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purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x dna decipher journal | july 2020 | volume 10 | issue 1 | pp. 29-32 29 pitkänen, m., multilocal viruses essay multilocal viruses matti pitkänen 1 abstract multi-local viruses are mysterious from the point of view of ordinary biology. the dna, rna, and proteins of these viruses divides into segments located at different host cells and can self-assemble back to the ordinary virus. various partitions of the virus are possible. tgd based view about space-time and quantum theory allows to understand these viruses as connected entities at the level of magnetic body (mb). mb containing dark matter in tgd sense would control the dynamics of what looks like multi-local entity at the level of ordinary matter. also bacteria could be seen as multi-local entities of this kind and the recent findings about states of bacterial colonies analogous to multi-cellulars resembling embryos of multi-cellulars suggests how multi-cellulars evolved from monocellulars. an interesting application is to the tgd view about cambrian explosion in which highly evolved multi-cellulars evolved. ontogeny recapitulates phylogeny principle provides support for the view that multicellular life evolved in underground oceans defining the womb of mother gaia and bursted to the surface as the radius of earth doubled in a phase transition reducing the value of local cosmological constant. 1 introduction i learned about very interesting piece of strangeness in biology known already for half a century (see http://tinyurl.com/yyh5s2c8): there are viruses, which can split into segments going into different host cells, replicate and produce proteins there, and self-assemble to original virus after this. virus (see http://tinyurl.com/owuwgfk) consist of dna or rna, protein coat, and in some cases outside envelope consisting of lipids and analogous to cell membrane. typically viruses consist of dna or rna decomposing to short segments coding for single protein. the reason for this is that rna replication is prone to errors and for short segments these errors are not so fatal. also dna can be segmented but the segments are longer. rna can be have positive sense in which it can be directly translated to protein or negative sense in which case replication producing positive sense rna is needed made possible by an enzyme contained by the virus. the usual thinking about viruses is that virus finds its way to cell and then uses the genetic machinery of the cell to replicate its dna and rna and produce also proteins. this does not not occur in the case of multipartite viruses infecting plants. the virus can split into segments infecting host cells separately. the segments of rna and proteins contained by the virus are thus shared by different cells are replicated and coded to proteins. the outcome of the process is then brought together in some cell which need not contain gene segments in it and self-assembly to full virus can occur. also fractured viruses can flourish and can infect some other plant. it has been found that the full complement of most viral segments is missing from most plant cells. protein required for viral replication present in cells that did not have genome for producing it so that the produced proteins can be transferred from the cell where they are produced to neighboring cells: it is though that so called plasmodesmata connecting cells to a network make this possible. in standard view assuming that the viral segments are completely independent systems multi-partitioning has high risks. in this view theoretically not more than 4 segments are possible. for instance, 8 has been observed in the examples discussed. even flu virus decomposes into 8 dna segments with the cell inside which it replicates. multi-partitioning produces also problems for spreading. in the case of fbnsv 1correspondence: matti pitkänen http://tgdtheory.com/. address: rinnekatu 2-4 a8, 03620, karkkila, finland. email: matpitka6@gamail.com. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/yyh5s2c8 http://tinyurl.com/owuwgfk http://tgdtheory.com/ mailto:matpitka6@gmail.com dna decipher journal | july 2020 | volume 10 | issue 1 | pp. 29-32 30 pitkänen, m., multilocal viruses viruses mentioned in the article on the insect aphideating fbnsv spreads the virus to plants. how can it get all 8 parts of virus simultaneously? this is very difficult to understand if the segments are really independent. this suggests that the view about these viruses somehow wrong. multi-partitioning happens and standard view does not allow it. 2 tgd based model for multi-local viruses one can start by asking why the multi-partitioning implying modular reproduction (something analogous to that in industry!)? one good reason is that host cell might not be able to recognize the segments. also transcription of too large number of rnas might be too much for the host and kill it. it seems that viruses act as populations. tgd based model is based on familiar basic notions [2, 5]. 1. the basic mystery of the biology is coherence of organisms. bio-chemistry alone cannot explain it. in tgd quantum coherence of dark matter identified as heff = nh0 phases of ordinary matter at magnetic flux tubes of the magnetic body (mb) of the system is quantum coherent in long scales and this quantum coherence forces the coherence of ordinary living matter. biological self-organization and metabolism reduce in zero energy ontology (zeo) to dissipation in non-standard direction of space-time [4]. 2. the flux tubes of mb connect cells to larger networks (tensor networks). in particular the segments of virus can be connected to a network in this manner. the segments would be effectively free but their behavior would be correlated. virus would be multi-local entity at the level of ordinary matter but single connected structure at the level of mb. 3. the tgd based model for bio-catalysis and replication and the model for monopole flux tubes suggests that the phase transition increasing heff/h0 = n increases the length of the flux tube. this process requires metabolic energy since quite generally the energy of system increases with n serving as a kind of iq of the system measuring its algebraic complexity and identifiable as the dimension of extension of rationals assignable to the system. multi-partitioning requires metabolic energy presumably given by a host cell. the components of multi-partitioned virus are virtually independent but flux tube connections are not lost. there are very many possible multi-partitions and the individual host cell can contain several segments. 4. if the decay of virus to multi-partition corresponds to ordinary state function reduction (”big” state function reduction (bsfr) in zero energy ontology (zeo) [6], the arrow of time changes at the level of mb of virus (dark matter). n increases in statistical sense in bsfr so that the multi-partitioned state should have higher iq and is thus favored by quantum tgd. one might perhaps say that when virus is not active it does not need too much iq: iq requires metabolic energy feed and low iq is the most economical choice in the dormant space. when virus infects the host it become active and and increase of n makes it multi-local at the level of ordinary matter. if this view is correct, the self-assembly of the virus would lead back to dormant state with opposite arrow of time. that dormant state of virus would correspond to opposite arrow of time for ”virus self” would conform with the general view that observer with opposite arrow of time than conscious entity experiences it as sleeping. one must be of course however very cautious with interpretations. 5. these dormant states would not be specific to viruses. also folded protein would be dormant. external perturbation would feed metabolic energy feed waking up the dormant protein and protein would un-fold and become active and intelligent. same applies to multi-locality. also bacterial colony could be seen as single organism multi-local only at the level of ordinary bio-matter. when bacterial colony suffers starvation the bacteria form issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2020 | volume 10 | issue 1 | pp. 29-32 31 pitkänen, m., multilocal viruses a single tightly connected structure also at the level of ordinary bio-matter. in the absence of metabolic energy feed the values of n associated with the flux tubes would be reduced and they would shorten causing the phenomenon. for cellular organisms the multi-locality at the level of ordinary bio-matter be realized for cell but the distances of cells would be fixed. also at the level of dna, rna, trna and amino-acids multi-locality would be realized but the distances would not be fixed. in bio-catalysis the reactants are brought together and here heff reducing phase transition would take place providing also the energy needed to overcome the potential wall making the reaction extremely slow otherwise. in tgd based model for replication, transcription, and translation this flexible multi-locality is indeed assumed [5]. 6. how sexual reproduction (see http://tinyurl.com/kuvswc9) emerged is one of the mysteries of biology. the formation of tightly bound multi-local states of mono-cellulars would have increased the probability for lateral gene transfer between neighboring cells, and also the replacement of mere replication with a two-step process consisting of replication followed by meiosis and fertilization as its inverse. the reconnection of flux tubes assignable to dna is a prerequisite of this process in tgd framework so that the formation of states analogous multi-cellulars would have made this process plausible. it has been found (http://tinyurl.com/qkzwk5t, thanks for nikolina bendedikovic for a link) that multicellulars have monocellular colonies as predecessors in the sense that the bacteria (monocellulars) form temporarily tight structures resembling multicellular embryos. the transition from loose multilocality to a more tight one suggets itself. when metabolic energy feed is low bacteria form tightly bound non-multilocal structures analogous to multi-cellulars. the flux tubes are shorten and metabolic energy is liberated, and also the need form metabolic energy is lower when flux tubes have lower values of heff . multi-cellulars would be permanently in this configuration and their intelligence coded by distribution of heff :s would be realized differently. multi-cellulars would have been formed when these multi-cellular like bacterial colonies became permanent and began to evolve from embryos to more developed forms [1, 3]. hitherto i have assumed that multi-cellulars were formed already before the cambrian explosion assumed to be induced by a relatively rapid phase transition increasing reducing the local cosmological constant by factor 1/2, and increasing the radius of earth by a factor 2. this transition would have brought multi-cellulars to the surface from underground oceans giving also rise to the ordinary oceans. i have compared underground oceans to a womb of magnetic mother gaia. ontogeny recapitulates phylogeny principle suggests that the life of the multicellular embryo in womb corresponds to the period of multicellular life in underground oceans. second possibility is that the multi-cellulars emerged from underground mono-cellulars during this transition or immediately after it. could the emergence of bacterial colonies to the surface perhaps providing less metabolic energy feed forced them to form tightly bound colonies forcing the evolution of multi-cellulars? references [1] pitkänen m. expanding earth model and pre-cambrian evolution of continents, climate, and life. available at: http://tgdtheory.fi/public_html/articles/expearth.pdf, 2018. [2] pitkänen m. getting philosophical: some comments about the problems of physics, neuroscience, and biology. available at: http://tgdtheory.fi/public_html/articles/philosophic.pdf, 2018. [3] pitkänen m. could mars have intra-planetary life? available at: http://tgdtheory.fi/public_ html/articles/mars.pdf, 2019. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/kuvswc9 http://tinyurl.com/qkzwk5t http://tgdtheory.fi/public_html/articles/expearth.pdf http://tgdtheory.fi/public_html/articles/philosophic.pdf http://tgdtheory.fi/public_html/articles/mars.pdf http://tgdtheory.fi/public_html/articles/mars.pdf dna decipher journal | july 2020 | volume 10 | issue 1 | pp. 29-32 32 pitkänen, m., multilocal viruses [4] pitkänen m. quantum self-organization by heff changing phase transitions. available at: http: //tgdtheory.fi/public_html/articles/heffselforg.pdf, 2019. [5] pitkänen m. some applications of tgd inspired quantum biology: bio-chemistry, metabolism, replication. available at: http://tgdtheory.fi/public_html/articles/bioexamples.pdf, 2019. [6] pitkänen m. some comments related to zero energy ontology (zeo). available at: http:// tgdtheory.fi/public_html/articles/zeoquestions.pdf, 2019. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.fi/public_html/articles/heffselforg.pdf http://tgdtheory.fi/public_html/articles/heffselforg.pdf http://tgdtheory.fi/public_html/articles/bioexamples.pdf http://tgdtheory.fi/public_html/articles/zeoquestions.pdf http://tgdtheory.fi/public_html/articles/zeoquestions.pdf introduction tgd based model for multi-local viruses login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x dna decipher journal | june 2013 | volume 3 | issue 2 | pp. 122-125 122 pitkänen, m., introduction article introduction matti pitkänen 1 abstract this second series of articles are devoted to tgd inspired ideas related to biological evolution. in the first article the basic facts believed to be known about pre-biotic evolution are discussed and the tgd inspired vision about prebiotic evolution is introduced. in the second article a tgd inspired physical model for the genetic code and its evolution is introduced and mcfadden’s views are compared with tgd views. in the third article a general vision about biological evolution, evolution of brain, and cultural evolution is discussed. in the fourth article quantum variant of expanding earth model and pre-cambrian evolution of continents, climate, and life is developed. the ideas are highly speculative and challenge the existing beliefs, and the defense is that they follow rather naturally from the basic tgd. this second series of articles are devoted to tgd inspired ideas related to biological evolution as it might have occurred in tgd universe. tgd inspired vision about quantum biology and consciousness has evolved during last two decades and reader might benefit of having a brief summary about the process and its outcome. 1. the original inspiration came from the notion of many-sheeted space-time and the failure of strict non-determinism for the basic variational principle dictating the dynamics of space-time-surfaces. the study of the preferred exremals of kähler action demonstrated that the notion of classical field differs from that of electrodynamics. topological field quantization meaning that field decomposes to magnetic flux quanta, electric flux quanta, and topological light rays analogous to laser beams takes place and means that space-time surface itself is quantized. this has profound implications: for instance topological light rays parallel to magnetic flux tubes make possible precisely target communications with maximal signal velocity and without dispersion. each physical system is accompanied by a field body and magnetic body becomes especially interesting in the case of living systems and allows to understand various strange findings about the effects of elf em fields on living matter one of the first biological applications that emerged already around 2000 in its preliminary form [?]tubuc. one of the first applications of the many-sheeted space-time was to the description of dna as many-sheeted structure [?]genecodec. the modular structure of genome could be understood if genes are accompanied by magnetic flux tubes carrying also helical electric fields and electronic supra currents: this implies a direct connection with the tgd based explanation of dc currents of becker [13]. 2. the conjecture that dark matter in tgd universe corresponds to a hierarchy of phases of ordinary matter characterized by an effective value of planck constant ~eff coming as an integer multiple of ordinary planck constant emerged around 2005. it inspired the vision that macroscopically quantum coherent dark matter in macroscopic quantum coherence with large planck constant can be seen as an intentional agent using biological body as a motor instrument and sensory receptor. this explains eeg and its various scaled up variants as communication and control tools of the system formed by magnetic body and biological body [2]. this conjecture is especially interesting if one wants to understand dna and the basic processes such as transcription, translation, and replication. the phase transitions changing planck constant 1correspondence: matti pitkänen http://tgdtheory.com/. address: köydenpunojankatu 2 d 11 10940, hanko, finland. email: matpitka@luukku.com. issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.com/ mailto:matpitka@luukku.com dna decipher journal | june 2013 | volume 3 | issue 2 | pp. 122-125 123 pitkänen, m., introduction imply scaling of quantum lengths and in the case of magnetic body should correspond to processes in which flux tubes change their length correspondingly. this provides a mechanism of biocatalysis based if biomolecules and also other biological structures are connected by magnetic flux tubes to form a kind of indra’s net. the reconnections of magnetic flux tubes provide second control mechanism and the reconnection process for the flux tubes of disjoint magnetic bodies could be seen as space-time correlate for directed attention involving generation of quantum coherence in the scale of the resulting system. one of the implications is the identification of biophotons as ordinary photons resulting when dark photons transform to ordinary photons with the same energy [?]persconsc,biophotonslian. dark photons rather than biophotons would be the basic signalling and control tool in living matter and biophotons would represent kind of leakage. the hierarchy of planck constants suggests that great leaps in evolution mean emergence of new levels to the hierarchy of planck constants. also the notion of collective gene expression is highly suggestive, and suggests that cultural/social evolution corresponds to the evolution of magnetic body. dna as topological quantum computer is one of the applications. cyclotron bose-einstein condensates at the magnetic flux tubes and dark photons with low cyclotron frequencies (even in eeg range and below) but energies above thermal threshold are expected to be important in living matter. also josephson junctions at least the junction formed by the lipid layers of cell membrane are assumed to play key role. this picture leads also to a quantum models of nerve pulse and eeg [?]pulse,eegdark. the frequencies of josephson photons are inversely proportional to ~eff so that even the radiation in eeg frequency range can be interpreted as dark josephson radiation generated by cell membrane. 3. also p-adic physics has served as a source of inspiration. one of the big ideas was that p-adic space-time sheets could serve as geometric correlates of intentions and cognitions representing the ”mind stuff” of descartes. mersenne primes and their gaussian counterparts are of special interest physically and the biologically especially interesting length scale range 10 nm-2.5 µm contains as many as four gaussian mersennes. furthermore, the mersenne prime m127 = 2127 − 1 characterizing electron corresponds to secondary p-adic time scale of .1 as and thus to 10 hz fundamental biorhythm. these observations suggest that p-adic length scale hierarchy defines a hierarchy of control levels in living matter. one particular application was motivated by the so called combinatorial hierarchy emerging naturally from p-adic considerations and leading to the conjecture that besides genetic code also memetic code assignale with the mersenne primes m127 = 2127 − 1 with code words consisting of 126 bits representable as sequences of 21 dna codons might be associated with living matter [?]genememec. the notion of negentropic entanglement is one of the basic notions inspired by p-adic physics. number theoretic entropy defined by shannon’s formula by replacing the logariths of probabilities with their p-adic norms is well-defined if the probabilities belong to algebraic extension of rationals. the resulting entropy can be negative and has interpretation as a measure for the negentropy associated with the entanglement carrying information as a rule telling which state pairs are correlated (thermodynamical entanglement entropy characterizes the lack of information about the state of either entangled particle). life as something residing in the intersection of real and p-adic worlds is the emerging vision. 4. zero energy ontology (zeo) is also a notion that emerged around 2005. zeo was inspired by the failure of the strict determinims of kähler action and also by the need to fuse real and p-adic physics to a larger structure [?]tgdnumber. causal diamond (cd) becomes the geometric correlate for the spotlight of consciousness in zeo. zeo has led to a rather detailed view about quantum jump identified as moment of consciousness in tgd inspired theory of consciousness [?]consccomparison. issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | june 2013 | volume 3 | issue 2 | pp. 122-125 124 pitkänen, m., introduction the basic challenge has been the understanding of the relationship between subjective time define by the sequence of quantum jumps and geometric time, and zeo has led to a radical modification of the basic beliefs about time [?]timenature. quite recently it became clear that the sequence of state function reductions to opposite boundaries of cd is very much analogous a sequence of pairs consisting of sensory perception followed by motor action, and that this structure appears in all scales. furthermore, sensory perception and motor action can be seen as time reversals of each other and one must generalize the second law of thermodynamics to a form in which thermodynamic arrow of time corresponds to that for subjective time whereas the imbedding space arrow of time is opposite for the zero energy states which result in the state function reduction to the opposite boundaries of cd. even the second law itself must be challenged. 5. in the earlier approach self was identified as quantum jump in conflict with the fact that self represents something which remains invariant in quantum jumps. negentropic entanglement together with negentropy maximization principle (nmp) allows to have representations which are approximate invariants under quantum jump sequence. this suggests that self should be replaced with self representation -”akashic records”. the conscious reading of the representations is possible by interaction free measurements in arbitrarily good approximation and gives rise to declarative memories, internal speech, and imagination. the necessary quantum jumps giving rise to the reflective level of consciousness (internal speech and imagination) takes place for the ”detectors” absorbing the dark photons (or dark phonons) scattered from the representation realized at the magnetic body. the braiding of flux tubes provides a geometric correlate for the negentropic entanglement and the ”long” parts of closed flux tubes and large flux sheets carry the cyclotron bose-einstein condensates defining the ”detectors” [?]consccomparison. what happens if the representations are not read? is there still a conscious experience? there could be a conscious experience also in this case, and the reports of mystics about higher states of consciousness suggest that it corresponds to an experience of understanding without ability to express what it is that one understands: also the presence of invariant parts of under quantum jumps could be experienced consciously but the contents of the experience would not be communicable. one of the first applications of the notion of many-sheeted space-time was to the pre-biotic evolution of the genetic code. later the topic of the corresponding chapter [?]prebio was extended to evolution in general. this issue contains four articles about about evolution in many-sheeted space-time. the articles of this issue have been prepared from two chapters of ”genes and memes”: the first version of [?]genememe has emerged during the period 2000-2006, and that of [?]expearth after 2006. the chapters have been subject to a continual updating, and therefore reflect the development of general vision about tgd. i have done my best to update the material and provide references to the recent tgd inspired vision about quantum biology: yet there might be some internal inconsistencies present. i have also done considerable work in removing obsolete arguments and added references to the recent understanding of the situation. i hope that this makes it easier for the reader to develop an overall view about the theory. in the first part the basic facts believed to be known about pre-biotic evolution are discussed and the tgd inspired vision about prebiotic evolution is introduced. in the second part a tgd inspired physical model for the genetic code and its evolution is introduced and mcfadden’s views are compared with tgd views. in the third part a general vision about biological evolution, evolution of brain, and cultural evolution is discussed. in the fourth part quantum variant of expanding earth model and pre-cambrian evolution of continents, climate, and life is developed. the ideas are highly speculative and challenge the existing beliefs, and the only defense form the is that they follow rather naturally from the basic tgd. references [1] m. pitkänen. about nature of time. in tgd inspired theory of consciousness. onlinebook. http://tgdtheory.com/public_html/tgdconsc/tgdconsc.html#timenature, 2006. issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.com/public_html/tgdconsc/tgdconsc.html#timenature dna decipher journal | june 2013 | volume 3 | issue 2 | pp. 122-125 125 pitkänen, m., introduction [2] m. pitkänen. dark matter hierarchy and hierarchy of eegs. in tgd and eeg. onlinebook. http://tgdtheory.com/public_html/tgdeeg/tgdeeg.html#eegdark, 2006. [3] m. pitkänen. evolution in many-sheeted space-time. in genes and memes. onlinebook. http: //tgdtheory.com/public_html/genememe/genememe.html#prebio, 2006. [4] m. pitkänen. genes and memes. in genes and memes. onlinebook. http://tgdtheory.com/ public_html/genememe/genememe.html#genememec, 2006. [5] m. pitkänen. genes and memes. onlinebook. http://tgdtheory.com/public_html/genememe/ genememe.html, 2006. [6] m. pitkänen. many-sheeted dna. in genes and memes. onlinebook. http://tgdtheory.com/ public_html/genememe/genememe.html#genecodec, 2006. [7] m. pitkänen. quantum antenna hypothesis. in quantum hardware of living matter. onlinebook. http://tgdtheory.com/public_html/bioware/bioware.html#tubuc, 2006. [8] m. pitkänen. quantum model for nerve pulse. in tgd and eeg. onlinebook. http://tgdtheory. com/public_html//tgdeeg/tgdeeg/tgdeeg.html#pulse, 2006. [9] m. pitkänen. tgd as a generalized number theory. onlinebook. http://tgdtheory.com/public_ html/tgdnumber/tgdnumber.html, 2006. [10] m. pitkänen. are dark photons behind biophotons. in tgd based view about living matter and remote mental interactions. onlinebook. http://tgdtheory.com/public_html/pdfpool/ biophotonslian.pdf, 2013. [11] m. pitkänen. comments on the recent experiments by the group of michael persinger. in tgd based view about living matter and remote mental interactions. onlinebook. http://tgdtheory. com/public_html/pdfpool/persconsc.pdf, 2013. [12] m. pitkänen. comparison of tgd inspired theory of consciousness with some other theories of consciousness. in tgd based view about living matter and remote mental interactions. onlinebook. http://tgdtheory.com/public_html/pdfpool/consccomparison.pdf, 2013. [13] m. pitkänen. quantum model for the direct currents of becker. http://tgdtheory.com/public_ html/articles/dcbio.pdf, 2012. issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.com/public_html/tgdeeg/tgdeeg.html#eegdark http://tgdtheory.com/public_html/genememe/genememe.html#prebio http://tgdtheory.com/public_html/genememe/genememe.html#prebio http://tgdtheory.com/public_html/genememe/genememe.html#genememec http://tgdtheory.com/public_html/genememe/genememe.html#genememec http://tgdtheory.com/public_html/genememe/genememe.html http://tgdtheory.com/public_html/genememe/genememe.html http://tgdtheory.com/public_html/genememe/genememe.html#genecodec http://tgdtheory.com/public_html/genememe/genememe.html#genecodec http://tgdtheory.com/public_html/bioware/bioware.html#tubuc http://tgdtheory.com/public_html//tgdeeg/tgdeeg/tgdeeg.html#pulse http://tgdtheory.com/public_html//tgdeeg/tgdeeg/tgdeeg.html#pulse http://tgdtheory.com/public_html/tgdnumber/tgdnumber.html http://tgdtheory.com/public_html/tgdnumber/tgdnumber.html http://tgdtheory.com/public_html/pdfpool/biophotonslian.pdf http://tgdtheory.com/public_html/pdfpool/biophotonslian.pdf http://tgdtheory.com/public_html/pdfpool/persconsc.pdf http://tgdtheory.com/public_html/pdfpool/persconsc.pdf http://tgdtheory.com/public_html/pdfpool/consccomparison.pdf http://tgdtheory.com/public_html/articles/dcbio.pdf http://tgdtheory.com/public_html/articles/dcbio.pdf observation of radiated spectra and comparison with predictions of stefan’s and wein’s laws dna decipher journal | december 2015 | volume 5 | issue 3 | pp. 195-205 tertyshniy, g. g., gariaev, p. p. & leonova, e. a., polarization-holographic processes in biosystems issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 195 article polarization-holographic processes in biosystems g. g. tertyshniy, peter p. gariaev * & e. a. leonova institute of quantum genetics llc, moscow, russia abstract a proposed physical-mathematical model that describes a version of the polarization-holographic vector-shaped calibration of potential spatio-temporal dynamic processes of higher biosystems in their development and in adulthood. keywords: dna, light radiation, chromosomal continuum, polarization, hologram. let’s record a vector diffraction kirchhoff’s integral in paraxial approximation [10], which describes wave field, for instance photon field, formed by a non-stationary fragment of a biosystem. these coherent photon fields may radiate from the liquid crystal continuum of a chromosome (lccc) in vivo [27]. this type of radiation may be expressed by the following equation: ( (1) where c — speed of light; ω — frequency; x0, y0, z0, t0 и x, y, z, t – space-time coordinates of a lccc’s point and an observation point, respectively; r -distance between these points; s0, t0 time-space interval, occupied by lccc; ds=dx0, dy0 in the equation (1), eob (x0, y0, z0, t0) represents distribution of field amplitude of lccc. this field is present for every polarization mode which are orthogonal and are independent until a turn occurs in their planes from their initial positions of vectors of median frequency waves of ω0 (which are polarized mono-frequency waves, slightly shifted by frequency in relation to one another), propagating along z axis with jones vector [11]. remember, chromosomes are characterized by high optical activity, expressed by optical spin dispersion and spherical dichroism that is a prerequisite for formalism. *correspondence: peter gariaev, ph.d., quantum genetics institute, maliy tishinskiy per. 11/12 25, moscow 123056, russia. email: gariaev@mail.ru mailto:gariaev@mail.ru dna decipher journal | december 2015 | volume 5 | issue 3 | pp. 195-205 tertyshniy, g. g., gariaev, p. p. & leonova, e. a., polarization-holographic processes in biosystems issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 196 (2) field e0 passes via non-stationary fragment of lccc with jones matrix. for simplification we will consider that non-stationary lccc is not a function of the frequency of translucent light [12, 13]. both polarization modes of coherent light are depolarized by gene-sign non-stationary nature of lccc (discussed above [22]) and are partially elliptically polarized. at the same time, they may interfere with formation of speckle patterns, and their total intensity is transferred from one mode to another by means of an earlier postulated way [25]. this in turn, leads to modulation of radio waves, formed from chromosomal photons by the mechanism of their delocalization [24]. according to [14], immediately behind the object, modified johns’ vector of orthogonally polarized passed waves may be represented in a form of partially coherent orthogonal components of elliptical polarization (3) where – a sign of non-coherent sum of amplitudes, which [14] is introduced for partially polarized light; ea – complex amplitude of one basis component; eb – complex amplitude of another basis component, orthogonal to the previous one and noncoherent. in a biosystem in the composition of lccc (with only one polarization component) as a hypothetical we use a carrying wave, which passed, for instance, through an infinitely narrow time shutter lock, possessing δ like characteristic of time transmission. such a shutter lock dna decipher journal | december 2015 | volume 5 | issue 3 | pp. 195-205 tertyshniy, g. g., gariaev, p. p. & leonova, e. a., polarization-holographic processes in biosystems issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 197 completely depolarizes the initially polarized wave [14]. the resulting wave, passed behind the shutter lock, is characterized by a continuous spectrum in the whole range with evenly distributed spectral density, and the modified vector of the carrying wave has a form of orthogonal basis of elliptical polarization: (4) where – amplitudes; ϕ, φ – initial phases of two mutually non-coherent components. for our case, where sometimes both polarization components are employed, the above assumption about the infinitely narrow time shutter lock is not necessary, and the sum of the field in the plane of the polarized hologram has the following form: (5) the real part of equation (5) represents the tension of electrical vector of the aggregate wave [16]. dna decipher journal | december 2015 | volume 5 | issue 3 | pp. 195-205 tertyshniy, g. g., gariaev, p. p. & leonova, e. a., polarization-holographic processes in biosystems issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 198 (6) parameters of the ellipse p and g are defined via ellipse components of polarization of each basis а and в, as in paper [14] (7) endogenous biological registration of the aggregate wave field (5) pertaining to lccc as a basic element of dna-wave bio-computer [26], implies the presence of polarization-sensitive medium in organisms [17,18], which is spectrally non-selective across the whole range of active frequencies (like non-stationary fragments of a biological object, for instance lccc). the polarization characteristics of the inducing light [19, 20] in the light-sensitive registering medium of lccc allow photo-anisotropy and photo-gyrotropy. to describe the vector photoresponse of polarized-sensitive media in the papers [19, 20, 21] functions of isotropic s, anisotropic νl and gyrotropic νg reactions are introduced, which are constant for all frequencies of active radiation. using johns’ matrices [8, 11] and rules of their formation [20] for cases of partially polarized inducing radiation, for the resulting johns’ matrix we get: (8) dna decipher journal | december 2015 | volume 5 | issue 3 | pp. 195-205 tertyshniy, g. g., gariaev, p. p. & leonova, e. a., polarization-holographic processes in biosystems issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 199 where in (8) – the length of the initial translucent endogenous wave (for instance, photonic radiation of chromosomes in vivo); d – thickness of registering lccc; n0 – complex coefficient of diffraction of lccc in its original, non-irradiated state; (i1+i2)a и (i1+i2)b – first stokes’ parameter; (i1-i2)a and (i1-i2)b – second stokes’ parameter; (i±-i±)a and (i±-i±)b – fourth stokes’ parameter for a and b components; θa and θb – orientational angles of the large ellipse’s polarization axis for aand b components, respectively measured counter-clockwise in relation to x axis. expressing in (8) stokes’ parameters via pa, pb, ga ,gb [8], for holograms’ matrix represented as a sum of the three matrices, in the whole range of active frequencies we will get: (9) where m0 – matrix describing non-diffracted beams; (10) m-1 – matrix describing virtual image; (11) with matrix elements dna decipher journal | december 2015 | volume 5 | issue 3 | pp. 195-205 tertyshniy, g. g., gariaev, p. p. & leonova, e. a., polarization-holographic processes in biosystems issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 200 m+1 – matrix describing real image (12) with matrix elements here mij≡mij(x0,y0,z0,t0) – elements, depending on coordinates and time of the 2d matrix of non-stationary lccc fragment. under the condition of rationality in biological objects, interrelation between functions of media reaction may be the following: dna decipher journal | december 2015 | volume 5 | issue 3 | pp. 195-205 tertyshniy, g. g., gariaev, p. p. & leonova, e. a., polarization-holographic processes in biosystems issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 201 (13) and expressions (11) and (12) can be simplified. in publication [8] is noted, that conditions in (13) are met with a high precision for a very large class of polarized-sensitive media. provided that conditions in (13) are met, m-1 and m+1 matrices take the following form: (14) (15) in (14) and (15) lccc matrix mob is marked, and p represents the following matrix where p* mob* – hermitian adjoint matrices. publication [21] should be noted for the original approach to the solution of the image reconstruction problem, which we will be glad to use in relation to morphogenetic modelling. under condition of endogenous illumination of the received hologram by reconstructing nonpolarized waves with complex amplitudes endogenous or exogenous in relation to the biosystem, and frequency ω' dna decipher journal | december 2015 | volume 5 | issue 3 | pp. 195-205 tertyshniy, g. g., gariaev, p. p. & leonova, e. a., polarization-holographic processes in biosystems issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 202 (16) the wave passed through the biological hologram is formed as follows: (17) where s – fragment size of lccc’s hologram; r‘ – distance between the point on the hologram surface and observation point. then, successively substituting in (17) expressions for matrices (10), (14) and (15), let’s define null, virtual and real images, formed by the hologram. and only now determine, what endogenous or/and exogenous wave is necessary for the organism to utilize as to reconstruct the required fragment of the wave image in a virtual form. to achieve this, it is necessary to determine their own vectors and corresponding to them values of p matrix. it turns out that with a precision of up to a constant multiplier, the vectors of p matrix are in essence and with their respective values and . it follows that reconstruction should be performed by a wave identical to the one used during recording by the carrying wave. as apparently, in biosystems at lccc level recording and reconstruction happen either simultaneously or in accordance with the last condition, then the reconstructed virtual image depiction corresponds to the real one and is not subject to any distortions. the latter is of principle importance for preservation of the wave image-vectors of morphogenesis, despite of the biosystem mobility in general as well as its lccc in particular. nonetheless, the non-stationary nature of images will appear, though over long time periods during organism aging and its pathological states, for instance in the case of carcinogenesis. for a wave passed without diffraction [21], the null image has the following form: dna decipher journal | december 2015 | volume 5 | issue 3 | pp. 195-205 tertyshniy, g. g., gariaev, p. p. & leonova, e. a., polarization-holographic processes in biosystems issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 203 (18) where the virtual and real images are presented as: (19) (20) where integrals, pertaining to (19) and (20), as in paper [21] are solved in a linear approximation for distances r and r’ and for infinitely large areas of integration s, s0, t0, ω. integrals s and ω have a character of spatial and time δfunction respectively. the final expressions executed in a similar way as in paper [6], lead to the following equations for the formed space-time polarized hologram. for the formed virtual image under condition of from (19) we have: (21) dna decipher journal | december 2015 | volume 5 | issue 3 | pp. 195-205 tertyshniy, g. g., gariaev, p. p. & leonova, e. a., polarization-holographic processes in biosystems issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 204 an analysis of the last equation shows that with precision up to the multiplier it depicts complete reconstruction of space-time structure as well as polarization characteristics of the field of its non-stationary object wave for example, via lccc. it is convenient for the biosystem to use this structure-image to organize itself in time and space, as this structure-image fully preserves the original calibrating scale without any distortions imposed by the dynamic nature of the biosystem and reproduces it in adequate dimensions for a developing or an adult organism. four dimensional organization of metabolic flows and morphogenetic movement of cells and tissues during embryogenesis additionally partial regeneration of biosystems in case of damage occurs in accordance with reconstructed wave gradients of scanned polarization holograms (calibration of the potential space-time of the biosystem), and proven by us [22]. in application of equation (20) for the real image where we have: (22) from equation (22) it follows that the image with pseudoscopic spatial structure of the objective fragment of the lccc field is formed of distance , symmetrically to the virtual image (19) in relation to the hologram. wherein its circulation time profile occurs with a delay, caused by the light passing the distance of , equal to the distance from the point of observation to the point on the surface of the real image, with conversion of polarization state, determined by pa* and pb* types of matrices. references [1] gabor d. // proc. roy. soc. ser. a197. 1949. vol. 197.p.454_460. [2] denisyuk yu.n. // dan sssr. 1962. t. 144. № 6.s. 1275_1278. [3] zubov v.a., kraiskii a.v., kuznecova t.i. // pisma v jetf. 1971.t.13.s.443_446. [4] zuikov v.a., samarcev v.v., usmanov r.g. // pisma v jetf.1980.t.32 .s.293-295 [5] saari p.m._ kaarli r.k._ rebane a.k. // kvantovaya elektron. 1985. t.12. №4 s.672-682. [6] kakichashvili sh.d., kakichashvili e.sh pisma v jtf. 1998. t.24. vip. 11.s76-79. dna decipher journal | december 2015 | volume 5 | issue 3 | pp. 195-205 tertyshniy, g. g., gariaev, p. p. & leonova, e. a., polarization-holographic processes in biosystems issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 205 [7] kakichashvili sh.d. // opt. i spektr. 1972. t. 33. vip. 2. s.324-327. [8] kakichashvili sh.d. // polyarizacionnaya golografiya. l. [9] kakichashvili sh.d., kilosanidze b.n. // jtf. 1997. t.67.vip.6.s.136-139. [10] kakichashvili sh.d. // pisma v jtf.1994.t.20.vip.22.s.78-82. [11] jones r.c/ // josa.1941. vol. 31. n7.p.488-499. [12] kirhgof r.g. izbrannie trudi. m., 1988. 430 s. [13] kottler f. // progress in optics.1965.vol.4.p. 283-313. [14] kakichashvili sh.d.// jtf. 1995. t.65. vip.7.s. 200-204. [15] harkevich a.a. spektri i analiz. m._ 1962. 236 s [16] born m., volf e. osnovi optiki. m., 1970. 855 s. [17] weigert f. // verhandl. deutschen physik. ges. 1919. bd 21. s.479-483. [18] zocher h._ coper k. // z.phys. chem. 1928.bd 132. s.313-319. [19] kakichashvili sh.d. // opt. i spektr. 1982. t. 52. vip. 2. s. 317-322. [20] kakichashvili sh.d., kilosanidze b.n. // pisma v jtf. 1995. t. 21. vip.23. s. 6-9. [21] kilosanidze b.n., kakichashvili e.d., jtf, 2000. t. 70. vip. 7. s. 65-69. [22] prangishvili i.v., garyaev p.p., tertishnii g.g., a.v.mologin, e.a.leonova, e.r.muldashev .// datchiki i sistemi, 2000, № 2, s.312. [23] prangishvili i.v., garyaev p.p., tertishnii g.g., a.v.mologin, e.a.leonova, e.r.muldashev .// datchiki i sistemi, 2001, №1, s. 3-8. [24] prangishvili i.v., garyaev p.p., tertishnii g.g., maksimenko v.v., .mologin av., leonova e.a., muldashev e.r. // datchiki i sistemi, 2000, № 9, s.3-30. [25] garyaev p.p., volnovoi geneticheskii kod. 1997, monogr. s.92-102. [26] gariaev p.p., birshtein b.i., iaroshenko a.m., marcer p.j., tertishniy g.g., leonova k.a., and kaempf uwe // consciousness and physical reality, 2000, vol.2, no.2, c.26-34. [27] popp, f.a., 2004, quantum phenomena of biological systems as documented by biophotonics, in: quo vadis. quantum mechanics?, a.c. elitzur, s. dolev and n. kolenda, eds., springer, berlinheidelberg-new york, p.371-396. login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x dna decipher journal | september 2018 | volume 8 | issue 2 | pp. 124-128 124 pitkänen, m., new support for the view on cambrian explosion being caused by rapid increase of earth radius essay new support for the view on cambrian explosion being caused by rapid increase of earth radius matti pitkänen 1 abstract cambrian explosion during which highly advanced lifeforms suddenly emerged is one of the mysteries of biology. oxygenation of the environment was associated with this event as also a release of methane trapped to a crystal structure of water. oxygenation made possible the emergence of aerobic respiration and of animals. stem cells to not however tolerate oxygen. the so called hypoxia-inducible factors (hifs) make possible to shift metabolism from aerobic to anaerobic in hypoxic environment. in the case of cancer cells so called hif-2α allows this also in oxic environment. the geobiologis emma hammarlund and tumor biologist sven phlman conjecture that this true also for the ordinary cells. moreover, they propose that the event induced a genetic change leading to the emergence of what they call hif-1 as a predecessor of hif-2α. this allowed the organism to adapt to environments in which oxygen concentration varied so that stem cells survived in high-oxygen environment. the cause of the sudden oxygenation is not discussed in the article. the so called great oxygenation event (goe) occurred much earlier than cambrian explosion, and tgd inspired proposal is that this event drove the primitive life forms under the earth surface to underground oceans. the precambrian situation would have been very similar to that in recent mars. cambrian explosion was induced by a rapid expansion of earth size with radius increasing by a factor of 2. this led to the formation of cracks and oxygenation of underground oceans which in turn induced rapid evolution of animals from plant like predecessors. keywords: cambrian explosion, rapid increase, earth radius, tgd framework. 1 introduction there was an interesting popular article in quanta magazine titled ”oxygen and stem cells may have reshaped early complex animals” (see http://tinyurl.com/y86ta45l). the article dicusses the work of geobiologist emma hammarlund and tumor biologist sven phlman: their interdisciplinary hypothesis is published as article in nature [2] with title ”refined control of cell stemness allowed animal evolution in the oxic realm” (see http://tinyurl.com/y85ufngz). here is the abstract of their article. animal diversification on earth has long been presumed to be associated with the increasing extent of oxic niches. here, we challenge that view. we start with the fact that hypoxia (≤ 1−3 per cent o2) maintains cellular immaturity (stemness), whereas adult stem cells continuously and paradoxicallyregenerate animal tissue in oxygenated settings. novel insights from tumour biology illuminate how cell stemness nevertheless can be achieved through the action of oxygen-sensing transcription factors in oxygenated, regenerating tissue. we suggest that these hypoxia-inducible transcription factors provided animals with unprecedented control over cell stemness that allowed them to cope with fluctuating oxygen concentrations. thus, a refinement of the cellular hypoxia-response machinery enabled cell stemness at oxic conditions and, then, animals to evolve into the oxic realm. this view on the onset of animal diversification is consistent with geological evidence and provides a new perspective on the challenges and evolution of multicellular life. 1correspondence: matti pitkänen http://tgdtheory.com/. address: rinnekatu 2-4 a8, 03620, karkkila, finland. email: matpitka6@gamail.com. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/y86ta45l http://tinyurl.com/y85ufngz http://tgdtheory.com/ mailto:matpitka6@gmail.com dna decipher journal | september 2018 | volume 8 | issue 2 | pp. 124-128 125 pitkänen, m., new support for the view on cambrian explosion being caused by rapid increase of earth radius 1.1 the proposal of hammarlund and phlman cambrian explosion (see http://tinyurl.com/ntvx38e) during which highly advanced lifeforms suddenly emerged prolifiration and diversification of animal life are the terms used about this is one of the mysteries of biology. for most of its 4.5-billion-year history, earth has sustained life but that life was largely limited to microbial organisms: bacteria, plankton, algae. for about 540 million years ago did larger, more complex species are assumed to dominate the oceans, but within just a few tens of millions of years (very short time on the evolutionary timescale), the planet had filled up with all kinds of animals. the fossil record from that period shows the beginnings of almost all modern animal lineages: animals with shells and animals with spines, animals that swam and animals that burrowed, animals that could hunt and animals that could defend themselves from predators. also many lineages that disappeared were present as one learns from the book of stephen jay gould describing in detail the burgess shale finding that revolutionized the picture about evolutionary biology and remains still a puzzle (see http://tinyurl.com/y9orfy43). the belief is that the environment became considerable more oxic that is contained oxygen and lifeforms had to cope with this change. before the change the animals in seas (believed to exist!) were anaerobic. the shifting to aerobic respiration was however an enormous metabolic advantage since the effectiveness of metabolic energy gain become roughly 20-fold. increased metabolic feed in turn made possible the emergence of complexity during cambrian period. 1. the proposal of the authors is that the evolution of the capacity to maintain stem cells even in an oxic environment allowed the animals to keep stocks of stem cells needed for tissue growth and repair for that this required at gene level new genes coding for so called hifs. 2. stem cells require low oxygen levels to preserve their stemness. heightened oxygen levels cause them to differentiate abruptly. this explains why stems cells are often located in hypoxic regions of the body (say bone marrow) having low oxygen levels. there are however exceptions to this rule: stem cells can also survive in ocix regions such as skin or retina. cancers also utilize stem cells to achieve growth. 3. hammarlund and phlman turned their attention to hifs (hypoxia-inducible transcription factors), which are proteins, which for hypoxic environment shift the metabolism from aerobic to an-aerobic. for oxic environment they are not needed. hif-2α remains however active also in oxic environment and make the cells behave as if the environment were hypoxic. this would allow the stem cells to survive. hif-2α would however keep the stem cells in immature state also in the case of cancer. the hypothesis of hammarlund and phlman was that hif-2α functions similarly in normal animal tissues. they have seen some preliminary evidence for the hypothesis but further work is needed. 4. hifs could have helped the animals to survive in oxic environment. consider an organism as a blob of cells. before the oxygenation the stem cells would have been forced to the deep interior of the blob, where oxygen concentration was especially low. when oxygenation took place, and oxygen level varied, this trick did not work anymore and hifs had to be invented. 5. hammarlund and phman postulate what they call hif-1, which would have helped stem cells to behave as if the environment were hypoxic. later hif-2α unique to vertebrates emerged and improved the situation further. vertebrates are bigger and have longer time spans that invertebrates and they can live in oxygenated environments. inveratebrates such as insects live most of their life as larvae under low-oxygen conditions and they cannot regenerate tissues as vertebrates can. 6. cancer would be the price paid for this evolutionary advance since cancer cells can proliferate because hif-2 keeps the stem cells alive. oh present in oxygen rich environment is an oxidant causing cancer. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/ntvx38e http://tinyurl.com/y9orfy43 dna decipher journal | september 2018 | volume 8 | issue 2 | pp. 124-128 126 pitkänen, m., new support for the view on cambrian explosion being caused by rapid increase of earth radius what caused the oxygenation? so called great oxygenation event (goe,see http://tinyurl.com/ q7qfd55) is believed to have occurred about about 2.25 billion years ago and thus preceded cambrian explosion that occured about .5 billion years ago.the time lapse between these events is about 1.75 billion years and much longer than the duration of cambrian period, which was only tens of millions years. thus goe was not the reason for the cambrian explosion. what caused a further oxygenation or were the effects of goe somehow postponed (wink-wink!)? 2 tgd view my own proposal is that life evolved in underground oceans and entered to the surface of earth in cambrian explosion (see http://tinyurl.com/ntvx38e) when oceans were formed at the surface of eearth from cracks formed when earth expanded rapidly in geological time scale. before the explosion earth did not have oceans and continents and was like mars nowadays: even its radius was that of mars. this picture follows from tgd based variant of expanding earth hypothesis [10, 9] (see http: //tinyurl.com/yc4rgkco and http://tinyurl.com/yb68uo3y) . the habitat changed in the rapid expansion of earth from hypoxic to oxic and the emergence of the hypothetical hif-1 transcription factor would have been forced by this evolutionary pressure and made it possible for the lifeforms to adapt oxygen based metabolism. this would have led to a rapid evolution of animals and emergence of vertebrates. one can of course think that oxygenation developed already in the underground oceans as cracks caused in the crust by the expansion of earth began to develop and provided oxygen. the alternative not so plausible sounding option is that the highly developed organisms developed underground slowly and only bursted to the surface of earth in the explosion. 1. chemical markers (see http://tinyurl.com/ntvx38e) indeed indicate dramatic change in the environment at the start of the cambrian period. the markers are consistent with a massive warming due to the release of methane ice (clathrate hydrate, see http://tinyurl.com/peq9gmw) trapped within the crystal structure of water. methane clathrate is found deep under the sediments at the ocean floors. methane hydrates are believed to form by migration of gas from deep along geological faults (the cracks produced by rapid expansion of earth [9]!). 2. during the period before cambrian explosion earth would have been very much like in recent mars. even its radius would have been that of recent mars! one can ask whether goe forced the existing primitive lifeforms underground or saved only those already living underground. situation would have been be very much like in the recent mars, which also seems to possess undergound life. the development of hif proteins (hypoxia inducing factor) making possible for stem cells to survive in environments with varying and thus temporarily higher oxygen content would have been a natural reaction to the dramatic changes in habitat. what can one say about the emergence of animal life in tgd framework? 1. the rapid evolution leading to the emergence of animals if it was present would relate to the quantum criticality associated with the increase of the effective planck constant heff/h0 = n by factor 2 increasing the size scale of earth. the increase of heff/h0 = n might have occurred at several levels of dark matter hierarchy, also at biological relevant scales and led to an increase of biological ”iq” (note that evolution corresponds in tgd to gradual increase of number theoretical complexity and n characterizes the dimension of extension of rationals characterizing the complexity [6, 7]). 2. animals use oxygen for breathing and are multicellular eukaryotes having cell membrane enclosing nucleus and other membrane bound organelles. the quantum critical period could have led to the emergence of a kind of symbiosis of various kind of organelles within cell membrane bounded volume. the p-adic length scale l(k) determined by the value of n assignable to the outer membrane of issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/q7qfd55 http://tinyurl.com/q7qfd55 http://tinyurl.com/ntvx38e http://tinyurl.com/yc4rgkco http://tinyurl.com/yc4rgkco http://tinyurl.com/yb68uo3y http://tinyurl.com/ntvx38e http://tinyurl.com/peq9gmw dna decipher journal | september 2018 | volume 8 | issue 2 | pp. 124-128 127 pitkänen, m., new support for the view on cambrian explosion being caused by rapid increase of earth radius organelles could correspond to the prime k = 163 (or 167). inside plant cells having no cell membrane these organelles correspond to vacuoles (see http://tinyurl.com/yd879b2d). the outer membrane that emerged in the transition increasing heff/h0 meant increase of the scale of quantum coherence to a longer p-adic length scale say k = 167 (or k = 169 = 132 if doubling took place). 3. mitochondria would have emerged and made possible oxygen based respiration whereas plant like organisms preceding them utilized anaerobic respiration. methanogenesis (see http://tinyurl.com/ y97gkym8) utilizing carbon instead of oxygen and producing carbon-dioxide and methane ch4(water in o2 based respiration) is the most natural option. the large methane storages underground would be due to methanogenesis. the recent findings (see http://tinyurl.com/y735g9kn) indicate that there is life in mars: methane emissions occurring periodically with a period of martian year have been detected. this suggests that solar radiation is somehow able to enter to the interior of mars or that it heats the underground oceans. in tgd one can consider also the possibility that some part of solar photons transforms to dark photons and is able to propagate to the underground oceans through the martian crust [9]. 4. what was the primary source of metabolic energy? direct solar radiation was absent in underground oceans. the immediate source of metabolic energy for the plant like organisms might have been dark nuclei consisting of dark proton sequences and liberating energy in the transitions reducing of heff/h0 = n. dark proton triplets give rise to dark variants of dna, rna, trna, and aminoacids [4, 3, 11]. these dark proton sequences could have formed by pollack effect at the surface of earth possibly containing some water and could have propagated along dark flux tubes to the interior: also in ”cold fusion” dark nuclei would be formed. some fraction of them would transform to ordinary nuclei and liberate practically all the nuclear binding energy. also transitions to dark nuclei with a smaller value of heff/h0 is possible and liberates energy usable as metabolic energy. most dark nuclei could leak out along magnetic flux tubes [5]. the hen-egg problem which came first, metabolism or genetic code would trivialize in this framework. for p-adic length scale l(k = 149) = 5 nm thickness of cell membrane the typical dark nuclear excitation energy was about .5 ev, the nominal value of metabolic energy quantum. for l(151) = 10 nm (thickness of neuronal membrane and dna double strand its value is .25 ev. these estimates are based on the scaling of the typical nuclear excitation energy taken to be 1 mev and are uncertain by a factor of 2 at least. one of course expects also higher excitation energies even so high that they correspond to visible ordinary photons. metabolic energy could have been liberated as dark photons in dark nuclear transitions transforming to ordinary photons and absorbed by the photosynthetic machinery. the (rough) estimate for the typical value of the dark photon energy is considerably lower than in ordinary photosynthesis. pollack effect [1] occurring in presence of gel phase bounding water volume suggests that for k = 149 the transformation of dark proton sequences to ordinary ones: this mechanism would liberate energy per proton∼ 1.5 ev [8], which corresponds to infrared photon. the small value of the metabolic energy quantum need not be a problem: there is recent evidence that ir light with energy 1.76 ev can be used in photosynthesis (see http://tinyurl.com/yc6pqjed). issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/yd879b2d http://tinyurl.com/y97gkym8 http://tinyurl.com/y97gkym8 http://tinyurl.com/y735g9kn http://tinyurl.com/yc6pqjed dna decipher journal | september 2018 | volume 8 | issue 2 | pp. 124-128 128 pitkänen, m., new support for the view on cambrian explosion being caused by rapid increase of earth radius references [1] the fourth phase of water : dr. gerald pollack at tedxguelphu. available at: https://www. youtube.com/watch?v=i-t7tcmudxu, 2014. [2] von stedingk k hammarlund eu and p;hlman s. refined control of cell stemness allowed animal evolution in the oxic realm. nature ecology & evolution. available at:https://www.nature.com/ articles/s41559-017-0410-5, 2:220228, 2018. [3] pitkänen m. more precise tgd based view about quantum biology and prebiotic evolution. available at: http://tgdtheory.fi/public_html/articles/geesink.pdf, 2015. [4] pitkänen m. about physical representations of genetic code in terms of dark nuclear strings. available at: http://tgdtheory.fi/public_html/articles/genecodemodels.pdf, 2016. [5] pitkänen m. cold fusion, low energy nuclear reactions, or dark nuclear synthesis? available at: http://tgdtheory.fi/public_html/articles/krivit.pdf, 2017. [6] pitkänen m. philosophy of adelic physics. in trends and mathematical methods in interdisciplinary mathematical sciences, pages 241–319. springer.available at: https://link.springer. com/chapter/10.1007/978-3-319-55612-3_11, 2017. [7] pitkänen m. philosophy of adelic physics. available at: http://tgdtheory.fi/public_html/ articles/adelephysics.pdf, 2017. [8] pitkänen m. about dark variants of dna, rna, and amino-acids. available at: http://tgdtheory. fi/public_html/articles/darkvariants.pdf, 2018. [9] pitkänen m. expanding earth hypothesis, platonic solids, and plate tectonics as a symplectic flow. available at: http://tgdtheory.fi/public_html/articles/platoplate.pdf, 2018. [10] pitkänen m. expanding earth model and pre-cambrian evolution of continents, climate, and life. available at: http://tgdtheory.fi/public_html/articles/expearth.pdf, 2018. [11] pitkänen m. homonymy of the genetic code from tgd point of view. available at: http:// tgdtheory.fi/public_html/articles/homonymy.pdf, 2018. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://www.youtube.com/watch?v=i-t7tcmudxu https://www.youtube.com/watch?v=i-t7tcmudxu https://www.nature.com/articles/s41559-017-0410-5 https://www.nature.com/articles/s41559-017-0410-5 http://tgdtheory.fi/public_html/articles/geesink.pdf http://tgdtheory.fi/public_html/articles/genecodemodels.pdf http://tgdtheory.fi/public_html/articles/krivit.pdf https://link.springer.com/chapter/10.1007/978-3-319-55612-3_11 https://link.springer.com/chapter/10.1007/978-3-319-55612-3_11 http://tgdtheory.fi/public_html/articles/adelephysics.pdf http://tgdtheory.fi/public_html/articles/adelephysics.pdf http://tgdtheory.fi/public_html/articles/darkvariants.pdf http://tgdtheory.fi/public_html/articles/darkvariants.pdf http://tgdtheory.fi/public_html/articles/platoplate.pdf http://tgdtheory.fi/public_html/articles/expearth.pdf http://tgdtheory.fi/public_html/articles/homonymy.pdf http://tgdtheory.fi/public_html/articles/homonymy.pdf introduction the proposal of hammarlund and phlman tgd view login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x dna decipher journal | december 2024 | volume 14 | issue 1 | pp. 29-36 29 pitkänen, m., some mysteries of the biological evolution from the tgd point of view article some mysteries of the biological evolution from the tgd point of view matti pitkänen 1 abstract in this article 3 mysteries related to the origin of life on earth are discussed. the recent candidate for life’s universal common ancestor (luca) has a surprisingly large number of genes, much larger than the earlier candidate and it would be a rather complex life form. the sudden emergence of complex multicellular life forms in the cambrian explosion is the second mystery. the tgd proposal for the solution of the luca mystery relies on the solution of the mystery of the cambrian explosion. bacteria and archaea would have evolved at the surface of the earth and eukaryotes having a cell nucleus and reproducing sexually in the underground oceans. bacteria and archaea would have evolved from a counterpart of luca having a much smaller genome and eukaryotes would have evolved from an archaea with maximum size, which became the nucleus of the first eukaryote, luca. the third mystery relates to the asteroid ryugu, which was found to contain basic amino acids and also rna and microorganisms bacteria and microfossils resembling those living at earth were found. does this support the panspermia hypothesis? there are however strong objections against this hypothesis and it has been proposed that the microorganisms living on earth might have somehow colonized the ryugu sample. there is no known mechanism for how this could happen. the tgd based solution of the mystery relies on the prediction that life and its evolution are long length scale phenomena involving gravitational and electric field bodies, which can have an astrophysical size. 1 introduction biological evolution involves several deep mysteries. in this article 3 such mysteries are discussed. 1.1 the mystery of life’s origin deepens sabine hossenfelder told about new study, which deepens the mystery of life’s origin (see this). the key notion is luca, life’s universal common ancestor, whose genome should be common to all life forms, which in the most general case involves both archaea, prokaryotes (bacteria), and eucaryotes (plants, fungi and animals). the newest study gives a considerably larger number than the previous estimates. 1. luca would have 2,657 genes. luca would have had 2.7 million bps to be compared with about 3 billion bps of humans. luca would have lived about 4.2 billion years ago. 2. the proteins coded by the genes of luca suggest that hydrogen was important in the metabolism of luca. presumably luca lived near volcanoes. luca also had a rather complex metabolic circuitry and the genome suggests that it was a part of an ecosystem. the size of luca is 10 µm in size, which is also the size of cell nucleus, and it has a genome but no nucleus. 3. an interesting side observation is that 2,657 is prime and forms a twin prime together with 2659. maybe number theory is deeply involved with the genome. 1correspondence: matti pitkänen http://tgdtheory.com/. address: valtatie 8 as 2, 03600, karkkila, finland. email: matpitka6@gmail.com. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://backreaction.blogspot.com/2024/12/new-study-deepens-mystery-of-lifes.html http://tgdtheory.com/ mailto:matpitka6@gmail.com dna decipher journal | december 2024 | volume 14 | issue 1 | pp. 29-36 30 pitkänen, m., some mysteries of the biological evolution from the tgd point of view 4. the earlier estimate for the gene number of luca by bill martin’s team (see this) left only 355 genes from the original 11,000 candidates, and they argue that these 355 definitely belonged to luca and can tell us something about how luca lived. the problem is that there are two widely different candidates for the luca and the new candidate seems to be too complex if one assumes a single evolutionary tree. 1.2 the mystery of cambrian explosion cambrian explosion represents a long standing mystery [6] of evolutionary biology. the basic mystery is that highly evolved multicellular life forms emerged suddenly in the cambrian explosion about .5 billion years ago. there are much older fossils of monocellular life forms archaea and prokaryotes and they would have lived at the surface of earth as separate evolutionary lineages. the tgd based solution of the mystery mystery of cambrian explosion does not involve ets bringing multicellular life to the earth [7] [9, 8, 13]. 1. in the tgd universe, quantum gravitation is possible in arbitrarily long scales and cosmic expansion is replaced by a sequence of quantum phase transitions occurring in astrophysical scales as very rapid local expansions between which there is no expansion. 2. the life on earth could have evolved in two ways and as three separate evolutionary trees. multicellular life forms possible for sexually reproducing eukaryotes would have evolved in the underground oceans, where they were shielded from meteor bombardments and cosmic rays. there are indications that underground oceans and underground life are present on mars and possibly also some other places in the solar system. 3. in the cambrian explosion, identified as a short lasting rapid local cosmic expansion, the radius of earth would have increased by a factor of two. this hypothesis was originally inspired by the observation of adams [2] that the continents seem to fit nicely together if the radius of earth is taken to be 1/2 of its recent radius. this hypothesis would generalize the continental drift theory of wegener. rather highly developed photosynthesizing multicellular life forms would have bursted to the surface of earth from underground oceans and oceans were formed [7] [9, 8, 13]. the tgd proposal for the solution of the luca mystery relies on the solution of the mystery of the cambrian explosion. bacteria and archaea would have evolved at the surface of the earth and eukaryotes having a cell nucleus and reproducing sexually in the underground oceans. bacteria and archaea would have evolved from a counterpart of luca having a much smaller genome and eukaryotes would have evolved from an archaea with maximum size, which became the nucleus of the first eukaryote, luca. 1.3 perplexing findings about asteroid ryugu anton petrov told in in youtube video (see this) ”shocking discovery of earth bacteria inside ryugu asteroid samples + other updates” of highly interesting recent discoveries, which might provide very strong direct evidence for the tgd view of quantum biology. ryugu was found to contain basic amino acids and also rna and microorganisms bacteria and microfossils resembling those living at earth were found. the motivation for studying asteroids is that they could have been very important in the planetary formation. the panspermia hypothesis suggests that asteroids and similar objects could have also brought life to the earth and the findings about ryugu could at first be seen as a support for this hypothesis. one question raised by the study is whether the microorganisms living at the earth managed somehow to colonize the ryugu asteroid sample. in standard biology this should not be possible. the alternative possibility is that the evolution in earth and ryugu has been very similar: ryugu indeed orbits the sun at an on orbit for which the distance from the sun is smaller than the orbital radius of mars. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://phys.org/news/2018-12-luca-universal-common-ancestor.html#google_vignette https://www.youtube.com/watch?v=mo46cnftrds dna decipher journal | december 2024 | volume 14 | issue 1 | pp. 29-36 31 pitkänen, m., some mysteries of the biological evolution from the tgd point of view this would however require that the biological evolution is dictated by physics in a much longer length scale than the earth size scale. this is just what tgd predicts. these findings provide a test for the tgd view of life which suggests a very general basic mechanism for the emergence of life [10, 12, 14]. 2 luca from the tgd perspective in the following the explanation for the perplexing findings about luca are discussed from the tgd point of view. 2.1 some basic facts about evolution let us relate the proposed identification of luca with 2657 genes to basic facts about biology. 1. it is known that parasitic bacteria have 500–1200 genes, free-living bacteria have 1500–7500 genes, and archaea have 1500–2700 genes. prokaryotes and archaea are monocellular organism and do not have cell nucleus. eukaryotes differ from archaea and prokaryotes in that they can sexually reproduce: this means huge evolutionary step. 2. archaea (see this) are often thought to be more primitive than prokaryotes (see this) and eukaryotes (see this but it seems that they resemble eukaryotes more than prokaryotes. it should be noticed that mitochondria (see this) responsible for the metabolism have their own genome having only 37 genes to that one could (just for fun) argue that mitochondria are a natural identification of luca! 3. the lower bound for the gene number of free living bacteria and archaea is 1500 and smaller than 2657. it is however known that ancient bacteria had more genes than their recent forms. this might be due to the fusion of the genes to longer genes. they could be also predecessors of luca in some sense. 2.2 the number of genes for luca is upper bound for the genes of archaea: what does this mean? intriguingly, 2657 is near the upper limit 2700 for the gene number of archaea. this raises questions. 1. could the branches of the evolutionary tree have genuine dead ends, and are archaea and bacteria such dead ends? could prokaryotes and archaea correspond to separate lineages of the evolutionary tree and did eukaryotes evolve from archaea as the cell nucleus emerged? 2. was the gene number 2657 a critical gene number distinguishing between archaea and higher life forms? could this be the critical gene number above which the cell nucleus possessed by eukaryotes becomes possible and makes possible sexual reproduction and explosive evolution of new life forms. did the maximally complex archaea with 2657 genes become the first eukaryote nucleus, luca? if this was the case, did prokaryotes really share the genes of luca? also prokaryotes and archaea with shorter genomes exist. are these predecessors of the nucleus of luca? did prokaryotes with gene number larger than 2657 evolve from prokaryotes separately? 3. do prokaryotes and archaea have a common predecessor analogous to luca having much lower number of genes and is it the previous candidate for the luca having 355 genes. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://en.wikipedia.org/wiki/archaea https://en.wikipedia.org/wiki/prokaryote https://en.wikipedia.org/wiki/eukaryote https://en.wikipedia.org/wiki/mitochondrion dna decipher journal | december 2024 | volume 14 | issue 1 | pp. 29-36 32 pitkänen, m., some mysteries of the biological evolution from the tgd point of view 2.3 two mysteries with a common solution: cambrian explosion and the complexity of luca the complexity of the genome of luca looks like a mystery as also the existence of two widely different candidates for luca. one possible solution of the mystery relies on the panspermia hypothesis. most life forms would have arrived to the earth from elsewhere and only sufficiently complex organisms, whose genomes contained the luca genome, survived in the new environment. the tgd based solution of the mystery does not involve ets but relies on the tgd inspired solution of the mystery of cambrian explosion [7] [9, 8, 13]. in this framework, one can imagine three separate evolutionary lineages. 1. archaea and prokaryotes such as cyanobacteria, about which there are fossils much before the cambrian explosion, would have evolved at the surface of earth. note that cyanobacteria have about 559 core-genes (see this). 2. more complex multicellular eukaryotes, having a cell nucleus and reproducing sexually, would have evolved in the underground ocean oceans. the basic evolutionary step would have been the emergence of the cell nucleus, perhaps as a fusion of two monocellulars. this step could have led from luca as a maximally complex archaea to eukaryotes. for some reason, eukaryotes would have survived only in underground oceans. cosmic rays causing damage to the genes inside it might have made sexual reproduction too risky. 3. eukaryotes would have had the proposed luca as a common ancestor as the maximally complex archaea whereas the earlier candidate for luca would be the common ancestor of archaea and prokaryotes. 4. either all the organisms of the underground oceans contained the maximally complex archaea genome or only the organisms of the underground oceans having a genome not sorter than the luca genome were sufficiently complex to survive besides the prokaryotes present from the beginning at the surface of earth. luca as the first eukaryote, having the maximally evolved archaea as cell nucleus, would have had just the minimum number of genes needed to survive at the surface of the earth. the archaea and bacteria having a genome shorter than luca genome would have emerged in the evolution at the surface of the earth before the cambrian explosion. 5. a fusion of two unicellulars took place in the formation of luca and outer cell membrane emerged. an archaea with the genes of luca became the nucleus of the first eukaryote cell. the minimal choice for the second unicellular is mitochondria with 37 genes: this would give 2694 genes, almost the upper bound of 2700 for archaea. if cell membranes are an outcome of self-organization rather than being coded, this system might have been able to code itself. 3 the perplexing findings about the asteroid ryugu from the tgd perspective the tgd perspective about ryugu is based on the notion of long range quantum coherence predicting the notions of gravitational and electric magnetic body carrying phases of ordinary matter with a very large value of planck constant [11, 10, 12, 14]. these field bodies with sizes in astrophysical scales are predicted to be fundamental for life and its evolution and imply that the evolution of the chemical life is predicted to be induced by the evolution at the level of the field bodies. in this framework one can understand why ryugu can contain life forms resembling those on earth. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2015.00219/full dna decipher journal | december 2024 | volume 14 | issue 1 | pp. 29-36 33 pitkänen, m., some mysteries of the biological evolution from the tgd point of view 3.1 some facts about ryugu some basic facts about ryugu are in order. consider first the origin of ryugu. 1. the surface of ryugu is very young and has an age of 8.9 ± 2.5 million years. the composition of ryugu shows that its material has been at a rather high temperature about 1000 c and presumably near the sun. eventually rygu would have left the inner solar system and its composition suggests that it has been very near to the kuiper belt with distance 30-55 au. 2. the asteroid that arrived near the earth from outer space must have been for a long period in complete darkness. the object giving rise to ryugu could have originated far from jupiter, possibly near the kuiper belt. some compounds in ryugu can only form near the kuiper belt. a larger object of radius about 100 km could have suffered a collision near earth and produced ryugu with a size of 10 km near earth. 3. recently ryugu orbits the sun at a distance of 0.96-1.41 au once every 16 months (474 days (16 months); semi-major axis of 1.19 au). note that the distance of mars from the sun is about 1.5 au. its orbit has an eccentricity of 0.19 and an inclination of 6 degrees with respect to the ecliptic. the circumstances at ryugu are favorable for life. 1. the highest temperature on the ryugu asteroid reaches 100 degrees c, while the coldest regions sit at about room temperature. temperatures also change depending on the solar distance of the asteroid, lowering as ryugu moves further away from the sun. this would mean that the circumstances at ryugu become favourable for life as it passes earth. the lowering of the temperature at a large distance would not be fatal. hydration is essential for life. the required range of dehydration reaction temperature decreases with increasing substitution of the hydroxy-containing carbon: primary alcohols: 170–180 degrees c; secondary alcohols: 100–140 degrees c; tertiary alcohols: 25 degrees-–80 degrees c. primary/secondary/tertiary refers to the position of -oh substitution in carbon atom. 2. ryugu contains liquid water and also carbonated water. coral-like inorganic crystals are present. the sample contained carbon rich molecules, amino acids and components of rna and hydrated compounds! ammonium. 3. it has also been found that ryugu contains phosphorus rich samples. phosphorus plays a central role in metabolism and in the ”dark” realization of the genetic code in tgd. the abstract of the article [4] summarizes the findings. parent bodies of c-type asteroids may have brought key volatile and organic-rich compounds to the terrestrial planets in the early stages of the solar system. at the end of 2020, the jaxa hayabusa2 mission successfully returned samples from ryugu, providing access to a primitive matter that has not suffered terrestrial alteration. here we report the discovery of a peculiar class of grains, up to a few hundreds of micrometres in size, that have a hydrated ammonium–magnesium–phosphorus (hamp)-rich composition. their specific chemical and physical properties point towards an origin in the outer solar system, beyond most snow lines, and their preservation along ryugu history. these phosphorus-rich grains, embedded within an organic-rich phyllosilicate matrix, may have played a major role when immersed in primitive terrestrial water reservoirs. in particular, in contrast to poorly soluble calcium-rich phosphates, hamp grains favour the release of phosphorus-rich and nitrogen-rich ionic species, to enter chemical reactions. hamp grains may have thus critically contributed to the reaction pathways of organic matter towards a biochemical evolution. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2024 | volume 14 | issue 1 | pp. 29-36 34 pitkänen, m., some mysteries of the biological evolution from the tgd point of view 3.2 objections against the panspermia hypothesis as explanation of the findings about ryugu the panspermia hypothesis states that ryugu and similar objects could have served as a source of life on earth. 1. overpopulation problem is the theoretical objection against the panspermia hypothesis. no new forms of life are possible since no niches are left untouched. 2. there is also a second objection against the panspermia hypothesis as an explanation of these findings about ryugu. it has been claimed that the ryugu sample was contaminated by terrestrial microorganisms [3] (see this). nitrogen dioxide no2 is used in sterilization meant to remove, kill, or deactivate all forms of life present in fluid or on a specific surface. life forms of earth should not be able to colonize samples under extremely sterile conditions. if contamination occurred, its mechanism is unknown. the ryugu samples contained terrestrial microbes and they evolved with time. their dna has not yet been identified. they resemble bacilles, which are everywhere on the earth. 3. microfossils have been found in meteorites [5]. they have been found also in ryugu but only at the surface of ryugu and were reported to be new fossils. the reason could be that microbes have survived only at the surface of ryugu where they receive solar light necessary for photosynthesis. the proposal of [3] is that terrestrial organisms might by some unknown mechanism have contaminated the surface of ryugu and produced the microfossils. 3.3 the tgd view of ryugu neither panspermia hypothesis nor contamination look plausible in the tgd framework. life would have evolved by the same basic mechanism both at the earth and the asteroids and other similar objects. 1. ryugu stays relatively near the earth at its orbit. this could have also made possible the generation of organic matter inside the sample during the period that ryugu has spent at its orbit around the sun. this requires a model for how this happens and standard physics does not provide such a model. 2. the notion of the field body is central in the tgd inspired quantum biology and would act as controller of the biological body [10, 12]. ordinary genetic code is proposed to be accompanied by its dark variant realized at the field body for ordinary particles at it having a very large value of effective planck constant and behaving like dark matter. could the field body of the earth and sun have induced the generation of organic molecules and even bacterial life forms in the same way as they did this at the earth? 3. the notion of the gravitational magnetic body, characterized by gravitational planck constant introduced by nottale [1], containing protons behaving like dark matter, represents new quantum physics relevant to the tgd inspired quantum biology. oh-o− + dark proton qubits and their generalizations based on biologically important ions formed by salts would be the key element of life [14] suggesting besides chemical life also other forms of life. any cold plasma (plasmoids as life forms) and even quartz crystals could give rise to these qubits at temperatures near the room temperature around which the flips of these qubits are possible. the difference of oh bonding energy and o− binding energy determines the relevant energy. its nominal value is .33 ev and is near the metabolic energy quantum of about .5 ev and near to the thermal energy .15 ev at physiological temperatures. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://www.space.com/ryugu-asteroid-sample-earth-life-colonization dna decipher journal | december 2024 | volume 14 | issue 1 | pp. 29-36 35 pitkänen, m., some mysteries of the biological evolution from the tgd point of view 4. these qubits would make the matter living and life in this sense is universal. dark genetic code is predicted and corresponds to the ordinary chemical genetic code. basic biomolecules would give rise to analogs of topological quantum computers. the flipping of these qubits would make quantum computation like information processing possible? pollack effect by photon absorption can induce oh→ o− +dark proton transition and the reversal of this process and the reversal of this process can take place spontaneously. if o−+dark proton has a lower energy than oh, it can be also induced by a presence of electric field or absorption of photons by o− so that oh becomes the minimum energy state. could one understand the findings about ryugu in this framework? 1. the presence of gravitational magnetic bodies of earth and sun could have induced the formation of oh-o− qubits and more general qubits, not only at the earth but also at ryugu. the presence of oh bonds requires hydration and hydration is indeed possible at ryugu. therefore the same mechanism could have led to the emergence of the basic organic molecules at the earth, at mars and inside the ryugu asteroid and meteorites. since the minimal distance of the earth and ryugu from the sun is nearly the same, the temperature of ryugu is near its maximal value when it is near the earth so that the temperature would never get too hot. 2. ryugu is under the influence of the gravitational bodies of both the earth and the sun. ryugu passesnear the earth repeatedly with a period of 4 years. the organic molecules and various hydrated compounds could have gradually formed during about 10 million years as it passed near the earth. also bacterial life could have emerged in this way. therefore contamination need not be in question. received december 10, 2024; accepted december 31, 2024 references [1] nottale l da rocha d. gravitational structure formation in scale relativity, 2003. available at: https://arxiv.org/abs/astro-ph/0310036. [2] a challenge to all geologists of earth. available at: https://www.nealadams.com/challenge.html. [3] genege mj et al. rapid colonization of a space-returned ryugyu sample by terrestrial microorganisms. meteorites & planetary sciences, 2024. available at: https://doi.org/10.1111/maps.14288. [4] pilorget c et al. phosphorus-rich grains in ryugu samples with major biochemical potential. nature astronomy, 2024. available at: https://www.nature.com/articles/s41550-024-02366-w. [5] rozanov ayu et al. new findings of microfossils in the orgueil meteorite. palentological journal, 55:111–115, 2021.available at: https://link.springer.com/article/10.1134/ s0031030121010111. [6] gould sj. wonderful life. penguin books, 1991. [7] pitkänen m. expanding earth model and pre-cambrian evolution of continents, climate, and life. in physics in many-sheeted space-time: part i. https://tgdtheory.fi/tgdhtml/btgdclass1. html. available at: https://tgdtheory.fi/pdfpool/expearth.pdf., 2023. [8] pitkänen m. empirical support for the expanding earth model and tgd view about classical gauge fields. https://tgdtheory.fi/public_html/articles/expearthnewest.pdf., 2021. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://arxiv.org/abs/astro-ph/0310036 https://www.nealadams.com/challenge.html https://doi.org/10.1111/maps.14288 https://www.nature.com/articles/s41550-024-02366-w https://link.springer.com/article/10.1134/s0031030121010111 https://link.springer.com/article/10.1134/s0031030121010111 https://tgdtheory.fi/tgdhtml/btgdclass1.html https://tgdtheory.fi/tgdhtml/btgdclass1.html https://tgdtheory.fi/pdfpool/expearth.pdf https://tgdtheory.fi/public_html/articles/expearthnewest.pdf dna decipher journal | december 2024 | volume 14 | issue 1 | pp. 29-36 36 pitkänen, m., some mysteries of the biological evolution from the tgd point of view [9] pitkänen m. updated version of expanding earth model. https://tgdtheory.fi/public_html/ articles/expearth2021.pdf., 2021. [10] pitkänen m. comparison of orch-or hypothesis with the tgd point of view. https://tgdtheory. fi/public_html/articles/penrose.pdf., 2022. [11] pitkänen m. how animals without brain can behave as if they had brain. https://tgdtheory.fi/ public_html/articles/precns.pdf., 2022. [12] pitkänen m. about long range electromagnetic quantum coherence in tgd universe. https: //tgdtheory.fi/public_html/articles/hem.pdf., 2023. [13] pitkänen m. expanding earth hypothesis and pre-cambrian earth. https://tgdtheory.fi/ public_html/articles/prece.pdf., 2023. [14] pitkänen m. quartz crystals as a life form and ordinary computers as an interface between quartz life and ordinary life? https://tgdtheory.fi/public_html/articles/qcs.pdf., 2024. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://tgdtheory.fi/public_html/articles/expearth2021.pdf https://tgdtheory.fi/public_html/articles/expearth2021.pdf https://tgdtheory.fi/public_html/articles/penrose.pdf https://tgdtheory.fi/public_html/articles/penrose.pdf https://tgdtheory.fi/public_html/articles/precns.pdf https://tgdtheory.fi/public_html/articles/precns.pdf https://tgdtheory.fi/public_html/articles/hem.pdf https://tgdtheory.fi/public_html/articles/hem.pdf https://tgdtheory.fi/public_html/articles/prece.pdf https://tgdtheory.fi/public_html/articles/prece.pdf https://tgdtheory.fi/public_html/articles/qcs.pdf introduction the mystery of life's origin deepens the mystery of cambrian explosion perplexing findings about asteroid ryugu luca from the tgd perspective some basic facts about evolution the number of genes for luca is upper bound for the genes of archaea: what does this mean? two mysteries with a common solution: cambrian explosion and the complexity of luca the perplexing findings about the asteroid ryugu from the tgd perspective some facts about ryugu objections against the panspermia hypothesis as explanation of the findings about ryugu the tgd view of ryugu login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify 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journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x untitled dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 236-243 campbell, r., part i: a critique of river out of eden: on winning by cheating issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 236 article part i: a critique of river out of eden: on winning by cheating robert campbell * abstract dawkins attacks the idea that evidence against the darwinian paradigm implies that unusual features in nature must be perfect from the outset in order for them to work. the example that a specific wasp is attracted to an orchid the shape and smell of a female wasp can be explained by gradual steps, since appearance can vary with distance and angle and so could converge to the size and shape of a female wasp over time. however a wasp cannot mate from a distance so there could be no selection pressure and the orchid would somehow have to strike upon just the right smell from an unlimited variety of odors in a single mutation together with mutations in concert to achieve the right shape and size. similar arguments about honey bees and the evolutions of eyes would require multiple mutations in concert to produce selection pressure. all of this argues strongly against rare random mutations and natural selection as the sole evolutionary mechanism. key words: charles darwin, theory of evolution, cosmic order, intellegent direction, spirituality, atheist, richard dawkins. river out of eden – ch. 3 do good by stealth: double speak even creeps into the title of this chapter of dawkins’ book [3]. values, good and bad, are touted as both the motive and the modus operandi of a mindless creative process. the title refers to a discussion of how the orchid has evolved to imitate both the appearance and smell of the sex organ of the female wasp, thus attracting male wasps to copulate, philandering creatures that they are, and promoting its own pollination. dawkins gets into his discussion by quoting at length from a personal letter from an american minister who read of the phenomena in national geographic. the man was so impressed that he came to believe “...that some kind of god in some kind of fashion must exist, and have an ongoing relationship with the processes by which things come into being.” the man consequently abandoned atheism and embraced the church. this letter has apparently disturbed dawkins, for he responds publicly to the minister’s private letter at length: “...how, i want to ask the minister, can you be so sure that the wasp mimicking orchid (or eye, or whatever) wouldn’t work unless every part of it was perfect and in place? have you in fact given the matter a split second’s thought? do you actually know the first thing about orchids, or wasps, or the eyes with which wasps look at females and orchids? what emboldens you to assert that wasps are so hard to fool that the orchid’s resemblance would have to be perfect in * correspondence: rober campbell, independent researcher. website: http://www.cosmic-mindreach.com e-mail: bob@cosmic-mindreach.com note: the articles presented in this issue are based on my book “downsizing darwin: an intelligent face for evolution” self-published in 1996 [1]. more information is available at my website [2]. dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 236-243 campbell, r., part i: a critique of river out of eden: on winning by cheating issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 237 all dimensions in order to work” [3]. what follows from the pen of an eminent biologist obviously seeking converts to his mindless position is good cause to be disturbed, for he himself has no basis on which to be so sure of blind accident as the sole creative agent. his own logic is riddled with holes. dawkins states that “the purpose of this chapter is to destroy the argument that complicated contrivances have to be perfect if they are to work at all.” now despite what dawkins says, this really isn’t the purpose of the chapter. dawkins’ purpose is clearly to destroy any impression of intelligence at work in the creative order. since the minister linked an intelligent agent of some kind to perfection, dawkins wants to exploit this statement and erode any suggestion that complicated contrivances must be perfect from the outset, then maybe he can float this to triumph over any suggestion of intelligence at work at all in the evolutionary process. in other words, he hopes to succeed by stealth, which he feels would be good. he has contrived the approach to exploit the minister’s sentiments. although this is clearly his hope, the two things are not synonymous. intelligence does not imply perfection in all things from the outset. we know from experience that if we exercise a little intelligence that we can learn by degrees and adjust our course of action accordingly toward a satisfactory result. but the darwinian position does not allow of intelligent feedback or assessment of alternatives prior to selecting a course of action. evolutionary mutations are seen as rare random accidents that just happen to have a survival advantage that becomes established after the fact. there is no intelligent anticipation allowed in the process, no intelligent feedback, no prior value judgments to direct the evolutionary process toward a needed result. having created a straw man, dawkins sets out to destroy him by first running through many examples of creatures being fooled, from insect to human. male stickleback fish are excited to mating behavior by any pear shaped object. an oystercatcher bird will try to incubate an egg as big as an ostrich egg. some ground-nesting birds will roll anything remotely resembling an egg back into their nest. baby herring gulls peck at the red spot on the parent’s bill for food, and will peck at any red spot. black headed gulls will react typically to a dummy gull head mounted on a stick, minus a body. a deaf mother turkey will kill its own young as a predator response to motion alone because it cannot hear their distinctive chirps. bees will clear a live bee from the nest if it is daubed with oleic acid, because this acid is given off by decaying bees and triggers an undertaker response. a female digger wasp always inspects its nest before dragging its prey in, and if its prey is moved a few inches, will keep going back to inspect its nest each time. another digger wasp identifies its nest by landmarks of twigs etc. around its burrow, and if the twigs are moved a few feet, will dive into the ground where it thinks its burrow should be. one digger wasp provisions its larvae in several burrows, according to their daily growth assessed at a morning inspection, and subsequent switching of the larvae doesn’t bring corresponding adjustment in the provisions provided to each one. evolution certainly hasn’t had an easy time exploring the integration of experience. all of this is intended to show that a very crude resemblance between an orchid and a female wasp might well be sufficient. “the general lesson we should learn is never to use human judgment in assessing such matters.” yes, richard dawkins really says this in print. if we are not to use human judgment, what kind of judgment are we supposed to use? dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 236-243 campbell, r., part i: a critique of river out of eden: on winning by cheating issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 238 then he emphasizes again his stated purpose of the chapter, to defeat the fallacy of what he dubs “the argument from personal incredulity.” we are apparently not entitled to disbelieve the exclusive darwinian viewpoint. of these arguments he says, “time and again, it has proved the prelude to an intellectual banana-skin experience.” therefore it must always prove futile to disbelieve the darwinian paradigm, is the implication in his statement. now it must be conceded that not many people will take the time and effort to carefully sift through the verbiage masking and distorting the evidence, to sort out word by word the gross transgressions of common sense that pervade the literature. but that does not justify the darwinian position by default. dawkins further pursues his stealthy purpose by adopting the word “brittle” to describe a device that must be perfect if it is to work at all. our besieged minister surely made a poor choice of words and dawkins is going to milk them for all they are worth, despite the fact that they are really beside the point. man made articles are generally not brittle, says dawkins, for even a 747 can fly on two engines. after ten minutes of thought dawkins says that he can only come up with one near brittle man-made device, namely the arch, since its integrity obviously depends on the interdependence of its parts. now think for just one minute. will half a wheel work? or a gear without teeth? or a roof without supports? or a table without legs? or a pulley without an axle? or a lever without a fulcrum? or a window without a frame? or a door without a hinge and a latch? or a bucket without a bottom? its hardly worth pursuing this tiresome logic. a man can live without one arm or one ear, but not without a heart, or a head. some things are more essential than others to the integrity of the whole and this is no accident. experience is a highly structured affair. but not according to dawkins. he launches into attack against the straw man by listing various examples of mimicry in nature in addition to that displayed by the orchid. among those that he contends creationist propaganda has served up as “brittle” are the camouflage of the tiger and leopard; the fishing rod of the angler fish; femmes fatales fireflies that mimic the flash patterns of other species in order to cannibalize them; saber-toothed blennies that mimic fish that clean a host, then feed on the host; many animals that resemble bark, twigs, leaves, flowers, stones, and seaweed; ground nesting birds that fake injury to protect their young; cuckoo eggs that resemble those of their host species; female mouthbreeder fish with dummy eggs painted on their flanks to attract males to brood real eggs. throughout his argument dawkins focuses on that word perfect, maintaining that is the key contention that makes the creationists wrong and darwinists right. i’m not defending the creationists, only pointing out weaknesses in his arguments. he stresses that not only does visual acuity change from one species to another, so do the conditions. he maintains there will be a continuum of conditions from very bad to very good and then goes into a discussion to explain the obvious. of course visual acuity varies with distance and lighting and angle. we can’t see in the dark or through the back of our head. but then dawkins makes a giant leap of logic. with his smoke screen about perfection in place, holding the reader’s attention on the one hand, on the other hand he tries to float the whole darwinian position past like a magician doing a magic pass. he says, “as evolution proceeds, resemblances of gradually improving perfection can therefore be favored by natural selection, in that the critical distance for being fooled gradually moves nearer.” dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 236-243 campbell, r., part i: a critique of river out of eden: on winning by cheating issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 239 can a wasp copulate with an orchid from a distance? and the wasp is not a night time philanderer that can mistake a lover in the dark. and the wasp is attracted not only by shape and color but also by smell, and the size must be just right for pollination to occur. these are highly complex variables that must be selected together in concert through parallel sets of mutations. smell alone is as characteristic as fingerprints and so vast in its possibilities as to be virtually unlimited. shape and size can be almost anything, and large combinations of color are possible. yet the orchid’s survival depends upon selection from this unlimited range of options, with a very specific need for an insect pollinating vector. somehow this maze of possibilities converges upon a specific wasp sufficiently for the strategy to work, and we are asked to believe that the selection was achieved by repeated parallel sets of blind fortuitous accidents, completely at random. remember that the darwinian position is that mutations are rare accidents and only a rare few offer a survival advantage. earlier on dawkins cites odds of a million million million million million to one for the genetic code evolving twice by accident, so that we must all have evolved from a single cell. the odds of all of the factors coming together by parallel series of rare random mutations in order for the orchid to imitate the wasp in the required time for selection pressure to be effective are so complex as to be not computable, but they are at least of the same order of enormity as the odds that dawkins cites above. try to compute the odds of a fish sprouting a fishing pole complete with a bait on the end of its nose. before this succeeded there must be gillions upon gillions of extinct mistrials among many species of fish, with part poles growing out of their tails and bellies and sides. but dawkins directs the discussion to his liking where he can make a point or two and pretend this wraps up the whole case. by citing a little knowledge acquired by biological research, one is supposed to believe he has the weight of the entire scientific community behind him. he focuses on the eye, the creationist’s favorite conundrum, as he calls it. there is no intention here to defend the creationists’ traditional positions, especially the literal genesis account. the intention is only to explore the weaknesses in dawkins’ arguments for darwinism and show that the evidence is better explained by intelligent direction in the evolutionary process. eyesight, he observes, fades with age, being adaptable to a continuum of tasks, so there is no difficulty in understanding the gradual evolution of the eye. think about this for a moment. does the gradual wearing out of our biological machinery justify the darwinian stance that all life forms, including those complete with eyes, evolved not only gradually but also by blind luck in a game of chance atomic billiards? this is clearly the implication that he wishes to convey in argument after argument that is completely beside the point. i have pointed out before that intelligence allows for learning through intelligent feedback and consequent adjustments to intentionally converge toward an anticipated result. pure chance allows for no communicative feedback and no direction. he now enlists the enormity of geological time to make his case credible, citing the work of two researchers, nilsson and pelger, to show that the eye can evolve in a relatively short period of time. apparently, according to biologists’ reckoning, invertebrate eyes, employing at least nine different design principles, have independently evolved between forty and sixty times from scratch dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 236-243 campbell, r., part i: a critique of river out of eden: on winning by cheating issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 240 among many species. one might well wonder how nine different design principles were conceived. one might well wonder why all this diversity of accumulated information should be lost to the higher sentient evolution of the vertebrates, if evolution really is a linear branching affair that is not otherwise in communication with itself. one might also wonder why the vertebrates should not have to explore the same ground again in order to arrive at a suitable “camera” eye design. later we shall see that the vertebrates are thought to have branched off from the chordates, which diverged in the cambrain period, thus ignoring a couple hundred million years of other invertebrate evolution, including eyes. in any case nilsson and pelger had to start somewhere, he says, and make some assumptions in devising a computer model to simulate the number of generations required to evolve an eye. to start with, they had to assume that a light sensitive cell had already somehow evolved, although it could be of no selective advantage. selection pressure would require some kind of vision process in which the eye could be an integral part to offer a survival advantage. this question is set aside as “a nice subject for future study,” as the critical questions invariably are, since nobody knows how to study them within the darwinian paradigm. the paradigm fails completely with fundamental questions. nilsson and pelger worked at the level of tissues which can change according to random mutations. they began already well on the road to an eye, with a flat retina atop a flat pigmented layer and protected by a flat transparent layer. the critical elements in an eye are thus assumed as already given, arranged in the required order, in correct relative size, and in the correct position, without bestowing any survival advantage whatever to the animal. that surely makes things infinitely easier. how could such a meticulous arrangement of complex cells have happened by accident if it was useless as a functioning eye? we have not yet even mentioned the maze of neural connections from retinal cells to a brain that somehow becomes wired to portray the signals as a meaningful image to a resident observer of some kind, or how this is integrated with other sensory modalities together with visceral and somatic motor responses. in any case nilsson and pelger then let the refractive index of the transparent layer mutate while the shape of the model could deform at random, but under two all important constraints. any mutant change must be small, and it must represent an improvement. how is any improvement to be demonstrated by the creature if the proto eye is not already properly wired to a functioning brain and integrated to some functional extent with its whole nervous system? nilsson and pelger are cheating more than a little bit. but the whole field is so biased that this kind of procedure is allowed. and what basis is there for assuming that ordered hierarchies are not structured into the genetic expression of a host creature such that a comparatively small mutation on one level does not result in comparatively major changes on subsumed levels? hierarchically ordered homoeodomain proteins and homeotic genes that activate batteries of genes in an ordered sequence are recognized in biological text books. but that implies intelligence at work. hierarchical order is not consistent with random order. despite such gaping holes in the logic it was concluded from this hopelessly simplistic computer study that a good camera eye can evolve in fewer than four hundred thousand generations, and for dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 236-243 campbell, r., part i: a critique of river out of eden: on winning by cheating issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 241 small animals this amounts to less than half a million years. what they are talking about is only the evolution of the refractive index and the shape of the eye, and this with cheating. all the really hard stuff is ignored completely. yet dawkins concludes from this camera eye simulation: “there has been enough time for it (the camera eye) to evolve from scratch fifteen hundred times in succession within any one lineage.” is this good impartial science? dawkins [3] makes an admission here, as to his reasons for insisting that evolution must be gradual. “without gradualness in these cases we are back to miracle, which is simply a synonym for the total absence of explanation.” is intelligence a miracle? can we explain how intelligence works, how it’s ordered? we live with it every day, and from very modest self-observation we find that it seeks out spatially, temporally, and intuitively ordered patterns in order to cope with experience. the socio-economic organizations that we function in are also structured communications systems that we have patterned according to the way that experience is implicitly presented to us. we are not totally blind victims of chance in everything that we do. we can plan and be agents of responsible action. since we are also products of the evolutionary process, is it such a travesty of common sense to think that intelligence may also be at work in the evolutionary process? the point is that this avenue of research into the nature of intelligent order has been declared off limits by science while a host of clues abound right under our noses. this is an outrageously unscientific bias that is shared by most of the scientific community. of course eyes evolved. but they didn’t evolve, gradually or otherwise, by blind meaningless luck. dawkins’ whole argument is again completely beside the point. he is blowing smoke to screen the real issues. it is very hard to understand why intelligent academic leaders should devote such strenuous efforts to consign themselves and the whole of humanity to a mindless oblivion. only double speak saves true believers from this personal realization. dawkins [3] goes on to the “dance language” of honey bees in an effort to explain how it could have evolved gradually with intermediate steps. a foraging bee returns laden with pollen and nectar and then proceeds to communicate where the food supply is by doing a figure eight dance in the darkness inside the hive on a vertical comb. there is a straight section in the middle of the figure eight which is oriented like the needle of a compass to tell the direction in relation to the sun, and the position of the sun is adjusted for by an internal clock that bees have. the distance is communicated by the rate of a peeping sound the dancer bee makes, perhaps combined with its rate of turning and waggle. the other worker bees then leave the hive and fly in a straight line to the food supply. before going on let’s examine dawkins position closely again. ask yourself, is it sufficient to establish that evolution is a gradual process in order to prove the darwinian position that all advances are the result of rare random mutations that accidentally endow an incremental survival advantage? we all know that intelligence can gradually accomplish things. but as dawkins seems to see it there are only two contestants in the field, the darwinists and the biblical creationists with a genesis bent. he doesn’t seem to acknowledge the possibility that the whole creative process could itself be an intelligent process, with all of the properties that we normally ascribe to intelligence. this means that there is an intelligent order that is both transcendent and immanent through which all things are in some way interrelated. this approach at least has the advantage of dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 236-243 campbell, r., part i: a critique of river out of eden: on winning by cheating issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 242 explaining the natural emergence of our own intelligence and it is not necessarily opposed to a certain niche for both the darwinian adaptation of species, and also the essential values that have evolved through our various religious traditions. but dawkins’ extreme and exclusive stance keeps running into insurmountable difficulties even on the grounds that he chooses to prove its efficacy. dawkins goes on to point out that many insects navigate by the sun and bees can see the polarized direction of light, and thus can navigate on cloudy days. now this capacity to see the polarization of light, however gradually it may begin, must be the result of a fortuitous series of random sets of mutations, according to darwinism, even though fortuitous mutations are extremely rare. each mutation must be a set, because it must fully integrate specially designed emerging receptors in the bees’ eyes into the whole nervous system of the bee, together with its motor responses to survival needs, as the bee is genetically programmed to perceive and respond to them. it is very hard to imagine that one genetic mutation can accidentally alter the eyes together with a host of adjustments to the nervous system and behavioral responses. and if it is a set, similar complementary sets of mutations must occur many times in succession to effect the result gradually through selection pressure. and only rare mutations endow a survival advantage. how then can a random collection of mutations occur simultaneously to alter the eye and nervous system to act in concert in any meaningful way. a bee might well begin to grow antlers first. it is dawkins’ position that this capacity evolved as an adjunct to the evolving bee’s eye. it must also have evolved in parallel with the bee’s internal clock in such a way that both are linked to motor responses to need. the directional process is reversed for bees in the southern hemisphere, and reverses annually in the tropics, so a rare mutation must do more than just fortuitously hit on perceiving polarized light, and being able to use it. it must interpret the information, linking this to a specific spatial direction of motion with respect to the sun when it is shining in various parts of the world and also to an internal clock. if all of these things do not come together at once, at least to some extent, then no survival advantage can be demonstrated that will drive evolution in a positive direction according to the darwinist theory. if dawkins or anyone one else can conceive of how the complexity of this task can be accomplished without benefit of intelligent input from a broad base of experience, why don’t they explain it instead of producing peripheral smoke screen arguments that mask and ignore the main issues. dawkins deals only with what he portrays as the main problem, to establish a credible series of gradual intermediate steps. some tropical bees build exposed combs attached to a tree. one species is cited that dances on top of the comb such that the straight run of the dance points to the food, and the straight run may have begun with a few steps on take off that became ritualized. an obvious way to prolong the take off run is to repeat it, thus leading to a figure eight, dawkins says. it might be obvious to an intelligent human being. but is he now talking about a random genetic mutation that directs behavior, or is he investing the bee with an independent intelligence governing behavior to some extent, such that it also directs its genetic programming? dawkins own words imply the latter, which he earlier insists is utterly impossible. there is no intelligent feedback in the darwinian position. to this point, none of this discussion addresses the question of how the bees evolve the capacity to identify the message that is being transmitted through hearing and feel, and then translate it into the appropriate action. to perform the dance is one thing. to perceive and interpret it is another. dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 236-243 campbell, r., part i: a critique of river out of eden: on winning by cheating issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 243 why should the other bees pay any attention to one bee that has slowly begun to act just a little bit strange? why should they gradually intuit some meaning in this bee’s slight deviations from the norm. do bees have an empathy for one another? are they consciously aware to some extent? are they psychically bonded? are they in intimate communication? do they experience mutual needs? do they have some form of inter-bee value judgment? is there some level of intelligent comprehension of the dance that can be learned, as more advanced creatures do, by following adults when they are young and gradually making the necessary associations? could there be some collective patterned energy at work, in conjunction with their genetic make up, that they independently relate to and that guides them accordingly? or is their response to the dance only blindly genetically programmed by atomic billiards? in any of the former cases there is intelligence at work in the evolutionary process. in the latter case, the already prohibitive odds of a random collection of simultaneous parallel mutations working toward a concerted result are multiplied many orders of magnitude. “the steamhammer of geological time” is not long enough to crack this “peanut” as dawkins calls it, because concerted parallel mutations in a whole generation of individuals are necessary before they can even begin to demonstrate a selection pressure to their collective advantage. bees must slowly learn to dance according to where they found flowers. genetics must relate to direction and distance—to space and time. as if the odds against a concerted set of such mutations happening by accident once was not enough, another complementary set of complex mutations must again happen by chance, to interpret the dance—and again, and again, and again in generation after generation after generation, if the final result is to be achieved gradually by selection pressure. dawkins’ own argument of gradualness in the evolutionary order only compounds the already impossible odds against it happening by chance to more impossible levels. references 1. robert campbell, downsizing darwin: an intelligent face for evolution. mindreach library (1996). 2. http://www.cosmic-mindreach.com 3. richard dawkins, river out of eden: a darwinian view of life. basic books (1996). 4. richard dawkins, the blind watchmaker: why the evidence of evolution reveals a universe without design. w. w. norton & company (1996). 5. richard dawkins, the selfish gene. oxford university press (1990). login dna decipher journal open 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login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x dna decipher journal | july 2017 | volume 7 | issue 1 | pp. 17-26 vary, a., fibonacci sunflowers, mathematical objects & cubic electrons issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 17 article fibonacci sunflowers, mathematical objects & cubic electrons alex vary * abstract we examine the uncanny involvement and influence of mathematical truths on the minutest and largest properties and phenomena of the physical world and the remarkable effectiveness of mathematics in describing and predicting natural phenomena. indeed, mathematics a vast and ingenious conceptual structure without empirical content is an indispensable and powerful theoretical instrument for the scientific understanding of virtually every aspect of the physical world. selected examples show the remarkable associations among specific mathematical objects and macroscopic and quantum matter and phenomena. keywords: mathematical object, euler's identity fibonacci sequence, golden ratio, wave-particle, duality, heavy electrons, higgs boson. introduction space and time have been assigned aspects of empirical reality by geometers who invented the language and algebra of dimensionality. prior to that, space and time were indifferently perceived as amorphous realities, devoid of metrics. initially a tabulae rasae, with metrics, space and time became mathematical objects, e.g., geometric manifolds with measurable attributes: shapes, distances, topology, intervals. euclid and other ancient geometers gave spatial dimensions axiomatic meaning by positing mathematical objects such as lines, triangles, circles, spheres, cubes and other regular and irregular geometric solids. descartes recognized relations among geometric points and temporal instances, giving them meaning by means of algebraical coordinates and equations. this was followed by the notion of multi-dimensional spaces. then, theoretical physicists elaborated on the geometric details by imbuing space and time with material meanings and properties. accordingly, synthetical spaces ostensibly produce quantum particles, quantum waves and force fields that interact energetically, stochastically, and periodically in synthetical time. euclidian geometric space and various non-euclidian abstract spaces of gauss, lobachevsky, bolyai, and riemann maintained the notion of three ‘obvious’ spatial dimensions. then, along came the notion of four-dimensional 'spacetime' the union of the three dimensions of space with the single dimension of time to create a combined entity. the ‘deformation’ of synthetical spacetime ostensibly explains gravitation. the notion of spacetime was introduced in the twentieth century by hermann minkowski and elaborated upon by albert einstein in his general theory of relativity. current theoretical concepts of spacetime are not restricted to just four dimensions. in an attempt to explain quantum particles and waves, ‘string’ theory posits a ten-dimensional hyper-spacetime. ‘m-theory’, which is an elaboration of string theory, posits eleven-dimensional * correspondence: alex vary, phd, retired nasa scientist & independent researcher. email: axelvary@wowway.com mailto:axelvary@wowway.com dna decipher journal | july 2017 | volume 7 | issue 1 | pp. 17-26 vary, a., fibonacci sunflowers, mathematical objects & cubic electrons issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 18 hyper-spacetime and mathematical objects that reside in it. calabi-yau manifolds constitute an interesting class of synthetical geometric spaces, that is, mathematical objects which shing-tung yau showed to be possible upon proving the calabi conjecture [1]. these spaces or shapes are based on complex space-time coordinates which bifurcate into even numbers of ‘real’ and ‘complex’ dimensions. the six-dimensional case is of special interest to string theory, where it serves as a candidate for the geometry of the theory's six hidden, or extra 'compactified' dimensions. they are presumed to be compactified because they are not observed ­ they are infinitesimal in relation to the metrics of three dimensional space. this compactification notion is really an unnecessary ploy. after all, if we can assign four pseudo dimensions to spacetime, then we can keep adding more dimensions as needed to satisfy, perhaps never quench, the thirst analytical geometers and theoreticians have for even more multidimensional spaces. geometric compactification the 'rolling up of a space' so that it is minute yet definable is considered necessary for a viable string theory. in string theory different ways of compactifying, the extra dimensions lead to the notion that their modulations comprise elementary ‘physical objects’ such as electrons and photons. in this sense, synthetical spacetime ‘manifolds’ are considered to be able to manifest as physical objects. various ‘vibrational modes’ of these spacetime manifolds have been taken as being the origins and constituents of quantum particles, fields and forces that pervade the cosmos. thus, spacetime origami has emerged as a tool to fold-forge quantum particles. shin-tung yau in the shape of inner space holds that the study of calabi-yau manifolds has provided a promising laboratory for thought experiments a laboratory that can inform the physics of string theory and also cosmology. it is a testament to the agility of the human mind that we began thinking about calabi-yau's manifolds strictly as objects, albeit mathematical objects, before there was any obvious role for them in physics. yau writes, “we're not forcing calabi-yau's on nature, but nature seems to be forcing them upon us.” the study of these compactified multi-dimensional manifolds has enabled both physicists and mathematicians to learn many interesting and unexpected things about the likely nature of elementary particles. although calabi-yau spaces may not be the ultimate destination, they may well be important stepping-stones to the next level of understanding. yau’s comments echo what eugene wigner called "the unreasonable effectiveness of mathematics in the natural sciences." yau and wigner marvel that laws of physics closely complement the mathematician's penchant for what is ‘elegant and beautiful’. at the same time, they grapple with the deep mystery of why this should be the case. mathematical beauty & truth euler's identity is often cited as an example of deep mathematical beauty. it is also a precise statement of mathematical truth which links three basic arithmetic operations: addition, multiplication, and exponentiation and also links five fundamental mathematical constants: the number 0, the null identity, dna decipher journal | july 2017 | volume 7 | issue 1 | pp. 17-26 vary, a., fibonacci sunflowers, mathematical objects & cubic electrons issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 19 the number 1, the unit identity, the number π, which is ubiquitous in the geometry of euclidean space, the number e, the base of natural logarithms which occurs widely in mathematical analysis, the number i, the imaginary unit of the complex field of numbers. both π and e are transcendental numbers. euler's identity (named after the swiss mathematician leonhard euler) is the equality e iπ + 1 = 0 e is euler's number, the base of natural logarithms: 2.718281828 . . . i is the imaginary unit, which satisfies i 2 = -1, and π is the ratio of the circumference of a circle to its diameter: 3.14159265 . . . euler's identity is a special case from complex analysis, which states that for any real number x, e ix = cos x + i sin x where the inputs of the trigonometric functions sine and cosine are given in radians. when x = π radians, or one half-turn (180) around a circle: e iπ = cos π + i sin π since, cos π = -1 and sin π = 0 it follows that e iπ = 1 + 0i which yields euler's identity: e iπ + 1 = 0. it should not be surprising that euler's identity precisely describes, seemingly unrelated physical phenomena at macroscopic, microscopic, and quantum levels. figure 1 illustrates how the euler's identity is related to the -180 o flip of a playing card, which also corresponds to the act of turning a page, opening a book, a stenographer’s tablet, or a laptop computer. at the quantum level, euler's identity describes the behavior of entangled quantum particles. measurements of physical properties, such as spin, performed on entangled particles are found to be correlated by euler’s identity. for example, if a pair of particles is simultaneously generated in such a way that their total spin is zero, and one particle has a spin-vector ‘up’, then the spin-vector of the other particle is ‘down’, or a -180 o flip measured on the same coordinates axes. the entanglement paradox although described by euler’s identity is unexplained. it appears that one particle of an entangled pair ‘knows’ the spin measured on the other, even though there is no known means for such information to be communicated between the particles, which at the time of measurement may be separated by arbitrarily large distances [2]. dna decipher journal | july 2017 | volume 7 | issue 1 | pp. 17-26 vary, a., fibonacci sunflowers, mathematical objects & cubic electrons issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 20 fibonacci sequence & golden ratio fibonacci numbers appear unexpectedly and often in mathematics, so that there is an entire journal dedicated to their study. applications of fibonacci numbers include computer algorithms such as the fibonacci search technique and the fibonacci heap data structure. fibonacci numbers also appear in biological settings such as branching in trees, the arrangement of leaves on a stem, the fruit sprouts of a pineapple, the arrangement of a pine cone's bracts, and prominently in sunflower seed patterns. the incremental number of petals on flowers often follows the fibonacci sequence . . . 3, 5, 8, etc. so that four-leaf clovers are extremely rare. ratios of successive pairs of numbers in the fibonacci sequence converge to the ‘golden ratio’ which appears in logarithmic spiral patterns in nature, including the spiral arrangement of leaves and other plant parts, snail and nautilus shells, and the cochlea of the inner ear. the ancient greeks and modern architects and artists have felt compelled to apply the golden ratio in their structures and works to achieve elegance and beauty. the fibonacci numbers or fibonacci sequence are the numbers in the following integer sequence: 1, 1, 2, 3, 5, 8, 13, 21, 34, 55, 89, 144, . . . or the alternative sequence: 0, 1, 1, 2, 3, 5, 8, 13, 21, 34, 55, 89, 144, . . . by definition, the first two numbers in the fibonacci sequence are either 1 and 1, or 0 and 1, depending on the chosen starting point of the sequence, and each subsequent number is the sum of dna decipher journal | july 2017 | volume 7 | issue 1 | pp. 17-26 vary, a., fibonacci sunflowers, mathematical objects & cubic electrons issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 21 the previous two the fibonacci spiral an approximation of the golden spiral is a logarithmic spiral whose growth factor is φ, the golden ratio. that is, a golden spiral gets wider (or further from its origin) by a factor of φ for every quarter turn it makes. expressed algebraically, for two quantities (a) and (b) with (a) > (b) > 0, if (a + b)(a) = (a)(b), then, by definition (a)(b) = φ = (1+5)(2) = 1.618033988 . . . simplification and substitution of (b)(a) = 1φ yields the relation: φ 2 = φ + 1 = 2.618033988 . . . the sequence of the ratios of successive pairs of fibonacci numbers fn+1fn converges to φ. similarly, the sequence of the ratios of the sums of the first n fibonacci numbers fn fn converges to φ 2 . the latter relationship is illustrated in figure 2 and is ostensibly significant in delimiting the size of sunflowers, daisies, and other plants and perhaps even ‘arms’ of spiral galaxies. the seed number increments of a sunflower follow the fibonacci sequence as they fill the outside space away from the center. during the process, sunflower seeds form spiraling patterns. in some cases, the seed heads are so tightly packed that total number can get quite high as many as 144 or a higher fibonacci number. the total number of seeds tends to match a fibonacci number. but, since the fibonacci sequence never ends, what limits the total number of seeds in a sunflower? why are there no sunflowers as big as dinner plates or tractor wheels? the obvious answer is that plant physiology controls growth factors which limit the diameter and size peculiar to sunflowers, daisies, and other flora allowing the best exposure to sunlight and other factors. yet, we observe from the curve in figure 2 that beyond approximately fibonacci number 144 the golden ratio φ 2 is dna decipher journal | july 2017 | volume 7 | issue 1 | pp. 17-26 vary, a., fibonacci sunflowers, mathematical objects & cubic electrons issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 22 very quickly reached. we cautiously infer that the sunflower seed pattern spiral shape and size are governed and limited by the golden ratio φ 2 = φ + 1 = 2.618033988. the ‘arms’ of spiral galaxies tend to follow the fibonacci pattern and golden ratio. the milky way and neighboring andromeda galaxy have several spiral arms, each of them a logarithmic spiral. like sunflowers, spiral galaxies appear to conform to size limitations which may be attributed to a range in mass content consistent with the golden ratio. factors governing spiral galaxy size range apparently include so-called dark matter and dark energy and also the ‘winding’ constraints that typify the shape and extent of the spiral arms. wave-particle duality myth in the double-slit experiment light passing through two precisely cut parallel slits in a thin opaque plate is collected on a photo-sensitive detector screen. after the photons pass through the slits, the image produced on the detector screen consists of fringes, an interference pattern, with light and dark regions corresponding to where light waves have constructively and destructively interfered, figure 3. the interference pattern is taken as evidence of wave-particle duality, as inferred from the application of wave-function calculations. when photons or other quantum ‘particles’ pass through the double slit, a calculation which assumes that the photons behave as waves is needed to predict the interference pattern. when the fringe pattern is examined, it is evident that the pattern was built piecemeal quantum by quantum not by continuous wave fronts forming fringes composed of a patterned accumulation of random spots. during transit, each photon, from the source to detector screen through one or the other double slit evolves, according to the schrödinger wave-function, and spreads out in space as an assumed wave front. but the actual measurement on the detector screen finds each photon deposited as a quantum parcel at a particular spot on the detector surface. this is unanticipated by the wave-function it is called wave-function collapse. this is explained by assuming wave-particle duality, that is, photons in transit are waves which become particles as they impinge the detector dna decipher journal | july 2017 | volume 7 | issue 1 | pp. 17-26 vary, a., fibonacci sunflowers, mathematical objects & cubic electrons issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 23 screen. it is better to admit that photons are photons and to avoid describing photons as either waves or particles. interfering cylindrical wave fronts are mathematical objects which are assumed to describe photons in transit because they effectively predict the probable fringe pattern of illumination and photo-excitation of actual particles that comprise the detector screen photo-sensitive granules. the mystery still remains in that the pattern is built piecemeal quantum by quantum not by the diffuse spreading of continuous wave fronts. an alternative way to describe the transit of photons or other quantum ‘particles’ is based on a louis de broglie concept adopted and developed by david bohm. he postulated that photons travel through both slits, but that each photon has a well-defined trajectory and passes through exactly one of the slits. according to bohm, photon interactions govern the trajectory of each photon instant by instant. this implies a definable mathematical and empirical ‘configuration space’ which guides the photons to their destinations [3]. the de broglie bohm ‘pilot-wave’ theory attempts to explain the behavior of photons without reference to wave-particle duality the associated particle is superfluous since pure wave theory is deemed sufficient. super-heavy cubic electrons in 1936, einstein expressed the counter-intuitive notion that “perhaps we must give up, by principle, the spacetime continuum.” current quantum gravity models assume that spacetime is discontinuous and particulate that spacetime is a fractal substance and that the granularity of spacetime is on the scale of planck length (10 -33 centimeter) and planck interval (10 -43 second) [4]. in agreement, we postulate that spacetime consists of energetic ‘four-dimensional’ parcels dynamic mathematical objects which consist of cubical volumes (voxels) of space that oscillate in time and that spacetime is a deformable substance consisting of tightly tesselated voxels. this corresponds to einstein’s concept of a deformable spacetime, that is, a substantive material-like spacetime. the tensor calculus of his general theory of relativity demanded it. according to the theory, gravitational deformation of spacetime adjacent to the sun is analogous to the deformation of a trampoline surface by a heavy bowling ball tossed upon it. modified spacetime voxels (cubic spacetime units) are also proposed as fundamental building blocks of subatomic quantum parcels such as neutrinos, electrons, positrons. it will be seen that this leads to the prediction of heavy electron masses which agree with and surpass the standard model of particle physics. dimensional analysis of the equation, e = mc 2 indicates a profound relation between the ratio (e/m) and the space/time ratio [l/t] 2 . the explicit meaning of the equation is that nuclear binding energies and mass defects are related that matter (mass) and energy are interchangeable and complementary. the implicit meaning of e = mc 2 is that energy and mass are essentially properties of space and time, that is, space-displacement [δl] 2 and time-interval [δt] 2 . we postulate that select spacetime parcels (voxels) have energy and mass and contribute energy and mass when combined as components of sub-atomic quantum parcels. this idea is applied in an dna decipher journal | july 2017 | volume 7 | issue 1 | pp. 17-26 vary, a., fibonacci sunflowers, mathematical objects & cubic electrons issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 24 abstract cubic representation of electrons according to the following thought experiment which models electrons as cubelike mathematical objects [5]. the basic electron, as depicted in figure 4, is essentially naked and may enjoy only a transitory existence. the naked electron is represented by the intersection of three mutually orthogonal strings and branes which carry mass, spin, and charge (a borrowing from string and m-theory). these properties are purely energetic potentialities and at this stage are undefined as physically measurable properties. according to our cubic electron model, after the naked electron is cloaked with a cubic spacetime voxel, its electric charge, spin, and mass appear as measurable properties. it then becomes a generation 1 electron with measurable mass of 0.511 mev and also conforms with standard model electric charge (-1) and spin (½) properties. a generation 2 electron consists of 8 generation 1 modules and 2 3  0.511 = 4.088 mev. a generation 3 electron consists of 27 generation 1 modules and 3 3  0.511 = 13.797 mev. the charge (-1) and spin (½) remain the same for all generations of heavy electrons. we use the generation 3 cubic electron module for generating super heavy electrons (figure 4). a generation 4 electron consists of 8 generation 3 modules and 2 3  13.797 = 110.4 mev. a generation 5 electron consists of 27 generation 3 modules and 3 3  13.797 = 372.5 mev. a generation 6 electron consists of 64 generation 3 modules and 4 3  13.797 = 883.0 mev. a generation 7 electron consists of 125 generation 3 modules and 5 3  13.797 = 1724 mev. fermat’s last theorem seems to govern the formation of cubic electrons. for example, a generation 4 and a generation 5 cubic electron cannot be added together to form a more massive cubic electron because, according to the theorem, the sums of cubes of successive integers are not closed under addition. fermat’s last theorem states that for n > 2 no integers a, b, c, n can be dna decipher journal | july 2017 | volume 7 | issue 1 | pp. 17-26 vary, a., fibonacci sunflowers, mathematical objects & cubic electrons issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 25 found such that a n + b n = c n . the cubic electron model not only predicts the muon and tau (tauon) masses but shows seven generations (with more possible) where the standard model projects only two generations of heavy electrons. the slight discrepancies between the standard model and cubic heavy electron mass predictions may be due to measurement anomalies with these highly transient particles. the standard model holds that there are three generations of electrons: the first generation being the basic electron itself, while the second generation is the heavier muon, and the third, the even heavier tauon. all three possess the same charge (-1) and spin (½) as an electron but differ greatly in mass. muons were discovered by carl d. anderson and seth neddermeyer at caltech in 1936, while studying cosmic radiation. the muon is a theoretically predicted heavy electron with a mass of 105.7 mev. the tau was detected in a series of experiments between 1974 and 1977 by martin lewis perl with his colleagues at the slac national accelerator laboratory and the lawrence berkeley laboratory group. the tauon mass is adduced as 1777 mev. in their free state, these heavy electrons decay almost instantly. some types of heavy electrons are found within a number of lanthanide and actinide compounds, where they exhibit a large effective mass, comparable to the mass of a muon. heavy electron mass may reach 1,000 mev in exotic ‘heavy fermion’ materials. a microscope that was designed to image electron arrangements and interactions in crystals revealed electrons that possess extraordinary mass under certain extreme conditions. these heavy electrons appear to be confined electrons as they interact with crystal lattices that they traverse. apparently, under extreme conditions, unusual phase transitions occur in particular materials causing electrons to take on extraordinary mass. these heavy electrons are apparently unstable unless they interact with and acquire mass in certain crystalline lattice structures. this thought experiment adopts the idea that spacetime is particulate and substantive and that certain manifestations spacetime voxels appear as electrons. the standard model of particle physics postulates the existence of the higgs boson which imparts to electrons and other elementary particles gravitational mass and inertia. the higgs boson was inserted in the standard model ad hoc along with other elementary particles which are grouped in an arbitrary way and which depend on 24 numbers whose values cannot be deduced from first principles, but which need to be chosen to fit the observations. although the standard model is imperfect, it is considered adequate for present purposes. spacetime voxels, as conceived here, have the properties attributed to the higgs boson and may incrementally impart mass to elementary particles. dna decipher journal | july 2017 | volume 7 | issue 1 | pp. 17-26 vary, a., fibonacci sunflowers, mathematical objects & cubic electrons issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 26 conclusion the previous discussion elaborates on the uncanny relations among pure, perfect mathematical objects and physical, material, measurable, objects to the quantum level. in the case of euler’s identity we note that even one of the most esoteric mathematical statements relates to mundane objects and actions. the fibonacci sequence and golden ratio are so pervasive that one is tempted to conclude that objective reality is governed by the sequence and ratio. of course, they are simply mathematical descriptors which have observable manifestations. other mathematical constructs, such as the de broglie bohm ‘pilot-wave’ theory describe unobservable quantum phenomena and attempt to explain their measurable behavior. they are purely intellectual constructs without empirical content but necessary for scientific reasoning. the cubic electron conceptualization incorporates string theory to assign structure to an ostensibly structureless entity to explain experimental observations and measurements. mathematical conceptualizations may anticipate aspects of empirical reality later discovered by sophisticated observations and measurement techniques. the examples cited illustrate that “. . . mathematical as well as logical reasoning make explicit what is implicitly contained in a set of premises while contributing to the content of our knowledge of empirical matters . . . mathematics is entirely indispensable as an instrument for the validation and even for the linguistic expression of such knowledge” [6]. we note that mathematical truths which echo empirical observations and discoveries of experimental science illuminate and often predict them. references 1. shape of inner space, shing-tung yau and steve nadis, basic books, 2010. 2. my universe a transcendent reality (part three, pp. 147-149), a. vary, xlibris, 2011. 3. a suggested interpretation of the quantum theory in terms of hidden variables. david bohm, physical review 85: 166–179, 1952 4. three roads to quantum gravity, lee smolin, basic books, 2001. 5. cubic lattice nucleus model & cryogenic cosmology, a. vary, prespacetime j, vol. 7, no 2, 2016. 6. on the nature of mathematical truth, carl g. hempel, in the world of mathematics, vol. iii, james r. newman, ed., simon and shuster, 1956. login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other 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access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x dna decipher journal| november 2011 | vol. 2 | issue 3 | pp. 319-329 319 pitkänen m. oil droplets in water as a primitive life form? article oil droplets in water as a primitive life form? matti pitkänen 1 abstract the origin of life is one the most fascinating problems of biology. the classic miller-urey experiment was carried out almost 60 years ago. in the experiment sparks were shot through primordial atmosphere consisting of methane, ammonia, hydrogen and water and the outcome was many of the aminoacids essential for life. the findings raised the optimism that the key to the understanding of the origins of life. after miller’s death 2007 scientists re-examined sealed test tubes from the experiment using modern methods found that well over 20 aminoacids-more than the 20 occurring in lifewere produced in the experiments. the urey-miller experiments have yielded also another surprise: the black tar consisting mostly of hydrogen cyanide polymer produced in the experiments has turned out to be much more interesting than originally thought and suggests a direction where the candidates for precursors of living cells might be found. in earlier experiments nitrobenzene droplets doped with oleic anhydride exhibited some signatures of life. the droplets were capable to metabolism using oleic anhydride as ”fuel” making for the droplet to move. droplets can move along chemical gradients, sense each other’s presence and react to it and have also demonstrated rudimentary memory. droplets can even ”solve” a maze having ”food” at its other end. the basic objection against identification as primitive life form is that droplets have no genetic code and do not replicate. the model for dark nucleons however predicts that the states of nucleon are in one-one correspondence with dna, rna, trna, and aminoacid molecule and that vertebrate genetic code is naturally realized. the question is whether the realization of the genetic code in terms of dark nuclear strings might provide the system with genetic code and whether the replication could occur at the level of dark nucleon strings. in this article a model for oil droplets as a primitive life form is developed on basis of tgd inspired quantum model of biology. in particular, a proposal for how dark genes could couple to chemistry of oil droplets is developed. 1 introduction the origin of life is one the most fascinating problems of biology. the classic miller-urey experiment was carried out almost 60 years ago. in the experiment sparks were shot through primordial atmosphere consisting of methane, ammonia, hydrogen and water and the outcome was many of the aminoacids essential for life. the findings raised the optimism that the key to the understanding of the origins of life. after miller’s death 2007 scientists re-examined sealed test tubes from the experiment using modern methods found that well over 20 aminoacids more than the 20 occurring in life were produced in the experiments. the urey-miller experiments have yielded also another surprise: the black tar consisting mostly of hydrogen cyanide polymer produced in the experiments has turned out to be much more interesting than originally thought and suggests a direction where the candidates for precursors of living cells might be found. in the earlier experiments nitrobenzene droplets doped with oleic anhydride exghibited some signatures of life. the droplets were capable to metabolism using oleic anhydride as ”fuel” making it possible for the droplet to move. droplets sensed each other’s presence and reacted to it and also demonstrated rudimentary memory. in this article a model for the oil droplets as primitive life form is developed using as a constraint the tgd inspired quantum model for living matter. the key ingredients are the notions of magnetic body, the assignment of dark matter identified a hierarchy of macroscopic quantum phases to a hierarchy of planck constants, zero energy ontology, the model for dna-cell membrane system as topological quantum computer, and negentropy maximization principle combined with the notion of number theoretic entropy. this entropy can be negative for rational and even algebraic entanglement probabilities, which inspires the vision about life as something in the intersection of real and p-adic worlds. 1correspondence: e-mail:matpitka@luukku.com issn: 2159-046x dna decipher journa www.prespacetime.com published by quantumdream, inc. http://en.wikipedia.org/wiki/miller-urey mailtomatpitka@luukku.com dna decipher journal| november 2011 | vol. 2 | issue 3 | pp. 319-329 320 pitkänen m. oil droplets in water as a primitive life form? the basic objection against the identification of oil droplets as a primitive life form is that droplets have no genetic code and do not replicate. the tgd inspired model for dark nucleons however predicts that the states of dark nucleon are in one-one correspondence with dna, rna, trna, and aminoacid molecules and that vertebrate genetic code is naturally realized. the question is whether the realization of the genetic code in terms of dark nucleon strings might provide the system with genetic code and whether the replication could take place at the level of dark nucleon strings rather than droplets. tgd inspired quantum model of biology leads to a model for oil droplets as a primitive life form. in particular, a proposal for how dark genes could couple to chemistry of oil droplets is developed. 2 intelligent oil droplets new scientist tells about a new twist related to the urey-miller experiment. martin hanczyc and his colleagues of university of southern denmark in odense are doing research with a rather ambitious goal: the discovery of the recipe of life. the highly demanding challenge is to find candidates for the protocell that preceded the recent cell. what makes the task so difficult that it is not even clear what one should be searching for. for instance, what basic characteristics distinguishing living matter from inanimate systems protocell is expected to have before one can speak about primitive life form? and if one accepts the dogmas of standard biology, one encounters also the nasty hen-egg question which came first: metabolism or the genetic machinery. hanczyc and his colleagues have been experimenting with simple candidates for primitive life forms: oily nitrobenzene [17] droplets doped with oleic anhydride [19] immersed in alkaline aqueous solution (alkalinity is by definition an ability to reduce acidicity). they have found that these systems have some attributes generally associated with life. the recent experiments replaced oleic anhydrite with the black tar consisting of complex branched and fractal looking hydrogen cyanide (hcn) polymer [16] produced by urey-miller experiments and found that also now the droplets exhibit lifelike behavior: they sense and respond their neighbors and move towards ”food” sources. the earlier experiments using nitrobenzene droplets doped with oleic anhydridge immersed in alkaline solution began immediately to move along straight lines. what happened that the oleic anhydride at the surface of the droplet reacted with the water splitting to two oleic acid molecules [18] by hydration. this dropped the surface tension of the droplet and by a kind of spontaneous symmetry breaking the reaction rate had maximum at some point of the droplet and a ”hot spot” was generated drawing oleic anhydride from the interior of the droplet and generating a convective flow. a ph gradient develops along the surface. the oleic acid in turn moved along the droplet surface from the hot spot to the diametrically opposite side of the droplet (http://pubs.acs.org/doi/abs/10.1021/ja806689p) [21]. the net effect was a linear motion. ph gradient is claimed to be essential for the generation of motion but i must admit that i do not quite understand this point. a primitive metabolism liberating energy is obviously in question. by momentum conservation the total momentum for the convective flow and flow of oleic acid was compensated by a center of mass motion of the droplet. one could claim that this process belongs to the same class of self-organization processes as the generation of convection patterns as one heats liquid from below. other researchers have however discovered that the oil droplets can also travel along chemical gradients, something known as chemotaxis used by many bacteria to find food and void threats. one oil droplet managed even to solve” a complex maze containing ”food” at its other end [20]. whether this kind of behavior can be regarded as a mere chemistry is far from obvious to me. to me this a achievement look like a genuinely goal directed intentional behavior. hanczyc has also found that when the oil droplets approach each other they change course to avoid collision, or can circle each other-like partners in viennese waltz! oil droplets seem to have even memory. by videoing the paths of oil droplets hanczyc found that the decision to stop or continue was not random but the behavior at any point of orbits was affected by the earlier behavior. this is by the way an elegant experimental manner to show that non-deterministic behavior is not just randomness. the experiments have been also carried using instead of oleic anhydride mineral oil consisting of a mixture of alkanes having as building block polymers from from ch4 by dropping two hydrogen from each c as also lipids have (methane ch4 is the simplest alkane). what distinguishes mineral oil molecules from the oleic anhydride issn: 2159-046x dna decipher journa www.prespacetime.com published by quantumdream, inc. http://www.newscientist.com/article/mg20928023.900-primordial-pacman-oil-droplet-hints-at-lifes-origin.html http://www.revleft.com/vb/oil-droplets-hint-t151201/index.html?p=2042209 http://flint.sdu.dk/people/martin_hanczyc.html http://en.wikipedia.org/wiki/nitrobenzene http://www.wolframalpha.com/entities/chemicals/oleic_anhydride/zq/4d/dm/ http://en.wikipedia.org/wiki/alkaline http://faculty.uncfsu.edu/aumantsev/research/published/scannig_v25_19-24_2003.pdf http://en.wikipedia.org/wiki/oleic_acid http://pubs.acs.org/doi/abs/10.1021/ja806689p http://www.newscientist.com/article/dn18391-intelligent-oil-droplet-navigates-chemical-maze.html dna decipher journal| november 2011 | vol. 2 | issue 3 | pp. 319-329 321 pitkänen m. oil droplets in water as a primitive life form? molecules are the oxygen atoms in the middle of the reflection symmetric linear molecule. also now the droplets move although the process takes place with a slower rate. the basic objections against the identification of the oil droplets as a life form is that they do not replicate and there is no genetic code. one must be however very cautious with this kind of statements. maybe the primary life forms are not the droplets and the behavior of droplets reflects the control actions of these life forms on droplets. perhaps also genetic code could be realized at at totally different level. the recent findings of the group of hiv nobelist montagnier [23] indeed suggest a new realization of genetic code in water closely related to to water memory and tgd suggests a concrete realization of this code [5]. 3 some key ideas of tgd inspired quantum biology before proposing a model for intelligent oil droplets as a primitive life form its good to list some of the basic ideas of tgd inspired quantum biology., 1. the basic hypothesis is that the dark matter at the magnetic flux tubes of the magnetic body assignable to any physical system serves as an intentional agent controlling the behavior of the ordinary matter [2]. dark matter can correspond to just the ordinary particlesat least electrons and protonsin a phase with non-standard large value of planck constant forming macroscopic quantum phases. also biologically important ions could form this kind of phases. tgd inspired nuclear physics[7] allows also the bosonic counterparts of fermionic with same nuclear charge so that every fermionic ion could be accompanied by exotic bosonic ion so that bose-einstein condensates could become possible. 2. the model for dark nucleons [7, 5] as entangled triplets of three quarks leads to the identification of the counterparts dna, rna, trna, and aminoacids as three-quark states and one can identify also vertebrate genetic code. dna sequences correspond to dark nucleon sequences dark nuclei in this correspondence. the proposal is that dark proton sequences in water form dark nucleons with so large a planck constant that nucleon size corresponds to size of singe dna codon. there is indeed evidence that in attosecond time scale (time scale for corresponding causal diamonds) water obeys effective chemical formula h1.5o as far as scattering of electrons and neutrons is considered [9, 11, 12]. this would suggest that 1/4 of protons are in dark large planck constant phase in the experimental situation. this proportion is expected to depend on temperature and pressure and should explain the rich spectrum of anomalies of water [10] by regarding it as a two phase system [3]. perhaps these protons could form dark nucleon sequences realizing genetic code. these sequences could replicate and evolve and could define at least the analog of dna or rna. maybe even dna-mrna-aminoacids translation processing could take place. if a translation machinery transforming exotic dna to ordinary has developed during evolution, this fundamental realization of genetic machinery might make possible kind of research & development making possible to experiment with different genomes. evolution would not be a random process anymore [5]. 3. the proposal is that the ordered water layers associated with polar molecules dissolved in water are attached to the magnetic body of the molecule induced in water environment and that this magnetic body mimicking ithe original molecule is an essential element of this primitive life [5]. the selforganization processes of these layers induced by external perturbations could be the predecessor of processes like protein folding and de-folding. the mechanism of water memory could be based on dropping of the magnetic bodies of molecules as a result of repeated shaking involved with homeopathic procedure inducing a sequence of catastrophes driving the evolution of these primitive life forms. one can also ask whether these magnetic bodies could define the analog of proteins providing one realization of dark matter genetic code. 4. if dark nucleons have been the predecessors of chemical life forms, one can circumvent the hen-egg question about whether the genetic code or metabolism came first. in zero energy ontology negative energy signals propagating in the direction of geometric past would in turn provide fundamental mechanism of intentional action, metabolism, and memory. if this is the case, evolution would have issn: 2159-046x dna decipher journa www.prespacetime.com published by quantumdream, inc. http://www.springerlink.com/content/0557v31188m3766x/ dna decipher journal| november 2011 | vol. 2 | issue 3 | pp. 319-329 322 pitkänen m. oil droplets in water as a primitive life form? only led to a refinement of the fundamental mechanisms of life already existing: there would be no need to pull anything out of hat. the mechanisms for chemical storage and utilization of energy are needed and moving oil droplets would provide a primitive realization of these mechanisms. 5. the notion of negentropic entanglement makes sense if one accepts the role of p-adic number fields and the vision about life as something residing in the intersection of real and p-adic worlds [6]. entanglement probabilities for negentropic entanglement must be rational or algebraic numbers in the algebraic extension of p-adic numbers involved and there is unique prime for which this entanglement entropy is maximally negative. negentropic entanglement makes possible new kind of many particle states analogous to bound states but with negative binding energy. the reason is that negentropic entanglement is stable against state function reduction if negentropy maximization principle determines its dynamics also in the case of negentropic entanglement. the proposal is that the mysterious high energy phosphate bond corresponds to negentropic entanglement and carries both metabolic energy and information [1]. in this framework atp-adp cycle has also information theoretic interpretation as a transfer of conscious information. the model for dna as topological quantum computer [4, 8] led among other things to an identification of magnetic flux tubes connecting bio-molecules as a basic building bricks of living matter. 1. flux tubes are assumed to connect dna nucleotides to lipids of the nuclear and cell membranes. flux tubes could begin from =o in the double bonds r=o or from negatively charged oxygens. in the case of dna r would correspond to the basic unit in phosphate deoxiribose backbone consisting of aromatic 5-cycle and po4 containing one =o and one o− [15]. the lipid end would contain =o and -oh and the flux tube could end to either of these or possibly -oh ionized to -o− by a transformation of proton to dark proton. 2. the braiding of flux tubes makes topological quantum computation like processes possible [4]. the contractions and expansions of flux tubes induced by phase transitions changing the value of planck constant would be a basic control mechanism allowing to understand how two biomolecules (say dna and its conjugate) can find each other in the thick soup of organic molecules. the reconnections of the magnetic flux tubes would be second basic control mechanism and atp →adp process [13] involving splitting of phosphate group and liberating metabolic energy and its reverse would represent standardized reconnection process and its reversal. 3. the flux tube ends would contain quark and antiquark (u,d and their antiquarks are involved) coding for the four dna letters a,t,c,g so that also dark quarks and their antiquarks would provide an elementary particle level realization for the codons. note that topological quantum computation does not necessitate genetic code and therefore also the repeating dna sequences regarded as junk could be used for topological quantum computations. 4 general ideas about oil droplets as a primitive life form it is interesting to see what one obtains if one takes the dark nucleon realization of genetic code, the mechanism of water memory realized as magnetic bodies attached to the ordered water layers associated with polar molecules, the model for dna as topological quantum computer, and the ideas about magnetic body with dark matter as fundamental bio-control as basic ingredients of the model of intelligent oil droplets. 1. the formation of hot spot on the oil droplet resembles spontaneous symmetry breaking. the interpretation as a generation of magnetic body of approximately dipolar magnetic field is attractive. the magnetic body would control the droplet. the change of the direction of the motion of the oil droplet would correspond to the change of the orientation of the magnetic body and would thus reduce to a motor action of the magnetic body. 2. the flux tubes of the magnetic body would be most naturally parallel to the direction of the nitrobenzene polymer strands. oleic anhydride molecules and the hydrogen cyanid polymers would issn: 2159-046x dna decipher journa www.prespacetime.com published by quantumdream, inc. http://en.wikipedia.org/wiki/dna http://en.wikipedia.org/wiki/adenosine_triphosphate dna decipher journal| november 2011 | vol. 2 | issue 3 | pp. 319-329 323 pitkänen m. oil droplets in water as a primitive life form? be transferred along the magnetic flux tubes of an approximately dipolar magnetic field entering to the hot spot from interior and the oleic acid molecules could move along the flux tubes continuing along the surface of the droplet to the diametrically opposite point. the migration of birds along magnetic field lines is a direct analogy for this. 3. the dark matter at the magnetic body would give the oil drop its ”intelligence”. the dark nuclear genome could be realized at the magnetic body and the magnetic bodies might define the replicating life form as in the tgd based model of water memory for which the magnetic bodies represent molecules as far as low frequency electromagnetic fields characterized by cyclotron frequencies are considered. one could see intelligent oil droplets as manifestation of control actions of a life form defined by dark matter at magnetic flux tubes and the first step in the process eventually leading to a complex control and coordination of the behavior of ordinary matter. 4. the ability of droplets to react to the presence of other droplets would be due to the communications between magnetic bodies based on low frequency photons at cyclotron frequencies but having energy above thermal energy if the value of planck constant is large enough. at least oleic anhydrite, hydrogen cyanide, and mineral oil can serve as a fuel of oil droplets and this raises the question what might be the common property shared by them. certainly this property must relate to metabolism and the model for ordinary metabolism suggests that this property is shared also by the high energy phosphate bond. 1. oleic anhydrite is a lipid formed by as a fusion of two oleic acids consisting of a sequence of ch2 units and the characteristic (c=o)-(o-h) group at its end. the burning of the molecule splits it to two oleic acids by hydration meaning utilizing one water molecule. the formation of oleic acid in turn involves dehydration so that the burning process is analogous to depolymerization of dna or aminoacid sequence by hydration. 2. mineral oil is also a lipid and looks like oleic anhydride locally. in the ideal case however the crucial ..(c=o)-o-(c=o)-.. portions are lacking. oxygenation could however produce this kind of defects to the mineral oil molecules so that the mechanism of burning would remain the same. 3. hydrogen cyanide hcn involves valence bond of valence 3 between c and n. the polymers are constructed from h-c-n sequences with single valence bond between both c:s and n:s of two subsequent horizontal h-c-n units, which one can think of as being obtained from (h-c)-(h-c)... sequence and ..n-n-n... sequences with each n and c connected by horizontal valence bond. this polymer replaces oleic acid as a ”fuel” reacting with water and liberating metabolic energy. these polymers which would serve as primitive analogs of proteinswould be transferred along the magnetic flux tubes and burned at the hot spot by hydration. hcn has been proposed to have been a primitive precursor of both amino acids and nuclei acids. with motivations coming from the general vision about quantum biology, it will be proposed that also hydrogen cyanide polymers contain in their c-backbone ..(c=o)-o-(c=o)-.. portions as local defects due to oxygenation so that the burning would occur via hydration in all three cases. 5 what are the prerequisites for metabolism and topological quantum computation like processes? the basic question is whether metabolism interpreted in tgd framework as negentropy transfer and thus requiring the analogs of high energy phosphate bond and atp-adp cycle is possible. the high energy phosphate bonds make also possible flux tube structures serving as a prerequisite for topological quantum computation like process. both oleic anhydride, hydrogen cyanide and mineral oil can serve as a metabolic source and one should identify the common property of them making. this property should be the analog of high energy phosphate bond. 1. high energy phosphate bond carries metabolic energy. this bond is poorly understood and i have proposed that high energy phosphate bond carries negentropic entanglement which identified in issn: 2159-046x dna decipher journa www.prespacetime.com published by quantumdream, inc. http://www.wolframalpha.com/entities/chemicals/oleic_anhydride/zq/4d/dm/ http://en.wikipedia.org/wiki/mineral_oil http://en.wikipedia.org/wiki/hydrogen_cyanide dna decipher journal| november 2011 | vol. 2 | issue 3 | pp. 319-329 324 pitkänen m. oil droplets in water as a primitive life form? tgd framework as the basic characteristic of life [6]. in the middle of oleic anhydride there (c=o)o-(c=o) structure and its splitting in hydration liberates energy. this suggests that this structure also now carries the negentropic entanglement and the metabolic energy. the splitting process of oleic anhydrite occurring at the hotspot would be analogous to atp→adp process involving splitting of po4 molecule from atp. 2. oleic acid is a lipid containing at its second end the characteristic (c=o)-oh group assumed to serve as a terminal for the magnetic flux tubes in the model of dna-cell membrane system as quantum computer. in the presence energy feed one could imagine that the inverse process transforming oleic acid to oleic anhydride takes place and a primitive version of the metabolic cycle involving photosynthesis and cellular breathing can be imagined. metabolic and quantum information processing would be very intimately related. by dna as topological quantum computer analogy the magnetic flux tubes connecting oleic anhydride molecules would make be responsible for primitive topological quantum computation if present in the system. 3. also when the tar from urey-miller experiment replaces oleic anhydrite small amount of oleic anhydride was used to build a film around oil droplet to lower surface tension. this suggests that the oleic anhydride has a deeper purpose and defines the analog of cell membrane and make possible for the magnetic flux tubes from the interior of the droplet to attach to the lipids? this could occur at least in the hot spot and at point opposite to it so that magnetic flux tubes would connect the diametrically opposite points of the droplet oleic anhydride would therefore serve a dual purpose serving both as a metabolic resource and a building brick of the protocell membrane: metabolic energy would be accompanied by information. also in real life lipids -about which fats are a special casehave this double role. 4. the process occurs also both for hydrogen cyanide and mineral oil and and this raises obvious objections since the energy and information carrying (c=o)-o-(c=o) structures making also possible the flux tube connects are not present in the ideal situation. one must however remember that the situation in real life is far from ideal and the most obvious idea is that the polymers as such are not enough: oxygen is the basic metabolic resource and oxygenation serving as the loading of metabolic batteries might be the crucial element. (a) the backbone of both oleic acid, oleic anhydride, and of mineral oil polymers is ch2 sequence common to all lipids. if some fraction of mineral oil polymers contain (c=o)-o -(c=o):s serving as carriers of metabolic energy and information the situation reduces to that for oleic anhydride apart from effects caused by the fact that the density of metabolic energy per volume is expected to be lower, which would explain why the motion is slower. (b) also in the case of hydrogen cyanide polymers one can imagine the presence of similar defect structures due to oxygenation. a portion of ...(h-c)-(h-c)-(h-c).... sequence would be replaced with ....(h-c)-( c=o)-o-(c=o)-(h-c)... with three carbons lacking. the nitrogen sequence ...n-n-n-n-n.. would split to ...n-oh and oh-n... so that three nitrogens would be lacking. the total number of hydrogens would remain the same. under these assumptions the model explains all three cases using hydration as the basic mechanism of metabolism as well as the conditions required by dna as topological quantum computer model. note that the process consumes oxygen just as the ordinary breathing. 6 what about genetic code and counterpart of dna? consider next the possible realization of the genetic code. the first thing to notice is that even in the case that genetic code is not realized the braiding would make possible topological quantum computation like processes and a realization of memory in terms of braiding patterns. furthermore, chemical realization of the genetric code is not possible so that dark nucleons remain the only possibility in tgd framework. the challenge is to try imagine whether dna like structures having flux tube connections with the counterparts of lipids in the cell membrane could exist. the following suggestion is a product of free imagination based on analogies and reflects my amateurish skills in biochemistry. issn: 2159-046x dna decipher journa www.prespacetime.com published by quantumdream, inc. http://en.wikipedia.org/wiki/oleic_acid http://en.wikipedia.org/wiki/mineral_oil http://en.wikipedia.org/wiki/hydrogen_cyanide dna decipher journal| november 2011 | vol. 2 | issue 3 | pp. 319-329 325 pitkänen m. oil droplets in water as a primitive life form? 1. aromatic rings [14] are an essential element of both phosphate deoxiribose backbone of dna and of dna letters itself. nitrobenzene molecule obeys chemical formula (c6h−5)-no2 and contains benzene ring to which no2 nitro group is attached. the oily character is due to the benzene ring. benzene rings could serve as a counterpart for the hydrocarbon 5-cycles appearing in phosphate deoxiribose backbone. note however that in deoxiribose ring one carbon is replaced with o and two hydrogens with oh. moreover, single benzene molecule would correspond to the counterpart of dna triplet rather than single nucleoside. one could however argue that only a backbone is in question so that the differences might not matter. 2. one would naively expect that both nitrogen and phosphorus have same valence equal to three. in po4 phosporus has 5 valence bonds as a rule and the interpretation is that phosphorus tends to donate its valence electrons to get empty shell. this kind of states are known as oxidation states and are possible also for nitrogen: hydroxylamine no2h is one exmple of this kind of state. this inspires the idea that nitrogen takes the role of phosphorus at least partially. 3. if one does not allow oxidation states, the simplest manner to construct the analog of phosphate deoxiribose backbone is as structure ...x-x-x..., with x= r-o(r1-n)-o, where r denotes oleic anhydride and r1 is for benzene residue. the bridges connecting benzene rings would be reflection symmetric. the breaking of reflection symmetry is however essential since it determines the reading direction of dna. 4. if one accepts oxidation states, the simplest option is that in benzene-no2 complex no2 is replaced with (n=0)-o and the counterpart of phosphate deoxiribose backbone would have the structure ...x-x-x—, x=r(r1-n=0)-o with r denoting oleic anhydride and r1 benzene. oleic anhydride has valence bond to n so that n has 5 valence bonds as phosphorus in phosphate. also the crucial =o is present. the units connecting subsequent benzene rings are not reflection symmetric anymore as indeed required. there is however no charged oxygen as in the case of ordinary dna. 5. the two mirror image branches of oleic anhydride molecule consist of 15 carbon atoms and the structure is rather long as compared to the basic unit of phosphat edeoxiribose backbone so that the distance between subsequent benzene units would be rather longof order 10 angstroms. on the other hand, 10 dna codons correspond to 10 nm length in a good accuracy so that one codon would take 1 nm length also in this case. if double strand is formed, twisting is possible so that the scales could be the same. the size scale of the dark nucleon representing single dna codon should correspond to the size scale of single oleic anhydride molecule and the required value of planck constant would be of order 106 as the ratio of this scale and nucleon size of order 10−15 meters. 6. the counterparts of dna nucleotides forming a linear structure should join to the benzene rings. dark nucleon sequences remain the only possibility if one wants a realization of genetic code. each dark codon represented by dark nucleon would be connected by three flux tubes with quark and antiquark at their ends to single unit of the proposed structure. there would be three =o:s per single benzene ring. since single benzene ring corresponds to single dna codon three =o:s are indeed expected. therefore =o:s could indeed correspond to terminals for flux tubes coming from single dark nucleon representing single dna codon. 7. the division of oil droplet would be the analog of cell replication and would involve at the deeper level the replication of dark nucleon sequences. this requires the analog of dna double strand and the analogs of dna codons would be dark nucleons. genetic codons could be realized in terms of flux tubes connecting dark nucleon sequences to the oleic acids or oleic anhydrides at the surface of the droplet. it remains to be seen whether the division can be achieve in real world. to sum up, this model is rather direct application of tgd based vision about life and the killer test is whether the mineral oil oil molecules and hydrogen cyanide molecules are not ideal but actually contain the (c=o)-o-(c= o) pieces carrying energy and information and serve as terminals for the magnetic flux tubes. issn: 2159-046x dna decipher journa www.prespacetime.com published by quantumdream, inc. http://en.wikipedia.org/wiki/aromatic_rings dna decipher journal| november 2011 | vol. 2 | issue 3 | pp. 319-329 326 pitkänen m. oil droplets in water as a primitive life form? 7 another approach to protocell also the group led by jack. w. szostak, who was the 2009 nobel prize winner in physiology or medicine has carried out beautiful experiments in which they are able to create a candidate for protocell satisfying many of the basic requirements [22]. one such condition is the ability of protocell to transfer various nutrient molecules through the protocell membrane. in modern cell pumps and channels consisting of proteins are believed to serve that purpose (for a different view see the remark below). genetically coded proteins were however absent during the primordial era. therefore the membrane is constructed of branching lipids believed to exists during prebiotic era allowing sugars which are basic building bricks of dna to permeate to the protocell. given the dna template , the basic building bricks of dna molecule assemble to a copy of dna in this protocell. what is still lacking is the generation of the template strand of dna itself and also the replication of protocell. if dark dna in the form of dark nucleon strings is really there, the template could result as the assembly of the basic bricks of dna around it and above a proposal for the analog of this kind of process is suggested. the replication of the dark genes would have been also present from the beginning and would have preceded the replication of genes and protocell. biological evolution could be seen as a migration from dark space-time sheets to ordinary ones and somewhat analogous to the migration of life from sea to land. remark: there are puzzling experimental findings about quantal currents through cell membrane even in absence of metabolic sources. in many-sheeted space-time one could interpret these currents as various kinds of josephson currents running between cell interior and exterior along current carrying space-time shees. pumps and channels would be more like a diagnostic tool allowing cell to measure the concentrations of various important biomolecules and ions. at first sight the approaches of szostak and martin hanczyc look very different. these approaches have however a lot of common at deeper level if one accepts tgd based view as dna-cell membrane system or its more primitive version as a topological quantum computer like system relying on the braiding of magnetic flux tubes connecting the counterpart of dna nucleotides to the lipids of protocell membrane and on the prebiotic realization of genetic code at the level of dark nuclear physics. one could also argue that the protocell of hanczyk represents oil based life as opposed to life as we know it. in tgd framework this is a mis-interpretation. the protocells of hanczyk live in an aqueous environment. nitrobenzene oil is an aromatic compound as also sugars and contains nitrogen taking in the proposed scenario same role as phosphorus in ordinary life. oleic anhydride is lipid andwould provide basic building brick for a particular variant of dna like structure half-way between dark and completely chemical realization. oleic anhydride would provide also the building bricks of protocell membrane and serve as a nutrient just like fat moleculesalso lipidsserve in ”real life”. references books related to tgd [1] m. pitkänen. about the new physics behind qualia. in quantum hardware of living matter. onlinebook. http://tgd.wippiespace.com/public_html/bioware/bioware.html#newphys, 2006. [2] m. pitkänen. dark forces and living matter. in p-adic length scale hypothesis and dark matter hierarchy. onlinebook. http://tgd.wippiespace.com/public_html/paddark/paddark.html# darkforces, 2006. [3] m. pitkänen. dark nuclear physics and condensed matter. in p-adic length scale hypothesis and dark matter hierarchy. onlinebook. http://tgd.wippiespace.com/public_html/paddark/ paddark.html#exonuclear, 2006. [4] m. pitkänen. dna as topological quantum computer. in genes and memes. onlinebook. http: //tgd.wippiespace.com/public_html/genememe/genememe.html#dnatqc, 2006. issn: 2159-046x dna decipher journa www.prespacetime.com published by quantumdream, inc. http://www.hhmi.org/news/szostak20080604.html http://www.hhmi.org/news/szostak20091005.html http://tgd.wippiespace.com/public_html/tgdeeg/tgdeeg.html#pulse http://tgd.wippiespace.com/public_html/bioware/bioware.html#newphys http://tgd.wippiespace.com/public_html/paddark/paddark.html#darkforces http://tgd.wippiespace.com/public_html/paddark/paddark.html#darkforces http://tgd.wippiespace.com/public_html/paddark/paddark.html#exonuclear http://tgd.wippiespace.com/public_html/paddark/paddark.html#exonuclear http://tgd.wippiespace.com/public_html/genememe/genememe.html#dnatqc http://tgd.wippiespace.com/public_html/genememe/genememe.html#dnatqc dna decipher journal| november 2011 | vol. 2 | issue 3 | pp. 319-329 327 pitkänen m. oil droplets in water as a primitive life form? [5] m. pitkänen. homeopathy in many-sheeted space-time. in bio-systems as conscious holograms. onlinebook. http://tgd.wippiespace.com/public_html/hologram/hologram.html# homeoc, 2006. [6] m. pitkänen. negentropy maximization principle. in tgd inspired theory of consciousness. onlinebook. http://tgd.wippiespace.com/public_html/tgdconsc/tgdconsc.html#nmpc, 2006. [7] m. pitkänen. nuclear string hypothesis. in p-adic length scale hypothesis and dark matter hierarchy. onlinebook. http://tgd.wippiespace.com/public_html/paddark/paddark.html# nuclstring, 2006. [8] m. pitkänen. three new physics realizations of the genetic code and the role of dark matter in bio-systems. in genes and memes. onlinebook. http://tgd.wippiespace.com/public_html/ genememe/genememe.html#dnatqccodes, 2006. condensed matter physics [9] j. k. borchardt. the chemical formula h2o a misnomer. the alchemist, august 2003. [10] m. chaplin. water structure and behavior. http://www.lsbu.ac.uk/water/index.html, 2005. [11] r. a. cowley. neutron-scattering experiments and quantum entanglement. physica b, 350:243–245, 2004. [12] y. danon r. moreh, r. c. block and m. neumann. search for anomalous scattering of kev neutrons from h2o-d2o mixtures. phys. rev., 94, 2005. biology [13] adenosine tri-phosphate. http://en.wikipedia.org/wiki/adenosine_triphosphate. [14] aromaticity. http://en.wikipedia.org/wiki/aromatic_rings. [15] dna. http://en.wikipedia.org/wiki/dna. [16] hcn polymer. http://faculty.uncfsu.edu/aumantsev/research/published/scannig_v25_ 19-24_2003.pdf. [17] nitrobenzene. http://en.wikipedia.org/wiki/nitrobenzene. [18] oleic acid. http://en.wikipedia.org/wiki/oleic_acid. [19] oleic anhydride. http://www.wolframalpha.com/entities/chemicals/oleic_anhydride/zq/4d/ dm/. [20] b. grzybowski et al. maze solving by chemotactic droplets. jacs, 132(4):1198–1199, 2010. [21] m. hanczyc et al. self-propelled oil droplets consuming fuel surfactant. jacs, 131(14):5012–5013, 2009. [22] j. w. szostak et al. template-directed synthesis of a genetic polymer in a model protocell. nature. online publication. http://genetics.mgh.harvard.edu/szostakweb/publications/szostak_ pdfs/mansy_et_al_nature_2008.pdf. [23] s. ferris j.-l. montagnier l. montagnier, j. aissa and c. lavall’e. electromagnetic signals are produced by aqueous nanostructures derived from bacterial dna sequences. interdiscip. sci. comput. life sci., 2009. issn: 2159-046x dna decipher journa www.prespacetime.com published by quantumdream, inc. http://tgd.wippiespace.com/public_html/hologram/hologram.html#homeoc http://tgd.wippiespace.com/public_html/hologram/hologram.html#homeoc http://tgd.wippiespace.com/public_html/tgdconsc/tgdconsc.html#nmpc http://tgd.wippiespace.com/public_html/paddark/paddark.html#nuclstring http://tgd.wippiespace.com/public_html/paddark/paddark.html#nuclstring http://tgd.wippiespace.com/public_html/genememe/genememe.html#dnatqccodes http://tgd.wippiespace.com/public_html/genememe/genememe.html#dnatqccodes http://www.lsbu.ac.uk/water/index.html http://en.wikipedia.org/wiki/adenosine_triphosphate http://en.wikipedia.org/wiki/aromatic_rings http://en.wikipedia.org/wiki/dna http://faculty.uncfsu.edu/aumantsev/research/published/scannig_v25_19-24_2003.pdf http://faculty.uncfsu.edu/aumantsev/research/published/scannig_v25_19-24_2003.pdf http://en.wikipedia.org/wiki/nitrobenzene http://en.wikipedia.org/wiki/oleic_acid http://www.wolframalpha.com/entities/chemicals/oleic_anhydride/zq/4d/dm/ http://www.wolframalpha.com/entities/chemicals/oleic_anhydride/zq/4d/dm/ http://genetics.mgh.harvard.edu/szostakweb/publications/szostak_pdfs/mansy_et_al_nature_2008.pdf http://genetics.mgh.harvard.edu/szostakweb/publications/szostak_pdfs/mansy_et_al_nature_2008.pdf dna decipher journal| november 2011 | vol. 2 | issue 3 | pp. 319-329 328 pitkänen m. oil droplets in water as a primitive life form? 8 figures figure 1: nitrobenzene figure 2: oleic anhydride figure 3: oleic acid issn: 2159-046x dna decipher journa www.prespacetime.com published by quantumdream, inc. dna decipher journal| november 2011 | vol. 2 | issue 3 | pp. 319-329 329 pitkänen m. oil droplets in water as a primitive life form? figure 4: hydrogen cyanide and hydrogen cyanide polymer. figure 5: the analog of the deoxiribose phosphate backbone. r denotes oleic anhydride containing two =o:s and r1 benzene ring. issn: 2159-046x dna decipher journa www.prespacetime.com published by quantumdream, inc. introduction intelligent oil droplets some key ideas of tgd inspired quantum biology general ideas about oil droplets as a primitive life form what are the prerequisites for metabolism and topological quantum computation like processes? what about genetic code and counterpart of dna? another approach to protocell figures dna decipher journal | december 2016 | volume 6 | issue 3 | pp. 170-175 170 pitkänen, m., combinatorial hierarchy: two decades later exploration combinatorial hierarchy: two decades later matti pitkänen 1 abstract combinatorial hierarchy (ch) is a hierarchy consisting of mersenne integers m(n) = mm(n−1) = 2m(n−1) − 1 and starting from m1 = 2. the first members of the hierarchy are given by 2, 3, 7, 127, m127 = 2127 − 1 and are primes. the conjecture of catalan is that the hierarchy continues to some finite prime. it was proposed by peter noyes and ted bastin that the first levels of hierarchy up to m127 are important physically and correspond to various interactions. i have proposed the levels of ch define a hierarchy of codes containing genetic code corresponding to m7 and also memetic code assignable to m127. in this article i consider the argument that the hierarchy ends at m127 and find that it should end already at m7 for which the condition used saturates and which corresponds to genetic code in tgd interpretation. the failure of condition at m127 level has interesting ””gödelian interpretation”. i find also that in tgd universe genetic code and its memetic counterpart are realized at the level of fundamental particles. already earlier i have ended up with alternative realizations at the level of dark nucleons and sequences of 3 dark nucleons. 1 introduction combinatorial hierarchy (ch) [1, 2] is a hierarchy consisting of mersenne integers m(n) = mm(n−1) = 2m(n−1)−1 and starting from m1 = 2. the first members of the hierarchy are given by 2, 3, 7, 127,m127 = 2127−1 and are primes. the conjecture of catalan is that the hierarchy continues to some finite prime. it was proposed by peter noyes and ted bastin that the first levels of hierarchy up to m127 are important physically and correspond to various interactions (see http://tinyurl.com/hszo9wb). i have proposed the levels of ch define a hierarchy of codes containing genetic code corresponding to m7 and also memetic code assignable to m127 [3]. pierre noyes and ted bastin proposed also an argument why ch contains only the levels mentioned above. this has not been part of tgd view about ch: instead of this argument i have considered the possibility that ch does not extend beyond m127. with the inspiration coming from email discussion i tried to understand the argument stating that ch contains m127 as the highest level and ended up with a possible interpretation of the condition. zero energy ontology (zeo) and the representation of quantum boolean statements a→ b as fermionic parts of positive and negative energy parts of zero energy states is essential. this led to several interesting new results. 1. to my best understanding the original argument of noyes does not allow m127 level whereas prime property allows. states at m127 level cannot be mapped to zero energy states at m7 level. allowing a wild association with gödel’s theorem, one could say that that there is hube number of truths at m127 level not realizable as theorems at m7 level. a possible interpretation is that m127 level corresponds to next level in the abstraction hierarchy defined by ch and to the transition from imbedding space level to the level of ””world of classical worlds” (wcw) in tgd. the possible non-existence of higher levels (perhaps implied if mm127 is not prime) could be perhaps interpreted by saying that there is no ””world of wcws”! 2. rather remarkably, for m7, which corresponds to genetic code [3], the inequality serving as consistency condition is saturated. one can say that any set of 64 mutually consistent statements at m7 1correspondence: matti pitkänen http://tgdtheory.com/. address: köydenpunojankatu 2 d 11 10940, hanko, finland. email: matpitka@luukku.com. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/hszo9wb http://tgdtheory.com/ mailto:matpitka@luukku.com dna decipher journal | december 2016 | volume 6 | issue 3 | pp. 170-175 171 pitkänen, m., combinatorial hierarchy: two decades later level can be represented in terms of 64 boolean maps at m3 level representable in terms of zero energy states. one obtains an explicit identification for the boolean algebras involved in terms of spin and isospin states of fermions in tgd framework at level m7 so that genetic code seems to be realized at the fundamental elementary particle level thanks to the dimension d = 8 of imbedding space. even more, the level m127 corresponding to memetic code emerges in the second quantization of fermions at m7 level. here color triplet property of quarks and color singletness of leptons and the identification of elementary particles as pairs of wormhole contacts are in essential role. the conclusion would be that in tgd universe genetic code and its memetic counterpart are realized at the level of fundamental particles. already earlier i have ended up with alternative realizations at the level of dark nucleons and sequences of 3 dark nucleons [l1]. 2 summary of combinatorial hierarchy i summarize first the basics of ch. 1. one considers the space algebra of boolean statements of n bits which can be also extended to complex linear space -quantum boolean algebra. one can give it linear structure as z2 algebra for binary coefficients with z2 sum having set theoretic interpretation. this linear space has some basis. that the coefficient field for linear structure is z2 does not seem to be absolutely essential. in tgd framework one considers the linear space defined by quantum boolean algebra with qubit interpretation generated by fermionic oscillator operators: one operator for every bit. 2. one assigns to the linear n-d space the n2-d space of linear maps of it to itself. one can also consider the space of maps of quantum boolean algebra to itself and also require that this defines a boolean homomorphism. dimensions would be the same: only coefficient field would be different. 3. to ch level, which corresponds to mersenne prime m(n) = mm(n−1) (n = 2, 3, 7, 127, 2127 − 1, ...) one assigns vector space with dimension d(n− 1) = [(m(n− 1) + 1)]2 , and requires that the space formed by d1(n) = (m(n) + 1)) 2 bit sequences, which represent a subset of mutually consistent boolean statements as subset of m(n) + 1 bit sequences are representable as a subset of bit sequences with d(n − 1) bits. this demands d1(n) ≤ d(n− 1) giving m(n) + 1) 2 ≤ [m(n− 1) + 1]2 . 4. this criterion is satisfied for the primes of ch up to m7 but not for m127: 2127 − 1 > 1282 so that m127 should not included if i have understood the criterion correctly. for m7 = 27−1 = 127 one obtains the condition 26 = 64 ≤ 8×8 = 64 so that condition is saturated. remarkably, 64 is the number of dna codons! issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2016 | volume 6 | issue 3 | pp. 170-175 172 pitkänen, m., combinatorial hierarchy: two decades later 5. the numbers of ch are also known as catalan mersenne numbers. catalan mersenne primes are special case of double mersenne primes mmn (see http://tinyurl.com/j4tqwch). catalan conjecture that catalan mersennes are primes up to some limit. after the first non-prime the remaining catalan mersenne numbers are necessarily composite. the known double mersennes are given by mmp : p = 2, 3, 5, 7. no other cases are known. these primes are good candidates for labelling scaled up variants of say hadron physics. to my opinion catalan criterion is more plausible. 6. classical number fields are in key role in tgd [9, 10, 11] and have dimensions d = 1, 2, 4, 8. also ch involves these dimensions. d(n− 1) = m(n− 1) + 1 giving dimensions 2, 4, 8 for m2,m3,m7. for m127 one would obtain d = 128, which does not correspond to any division algebra. this might relate to the above observation. 3 ch as a prediction of quantum tgd in the following the interpretation of boolean map in zeo is proposed. also it is shown that m7 level allows a natural realization in terms of spin-isospin states of fermions and that m127 level is obtained in second quantization meaning going from the level of imbedding space to the level of wcw. 3.1 interpretation of the lower level boolean map in terms of zeo one can ask, why one should have this kind of map? one interpretation is that the space of boolean statements at given level is imbeddable to the space of quantum boolean maps at previous level. quantum boolean maps would represent boolean rules a→ b, ””theorems” or ””laws of physics”. 1. in tgd framework the interpretation of ch would be as a hierarchy of statements about statements about... the number of statements about n statements is indeed 2n . one statement corresponding to all bits equal to 0 (in set theoretic realization empty set) is thrown away so that one has 2n − 1 statements instead of 2n . 2. zeo means that physical states are pairs of states with opposite conserved quantum numbers: they correspond to physical events, which replace states as fundamental entities in zeo. the fermionic parts of positive and negative energy parts of states would be pairs of many-fermion states allowing interpretation as elements of quantum boolean algebra. zero energy states themselves would correspond to pairs of these fermionic states and thus to ”theorems” a→ b or maps from boolean algebra to itself. the allowed statement pairs would satisfy fermion number conservation and conservation of various quantum numbers and would indeed represent laws of physics. 3. a possible interpretation of the map would be that the statements at given level m(n+ 1) must be representable as theorems at previous level m(n). for m(n) > m7 = 127 this would not hold true anymore. could this have some deep mathematical meaning as the wild association with goedel’s theorem suggests? in the model of genetic code and its generalizations [3] i have proposed that each level of ch defines a maximal number of mutually consistent statements identifiable as ””axioms”: the number is 2n−1 for 2n n-bit statements. for m7 = 127 the number is 64, the number of dna codons, which would thus have interpretation as axioms or ””fundamental truths”. in this case the representability would still hold and map would be bijection. at the next level one would have ””memetic code” with 2126 codons representable as sequences of 21 dna codons with stop codon included (126 = 21×6). by the proposed criterion, at memetic level only vanishingly small subset of truths would be representable as theorems at genetic level. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/j4tqwch dna decipher journal | december 2016 | volume 6 | issue 3 | pp. 170-175 173 pitkänen, m., combinatorial hierarchy: two decades later 3.2 representation of m7 level in tgd framework could the saturation for m7 have some physical meaning? the maps would be from 8-d space to itself. 1. bits can be represented in terms of spin and electroweak spin giving 2×2 = 4 states and imbedding space-spinors (h = m4 × cp2) of given h-chirality (quark or lepton like), given fermion number (fermion or antifermion) and physical helicity. if also unphysical helicities with fixed fermion number are allowed one would have 4 + 4 = 8 states. the condition that helicity is physical would reduce the number of states by one half. this applies to both quarks and leptons since color is not spin like quantum number in tgd (colored states correspond to partial waves in cp2). 2. what could be the interpretation for 27 − 1 = 127 states containing as subset n = 26 states. could n = 26 correspond to the number of states in the tensor product formed by pairs of 8 leptons and 8 antileptons allowed to have also unphysical polarizations? same would apply to quarks. allowing both quark-antiquark and lepton-antilepton type states one would have 128 states. the physicality condition for boson polarizations could drop the number of states to 64. what the dropping of one state would correspond: to the dropping of νr− νr pair having no electroweak and color couplings perhaps? one can imagine two alternative identifications for the two tensor factors. (a) in tgd framework fundamental bosons correspond to fermion antifermion pairs with members at opposite throats of wormhole contact connecting two space-time sheets. could the genetic code correspond to 64 elementary bosons with physical polarizations and the maps to those assigning to 8 fermions 8 antifermions? (b) an alternative identification is suggested by zeo. the tensor product of fermionic boolean algebras at opposite boundaries of causal diamond (cd) would replace that at opposite wormhole throats. this would in accordance with the interpretation of zero energy states as statements a→ b represented as boolean maps. 3.3 representation of m127 level in tgd framework what about the physical interpretation of m127 level in tgd framework? 1. the first thing to observe is that physically p = m127 corresponds in tgd to the p-adic prime p characterizing electron in p-adic mass calculations: compton length is proportional to the p-adic length scale and thus proportional to √ p. the remaining mersenne primes correspond to completely super-astrophysical compton lengths. hence m127 has a very special role. the mersenne primes 3, 7, 31, 127 giving rise to double mersenne primes correspond to extremely short p-adic length scales. recall that the ratio of mcp2 /me is approximately mcp2 /me = 2127/2/ √ 5 + x, where x ∈ [0, 1] characterizes the second order contribution to electron mass from p-adic mass calculations [5]. the ratio of planck mass to proton mass equals to mpl/mp = 1.307 × 1019. for x = 0 this gives mpl/mcp2 = (mp/me)× 3.96 = 7.271× 103, which is not far from 213 ' 8.912× 103. the value of 213 is very attractive number theoretically and would be obtained for x = .5, again power of 2. 2. the states at this level should correspond to statements about statements at the lower level represented in terms of quark lepton state space as many-fermion states assignable to wormhole throat or several wormhole throats (elementary corresponds to two wormhole contants and 4 wormhole throats). the construction of infinite primes can be interpreted as a process of forming repeatedly statements about statements and the physical analog is repeated second quantization [8]. in the recent situation second quantization would correspond to the formation of many-fermion states at partonic 2-surfaces defined by the throats of wormhole contacts. this would automatically give rise to m127 states if one has 127 single fermion states to begin with. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2016 | volume 6 | issue 3 | pp. 170-175 174 pitkänen, m., combinatorial hierarchy: two decades later physically this step would correspond to a step from the spinor modes of imbedding space to the spinor modes of wcw identifiable as fermionic fock states assignable to partonic 2-surfaces so that indeed a huge abstraction is in question. i have proposed that anyonic states could be this kind of states for large value of heff = n×h implying that the size of wormhole throat becomes nano-scopic [7]. 3. one has 127 boson states but how to obtain 127 (or 128 = 27) single fermion states? counting only spin and weak isospin gives n = 8 + 8 = 24 (n = 4 + 4 = 23) single fermion states if one allows (does not allow) also unphysical polarizations. the simplest option is that each single fermion state has 23 (24) additional states. the location of fermion at one of the 4 wormhole throat could give 4 additional degrees of freedom. this would leave 2 (4) additional states per fermion state still missing. 4. a good guess is that quark color realized as color partial waves comes in rescue and gives the needed states. light quarks must move in color triplet states and leptons in singlet states. thefore quarks have 3 × 8 = 24 modes and leptons 8 modes giving altogether 32 modes altogether. there are 4 wormhole throats so that 4× 32 = 128 modes are obtained and if right-handed neutrino is thrown out one has 127 states as required if no constraints on polarizations are posed. it therefore seems that tgd physics codes ch naturally at elementary particle level! there is indeed a rich set of ””vibrational” degrees of freedom giving also rise to color degrees of freedom. the symplectic group of ∆m4 ± assignable to either boundary of causal diamond (cd) defined as the intersection of future and past directed light-cones of m4 with points replaced with cp2 gives rise to products of s2 and cp2 partial waves. besides this there is a conformal weight labelling the states correlating with s2×cp2 partial wave light quarks massless before massivation by p-adic thermodynamics move in color partial waves and color triplets are obtained as the color excitations for them corresponding to higher conformal weights and having cp2 mass as mass scale. i have already earlier ended up with the proposal that genetic code is realized at the level of dark nuclear physics. either the states of dark proton or sequence of 3 protons could be organized naturally states corresponding to 64 dnas, 64 rnas, 20 aminoacids, and 40 trnas and vertebrate genetic code follows from very simple assumption that opposite spins are paired [6, 4] [l1] (see http://tinyurl.com/ jgfjlbe). these findings suggest that genetic code and memetic code are also realized at the elementary particle level. acknowledgements: i am gratetul for james bowery for raising the question about the possible relevance of ch for tgd. references [1] bastin t et al. 7:445, 1979. [2] noyes p. the combinatorial hierarchy an approach to open evolution. available at: http:// tinyurl.com/hszo9wb, 1980. [3] pitkänen m. genes and memes. in genes and memes. onlinebook. available at: http: //tgdtheory.fi/public_html/genememe/genememe.html#genememec, 2006. [4] pitkänen m. homeopathy in many-sheeted space-time. in bio-systems as conscious holograms. onlinebook. available at: http://tgdtheory.fi/public_html/hologram/hologram.html# homeoc, 2006. [5] pitkänen m. massless states and particle massivation. in p-adic physics. onlinebook. available at: http://tgdtheory.fi/public_html/padphys/padphys.html#mless, 2006. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/jgfjlbe http://tinyurl.com/jgfjlbe http://tinyurl.com/hszo9wb http://tinyurl.com/hszo9wb http://tgdtheory.fi/public_html/genememe/genememe.html#genememec http://tgdtheory.fi/public_html/genememe/genememe.html#genememec http://tgdtheory.fi/public_html/hologram/hologram.html#homeoc http://tgdtheory.fi/public_html/hologram/hologram.html#homeoc http://tgdtheory.fi/public_html/padphys/padphys.html#mless dna decipher journal | december 2016 | volume 6 | issue 3 | pp. 170-175 175 pitkänen, m., combinatorial hierarchy: two decades later [6] pitkänen m. nuclear string hypothesis. in hyper-finite factors and dark matter hierarchy. onlinebook. available at: http://tgdtheory.fi/public_html/neuplanck/neuplanck.html# nuclstring, 2006. 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[11] pitkänen m. from principles to diagrams. onlinebook.available at: http://tgdtheory.fi/ public_html/tgdquantum/tgdquantum.html#diagrams, 2016. [l1] pitkänen m. about physical representations of genetic code in terms of dark nuclear strings. available at: http://tgdtheory.fi/public_html/articles/genecodemodels.pdf, 2016. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.fi/public_html/neuplanck/neuplanck.html#nuclstring http://tgdtheory.fi/public_html/neuplanck/neuplanck.html#nuclstring http://tgdtheory.fi/public_html/neuplanck/neuplanck.#anyontgd http://tgdtheory.fi/public_html/neuplanck/neuplanck.#anyontgd http://tgdtheory.fi/public_html/tgdnumber/tgdnumber.html#visionc http://tgdtheory.fi/public_html/tgdnumber/tgdnumber.html#visionc http://tgdtheory.fi/public_html/tgdnumber/tgdnumber.html#visionb http://tgdtheory.fi/public_html/tgdnumber/tgdnumber.html#visionb http://tgdtheory.fi/public_html/tgdgeom/tgdgeom.html#wcwnew http://tgdtheory.fi/public_html/tgdgeom/tgdgeom.html#wcwnew http://tgdtheory.fi/public_html/tgdquantum/tgdquantum.html#diagrams http://tgdtheory.fi/public_html/tgdquantum/tgdquantum.html#diagrams http://tgdtheory.fi/public_html/articles/genecodemodels.pdf introduction summary of combinatorial hierarchy ch as a prediction of quantum tgd interpretation of the lower level boolean map in terms of zeo representation of m7 level in tgd framework representation of m127 level in tgd framework login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x dna decipher journal | december 2023 | volume 13 | issue 2 | pp. 144-150 144 pitkänen, m., on the mechanism of the energy transfer in photosynthesis essay on the mechanism of the energy transfer in photosynthesis matti pitkänen 1 abstract the basic mystery of photosynthesis is extreme energy efficiency. up to 95% of the photon’s energy is transmitted in a medium that would seem to be as inhospitable as possible for energy transmission with almost no dissipation. the use of very low temperatures, the shooting of monochromatic photons into a lattice, and superconductivity are out of the question. the incoming photons also have a wavelength distribution, which does not facilitate the energy transfer either. the recent experimental study of the lh2 antenna system has led to a view about how the photon energy is transferred to the reaction center where photosynthesis takes place. it is believed that the disorganization of the proteins is proposed to explain this. the proposed interpretation of the findings is as follows. a photon enters and excites the electron of the lh2 protein. when the electron is de-excited, one or more photons are generated which in turn excite the electrons of the next lh2 proteins. finally, the generated photons excite the electrons of the reaction center and these electrons are used in the photosynthetic process to produce sugar molecules. i find it difficult to imagine how the irregular positions of proteins could make possible the low dissipation, as proposed. the tgd based proposal for the mechanism involves two key ideas. the required long range quantum coherence is made possible by the proposal that dark matter corresponds to the phases of ordinary matter characterized by effective planck constant. the crystal structure making possible low dissipation would be icosa-tetrahedral hyperbolic honeycomb associated with a magnetic body of the system, which is central also in the dark realization of the genetic code in the tgd framework. low dissipation for electrons would be possible since dark electron-hole pairs would be transferred along the magnetic body. the gravitational magnetic body of earth could also play a central role. 1 introduction i learned about very interesting results related to photosynthesis. a popular article on the bigthink page (https://rb.gy/phb4c) tells about an article published in the journal pnas [2] (rb.gy/9zppa). the basic mystery of photosynthesis is extreme energy efficiency. up to 95% of the photon’s energy is transmitted in a medium that would seem to be as inhospitable as possible for energy transmission with almost no dissipation. the use of very low temperatures, the shooting of monochromatic photons into a lattice, and superconductivity are out of the question. the incoming photons also have a wavelength distribution, which does not facilitate the energy transfer either. consider first a summary of the basic findings and conclusions. 1. chlorophyll is the basic structure involved with photosynthesis. its basic function is to gather solar energy and transfer it to the reaction center where the energy is stored to various biomolecules. there are 2 wavelength bands, corresponding to 430 nm in blue and 662 nm in red, where the absorption is especially strong. the so-called lh2 proteins act as antennas absorbing photons. in the reaction center lh1 proteins perform photosynthesis by building biomolecules to which the solar energy is stored. 2. it has been observed that the lower limit of the size of the so-called light-absorbing lh2 antenna proteins is 2.5 nm. it is also the minimum distance between lh2 proteins. the proposal is that the lh2 antenna network could somehow make the transfer of energy almost without dissipation. 1correspondence: matti pitkänen http://tgdtheory.com/. address: rinnekatu 2-4 a8, 03620, karkkila, finland. email: matpitka6@gamail.com. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://rb.gy/phb4c rb.gy/9zppa http://tgdtheory.com/ mailto:matpitka6@gmail.com dna decipher journal | december 2023 | volume 13 | issue 2 | pp. 144-150 145 pitkänen, m., on the mechanism of the energy transfer in photosynthesis it is believed that the disorganization of the proteins might explain this. however, in the popular article there was no intuitive argument as to why this is so. the claim is made on the basis of computational models and empirical facts gained by studying the transfer process. i find it difficult to imagine how the irregular positions of proteins could promote the process. 3. the proposed interpretation of the findings is as follows. a photon enters and excites the electron of the lh2 protein. when the electron is de-excited, one or more photons are generated which in turn excite the electrons of the next lh2 proteins. finally, the generated photons excite the electrons of the reaction center and these electrons are used in the photosynthetic process to produce sugar molecules. 1.1 tgd view of the energy transfer the findings seem to resonate with two key views of the tgd inspired quantum biology. 1. photosynthesis involves at least a temporary storage of solar energy to quantum gravitational energy batteries [10, 9]. 2. there is dark variant of the genetic code and realization of dark dna double strand base on the icosahedral tessellation [11] of the hyperbolic 3-space h3, which is realized both as a mass shell in m4 ⊂ m8 and light-cone proper time=constant 3-surface in m4 ⊂ m4 × cp2. icosa-tetrahedral and possible other hyperbolic tessellations would be associated, not with the biological body, but with the magnetic body (mb) of the biosystem carrying dark matter identified as phases of the ordinary matter with effective planck constant heff = nh0. the location of dark matter at the field body would explain why dark matter has not been found in various searches. what are the tgd answers to the basic questions waiting for an answer? 1. why would the dissipation be so low? quantum coherence in a scale of at least the order of tens of nanometers could guarantee this. dark matter as phases with a large value of heff indeed implies a long quantum coherence scale. also a regular crystal structure is a natural prerequisite for a low dissipation. the dissipation is minimized if the energy, or possibly the electrons, are transferred through the hyperbolic tessellation of the mb carrying dark matter. 2. the minimum distance between lh2 proteins is about 2.5-4 nanometers, which corresponds to the dna codon size scale. in the tgd based model for genetic code, the dark realization of the genetic code and the dna double helix are connected to an icosa-tetrahedral honeycomb in hyperbolic 3-space h3 assigned with the mb [11]. could the crystalline structure be realized by using the same icosa-tetrahedral tessellation as associated with the dark dna and dark genome controlling the ordinary genome. if the transfer of energy to the reaction center occur at the mb as a transfer of dark electrons, the dissipation could be very small since there would be no direct interaction of the dark electrons with the ordinary matter if the interaction vertices can involve only particles with the same value of heff , as seems natural. 2 the tgd based model consider now the tgd proposal in more detail. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2023 | volume 13 | issue 2 | pp. 144-150 146 pitkänen, m., on the mechanism of the energy transfer in photosynthesis 2.1 quantitative data consider next the quantitative data. 1. the distance between lh2 proteins is in the range 2.5-3.1 nm. this scale corresponds to the dna codon size scale and to the cell size of the fundamental region of the icosa-tetrahedral tessellation, which has platonic solids as cells [11]. there are 12 icosahedrons, 20 tetrahedrons and 30 octahedrons forming a region of size 10 nm, which corresponds to the p-adic length scale l(151) (associated with a p-adic prime p ≃ 2k, k = 151) appearing as a characteristic length scale in bomatter. this region corresponds to 10 dna codons for which the total twist along the dna strand is 6π that is 3 full turns. 2. the size of the structure involved with the photosynthesis would be naturally cell size scale? the wavelength of the red light gives a length scale of order .5 µm and serves a natural lower bound. note that cell nucleus size is about 1 µm. 3. the time τ required for the energy transfer between adjacent antenna proteins varies from 5.7 to 14 ps. in time τ , the distance traveled by the light is l = 1.71 − 4.2 mm. interestingly, for earth the gravitational compton wavelength λgr(e) = gme/β0(e) is for β0(e) = v0/c = 1 equal to λgr(e) = 4.5 mm. gravitational compton frequency is fgr(e) = 67 ghz and corresponds to a time of about tgr(e) = 15 ps, the upper limit for the estimated time. fgr corresponds to a photon energy of egr = .27 mev. the electronic metabolic energy quantum in the case of the earth would be related by a factor me/mp the protonic metabolic energy quantum identifiable as standard metabolic energy currency. the model for the findings of andrew adamatsky [4] suggests that sponges have a language based on membrane potential oscillations with membrane potential variations of order mv. the tgd based model suggests the existence of metabolic energy quantum of this order of magnitude [10]! mev is also the energy associated with the miniature membrane potentials. could τ be identifiable as the gravitational compton time tgr at which the dark matter at the mb would oscillate? 2.2 how could the electrons be transferred to the reaction center as dark electrons? could the process at the level of lh2 antenna proteins correspond to the propagation of the dark electron and the hole associated with it? the dark electron would hop between the sites of the tessellation perhaps by quantum tunneling, which in tgd universe corresponds to a pair of ”big” (ordinary) state function reductions (bsfrs) changing the arrow of time temporarily. the dark electron current would be analogous to super current and the system ”hole + dark electron” would be analogous to a cooper pair. 1. the duration τ of a single step should correspond to the oscillation period τ ∼ tgr. if so, the oscillation would play the role of eeg resonance oscillation coordinating the transfer by induces the pairs of bsfrs. 2. the first guess is that electrons are converted to dark electrons with a large value of the gravitational planck’s constant ~eff = ~gr = gmm/β0(m) [1] located at the gravitational mb of the earth or sun. they would be transferred to the u-shaped monopole flux tubes and the reduction of the binding energy of the electron would be equal to the energy of the incoming photon absorbed by it. the reduction of the binding energy cannot be however purely gravitational. for electrons, the maximal gravitational binding energy in the case of the earth is about egr(earth, e) = .25 mev whereas the incoming photon has energy e ≃ x × .5 ev, where x is in the range 4 to 6 in the wavelength range considered. for the sun the maximal binding energy egr is reduced by the ratio issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2023 | volume 13 | issue 2 | pp. 144-150 147 pitkänen, m., on the mechanism of the energy transfer in photosynthesis [m(earth)/m(sun)]× [r(sun)/r(earth) = .071. in the case of protons with egr(earth, p) = .5 ev this gives to egr(sun, p) = .14 ev, which happens to be roughly twice the energy assignable to membrane potential. for electrons this gives egr(sun, e) = 1.8 µev. for the energy transfer in photosynthesis, the energy of the solar photon cannot therefore correspond to the change of gravitational binding energy in the case of electrons. rather, the energy must be identified as the change of electromagnetic binding energy as an atom is effectively ionized when an electron becomes a dark electron at the mb. this mb need not be gravitational and could also correspond to a relatively small heff > h. 3. what comes to mind are dark unpaired valence electron states of atoms in which the heff of an unpaired electron increases so that binding energy is scaled down by 1/h2 eff . the binding energy spectrum of the dark electron states is obtained by scaling the ordinary binding energy spectrum and these states are analogous rydgerg states in that the radius of bohr orbits is scaled up by h2 eff . if the valence electron becomes gravitationally dark (heff = hgr), the atom effectively suffers ionization to a state with vanishing energy and positive charge. dark ions could correspond to this kind of states. 4. how could the energy transfer to the reaction center take place? the simplest mechanism could be the following. one can charge the solar energy batteries by transforming ordinary electrons to dark electrons at the mb of the sun. at the reaction center the dark electrons drop back and transform to ordinary electrons and are available for the photosynthesis proper, storing the energy to biomolecules. the experimental findings could be consistent with the assumption that the pairs formed by a dark electron and hole move to the reaction center, and the movement of the dark electron is analogous to a conduction in a lattice by hopping. the lattice could correspond to the tetraicosahedral tessellation assignable also with dna and genetic code. the time for one transition would correspond to tgr(earth) ∼ 15ns. this supports the view that the mb of the earth is present. 5. why would the dropping down to earth take place in the reaction center? the holes have an effective positive charge because the dark electrons have a large distance to the surface of earth. if the reaction center has a negative charge, it attracts the positively charged holes. the holes move towards the reaction center and the dark electrons and gravitational monopole flux tubes and dark electrons follow. the electrons transform to normal ones and holes disappear. the predicted negative charge of the reaction center serves as a test for the proposal. 6. how this negatively charged region in the reaction center could be generated? pollack effect [5, 3, 7, 6], discussed from the tgd point of view in [8], is caused by (say) ir radiation in the presence of gel phase, and indeed generates negatively charged exclusion zones. the exclusion zones could be due the transfer of protons of water molecules to dark protons at the flux tubes of the mb,which is however not gravitational. both cells and dna represent examples of negatively charged objects. pollack effect is indeed a key element of the tgd inspired view of living matter. there it is natural to assume that the exclusion zone is present also in the reaction center. if the energies of dark electrons and holes are separately conserved, they can annihilate to the ordinary electron in the reaction center. can this be true? 1. why would the energy of the dark electron be conserved in the hopping along the tessellation? single step would correspond to a motion under the magnetic lorentz force, which conserves energy since force is orthogonal to the velocity. 2. what about the dark electron-hole interaction? this interaction is present if the flux tube follows the motion of the hole-dark electron pair. this pair would form a bound state analogous to the cooper issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2023 | volume 13 | issue 2 | pp. 144-150 148 pitkänen, m., on the mechanism of the energy transfer in photosynthesis pair and its energy would be conserved if its scattering would reduce to the magnetic scattering of the dark electron. the situation would be very much like in the case of superconductivity. 3. if the hole corresponds to a transition of an unpaired valence electron to a large heff analog of a rydberg state with a very large size, the binding energy and energy of the state is very near to zero. the ionization energy scale for valence electrons is measured in electron volts just like for the photons from the sun. the energy scale for icosa-tetrahedral honeycomb scaling like ~2eff/(2mel 2), l the size of the fundamental region, gives an estimate for the unit of energy quantization, which does not depend on ~eff . the energy scale is 102 ev for l = l(151) = 10 nm. this scale is expected to be very large as compared to the energy gap so that transitions are not possible. the situation would be like in superconductivity and superfluidity. 4. what about energy conservation in the motion of the localized valence hole? valence electron hole can be replaced with the valence electron of a neighboring atom and this makes possible its movement towards the negatively charged reaction center. the energy of the valence hole in the center of mass system of the atom is not changed but the ionized atom or the molecule containing it would experience the coulomb force assumed to be associated with the reaction center and its center of mass energy can change. how is it possible that the attractive coulomb field between the hole and the reaction center does not affect the energy of the valence hole? the question is well-motivated the coulomb energy between the hole and the reaction center is expected to be much larger than the energy gap. for instance, for distance of 1 µm the coulomb energy between unit charges is of order 10−2 ev. what prevents the valence hole from accelerating and getting more energetic? the u-shaped gravitational magnetic flux tube has a string tension and the lengthening of the flux tube could compensate for the coulomb force. the coulomb energy would be transformed to elastic energy of the flux tube. in the reaction center the flux tube would contract and the dark electron could fuse with the hole having the same energy. 2.3 is this picture consistent with the quantum gravitational storage of metabolic energy? is this picture consistent with the earlier proposal for the metabolic energy storage, which is based on the notion of gravitationally dark protons [10] and also predicts electronic metabolic energy currency of about .25 mev for which there is some evidence [4]? 1. the motivation for the proposal is that the gravitational potential energy of a proton at the surface of earth is .5 ev: this happens to be the nominal value of metabolic energy quantum. of course, since the electromagnetic binding energies in molecular scale are measured using ev as units, this might be a pure accident. the weaker optimistic interpretation is that this co-incidence makes possible interaction between quantum gravitational and quantum electromagnetic degrees of freedom. when the distance from the surface of earth in the direction of the sun, the gravitational forces of sun and earth are identical. this condition gives an upper bound for the distance r(earth) of the particle from the earth in the direction of sun as r(earth)/au−r(earth) = √ m(earth)/m(sun) giving r(earth) ≃ 100r(earth) to be compared to the distance of moon about r(moon) ≃ 60r(earth). the value of the gravitational potential difference as is 99% of the maximal one. the proposal [10] is that the transformation of protons of water molecules to gravitationally dark protons could serve as a mechanism for the storage of metabolic energy. if the metabolic energy quantum is determined solely by the gravitation of earth, this mechanism does not work at large distances from the surface of earth. the fact that moon travellers have issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2023 | volume 13 | issue 2 | pp. 144-150 149 pitkänen, m., on the mechanism of the energy transfer in photosynthesis survived does not favor a purely gravitational mechanism but the fact that molecular binding energies are of the same order, might save the mechanism. a more imaginative option is that the gravitational mb of the moon traveller is still associated with earth and makes it possible to store metabolic energy to the gravitational mb of earth. 2. dark protons triplets could serve as a storage of metabolic energy in the case of atp (high energy phosphate bond) and maybe even in the case of biomolecules. this is supported by the appearance of 3 protons as a kind of basic unit in atp→ adp metabolic machinery. 3. in the pollack effect, ir radiation effectively ionizes water molecules and produces effective stoichiometry h1.5o inside a negatively charged exclusion zone. the decrease of the electronic binding energy per water molecule in the pollack effect could be naturally given by the energy of the ir photon and would be rather small. if the coulomb binding energy of the dark proton triplets with the exclusion zone is equal the metabolic energy quantum e = .5 ev, the reduction of the gravitational binding energy in the transfer of dark proton triplet to the gravitational mb would be given by e and would lead to a zero energy state. could one the build-up the energy carrying bio-molecules by transferring dark proton triplet to the gravitational magnetic bodies of the biomolecules by using the energy liberated by dark electrons as they drop down and transform to ordinary electrons in the reaction center? received september 23, 2023; accepted december 9, 2023 references [1] nottale l da rocha d. gravitational structure formation in scale relativity, 2003. available at: https://arxiv.org/abs/astro-ph/0310036. [2] harris d wang d, fiebig oc and schlau-cohen gs. elucidating interprotein energy transfer dynamics within the antenna network from purple bacteria. pnas, 120((28)e2220477120), 2023. available at: https://doi.org/10.1073/pnas.222047712. . [3] the fourth phase of water: dr. gerald pollack at tedxguelphu, 2014. available at: https: //www.youtube.com/watch?v=i-t7tcmudxu. [4] adamatsky a. language of fungi derived from electrical spiking activity, 2022. available at: https: //arxiv.org/pdf/2112.09907.pdf. [5] pollack g. cells, gels and the engines of life. ebner and sons, 2000. available at: https: //www.cellsandgels.com/. [6] zhao q pollack gh, figueroa x. molecules, water, and radiant energy: new clues for the origin of life. int j mol sci, 10:1419–1429, 2009. available at: https://tinyurl.com/ntkfhlc. [7] pollack gh zheng j-m. long-range forces extending from polymer-gel surfaces. phys rev e, 68:031408–, 2003. available at: https://tinyurl.com/ntkfhlc. [8] pitkänen m. pollack’s findings about fourth phase of water : tgd view. available at: https: /tgdtheory.fi/public_html/articles/pollackyoutube.pdf., 2014. [9] pitkänen m. comparison of orch-or hypothesis with the tgd point of view. https://tgdtheory. fi/public_html/articles/penrose.pdf., 2022. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://arxiv.org/abs/astro-ph/0310036 h https://www.youtube.com/watch?v=i-t7tcmudxu https://www.youtube.com/watch?v=i-t7tcmudxu https://arxiv.org/pdf/2112.09907.pdf https://arxiv.org/pdf/2112.09907.pdf https://www.cellsandgels.com/ https://www.cellsandgels.com/ https://tinyurl.com/ntkfhlc https://tinyurl.com/ntkfhlc https:/tgdtheory.fi/public_html/articles/pollackyoutube.pdf https:/tgdtheory.fi/public_html/articles/pollackyoutube.pdf https://tgdtheory.fi/public_html/articles/penrose.pdf https://tgdtheory.fi/public_html/articles/penrose.pdf dna decipher journal | december 2023 | volume 13 | issue 2 | pp. 144-150 150 pitkänen, m., on the mechanism of the energy transfer in photosynthesis [10] pitkänen m. how animals without brain can behave as if they had brain. https://tgdtheory.fi/ public_html/articles/precns.pdf., 2022. [11] pitkänen m. about tessellations in hyperbolic 3-space and their relation to the genetic code . https://tgdtheory.fi/public_html/articles/tessellationh3.pdf., 2023. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://tgdtheory.fi/public_html/articles/precns.pdf https://tgdtheory.fi/public_html/articles/precns.pdf https://tgdtheory.fi/public_html/articles/tessellationh3.pdf introduction tgd view of the energy transfer the tgd based model quantitative data how could the electrons be transferred to the reaction center as dark electrons? is this picture consistent with the quantum gravitational storage of metabolic energy? login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x dna decipher journal | december 2024 | volume 14 | issue 1 | pp. 44-55 44 pitkänen, m., updated view on the rice experiments of masaru emoto essay updated view on the rice experiments of masaru emoto matti pitkänen 1 abstract masaru emoto has carried out extremely interesting experiments with water at the critical point against freezing. emoto reports that words expressing emotions are transmitted to water: the expression of positive emotions tend to generate beautiful crystal structures and negative emotions ugly ones. also music and even pictures are claimed to have similar effects. emoto has also carried out similar experiments with rice in water at physiological temperature. rice subjected to words began to ferment and water subject to words expressing negative emotions began to rotten. i have already earlier discussed a model for the findings of emoto. in this article i update the model. i will also ask new questions. how emotions are communicated at the fundamental level and how a conscious entity can perceive the emotional state of another conscious entity and possibly affect it? what does emotional intelligence mean? how could one assign a measure of conscious emotional information to the emotional state? how certain sounds or gestures with emotional contents or even pictures can induce emotional response at the fundamental dna level? 1 introduction masaru emoto has carried out extremely interesting experiments with water at a critical point against freezing. emoto reports that words expressing emotions are transmitted to water: positive emotions tend to generate beautiful crystal structures and negative emotions ugly ones. also music and even pictures are claimed to have similar effects. emoto has also carried out similar experiments with rice in water. rice subjected to words began to ferment and water subject to words expressing negative emotions began to rotten. remark: fermentation is a metabolic process consuming sugar in absence of oxygen. metabolism is a basic signature of life so that at least in this aspect the water+rice system would become alive. the words expressing positive emotions or even music would serve as a signal ”waking up” the system. 1.1 summary of emoto’s findings the wikipedia article about masaru emoto (see http://tinyurl.com/pqy57jj) provides a good summary of the experiments of emoto and provides a lot of links so that i will give here only a brief sketch. emoto believed that water was a ”blueprint for our reality” and that emotional ”energies” and ”vibrations” could change the physical structure of water. the water crystallization experiments of emoto consisted of exposing water in glasses to different words, pictures or music, and then freezing and examining the aesthetic properties of the resulting crystals with microscopic photography. emoto made the claim that water exposed to positive speech and thoughts would result in visually ”pleasing” crystals being formed when that water was frozen, and that negative intention would yield ”ugly” crystal formations. in 2008, emoto and collaborators published an article titled ”double-blind test of the effects of distant intention on water crystal formation” about his about experiments with water in the journal of scientific exploration, a peer reviewed scientific journal of the society for scientific explorations (see http://tinyurl.com/ycsnu2oc). the work was performed by masaru emoto and takashige kizu of emoto’s own ihm general institute, along with dean radin and nancy lund of the institute of noetic 1correspondence: matti pitkänen http://tgdtheory.com/. address: valtatie 8 as 2, 03600, karkkila, finland. email: matpitka6@gmail.com. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/pqy57jj http://tinyurl.com/ycsnu2oc http://tgdtheory.com/ mailto:matpitka6@gmail.com dna decipher journal | december 2024 | volume 14 | issue 1 | pp. 44-55 45 pitkänen, m., updated view on the rice experiments of masaru emoto sciences, which is on stephen barrett’s quackwatch (see http://tinyurl.com/y99kol2e) blacklist of questionable organizations. pss are the modern jesuits and for jesuits the end justifies the means. emoto has also carried experiments with rice samples in water. there are 3 samples. first sample ”hears” words with positive emotional meaning, second sample words with negative emotional meaning, and the third sample serves as a control sample. emoto reports (see https://youtu.be/wc-zmvxfbxe) that the rice subjected to words with positive emotional content began to ferment whereas water subject to words expressing negative emotions began to rot. the control sample also began to rot but not so fast. 1.2 but has anyone replicated the experiments of emoto? has anyone replicated the experiments of masaru emoto? this was the question posed to me by alain jutras on fb. in the research community very few people want to get a label of crackpot by trying to do something like this. the experiments are however simple and ordinary laymen can do the replication (for a successful replication see this). when we are talking about emoto’s experiment we make head on collision with physicalism, which identifies as the core of scientific thinking the belief that consciousness has no causal effects so that our desires and intentions cannot have any effects on anything. giving up this belief would of course pose strong challenges for experimentation: how can we know the desires of the experimenter have not affected the outcome of the experiment? for the skeptic, also free will is an illusion (this implies that also moral and ethics are illusory but usually even the most hardfore skeptics avoids saying this aloud). some extremists believe that even consciousness is an illusion. just for fun i looked at some urls on the web and found that the typical reaction was that it does not matter whether emoto’s experiments can be replicated or not. emoto must be a crackpot of fraud. this is idiotism in the veil of scientific thinking and i have learned during years that it is useless to argue with an idiot. there are of course numerous phenomena suggesting remote mental interactions, where skeptics are forced to give up logical thinking. 1. for instance, in medical experiments, a placebo can produce the same effect as real medicine. for skeptics this shows that the idea about the mind-matter interaction is deadly wrong. skeptic does not (want to) realize the very placebo effect proves that mind can affect matter! 2. the so-called experimenter effect is well-known and well-documented and is an example of the effect of the desires of experiment on the results (very probably) involving no fraud. in the development of a new medicine the test results can be phantastic but when the tests are repeated years later there is no effect. the reason could be that the interest of experimenters has already faded, and their desire to get nice results has vanished. the nice results were the outcome of desire, which is just the remote mental interaction! 3. some experimenters get fantastic results from tests of some paranormal effect but it turns out that the results cannot be replicated. the very fact that this could well be the case without fraud shows the existence of remote mental interactions but skeptics manage to not notice this in their arguments. and of course, there is always the easy explanation: an experimenter is a swindler or crackpot or something like that. the researchers of paranormal phenomena are martyrs of modern science! 4. water memory and homeopathy is a further example: nobel level scientists have demonstrated it but have been labelled either swindlers or fools. the attitudes to ”cold fusion” is a further example of anti-intellectualism in the veil of scientism. 5. the final example is skeptic himself: at least outside the academic environment he believes that he has command of his actions over his body. why should he have this belief if it is a mere illusion? this question skeptic manages to unask. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/y99kol2e https://youtu.be/wc-zmvxfbxe https://www.youtube.com/watch?v=okwyk1ccxm0 dna decipher journal | december 2024 | volume 14 | issue 1 | pp. 44-55 46 pitkänen, m., updated view on the rice experiments of masaru emoto the emoto experiments are especially vulnerable against the attacks of skeptics. first of all, the experimenter must be able to take seriously the idea that the system studied can have emotions, he must be able to perceive the emotional state of the system and be even able to affect it. the attempt to affect water at freezing point or the rice in a water bottle requires remote mental interaction: one might say that at the level of conscious experience one must be able to fuse with the water. this kind of ability, emotional intelligence, probably requires an empathetic personality and also a long period to develop since developing a deep emotional relationship with a rice bottle is not a one-night stand. if a skeptic (usually not a very empathetic person) tries to replicate the experiments, he probably fails since he wants to fail and because for him the rice is dead matter (as also other people and skeptic himself, if he thinks completely logically). there is no way to prove to skeptics that these effects are real since in his world view these effects are impossible. therefore i think that there is only one way to proceed. a new view of fundamental physics based on good philosophy respecting internal logical consistency, consistent with existing physics, solving the anomalies of the existing physics, and predicting a lot of new phenomena is the only way to proceed. even skeptics must eventually bow to the power of logic. this theory must explain what consciousness and life are and must provide an elegant identification for emotions as a universal panpsychic phenomenon appearing already at dna level. this theory must explain emotional intelligence as the ability to sense the emotional state of another system and explain how emotions are expressed, transferred and induced. if this kind of theory exists, there are hopes that human kind eventually gains the ability to study consciousness instead of denying it. 1.3 tgd view of the findings in the sequel i will consider the working hypothesis that the effects are real, and develop an explanation based on tgd inspired quantum biology [11, 10, 9]. i have developed a model for the findings of emoto already earlier [7][15] but the updated version of the model involves new elements related to the progress of tgd. i will also ask new questions. how emotions are communicated at the fundamental level and how a conscious entity can perceive the emotional state of another conscious entity and possibly affect it? what does emotional intelligence mean? how could one assign a measure of conscious emotional information to the emotional state? how certain sounds or gestures with emotional contents or even pictures can induce emotional response at the fundamental dna level? the basic ingredients of the model are following: magnetic body (mb) carrying dark matter as heff/h = n phases of ordinary matter; communications between mb and biological body (bb) using dark photons able to transform to ordinary photons identifiable as bio-photons; the special properties of water explained in tgd framework by assuming dark component of water implying that criticality for freezing involves also quantum criticality; the special properties of water at the quantum criticality for pollack effect at physiological temperature, and the realization of genetic code and counterparts of the basic bio-molecules as dark proton sequences and as 3-chords consisting of light or sound providing a universal language allowing universal manner to express emotions in terms of bio-harmony realized as music of light or sound. the entanglement of water sample and the subject person (with mbs included) realized as flux tube connections would give rise to a larger conscious entity expressing emotions via language realized in terms of basic biomolecules in a universal manner by utilizing genetic code realized in terms of both dark proton sequences and music of light of light and sound. 2 bioharmony and the genetic code the notions of genetic code and bioharmony have evolved gradually during years. the following gives a brief summary of the basic ideas. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2024 | volume 14 | issue 1 | pp. 44-55 47 pitkänen, m., updated view on the rice experiments of masaru emoto 2.1 basic ideas of bioharmony 1. the notion of bioharmony is based on the observation that 12-note-scale could correspond to a hamilton cycle at an icosahedron containing 12 vertices [12, 16, 17, 18, 22]. the scale would correspond to a hamilton cycle going through all the vertices just once. quint cycle is a very attractive identification for the representation of the scale in the sense that neighboring points of the icosahedron correspond to scaling of frequency by factor 3/2 and so that octave equivalence characterizing musical perception gives 12-not scale spanning a single octave. 2. for a given hamilton cycle, the 20 faces of the icosahedron define 3-chords proposed to correspond to an icosahedral harmony. one obtains a large number of different hamilton cycles characterized by a symmetry group which is either z6, z3 or z2, which can be generated by reflection or a rotation by π. there are also 6 hamilton cycles with trivial symmetries (z1). hamilton cycles without any symmetries have an interpretation as disharmonies. 3. the surprising finding was that the 3 icosa tetrahedral 20-chord harmonies: the unique z6 harmony, z4 harmonies and considerable larger number of z2 harmonies give rise to a partial representation of the genetic code in the sense that the orbits of these symmetry groups correspond to amino acids. the number of triangles at a given orbit zn is the same as the number of dnas coding the corresponding amino acid. 4 codons from 64 codons are however missing. these are obtained by adding a tetrahedral hamilton cycle with 4 chords and 4 vertices. the conclusion is that genetic code and music harmony might be deeply related. 4. icosa tetrahedral hyperbolic tessellation [22] emerges as a unique hyperbolic tessellation involving 3 platonic solids tetrahedron, octahedron and icosahedron. the proposal is that it could provide a universal representation of the genetic code and associated bioharmony, which is not restricted to biology but applies to all kinds of systems in all scales. one could say that the tessellation is induced (projected) to the 3-surface at hyperbolic space h3 (light-cone proper time constant surface in m4 and defines a genetic code for almost any system. the 3 hamilton cycles as representations of 12-note scale give 20+20+20 =60 chords and the tetrahedral hamilton cycle gives 4 chords. these 64 chords would correspond to genetic codons represented as faces of icosahedron and tetrahedron. 2.2 the quantum realization of bioharmony how to realize bio-harmonies physically if the tgd view of dark matter residing at monopole flux tubes and controlling biomatter is assumed? 1. dark genome at the magnetic monopole flux tubes paired with dna and realized in terms of dark protons. dark 3-proton triplets would represent the 3-chords of the icosa tetrahedral bioharmony. chords would be assignable to cells of a unique hyperbolic icosa tetrahedral tessellation containing icosahedron, octahedron and tetrahedron as basic units. these three platonic solids have triangular faces so that they can be glued together. the icosa tetrahedral tessellation of h3 would induce a tessellation of the 3-surface x3 = x4 ∩ h3 ×cp2, where x4 ⊂ h3 ×cp2 denotes the space-time surface [22]. the octahedrons belonging to the tessellation would have naturally a passive role since all faces could be regarded as either icosahedral or tetrahedral. codons would be realized in terms of dark proton triplets assigned to vertices of the triangular faces of the tessellation. 2. dark photon triplets as cyclotron frequency triplets, 3-chords, induce transitions between the states of dark proton sequences. differences of cyclotron frequency triplets would correspond to dark issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2024 | volume 14 | issue 1 | pp. 44-55 48 pitkänen, m., updated view on the rice experiments of masaru emoto photon triplets which can induce transitions between dark proton triplets. this realization came rather recently and it is still somewhat unclear whether the chords correspond to the differences of the triplets or to triplets. also pairs of frequencies and even a single frequency can induce transitions in which 2 or only one frequency of the chord changes. 3. tgd leads also to a speculative generalization of genes. not only dark codons would be possible but also sequences of dark codons forming dark 3n-protons behave as quantum units, dark genes. they can emit and absorb dark 3n-photons inducing transitions between dark genes as 3n resonances. for a given bioharmony, the dark codons and dark genes would effectively serve as addresses and given dark 3n-photon could induce transitions only between dark genes for which its 3n cyclotron frequencies would correspond to differences of the cyclotron frequencies. also partial resonance is enough and even a single dark photon can induce transition between two dark genes. several transitions are possible if only a single dark proton makes a cyclotron transition. it is also possible that the transformed dark gene belongs to a different bioharmony. this leads to a view of how dark genes control ordinary genes. 1. dark biomatter as heff = nh0 phases at magnetic monopole flux tubes of the magnetic body (mb) of the system should act as a boss receiving information from the ordinary biomatter controlling it. this strongly suggests that the dark and ordinary information molecules, in particular genes are paired and form helical structures. a rather detailed view of this idea was developed in [22]. 2. the control and communication between dark and ordinary genes would involve the transformation of dark photons to ordinary photons, possibly identifiable as bio-photons, or vice versa. this applies also to the communications of dark and ordinary counterparts of the other information molecules and would be essential in the processes like transcription and translation. dark 3n-photons as quantum coherent units could decay to 3n ordinary photons. the communication would involve energy resonance but not frequency resonance since heff changes. a full 3n-resonance is not needed. 3. the resonance condition requires that the dark cyclotron energies and corresponding transition energies assignable to ordinary dna are identical. the frequency increases since heff decreases. the transitions of ordinary information molecules need not be cyclotron transitions but can correspond to ordinary chemical transitions. this gives a strong constraint to the values of heff . this poses strong constraints on both the ordinary and dark information molecules and could have led to a selection of the dna, rna and trna codons and amino-acids. 4. the original long held belief was dark genes as sequences if 6 bits are identical with the ordinary genes. there is actually no need to assume this. both the bioharmony and bits can be dynamical. even the bioharmionies of the dark codons can be dynamical and the dark bioharmony should be consistent with the transition energy spectrum of the ordinary genetic codons only during their mutual communications. 3n-photons of dark genes or thei substructures should induce transitions of ordinary genes in order to make control possible. dark genes pairing with dna would make the dna a cognitive unit consisting of units of 6 bits, an intelligent entity. it would also have emotions and perhaps also emotional intelligence due to the existence of several bio-harmonies. 2.2.1 about the symmetries of dark codons before continuing one must consider the symmetries of the bioharmony. 1. an open question is whether the dark 3-chords related by a permutations of vertices should be identified or not. if they are regarded as different, there are (3!=6 non-equivalent chords). if a full permutation invariance is allowed, it does not make sense to speak of permutations of the vertices of f and the transitions inducing changes of the 3-chord would not be possible since they could correspond to vanishing energy change of cyclotron energy. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2024 | volume 14 | issue 1 | pp. 44-55 49 pitkänen, m., updated view on the rice experiments of masaru emoto 2. in the case of ordinary dna the order of nucleotides matters and one has 3! different orderings. now however the codons are quantum entangled units of 3 dark protons so that the situation is not so simple. if the cyclotron frequency spectra assignable to the vertices are not identical then one can say that dark protons are ordered. in this case either of these options is relevant. 3. an interesting possibility is that the 3-chords related by cyclic permutations are equivalent. there would be only 2 non-equivalent 3-chords with different total cyclotron energies and they would have opposite orientations which might be interpreted in terms of parity violation. this would double the number of physically realizable chords and the problem associated with the physical realization of the codons is that the number of codons is by a factor 1/2 too small for the simplest proposals. 4. if a full permutation invariance is allowed it does not make sense to speak of permutations of the vertices of f and the transitions inducing changes of the the 3-chord would not be possible since they could correspond to vanishing energy change of cyclotron energy. if only cyclic invariance is assumed, one can reach 2 vertices/notes from a fixed vertex/note of f by a reflection which permutes the vertices and changes the total cyclotron energy. 2.2.2 does the notion of bioharmony relate to the ordinary notion of harmony it would be nice to have a contact with the ordinary notion of harmony in which the numbers of chords are small and the 12-note scale is replaced by the 8-note scale or 5-note scale and one has minor and major scales or fusion of them to a scale containing 9 notes. at the fundamental level music should induce transitions between the codons of a bioharmony so that it is natural to study the transitions changing the dark codons. consider now the possible transitions changing the 3-chord represented as 3-proton state and induced by one or more dark photons. 1. for a given icosahedral triangular face f and given bioharmony, one can consider the neighboring faces of f, which have either 3, 2, 1 common vertices reachable by a transition induced by be keeping the face/3-chord fixed, keeping one edge (2 notes) fixed, or keeping 1 vertex/note fixed. if there are no common vertices, the initial and final chords have no common frequencies. also these transitions are possible. 2. for transitions leaving a single edge e/note pair fixed, there are 3 faces/3-chords reached by reflection with respect to e. one could call them inner faces/chords. there are 6 faces/chords reached by keeping a single vertex/note fixed: these faces/chords could be called outer chords. the total number of faces/chords reached by edge and face preserving transitions is 6+3=9=10-1, where 10 is half of the number of faces of the icosahedron. if the orientation of the fae matters, 10 faces are reached. the faces belonging to the complement of these 10 faces require the change of all frequencies. the inner 3+1=4 faces define 4 3-chords and 6 outer faces define 6 3-chords: 10 chords altogether making 1/2 of all 3-chords. could they be regarded as simpler sub-harmonies of the 64 chord harmony? 3. the hamiltonian cycle has 12 vertices and 3 of them must belong to the complement of the reachable region and should define a triangle by the reflection symmetry of the icosahedron. one would have dual sub-harmonies. could they somehow relate to the minor and major scales? or could they relate to dna strand and conjugate strand? the outer faces contain 6 vertices, which do not belong to f so that the reachable region contains 6+3=9 vertices. could this have something to do with the 8-note scale which has actually only 7 notes by octave equivalence. the minor scale has two additional notes since the scale (ahcdef♯f♯a differs from its reversal agfedcha: this would make 9 notes/vertices. for a given base note the number of notes of minor and major scale is 9. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2024 | volume 14 | issue 1 | pp. 44-55 50 pitkänen, m., updated view on the rice experiments of masaru emoto 4. from a given vertex of f, one can reach 3+1 outer vertices and 2 vertices of f if reflection symmetry is not true. could the pairs formed by the fixed vertex of f and these vertices define 6 notes which define allowed changes of notes for a melody. interestingly, the 8-note scale (c,d,e,f,g,a,h) allows 6 non-trivial intervals ({(c,d), (c,e), (c,f), (c,g), (c,a),(c,h)}). 3 the interpretation of bioharmonies in the framework of the tgd inspired theory of consciousness the key idea is that music expresses and generates emotions. harmony dictates the emotional tone of music and this suggests that bioharmonies are correlates for emotions and that emotions are realized already at the molecular level. 3.1 empirical support for the notion of bioharmonies as correlates for emotions there is empirical support for the idea that bio-harmonies correlate with emotions. 1. rna seems to represent and transfer emotions [6] (see http://tinyurl.com/y92w39gs) [7]. rna from the brain of a snail conditioned by a painful stimulus is transferred to the preparation made from neurons of sea slug. neuron preparation in the petri dish reacts to the conditioning stimuli as if it were itself conditioned. 2. somehow rna is able to transfer emotions. the tgd inspired proposal [12, 21, 13, 17, 7, 14] is that dark dna and rna represent emotions as sequences of 3-chords made of dark photons of dark rna form 3n-dark photons behaving like a single quantum coherent unit. the representation of the genetic code would rely on icosa-tetrahedral representation in which the 3-chords would correspond to triangular faces of icosahedron and tetrahedron to which 3-chords are assigned. 3. the first proposal was that the induction of emotions could take place by 3n-resonant cyclotron absorption of dark 3n-photons by dark genes represented as sequences of 3n dark proton triplets at monopole flux tubes of mb. also the absorption of dark photon singlet or doublet by a dark codon is enough to induce transition between dark codons and therefore between dark genes. this would ”wake-up” the dark gene and induce emotional response. 3.2 emotions are expressed and emotional expression induces emotions assume that emotions reduce to the dna level or at least, that they are realized at dna and biomolecular level. one can pose several questions. what are emotions? how are they expressed? how does emotional expression induce emotions? how are emotions perceived? 1. the universality and uniqueness of the hyperbolic tetra icosahedral tessellation suggests that the notions of bioharmony and moods are universal and can be defined at the level of dna and other bio-molecules and could even generalize to even larger structures by inducing the icosa-tetrahedral structure to the 3-surface associated with the structure. 2. moods at the bio-molecular level would correspond to bio-harmonies realized in terms of dark genes represented as sequences of dark codons representable as dark proton triplets. the dark genes would be dynamical unlike the ordinary genes and dark bioharmony would only correspond to the transition energies of dna only during control and communications. dark genes would therefore represent intelligence in both cognitive (bit) sense and emotional sense. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/y92w39gs dna decipher journal | december 2024 | volume 14 | issue 1 | pp. 44-55 51 pitkänen, m., updated view on the rice experiments of masaru emoto 3. the basic idea is that music induces emotions and expresses them.how this would be realized at the level of bioharmonies. the first guess is that the emotional state is represented by 3n-chords defining a bioharmony and identified as dark proton triplets, dark genetic codons. the original proposal was that dark photon triplets define another representation of the dark code. this would not be the case: dark photon frequency triplets could correspond to differences of the frequency triplets assignable to dark proton triplets. with this interpretation the notes and chords of music would correspond to the differences of chords and notes for the bio-harmonies. this interpretation also allows us to consider temporal patterns of dark codons defining a sequence of 3-chords as a kind of music piece. the dark 3n-photon triplets and also dark photon singlets and doublets induce cyclotron transitions between these triplets if the bio-harmonies of the sender and receiver are the same. otherwise only some chords induce transitions or only some notes of a given chord. one can even consider transition of entire dark genes by using dark 3n-photons. 4. systems a and b with the same bioharmony, have the same emotional state, can be in emotional resonance. transitions between different chords induced by dark photon triplets generated by codon a induce transitions of codon b producing temporal sequences of 3-chords, music pieces! 5. the resonance can be also partial so that all notes of the dark codon are not affected. for instance sequence of notes can induce transitions between chords if the two chords belong to the same 20-codon bioharmony. this is the case always for the codons with z6 symmetry. a melody, which is consistent with a given bioharmony, involves only notes belonging to the chords of the harmony so that it can induce a transition at a level of single chords. the number of these notes should be maximal. an emotionally intelligent conscious entity should have a wide repertoire of bio-harmonies and be able to rapidly find a bioharmony to generate emotional resonance to the signals of another conscious entity. 6. cyclotron transitions would form a representation of bioharmony analogous to music piece. reading of a gene could give rise to a music piece as a sequence of 3n-chords. the interpretation as a melody consistent with given bioharmony should make sense. 3.3 how to perceive the bioharmony, resonate with it, and modify it? in the sequel i christen the sender of emotional signal alice and its receiver bob since the world of physics contains only spherical cows besides alice and bob. human interaction involves emotional aspects. in the ideal case, alice and bob are able to sense each other’s emotional states and are able to communicate their emotions. empathetic alice with noble goals can even change the mood of bob from confused or sad to vsl and happy. empathy does not mean benevolence. hitler was known as a very empathetic person. empathetic but malevolent alice can do the opposite. what could be the description of this at the fundamental level? 1. even a single note of a melody can induce a transition between chords of a given bioharmony represented as dark codons if it corresponds to a difference of notes of two chords. note or several of them can change the chord so that it does not belong to the same bioharmony anymore. this would tend to change the mood. if alice is an empathetic listener not trying to affect the mood of bob, she must use frequencies, which resonantly induce transitions between the chords of the bioharmony of bob. alice and bob must be tuned: i.e. they must have the same bioharmony with the same frequency scale. 2. the ability to resonate with bob requires that the signal sent by alice contains peak frequencies, which belong to the bioharmony of bob. to be empathetic, alice should be able to sense the frequencies associated with the chords of bob’s bioharmony. from these frequencies alice might be even able to deduce the chords of the bioharmony of bob. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2024 | volume 14 | issue 1 | pp. 44-55 52 pitkänen, m., updated view on the rice experiments of masaru emoto if alice manages to do this, she has the gift of empathy or emotional intelligence. autists might be regarded as people with a low level of emotional intelligence and the reason might be that they are not able to perceive the needed frequencies. perhaps mirror neurons play an essential role here in detecting these frequencies. empathy has nothing to do with the moral or ethical standards of alice. alice can do several things. she can generate resonant transitions supporting the bioharmony of bob. she can also try to modify the mood of sad bob, say comfort him. alice can do this by generating frequencies which affect the chords of the bioharmony of bob so that it changes. if alice is malevolent, she can modify the bioharmony of bob so that his mood becomes sad or depressed. if alice is a psychopath, she can even force a disharmony without any symmetries leading to a total emotional confusion. basically alice makes a choice between good and evil. perhaps the ugly words do just this at the level of the dna of rice in emoto’s experiments whereas nice encouraging words do the opposite. how the voices or gestures of alice are transformed to dark photons, their triplets or even dark genes? 1. the voice of alice could be transformed to dark photons with the same frequency spectrum by a generalization of the piezoelectric effect (see this). these dark photons should affect the dark proton sequences of the mb of bob at the biomolecular level in order to generate an emotional response. 2. the frequencies must be consistent with the bioharmony of bob and define the emotional color of the speech of alice, which can be warm or cold or lacking emotional content altogether if alice and b are not emotionally ”tuned”. also the gestures of alice should be coded to the sequences of dark photons or even of dark photon triplets representing kind of emotional music pieces. the notes of the melody should correspond to differences for the chords of the bioharmony in question. 3.4 negentropy of bioharmony dark genetic code consists of 6-bit units and this aspect corresponds to the ordinary dna as a bit sequence. besides this there is bioharmony which relates to the information represented as emotions instead of bits. emotional intelligence measures the ability to perceive the emotional state. one cannot give a simple measure for this ability. one can however consider information measures for the bioharmonies. 1. one can assign to the bioharmony a measure of its algebraic complexity and information content. the value of heff = nh0, where n is a dimension of algebraic extension involved, would define a kind of iq and perhaps also eq. one can also assign a negentropy to the bioharmony, which could measure its information content. of course, the eq characterizes the ability to perceive the emotional state, and is not a property of bioharmony. 2. the intuitive picture is that the negentropy of the bioharmony characterizes the symmetries of the bioharmony. for a given bioharmony, one has 3 icosahedral symmetry groups z6, z4, and z2 corresponding to the 3 20-codon bio-harmonies. the symmetry group of a given 20-codon icosahedral code has orbits such that each codon at a given orbit codes for the same amino acid. there can be several orbits coding for the same amino acid. the k:th orbit contains nk codons. 3. consider first the definition of the entropy. the expression for the entropy of given bioharmony could be defined by the probabilities that a given chord belongs to the k:th orbit with nk chords. the 3 20-chord harmonies are independent and the icosahedral contribution to the entropy is the sum ∑3 k=1 sk of the entropies sk associated with them. also the tetrahedral contribution is present. one would have s = − ∑ pklog(pk). pk would be given by pk = nk/n , where n = 20 is the total number of chords in the icosahedral case n = 4 is the total number of chords in the tetrahedral case. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://en.wikipedia.org/wiki/piezoelectricity dna decipher journal | december 2024 | volume 14 | issue 1 | pp. 44-55 53 pitkänen, m., updated view on the rice experiments of masaru emoto 4. one wants to assign an information measure, negentropy to cognition. p-adic number fields serve as correlates of cognition. formally the definition is similar to that for entropy: one sums over the contributions of 3 icosahedral harmonies and the unique tetrahedral harmony. for a given p-adic prime p, one can define p-adic negentropy np = ∑ pklog(np(pk)), where np(pk) is the p-adic norm of the probability. rather remarkably, this negentropy can be positive unlike entropy. one can also define the sum ∑ p np of the p-adic negentropies as the total p-adic negentropy. this sum involves only a finite number of terms since the probabilities are rational numbers and the p-adic norm differs from unity only if p divides the numerator or denominator of p. in this way one obtains non-negative information measure. it can be shown that the difference n-s is non-negative. 4 how to understand emoto’s experiments with freezing water and rice? in emoto’s experiments with water at freezing point and with rice the emotional tone of the spoken words has a surprising effect on the system. how to understand this? water is fundamental for life and in the tgd based view of life quantum criticality is fundamental for life and conscious intelligence. water makes possible quantum critical fluctuations involving large values of heff measuring the algebraic complexity of the quantum state and also serving as a kind of iq. the criticality for freezing and also other phase transitions would be basically quantum criticality and could have been essential for the emergence of primordial life. the ice crystals found by emoto in the experiments could be corpses of small primordial life forms formed by water molecule clusters. they would be especially favored at quantum criticality and would have dark genetic code which would make it possible for these life forms to experience emotions. the biochemical realization of the genetic code would have emerged much later but would not be essential for the conscious emotional experience. in the rice experiments, the pollack effect [3, 2, 5, 4] could play a key role [20, 19]. the physiological temperature would be the quantum critical temperature for the phase transition taking place in the pollack effect. pollack effect creates matter with a very large value of ~eff = ~gr, where ~gr is gravitational planck constant introduced by nottale [1] characterizing the monopole flux tubes of the gravitational fields of the sun, earth and also other planets. in the pollack effect, incoming photons kick protons to dark protons at the gravitational magnetic flux tubes. this gives rise to negatively charged exclusion zones characterizing cells and dna. pollack effect would be associated with the sol-gel phase transition. pollack effect is also essential for the metabolism and photosynthesis. pollack effect requires energy feed and for instance solar radiation can provide it. also the formation of molecules from atoms can liberate the needed energy. the dark protons would be associated with the magnetic bodies of water molecule clusters. water memory and homeopathy would involve pollack effect and would be associated with primordial life forms formed by water clusters [8]. water memory would allow the magnetic bodies to recognize and mimic the magnetic bodies of the invader molecules as small life forms with the same cyclotron energy spectrum. this would make possible the evolution of the immune system and of chemical life. also the electric counterpart of the gravitational quantum coherence is possible in the long range classical electric fields of sun, earth and also of smaller objects is an essential element of life [23]. the long range electric fields associated with the central nervous system might involve macroscopic quantum coherence with a large value of hem. an induction of emotions similar to that occurring in human interactions could take place in the experiments of emoto and transform the words of the experimenter to dark photon signals affecting the dna and rna of the rice. it is the peak frequencies determining the emotional tone which matter, not the content of the words in the usual sense. if the emotions are indeed universal at the level of dark genes, the emotional aspects of voice would be emotional also from the point of view of rice in water. the words with an unfriendly tone would change the bioharmony to a less negentropic one. friendly issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2024 | volume 14 | issue 1 | pp. 44-55 54 pitkänen, m., updated view on the rice experiments of masaru emoto words would cause the opposite. this would not be about a direct modification of the metabolic energy feed but about its utilization: depressed people lose their appetite and this leads to metabolic deprivation. the sum of p-adic negenetropies provides a quantitative measure for the negentropy of the bioharmony and it also could also serve as a parameter characterizing the mood. received march 24, 2024; accepted december 31, 2024 references [1] nottale l da rocha d. gravitational structure formation in scale relativity, 2003. available at: https://arxiv.org/abs/astro-ph/0310036. [2] the fourth phase of water: dr. gerald pollack at tedxguelphu, 2014. available at: https: //www.youtube.com/watch?v=i-t7tcmudxu. [3] pollack g. cells, gels and the engines of life. ebner and sons, 2000. available at: https: //www.cellsandgels.com/. [4] zhao q pollack gh, figueroa x. molecules, water, and radiant energy: new clues for the origin of life. int j mol sci, 10:1419–1429, 2009. available at: https://tinyurl.com/ntkfhlc. [5] pollack gh zheng j-m. long-range forces extending from polymer-gel surfaces. phys rev e, 68:031408–, 2003. available at: https://tinyurl.com/ntkfhlc. [6] bedecarrats a et al. rna from trained aplysia can induce an epigenetic engram for long-term sensitization in untrained aplysia. eneuro.0038-18.2018, 2018. available at:https://www.eneuro. org/content/early/2018/05/14/eneuro.0038-18.2018. [7] pitkänen m. emotions as sensory percepts about the state of magnetic body? in tgd and eeg: part i. https://tgdtheory.fi/tgdhtml/btgdeeg1.html. available at: https://tgdtheory.fi/ pdfpool/emotions.pdf, 2023. [8] pitkänen m. homeopathy in many-sheeted space-time. in tgd universe as a conscious hologram. https://tgdtheory.fi/tgdhtml/bholography.html. available at: https://tgdtheory.fi/ pdfpool/homeoc.pdf, 2023. [9] pitkänen m. quantum mind and neuroscience. in tgd and eeg: part i. https://tgdtheory. fi/tgdhtml/btgdeeg1.html. available at: https://tgdtheory.fi/pdfpool/lianpn.pdf, 2023. [10] pitkänen m. quantum mind, magnetic body, and biological body. in tgd and quantum biology: part i. https://tgdtheory.fi/tgdhtml/bqbio1.html. available at: https://tgdtheory. fi/pdfpool/lianpb.pdf, 2023. [11] pitkänen m. tgd based view about living matter and remote mental interactions. online book. available at: https://www.tgdtheory.fi/tgdhtml/tgdlian.html, 2023. [12] pitkänen m. geometric theory of harmony. available at: https://tgdtheory.fi/public_html/ articles/harmonytheory.pdf., 2014. [13] pitkänen m. about the correspondence of dark nuclear genetic code and ordinary genetic code. available at: https://tgdtheory.fi/public_html/articles/codedarkcode.pdf., 2018. [14] pitkänen m. could also rna and protein methylation of rna be involved with the expression of molecular emotions? available at: https://tgdtheory.fi/public_html/articles/ synapticmoods.pdf., 2018. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://arxiv.org/abs/astro-ph/0310036 https://www.youtube.com/watch?v=i-t7tcmudxu https://www.youtube.com/watch?v=i-t7tcmudxu https://www.cellsandgels.com/ https://www.cellsandgels.com/ https://tinyurl.com/ntkfhlc https://tinyurl.com/ntkfhlc https://www.eneuro.org/content/early/2018/05/14/eneuro.0038-18.2018 https://www.eneuro.org/content/early/2018/05/14/eneuro.0038-18.2018 https://tgdtheory.fi/tgdhtml/btgdeeg1.html https://tgdtheory.fi/pdfpool/emotions.pdf https://tgdtheory.fi/pdfpool/emotions.pdf https://tgdtheory.fi/tgdhtml/bholography.html https://tgdtheory.fi/pdfpool/homeoc.pdf https://tgdtheory.fi/pdfpool/homeoc.pdf https://tgdtheory.fi/tgdhtml/btgdeeg1.html https://tgdtheory.fi/tgdhtml/btgdeeg1.html https://tgdtheory.fi/pdfpool/lianpn.pdf https://tgdtheory.fi/tgdhtml/bqbio1.html https://tgdtheory.fi/pdfpool/lianpb.pdf https://tgdtheory.fi/pdfpool/lianpb.pdf https://www.tgdtheory.fi/tgdhtml/tgdlian.html https://tgdtheory.fi/public_html/articles/harmonytheory.pdf https://tgdtheory.fi/public_html/articles/harmonytheory.pdf https://tgdtheory.fi/public_html/articles/codedarkcode.pdf https://tgdtheory.fi/public_html/articles/synapticmoods.pdf https://tgdtheory.fi/public_html/articles/synapticmoods.pdf dna decipher journal | december 2024 | volume 14 | issue 1 | pp. 44-55 55 pitkänen, m., updated view on the rice experiments of masaru emoto [15] pitkänen m. the experiments of masaru emoto with emotional imprinting of water. available at: https://tgdtheory.fi/public_html/articles/emoto.pdf., 2018. [16] pitkänen m. an overall view about models of genetic code and bio-harmony. available at: https: //tgdtheory.fi/public_html/articles/gcharm.pdf., 2019. [17] pitkänen m. how to compose beautiful music of light in bio-harmony? https://tgdtheory.fi/ public_html/articles/bioharmony2020.pdf., 2020. [18] pitkänen m. is genetic code part of fundamental physics in tgd framework? available at: https: //tgdtheory.fi/public_html/articles/tih.pdf., 2021. [19] pitkänen m. comparison of orch-or hypothesis with the tgd point of view. https://tgdtheory. fi/public_html/articles/penrose.pdf., 2022. [20] pitkänen m. how animals without brain can behave as if they had brain. https://tgdtheory.fi/ public_html/articles/precns.pdf., 2022. [21] pitkänen m. the realization of genetic code in terms of dark nucleon and dark photon triplets. https://tgdtheory.fi/public_html/articles/darkcode.pdf., 2022. [22] pitkänen m. about tessellations in hyperbolic 3-space and their relation to the genetic code . https://tgdtheory.fi/public_html/articles/tessellationh3.pdf., 2023. [23] pitkänen m. about long range electromagnetic quantum coherence in tgd universe. https: //tgdtheory.fi/public_html/articles/hem.pdf., 2023. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://tgdtheory.fi/public_html/articles/emoto.pdf https://tgdtheory.fi/public_html/articles/gcharm.pdf https://tgdtheory.fi/public_html/articles/gcharm.pdf https://tgdtheory.fi/public_html/articles/bioharmony2020.pdf https://tgdtheory.fi/public_html/articles/bioharmony2020.pdf https://tgdtheory.fi/public_html/articles/tih.pdf https://tgdtheory.fi/public_html/articles/tih.pdf https://tgdtheory.fi/public_html/articles/penrose.pdf https://tgdtheory.fi/public_html/articles/penrose.pdf https://tgdtheory.fi/public_html/articles/precns.pdf https://tgdtheory.fi/public_html/articles/precns.pdf https://tgdtheory.fi/public_html/articles/darkcode.pdf https://tgdtheory.fi/public_html/articles/tessellationh3.pdf https://tgdtheory.fi/public_html/articles/hem.pdf https://tgdtheory.fi/public_html/articles/hem.pdf introduction summary of emoto's findings but has anyone replicated the experiments of emoto? tgd view of the findings bioharmony and the genetic code basic ideas of bioharmony the quantum realization of bioharmony about the symmetries of dark codons does the notion of bioharmony relate to the ordinary notion of harmony the interpretation of bioharmonies in the framework of the tgd inspired theory of consciousness empirical support for the notion of bioharmonies as correlates for emotions emotions are expressed and emotional expression induces emotions how to perceive the bioharmony, resonate with it, and modify it? negentropy of bioharmony how to understand emoto's experiments with freezing water and rice? untitled dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 304-322 campbell, r., part ii: an intelligent face to evolution: the vertebrates exploring knowledge of emotive behavior issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 304 article part ii: an intelligent face to evolution: the vertebrates exploring knowledge of emotive behavior robert campbell * abstract the parallels in the natural record continue to confirm the self-similarity implicit in the evolutionary order, from the form level in the plants, up through the routine level in the invertebrates, to the knowledge level in the vertebrates. we may expect the pattern to continue with humanity’s cultural evolution at the idea level in the hierarchy, but we will not find four levels completely delegated within this level. we shall see that in our brief journey out of the jungle that we have barely reached the stage of developing global technologies associated with our collective routines. even at this level we are threatening our own survival. man’s evolution is far from complete, but we are slowly becoming aware of our own evolution and the impact that our endeavors are having on the biosphere. a few hundred thousand years ago, homo erectus had a brain close to the size of our own. he lived and hunted in groups, erected dwellings, made use of fire, and hunted big game. he must have possessed at least rudimentary language skills to accomplish these things, and he could make limited plans. these ground breaking achievements were the inheritance of homo sapiens who brought sharper perceptions and talents to bear on the development of early human cultures. with the emergence of a single species, about thirty-five thousand years ago, human evolution graduated from our biological roots to become a distinctively cultural affair within a relatively fixed biological form. key words: cosmic order, evolution, intelligence, integration, idea, form, routine. knowledge-form: the hagfish and lampreys are the last survivors of the earliest vertebrates: the jawless fish, called agnathans. early versions of jawless fish became widespread in the seas of the cambrian and ordovician periods some 500 million years ago, but they were quite different from their modern descendants. they had thick bony plates covering their bodies that probably evolved as a defense again giant sea scorpions two meters long with pincers that could crush an unprotected animal. these early fish began to give way to the cartilaginous fish, such as the sharks, and the bony fishes, beginning in the devonian period, about 400 million years ago. by the mid devonian, about three hundred and eighty million years ago, some species of fish had developed both gills and lungs, together with fins that were attached to four lobes that contained bones and muscles inside. these lobe fins could be used for crawling, so these fish could breathe air and drag themselves over land for short distances. it is believed that amphibians developed in a gradual way from these lobe-finned fish by random mutations, although amphibians go through a * correspondence: rober campbell, independent researcher. website: http://cosmic-mindreach.com e-mail: bob@cosmic-mindreach.com note: the articles presented in this issue are based on my book “downsizing darwin: an intelligent face for evolution” self-published in 1996 [1]. more information are available at my website [2]. dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 304-322 campbell, r., part ii: an intelligent face to evolution: the vertebrates exploring knowledge of emotive behavior issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 305 tadpole stage and their skeletal structures are refined into leveraged jointed legs and digits, together with a host of other differences. in any case, by the late devonian a few amphibians had established themselves on land with the well defined jointed quadruped limb structure that we know today. they could lift their bodies off the ground and walk, and they had a strong rib cage with adaptations to keep their organs from collapsing under their weight. they also had a shoulder collar separate from a head, so that they could move the latter independently. amphibians became dominant land animals in the swamp forests of the carboniferous period, a few reaching lengths of over four meters. they were weakjawed lizard-like creatures that developed through a tadpole stage. the vertebrate head brain consists of cerebral hemispheres that have blossomed above primary structures closely associated with the brain stem at the top end of the spinal cord. the autonomic nervous system also developed in concert with the cerebral hemispheres. the cerebral hemispheres became progressively more convoluted as their surface area increased in the higher vertebrates. the external surface layer of the hemispheres is associated with higher levels of consciousness and intelligence. this outer rind of the hemispheres consists of densely packed layers of nerve cells a few millimeters thick, called the cortex, hence the term cerebral cortex. in humans it contains a few hundred billion nerve cells. the two hemispheres function with a degree of independence and yet they are interconnected through nerve bundles called commissures, the largest by far being the corpus callosum. previously it was pointed out that the cerebral hemispheres, including the cortex, developed in three stages associated with the reptile, the lower mammal and the higher mammal. these three developments, old, median, and new, correspond to what are called the archicortex, the mesocortex, and the neocortex, all of which were present in undeveloped form in early vertebrate amphibians. although the three brains were undeveloped, they represented an indication of developments to follow. in other words they indicated a development plan anticipating events far in the future, contrary to the darwinian view. the reptiles largely replaced the amphibians after about eighty million years, during the carboniferous period as forests appeared. they developed a watertight egg that freed them from a tadpole water stage, allowing them to become fully terrestrial. the amniotic egg has an outer shell that protects the developing embryo with the help of three additional membranes within. one membrane encloses the embryo itself. another membrane acts as a collecting bag for waste, also functioning as a respiratory organ. the third encloses the other two together with the yolk, thus separating them from the albumen, a reservoir of water and protein. the reptiles also developed a modified skull with powerful jaws and teeth. at the same time the continents were converging into the supercontinent pangea, and this allowed a common vertebrate format to become established throughout the world. it’s a curious thing that very early in their development the reptiles explored mammalian characteristics. the pelycosaurs included both mammal-like carnivores and herbivores and were replaced in the early permian, about 260 million years ago, by more advanced mammal-like reptiles, the therapsids. some species, up to five meters long, lost most of their teeth and developed beaks, becoming the dominant herbivores. some early carnivores were like saberdna decipher journal | november 2012 | volume 2 | issue 3 | pp. 304-322 campbell, r., part ii: an intelligent face to evolution: the vertebrates exploring knowledge of emotive behavior issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 306 toothed cats, some were dog-like, others were smaller shrew-like creatures. more advanced carnivores may have had hair, and some of them may have been warm blooded. they had longer legs which later moved under their bodies, rather than sticking out sideways as in living reptiles. although they may have been mammal-like in form, it is very unlikely that these early reptiles were mammal-like in behavior. they lacked the cerebral capacity to select a variety of behavioral patterns and moods and thus were more limited than mammals in their ability to modulate their behavior. they integrated experience more directly at a spinal level, with minimal conscious input. in this way each species was more stereotyped in a reptilian way, being locked into fixed behavioral responses to their environment. the large variety of species nevertheless explored a broad range of behavioral forms just before pangea began to break up, about two hundred million years ago, toward the end of the triassic period, there was a mass extinction in which many species disappeared, including most mammal-like reptiles that had evolved a variety of mammalian features. during the jurassic and cretaceous periods that followed two archosaur lines, the crocodiles and dinosaurs, emerged as dominant. the dinosaurs began as small and medium sized creatures, however their legs moved underneath the body allowing them to later support enormous weights as they explored the upper limits to size. some dinosaurs reached lengths well over a hundred feet. one flying pterosaur reached a wing spread of forty-nine feet. they all became extinct at the end of the cretaceous, about sixty-five million years ago. by then the flowers had arrived in abundance to foretell their doom. the indian subcontinent was speeding into asia at 6 inches a year gobbling up the sea floor and plowing some of it into the richest oil deposits on earth in the arabian gulf, while placing the continental plates in compression, raising mountain ranges in asia. mountain building proceeded also in europe and the americas. east africa, the american west and the tibetan plateau were raised. these events were associated with the largest volcanic outflow in the planet’s history. the deccan traps originally covered about half of india’s 1.2 million square miles. depleted in area by erosion today they still cover an area of 200,000 square miles over a mile deep. it is noteworthy that a study by m.j. benton shows that the cretaceous extinction didn’t have a major impact on other land animals and plants, although it affected marine life. yet the dinosaurs were exterminated. if the extinction was caused by a huge asteroid impact bringing on a nuclear winter scenario, as some believe, then why wouldn’t many species of plants, and most other land animals be eliminated also?1 there have been other large asteroid impacts in geological history that didn’t bring mass extinctions as well as mass extinctions that did not align with asteroid impacts. be that as it may, reptilian evolution remained anchored to a common skeletal, visceral, sensory and motor arrangement. none developed six or eight legs or multiple eyes as some invertebrates did. the archicortex of the reptiles blossomed, and there was a lesser expansion of the mesocortex 1 benton, m. j., diversification and extinction in the history of life, science, 268, 52, 1995. the evidence does not confirm a regular period to mass extinctions such as might be associated with periodic cataclysmic physical causes raining from the heavens. dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 304-322 campbell, r., part ii: an intelligent face to evolution: the vertebrates exploring knowledge of emotive behavior issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 307 associated with the lower mammals, with little change in the neocortex. mammalian features survived, consolidated in a few small rodent-like mammals that made their appearance well over two hundred million years ago. typically, the mammals diverged early in the reptilian period and not as a gradual evolution from the dinosaurs that came later. the cerebral expansion of the reptilian archicortex and the lower mammalian mesocortex in the reptiles was complemented by comparable refinements to the autonomic nervous system. the latter is geared to the automatic function of the body to fuel its emotive and emotional needs. it provides energy to the body’s organs and muscles in patterns suited to certain actions, while at the same time providing patterned emotional feedback to conscious awareness. the cerebral hemispheres work something like a tv screen upon which emotional energies can be reflected for conscious observation. so the reptiles developed a limited cerebral capacity to consciously reflect on their needs as they relate to the behavioral form of the body and its functions. they acquired an awareness of exertion or the lack of it, and of the pattern of energy associated with specific actions. each species explored their patterns of behavior to their limits. there is awareness of lunging after prey, struggling to escape, fighting, seeking shelter, basking in the sun, suffering hunger, thirst, injury, birth, death, all relating to the many reptilian species of vertebrate form. a broad spectrum of experience was explored in the conscious awareness of reptiles. these patterned energies that were reflected in awareness integrated a vast spectrum of behaviors that span space and time, since each energy pattern involves action through space and time. although behavior was stereotyped according to species, many species appeared during the reptilian reign of more than two hundred million years. in the reptiles there was thus an exploration in conscious knowledge of the basic vertebrate form in a huge variety of species of all shapes and sizes under many conditions. to a lesser extent this is true of the fish and amphibians also, from which the reptiles emerged. the integration of experience spanning space and time is facilitated through the agency of the timeless and boundless void. knowledge-routine: a reptile is not a very expressive beast. a crocodile sleeps, swims, or eats without showing a variety of moods or emotional modulation in the character of its behavior. its emotive energies are reflected in cerebral awareness through an expanded archicortex, but it can’t do much to alter their pattern because the mesocortex is less developed, and the neocortex is undeveloped. a reptile’s somatic motor functions are largely integrated at a spinal level with minimal conscious involvement. it is not much different to a fish or a primitive amphibian in this respect and it has minimal capacity to transcend the organic dictates of its species. it can’t reflect well on the pattern of reflection because the neocortex is undeveloped. the mesocortex blossomed with the lower mammals, together with limited but significant expansion of the neocortex. with it came a much improved capacity to modulate their emotive energies. anyone who has ever watched young colts, or calves, or lambs romp and frolic can attest to this. they play at mock aggression and the chase, or simply thrill at their own antics. these animals can also emotionally bond to humans, sense our moods and intentions, and be trained to dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 304-322 campbell, r., part ii: an intelligent face to evolution: the vertebrates exploring knowledge of emotive behavior issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 308 some extent. they have knowledge of various behavioral routines. crocodiles don’t care much about feelings of anything apart from primal appetites. as the dinosaurs perished, the mammals rapidly diversified in three groups. a few egg laying monotremes, the duck-billed platypus and the spiny anteaters, still survive. in the pouched marsupials, the labor of birth falls to the tiny undeveloped fetus which must crawl unaided into the mother’s pouch and attach itself to a nipple for the remainder of its development. in the placental mammals the fetus develops in the womb and the labor of birth falls to the mother. the placenta derives from the second membrane in the amniotic egg, the fetus receiving oxygen and nutrients from it and discharging wastes into it, without the mixing of blood between mother and infant. all mammals nurse their young, including the few surviving species of monotremes. although monotremes have no nipples, milk is secreted from pores on the mother’s belly. there is a period of parental supervision in all mammals that increases with more evolved species of placental mammals. there are many anatomical and physiological modifications in the mammals. for example, unlike most reptiles (not all), mammals have a four chambered heart, two auricles and two ventricles, with separate circulation to the lungs for the more efficient respiration needed to support a higher metabolic rate. mammals have internal temperature control, usually assisted by a warm layer of body hair, they have improved kidneys, a better system of bone growth that allows highly leveraged activity in the young, and they generally have more efficient organs. these anatomical refinements made a much greater diversity of behavioral routines possible, from the seasonal migratory patterns of caribou, to the bat’s mastery of flight. the lower mammals, small at first, re-explored the limits to size after the dinosaurs. the early dog-sized rhinoceros of the eocene period grew into a sixteen ton baluchiterium that stood eighteen feet high at the shoulder. the somewhat larger indricotherium or “giraffe-rhinoceros” had a long neck in addition and could graze from the tops of moderately sized trees. they lived during the oligocene epoch among lesser giants, about thirty million years ago. in those days there were also some fearsome carnivores, such as the wolf-like andrewsarchus that was sixteen feet long with a head three feet long. during the miocene there was dinohyus, a pig as big as an ox, and moropus, an oversized horse-like creature with claws. giant building continued in successive waves into the pleistocene epoch of the ice ages, with daedicurus, an armadillo over ten feet long, and the six meter tall giant ground sloth. the marsupials also produced giants during this time, including a wombat as big as a grizzly. many parallels were explored between the marsupial and the placental mammals even though they diverged shortly after the demise of the dinosaurs. the marsupials evolved forms very similar to many species of placentals in complete isolation from them, especially in australia, which has been isolated from the rest of the world for about sixty million years, since the end of the cretaceous. there have been marsupial counterparts to the wolf, cat, mouse, rat, mole, bat, anteater, bear, squirrel (including a gliding version), monkey, and others. this is another strong indication of cross species communication in a global evolutionary context. that the same forms should have evolved, together with very similar equipment, from nostrils to dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 304-322 campbell, r., part ii: an intelligent face to evolution: the vertebrates exploring knowledge of emotive behavior issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 309 eye lashes, to complex neurological organization and function is uncanny evidence of biospheric resonance at work. in light of this obvious parallel evolution in a common form and pattern of integration, even the most biased observer should find it very hard to believe that this could be the result of countless sequences of random chance, especially when other major fundamental differences have persisted between the two groups. a remarkable difference in the marsupial brain (as well as in fish, amphibians and birds) is the lack of a corpus callosum. this huge nerve bundle interconnects most areas of the right and left hemispheres in the placental mammals, although interconnections tend to be sparse or lacking in the freer more distal limb segments such as the hands and fingers that function more independently in humans. in marsupials transfer between both hemispheres is accommodated by their smaller but more developed anterior commissure, but in a more generalized manner. in the diprodontia marsupials such as the kangaroos and wombats there is an additional commissure called the fasciculus aberrans.2 it interconnects more dorsal areas of the neocortex that are generally associated with sensory integration. these differences between marsupial and placental mammals allow differences in bilateral behavior patterns to be explored since the two hemispheres in marsupials are required to function more independently, while still being anchored to a common emotional apparatus and receiving similar sensory input. a major degree of bilateral polarization of brain function, such as that so markedly associated with language in humans (and probably to a degree in some higher placental mammals) was forestalled in the marsupials. this means that the intuitive planning of marsupial behavior, distinct from the explicit formulation of behavior, tends to be worked out more independently in each hemisphere of the marsupial brain. obviously the right and left hemisphere versions have to complement one another in the bilateral integration of movement. one side of the body must be coordinated with the other side. this is basic to routine behavior. in both marsupial and placental mammals routine behaviors become automated at the spinal level and conscious integration is also facilitated by the cerebellum. the independent intuitive planning of behavior in each hemisphere requires secondary sensory and motor areas in each hemisphere to sustain polar relationships between the intuitive integration of meaning and the explicit technique of behavior. (see appendix 1 and 3) the situation in marsupial and placental mammals is similar, so far as working out separate yet complementary behavioral patterns for the two sides of the body is concerned, except that in the placental mammals one side is a more completely hard wired referent to the other side via the corpus callosum. the sensory areas, operating in polar relation to motor areas, assimilate the intuitive patterns for each sequence of movement for each half of the body. this is then translated into specific action by the primary motor area on one side of the new brain which transmits the pattern to the muscles on the opposite side of the body. the change in position of one arm or one leg is monitored by proprioceptive feedback to the sensory areas which assimilate the next sequence of movement, and 2 heath cj., jones eg. interhemispheric pathways in the absence of a corpus callosum. j. anat. (1971), 109, 2, pp. 253-270 dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 304-322 campbell, r., part ii: an intelligent face to evolution: the vertebrates exploring knowledge of emotive behavior issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 310 so on.3 the proprioceptive nervous system rapidly feeds back information about the relative position of the body in space to both the cerebellum and the cerebral cortex. the hippocampal commissure provides a route to the hypothalamus and the reticular system that regulate the independent activity of the autonomic nervous system and allows emotional feedback from the primitive limbic system to neocortical awareness. the independent capacity of the new brain to reflect upon and modify the emotional patterns of the reptilian brain provides both marsupial and placental mammals an enhanced degree of freedom to tailor their actions to better suit the needs of circumstance, albeit more limited in the case of marsupials. the spinal cord is also organized in sensory and motor areas with proprioceptive input that allows for local spinal integration of simple sensory-motor behavior. minimal conscious participation on the part of the host is needed, as in the more stereotyped behavior of the reptiles. it also requires minimal conscious participation in mammals and humans when repetitive motions such as walking have been automated and delegated to the spinal level. the absence of a corpus callosum places marsupials under somewhat of a handicap when it comes to consciously integrating complementary behavior on the two sides of their bodies. the topological representations, called homunculi, are paired in motor and sensory sets. since one set is essential to developing the intuitive idea and another set is essential for its explicit motor enactment, two sets are thus essential in each hemisphere if it is to function independently of the other hemisphere.4 ’ 5 this neural organization is especially essential in the lower mammals for the bilateral organization of more flexible and refined body movements in both the marsupials and the placentals. in more developed form it is essential for the bilateral polarization of brain function associated with language and human creativity. in the marsupials, however, the complementary patterns for each hemisphere must be intuited more independently, without the same benefit of a more complete hard wired referent to the other hemisphere. it seems likely that the exploration of a variety of marsupial forms with close placental counterparts facilitated the bilateral organization of brain function in both classes of mammals. patterned energies have been mutually accessible to similar species of different classes, facilitating both their biological and their behavioral evolution. otherwise there would be no mutual referents to independent yet complementary motor patterns by which to refine behavior consciously, either in the marsupials or in the placentals. the 3 the description given here is very general. for a complete description of how the human nervous system works synapse by synapse see campbell rc. (2006). the nervous systempart 1spinal integration: http://www.cosmic-mindreach.com/system4_sequence_steps.html and part 2the cerebellum: http://www.cosmic-mindreach.com/system4_sequence_part_2.html. 4 woolsey cn, organization of somatic sensory and motor areas of the cerebral cortex in biological and biochemical bases of behavior, harlow hf, woolsey cn eds, university of wisconsin press, madison, 1958. 5 the intuitive idea is developed as a sensory pattern relating to a motor context, and the explicit technique is developed as a motor pattern relating to a sensory context. idea development takes place to the rear of the central sulcus, motor development takes place in front of it. this complements the organization of the spinal cord, where the sensory areas are in the dorsal horns and the motor areas are in the ventral horns. dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 304-322 campbell, r., part ii: an intelligent face to evolution: the vertebrates exploring knowledge of emotive behavior issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 311 marsupials needed the placentals to refine complementary topological patterns, while the placentals needed the marsupials to refine independent topological patterns. without this interplay, accessible through biospheric resonance6, the mammals would be left completely to the vagaries of trial and error. it appears that placental evolution has been globally enhanced as a consequence. the higher placental mammals have clearly outpaced the marsupials. the above discussion illustrates problems associated with hard wiring routines of behavior genetically that are subject to volitional control, since it can’t be done solely either with or without the conscious participation of the animal. behavioral patterns are subject to change at the individual creature’s discretion, utilizing the same anatomical and physiological organization.7 this becomes increasingly significant with the lower mammals. even at this level mammals are not complete slaves of their genetic programming. they are sentient creatures capable of sensing a variety of patterns and modulating their behavior in the task of integrating space and time. complementary routines of behavior are thus worked out in knowledge at this knowledge-routine level of the lower mammals. knowledge-knowledge: in the higher mammals there is an explosive development of the neocortex, or new brain, such that it outreaches the mesocortex and archicortex of the lower mammals and reptiles and enfolds them inward around the top of the brain stem. the archicortex and mesocortex form the edge, or limbus, of the hemispheres and together with certain structures in the brain stem become a functionally integrated apparatus, known as the limbic system. in the development of the brain in higher mammals the old brains don’t get thrown away. rather they get rearranged to incorporate control over emotive energies, that is over “feelings” that have ancient origins and the corresponding patterned energies that mobilize the body. the limbic system is a common feature throughout the mammalian lineage but it becomes more pronounced with the explosion of the neocortex in the higher mammals and especially in humans. it works in close association with the autonomic nervous system.8 (see appendix i.) together this division of emotional and conscious knowing bestows a knowledge of knowing on the higher mammals, especially humans. 6 experience is quantized into discrete episodes that become structurally integrated as elements of memory in the quantum sensorium, the void. quantized elements are recalled to form in the oscillating dance between particulate form and quantized emptiness that makes up the cosmic movie. the biosphere is a living whole that seeks balance and equilibrium between the myriad living organisms on every level that make up the sphere of life that surrounds the planet. it seeks resonance and harmony with itself in its oscillating dance, as surely as beating a drum head or strumming a string on a banjo. experience explored in one part of the biosphere does not exist in isolation, even though it may be geographically isolated. it is integrated with and accessible to experience in other parts of the biosphere through biospheric resonance. there are countless instances of evolutionary copying between unrelated species, wherever they can exploit a complementary niche in the biosphere. simply calling this convergent evolution on the assumption that it happens by a series of fortuitous accidents explains nothing. 7 established behavioral patterns become quantized elements of technique and are preserved as elements of memory in the sensorium or void. they are accessible through the structured relationship of the individual to the species, genus, order, class, etc., to the extent that taxonomy reflects the evolutionary order. they are also accessible between different lineages where resonance renders this feasible. 8 in 1878 broca demonstrated that a large cerebral convolution which he called the great limbic lobe is found as a common denominator in the brains of all mammals, forming a border around the brain stem. broca, p., anatomie dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 304-322 campbell, r., part ii: an intelligent face to evolution: the vertebrates exploring knowledge of emotive behavior issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 312 we retain emotional access to the patterned energies explored by our reptilian and lower mammalian roots. they become especially apparent during moments of raw unbridled reactions, as in moments of rage, fear, fervor, lust, greed, hunger, satiation. we remain indebted to ancestors that have long since perished from the planet, and in a sense we are obliged to repay the debt. we continue to refine and tailor their primitive energies in more appropriate ways in everything that we think and do. we still have their primitive brains incorporated into our limbic system that fuels the emotional energy for our every action. this reflux and refinement of behavioral energy seeking balance up and down the levels of the evolutionary hierarchy has been going on for hundreds of millions of years, and its character has evolved at each level as the process proceeds. as the most recent player on the highest level of the hierarchy we span the greatest expanse of history, and we face the greatest challenge in its integration. the human heart is an ancient thing indeed, and we are biologically obliged to consciously cope with primitive energies and emotions.9 even within this primitive limbic system there is some degree of emotional regulation at a lower mammalian level of awareness. the mesocortex that bloomed with the lower mammals is more developed than the reptilian archicortex and it has some degree of independence from it. so there can be a degree of emotional reflection on primary reptilian emotions, albeit within the context of the emotional apparatus of all mammals. keep in mind that the cerebral cortex is like a screen on which emotional experience is projected in conscious awareness. since the lower mammalian screen has a degree of independence from the reptilian screen, there can be a degree of emotional awareness of emotion. this is characteristic of the way the creative process elaborates within itself. it is especially true in the higher mammals and humans. we have an emotional brain that is distinct from and yet related to, the new brains of our two hemispheres. at this point it should be emphasized that the limbic cortex is structurally primitive compared to the neocortex, and it shows a similar degree of organization in all mammals. unlike the neocortex, the limbic cortex has strong reciprocating connections with the hypothalamus which integrates autonomic functions. (see appendix ii.) this means that there is a strong projection of visceral emotions onto the limbic screen that colors sensory perceptions. by contrast the neocortex or new screen has expanded immensely with the development of the higher mammals, with consequent enhancement of our intellectual potential. the neocortex integrates sensory impressions of the external world with minimal emotional content. the limbic cortex and the neocortex thus function in independent yet mutually related realms. p. d. maclean, who did much of the early research on the limbic system, called this split between the intellect and emotion a built-in schizophysiology in humans.10 as arthur koestler put it, the comparée des circonvolutions cérébrales. le grand lobe limbique et la scissure limbique dans la série des mammifères. rev. anthrop., 1: 385, 1878. 9 papez first advanced the idea that the limbic cortex and related structures provide the anatomical substratum of emotional behavior. papez, j.w., a proposed mechanism of emotion, arch. neurol. &psychiat., 38, 725, 1937. 10 in 1949 paul maclean first introduced the idea that there is a built in schizophysiology between the neocortex and the limbic system, since the former has no built-in biological controls over the latter. many articles including: maclean, p.d., contrasting functions of limbic and neocortical systems of the brain and their relevance to psychophysiological aspects of medicine, the journal of american medicine, 1958, 25, 611. dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 304-322 campbell, r., part ii: an intelligent face to evolution: the vertebrates exploring knowledge of emotive behavior issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 313 immense intellectual capacity of our neocortex, capable of building atomic bombs and sending rockets to the moon, is biologically harnessed to the emotional capacity of a crocodile and a horse.11 judging by our tragic history of destructive violence it seems an accurate assessment of our human situation. one might like to hope that the main potential for emotional tailoring and regulation in the higher mammals derives from the much larger neocortex. it doesn’t happen through hard-wired control of the neocortex over the limbic system, however, because the neural connections are just not there to allow it. in all mammals emotional energies become reflected in cerebral awareness and they must be regulated through a degree of intuitive insight into the dynamics of experience that can find appropriate expression in explicit behavior. this process must be integrated through the motorsensory topology of the neocortex according to the perceived needs of circumstance. neither the neocortex nor the limbic cortex has dominion over the other. this simply means that emotion and intellect are constrained to live independently in the same house together and must seek a satisfactory balance in the integration of experience. thus we find that in dogs, cats, porpoises, whales, elephants, seals, monkeys, apes, and so on, there is a considerable degree of intelligent reflection and behavioral refinement of emotive experience. the higher mammals can modulate their emotive experience more flexibly over a wider range than the lower mammals can and they display more distinctive personalities. they can show anger, fear, joy, anguish, affection, contempt, interest, indifference, trust, a whole range of emotions of a similar nature to humans. values begin to blossom with the higher mammals. a conscious evaluation and intentional selection of various emotional patterns becomes possible. this means that explicit knowledge of various emotional patterns is reflected for assimilation with other factors. at this conscious level of knowledge appropriate discretionary choices can be made between them. there is a knowledge of knowing alternatives that form the basis of value judgments. this entails a conscious anticipation of the future that spans space and time introduced into the process of integrating history. it’s worth pointing out that the body is also topologically represented by three homunculi in the cerebellum, the large folded structure to the rear of the brain stem at the base of the cerebrum. one homunculus is centrally inverted on the older part of the spino-cerebellar cortex. the other two are bilateral representations of each half of the body. the cerebellum controls equilibrium and muscle tone and it is also involved in coordinating skilled voluntary movements. to do this it must reconcile spinal inputs, including proprioceptive sensory feedback from simulations in muscle spindles, with conscious simulations of anticipated patterns of behavior. in short it must reconcile spinal cord and cerebral functions. it tends to be especially 11 koestler, a., the ghost in the machine, pan books, london, 1970. dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 304-322 campbell, r., part ii: an intelligent face to evolution: the vertebrates exploring knowledge of emotive behavior issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 314 well developed in birds and bats in order to meet the challenges of flight. (approximately one quarter of mammalian species are bats.) motor-sensory topology is closely related to the proprioceptive nervous system that monitors the relative position of the body’s joints, tendons and muscles through feedback from complex sensory organs. it gives us our perception of the body’s orientation in space. included are muscle-spindle organs distributed throughout the muscles of the body that consist of special bundles of muscle fibers enclosed within a sheath. these relatively small spindle fibers receive an independent “gamma” motor supply (small motor neurons) from the ventral horns of the spinal cord, regulated by descending tracts from the brain. these small gamma motor neurons constitute about 30% of the motor neurons in the ventral horns of the spinal cord. this independent motor supply to the muscle spindles allows them to be flexed independently of the muscles they monitor. the spindles in turn transmit two kinds of sensory signals, measuring the degree and the rate of flexion, back to the dorsal horns of the cord at various levels. the same sensory feedback also has collateral branches extending into the motor centers of the ventral horns, as well as transmitting to brain centers, including the homunculi of the cerebrum and cerebellum. this muscle spindle arrangement allows for an electronic “gamma” motor simulation in the ventral horns of the cord, initiating a simulation in the muscle spindles distributed throughout the muscles of the body, without affecting the skeletal muscles themselves. the simulation generates patterned feedback from the spindles, via the large rapidly transmitting proprioceptive sensory fibers, thus allowing for anticipated future patterns of action involved in the selection of actual motor patterns.12 we are often aware of sensing the simulation of the next action sequence prior to enacting it, even in the process of ongoing activity. we can also consciously simulate actions, as in learning dance steps, or any planned sequence of actions. we can also just feel the rhythm of music through the body, as if dancing or marching. the intuitive perception and planning of the body’s movements thus needs one set of sensory-motor topology to integrate proprioceptive feedback distinct from a second set of motor-sensory topology for integrating the actual execution of movement in each cerebral hemisphere. the passive cerebral reflection of emotive patterns of behavior in conscious awareness thus has another dimension added to it in the higher mammals with a more developed neocortex. the higher mammals can intentionally simulate and integrate a variety of behavioral patterns in anticipation of a future outcome, all within the biological format of a single individual. the capacity to reflect on emotional experience is not confined to an individual’s history, nor to that of the species. the higher mammals are quite responsive to the emotions that humans project. they pick up our feelings, emotions and intentions, and this certainly isn’t hard wired across species. some dogs assume characteristic traits of their masters. they can learn to understand 12 campbell r. the nervous systempart 1spinal integration, 2006: http://www.cosmicmindreach.com/system4_sequence_steps.html dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 304-322 campbell, r., part ii: an intelligent face to evolution: the vertebrates exploring knowledge of emotive behavior issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 315 verbal commands, and most higher mammals, as well as some birds, can be highly trained. we can also consciously pick up their feelings if we make a modest effort to be sensitive toward them. and there needn’t be a human involved, since social animals bond in groups. some animals and birds chose one mate for life, and the period of adult supervision and training of the young in some higher mammals spans a number of years. animals sometimes bond across species, even natural enemies like dogs and cats. even in aggressive confrontation animals pick up the feelings of others. this capacity to tune into the emotive feelings of others is facilitated via the quantum sensorium, spanning space and time and integrating history. it is obvious from these observations that the integration of experience is not just an individual or a species affair. as higher mammals we are attuned not only to private aspirations which influence human affairs, but also to the energies of other species with whom we share the biosphere, while sharing also a common basis to emotive experience through our limbic ancestry. among the higher mammals the significance of a common limb structure, together with a very similar visceral and neurological organization, becomes especially apparent. the motor-sensory topology of the neocortex, which must always seek a balance with the primitive limbic system, is instrumental in integrating the experience and history of the biosphere in the higher mammals and especially in man. this implicitly requires a common mammalian format with the evolved cerebral capacity to consciously span space and time in knowledge extended far beyond the constraints of individual concerns. the knowledge implicit in the mammalian format accesses knowledge across epochs, eras, species, classes and continents as it seeks balance in biospheric resonance. the relationship of the neocortex to the limbic system bestows a knowledge of knowing on the individual in the higher mammals, especially in humans. through our often destructive endeavors the human being has assumed a position at the top of the biological hierarchy and we are just beginning to learn the responsibility attached. we are more than our social identities going back a few decades to when our mothers gave birth. the human heart is ancient, embracing the entire vertebrate lineage for four hundred million years of evolutionary history. knowledge-idea: the conscious development of creative ideas which can give implicit direction to knowledge, routine and form, is a capacity that has developed from early primate origins, through anthropoid and hominid ancestors, to eventually find consolidation in one species, homo sapiens. not only are we humans able to create highly independent ideas, it seems that this has been the integrating idea involved in the whole evolutionary process over the last several billion years. we potentially have the capacity to become aware of our own evolution, to consciously participate in the process by learning to respond responsibly to one another and our role in the biosphere. it is believed that primates diverged from primitive tree shrews that lived in the cretaceous period during the hey day of the dinosaurs. present day shrews are very small, from less than two inches to at most a few inches long. they are extremely active, aggressive, nervous, solitary and territorial. they are easily frightened to death. they have the highest metabolic rate of any animal on earth, with a heart rate as high as 800 beats a minute. they must constantly search for food and dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 304-322 campbell, r., part ii: an intelligent face to evolution: the vertebrates exploring knowledge of emotive behavior issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 316 will eat anything, sometimes preying on animals larger than themselves. if deprived of food most of them face starvation in a half a day. they in any case only live for about fifteen months, so if biologists are correct, we had rather shaky beginnings. small prosimians, or pre-monkeys, were common in north america and europe during the paleocene to the mid eocene, from about sixty to forty-five million years ago. the first new world monkeys appeared in argentina by the late oligocene or early miocene, about twenty-five million years ago. the old world monkeys and apes, from which humans descended, seem to have evolved from different prosimian stock, the earliest cat-sized fossils from egypt being dated at about thirty million years ago. during the miocene, from twenty-three to fifteen million years ago, several fossil species are known which were probably relatives of both human and african ape ancestors. the first evidence of a distinctively hominid line is found in the so-called ground apes, the first named ramapithecus that appeared from fifteen million to about eight million years ago in east africa, eastern europe, turkey, pakistan, india, and china. primates have several features which have contributed toward developing their intelligence. their faces are flattened so that their eyes focus together to provide stereoscopic vision, with enhanced depth perception. their hands and feet have fingers and toes capable of grasping, with flattened nails rather than claws. in many the thumb or toe works in opposition to the other four digits, facilitating the holding and manipulation of objects. they sit in an upright position and some are partially bipedal, freeing the arms and hands for separate tasks. most live in trees where they use their hands and arms in swinging with a high level of agility. the primates tend to be anatomically unspecialized, so that the group as a whole is better characterized by increasing levels of dexterity and intelligence. all of the higher primates have some degree of social organization, they care for their young over extended periods, and possess a rudimentary level of communication. hominid species began to walk upright and clearly differentiate over four million years ago in africa. paleoanthropologists have dated fossils of ardipithicus ramidus found in ethiopia in 1992 and 1993 at 4.4 million years old, pushing the date back nearer to the time when hominids diverged from the chimpanzee line. considered to be ancestral to the genus australopithicus, it had many features in common with the chimpanzee and other features common to later hominids that indicated an upright stance. it lived at least part of the time in wooded areas, challenging beliefs that upright walking began in the open savanna. fossils of a number of species of australopithecus dating from 4 million years to 1.25 million years ago have been found. at some point, just over 2 million years ago, a new genus, homo (to which our species homo sapiens belongs), evolved from one of the species of australopithecus, and it appears from the evidence so far that two or three early species of homo coexisted for a time. homo habilis used stone tools and had a significantly larger cranial capacity than australopithecus, about 750 cc as compared to 600 cc at most for the latter. although the evolutionary tree has a tendency to grow branches as more fossil finds are made, homo erectus came on the scene about 1.8 million years ago. he was larger, more adventuresome and brighter than habilis, with a cranial capacity ranging from 900 cc to 1050 cc and more near the end of his time. homo erectus survived until at least two hundred thousand years ago, and perhaps later in dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 304-322 campbell, r., part ii: an intelligent face to evolution: the vertebrates exploring knowledge of emotive behavior issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 317 places. he migrated out of africa to asia, indonesia, and europe, displaying considerable adaptability and ingenuity in employing tools and techniques to meet different circumstances. he hunted big game, made use of fire, and must have had some command of language to organize collective efforts, as in hunting. he was followed, or perhaps paralleled, by archaic forms of homo sapiens, assigned by some to the species homo heidelbergensis13. in any case the sparse fossil record indicates that we first emerged very close to our present form, with an average cranial capacity of 1350 cc, about 100,000 years ago or more in s. africa, radiating north through palestine and lebanon, and appearing about 40,000 years ago in europe. however neanderthal man, a sub-species of homo sapiens, emerged mysteriously on the scene in europe about 130,000 years ago. he was more robust than our sub species, which is sometimes called homo sapiens sapiens. neanderthals had large brow ridges, a receding chin, and a somewhat larger brain, up to about 1600 cc. they were contemporary with modern man and they had some language skills. they buried their dead with some evidence of ritual, indicating spiritual beliefs, but they generally left little evidence of an interest in aesthetic values. neanderthals disappeared about 35,000 years ago, leaving us as the sole beneficiary of the human form. our brain and body size also seems to have peaked about thirty thousand years ago and declined about ten percent since. there is some evidence that neanderthals and home sapiens may have interbred. the upper paleolithic cultures of homo sapiens were much improved, with finely crafted stone and bone tools, and shell and ivory jewelry. human knowledge and values had advanced to appreciate beauty and craftsmanship in created ideas. this is clear evidence of efficient language skills coupled to discriminating intuitive perceptions. the bilateral polarization of human brain function was well under way, with the energies of limbic reptilian and mammalian ancestors being refined anew. cave paintings14,15,16 dating back 35,000 years in europe, at least 30,000 years in australia,17,18,19 and perhaps as much as 100,000 years in south africa20,21 captured the animating spiritual essence of animals and events. aboriginal 13 lozano m, mosquera m, de castro j, arsuaga j, carbonell e. right handedness of homo heidelbergensis from sima de los huesos (atapuerca, spain) 500,000 years ago. evol human behav 2009; 30:369-76. 14 curtis g. the cave painters. new york: anchor books, 2006. 15 clottes j. in: bahn pg, trans. chauvet cave: the art of earliest times. salt lake: u of utah press, 2003. 16 whitley ds. cave paintings and the human spirit: the origin of creativity and belief. amherst ny: prometheus books, 2009. 17 bednarik rg, the earliest evidence of palaeoart. in: rock art research 2003; 20:89-135. 18 mcdonald j, haskovec ip, eds. state of the art: regional rock art studies in australia and melanesia, proc of the first aura congress. melbourne: aust rock art research assoc. publication no 6, 1988. 19 kleinert s, neale m, eds. the oxford companion to aboriginal art and culture. melbourne: oxford university press, 2000. 20 villa p, soressi m, henshilwood cs, mourre v. the still bay points of blombos cave (south africa). j arch sci 2009; 36:441-60. dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 304-322 campbell, r., part ii: an intelligent face to evolution: the vertebrates exploring knowledge of emotive behavior issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 318 cultures all over the world consider the earth to be sacred and regard themselves as an integral part of this holistic and living landscape. they belong to the land and are at one in it with animals, plants, and ancestors whose spirits inhabit it along with transcendent archetypal spirits. these spiritual beliefs still in evidence today pervade the aboriginal australian, african,22 native american23, 24 and east asian25 cultures, the native americans having arrived from east asia during the last ice age with no prior evidence of human habitation. the aboriginals of australia arrived about 60,000 years ago. in a recent find a vast rock wall of about 1500 paintings chronicles the history of australian aboriginal contact with outsiders, including european sailing ships, 19thcentury steamships and a world war ii battleship, alongside exquisite rock art more than 15,000 years old.26 with over 200 languages, 600 dialects and no formal script, they continue to communicate with message sticks consisting of picture sequences that communicate a message.27 various authorities ascribe the origin and significant of cave paintings to shamans who translated experiences in trance states.28,29 according to leon jaroff 30 "wildlife and humans tend to get equal billing in african rock art (in the caves of western europe, by contrast, pictures of animals cover the walls and human figures are rare). in southern africa, home to the san, or bushmen, many of the rock scenes depicting people interpret the rituals and hallucinations of the shamans who still dominate the san culture today. among the most evocative images are those believed to represent shamans deep in trance: a reclining, antelope-headed man surrounded by imaginary beasts, for example, or an insect-like humanoid covered with wild decorations." spirit possession is widely practiced in africa31 and asia32,33 today. it requires an intuitive connection that implicitly invites a spirit to enter their organic body in place of their own. ancient rock art in australia is attributed by the indigenous people to dreaming beings. it is regarded as sacred because it shows a continuing ancestral presence that spans space and time.34 the paintings indicate that human perceptions and creative abilities had matured to a level comparable to humans today. they could deal with experience in abstraction with a good degree of sophistication. this clearly indicates well developed left brain language skills differentiated from a right brain capacity for intuitive insight. 21 mourre v, villa p, henshilwood cs. early use of pressure flaking on lithic artifacts at blombos cave, south africa. science 2010; 330:659-62. 22 mbiti js. introduction to african religion. nairobi: east african educational publishers, 1991. 23 blondin g. trail of the spirit: the mysteries of medicine power revealed. edmonton: newest press, 2006. 24 blondin g. yamoria the lawmaker: stories of the dene. edmonton: newest press, 1997. 25 dr. cheu hock tong. the nine emperor gods: a study of chinese spirit medium cults. singapore: times books intl, 1988. 26 http://www.smh.com.au/news/national/rock-art-redraws-our-history/2008/09/19/1221331206960.html . 27 http://australia.gov.au/about-australia/australian-story/austn-indigenous-tools-and-technology . 28 hedges k. traversing the great gray middle ground. an examination of shamanistic rock art interpretation. rock art res 2001; 27:123-36. 29 eliade m. shamanism: archaic techniques of ecstasy. princeton: princeton u press, 1964. 30 jaroff l. etched in stone. new york: time mag article june 2, 1997. 31 behrend h, luig u, ed. spirit possession, modernity, and power in africa. madison: u of wisc press, 1999. 32 smith fm. deity and spirit possession in south asia. delhi: motilal banarsidass, 2009. 33 pak ok. spirit possession phenomena in east asia. london: sage publications, 1996. 34 http://australia.gov.au/about-australia/australian-story/austn-indigenous-art . dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 304-322 campbell, r., part ii: an intelligent face to evolution: the vertebrates exploring knowledge of emotive behavior issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 319 the neocortical expansion and development which has taken place with the lower and higher mammals was largely symmetrical in both hemispheres. it relates primarily to integrating the bilateral symmetry of the body and its consciously controlled movements. it is quite apparent in the higher mammals, and especially in the primates, that neocortical development has resulted in more fluidly perfected and automated behavioral patterns. language superimposes upon this bilateral symmetry of the new brain the polarization of right brain intuition and left brain technique. the human capacity for generating creative ideas and translating them into explicit forms is not symmetrically organized in the neocortex of the brain. this extraordinary fact of the bilateral polarization of the new brain in humans was most dramatically demonstrated by the experiments of roger sperry in the 1960’s. he performed extensive tests on a number of patients who had undergone surgical deconnection of their cerebral hemispheres in an effort to control repeated severe epileptic seizures.35 these patients had their corpus callosum cut in two so that the epileptic focus that caused the seizures in one hemisphere could not transmit to the other hemisphere through this massive nerve bundle. following this drastic surgery, each hemisphere of these people’s brains had to function independently. under normal conditions, however, both hemispheres are presented with the same sensory input, even though they are separated, and both remain harnessed to a common emotional limbic apparatus. each hemisphere also possesses the essential major and minor sensory and motor homunculi that allow the independent yet related development of the essential polar relationships. there was therefore little noticeable change in their behavior, except that their epileptic condition was improved. sperry, however, devised a means of testing the visual perceptions of these people. if they focused at the center point of a screen, and a picture was flashed very quickly on one half of the screen, the image would only register on the opposite hemisphere of the brain. if a picture was flashed on the left side, say of a pencil, it would only register on the right brain. if the person was then asked what they saw, they could not reply correctly. the right hemisphere cannot speak in right handed people. if then asked to pick the pencil out from a number of concealed articles by touch, their left hand could readily do it, since it is controlled by the right hemisphere. when the picture was flashed on the right screen, registering on the left hemisphere, the left hand could not pick the article out, yet the person could readily say what it was when asked. the left hemisphere has motor control of speech, but not of the left hand. by extensive testing sperry was able to show that there are different mental functions being performed completely independently in each hemisphere, each with a completely separate memory track. there are two minds in one body, so to speak, both of them harnessed to a third emotional or limbic mind that tends to respond through grunts and grimaces. the left brain in right handed people concerns explicit functions that involve language. this includes nearly all of human 35 many articles including: sperry, r.w., gazzaniga, m.s., and bogen, j.e., interhemispheric relationships: the neocortical commissures; syndromes of hemispheric deconnection, handbook of clinical neurology, 4, 1969. sperry, r.w., hemisphere deconnection and unity in conscious awareness, amer. psychol., 1969. dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 304-322 campbell, r., part ii: an intelligent face to evolution: the vertebrates exploring knowledge of emotive behavior issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 320 behavior, encompassing all socially learned techniques of performance, including science. the intuitive right brain excels at spatio-temporal organization, intuitive appreciation of art, music, aesthetics, the spiritual sense and the like. so this pattern of three polar focal points to human mental activity is a very real and distinct thing. it is not genetically programmed because the meaning inherent in language must be learned through intuitive access to a reservoir of cultural experience associated with the social tradition in which the individual grows up. a chinese infant adopted by american parents will become thoroughly american, and vice-versa. even if there is a limited genetic component to the overall triadic pattern of thought and behavior, the genes are themselves determined by the self-similar universal pattern, not vice-versa. three focal points are inherently necessary for creative ideation. there must be an intuitive insight into the spatio-temoral dynamics of any process in order to develop an idea in abstraction. that idea must then find translation into an appropriate technique to make it an explicit reality. it’s of little use to try to fly like a bird without an insight into the dynamics of flight, and without some means of developing the technique to actually do it. all the bird-like feelings of flying in the world won’t accomplish the task, and yet the energy that fuels the necessary thought processes must derive from our limbic emotional apparatus, since we are spiritually animated creatures. this fundamental pattern of three focal points involved in the creative process transcends space and time, since it integrates space and time. the pattern is a self-similar reflection of the cosmic order through which the whole of experience is integrated in a perpetual state of evolution and renewal. the creative process is in communication with itself and is therefore implicitly intelligent. we would be a long time waiting for monkeys to bang an airplane together by accident. (see appendix iii.) we find then that by late paleolithic times human beings had arrived on the scene well equipped for abstracting experience through intuitive insight and giving direction to knowledge through creative ideas. as individuals humans could independently perceive and communicate ideas from what they learned in experience. they became able to distinguish individual differences and similarities more acutely, but they were also aware that they needed to reconcile the gulf between self and other in order to meet the challenge of group survival. they could consciously develop independent ideas to integrate their collective knowledge and direct their routines in social forms of behavior. this capacity became the dominant factor in human social evolution. the universal and particular aspects of experience are always there, defining one another and seeking mutual reconciliation. phenomenal experience has a universal archetypal component as well as a particular individual component. *** commentary: the parallels in the natural record continue to confirm the self-similarity implicit in the evolutionary order, from the form level in the plants, up through the routine level in the dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 304-322 campbell, r., part ii: an intelligent face to evolution: the vertebrates exploring knowledge of emotive behavior issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 321 invertebrates, to the knowledge level in the vertebrates. we may expect the pattern to continue with humanity’s cultural evolution at the idea level in the hierarchy, but we will not find four levels completely delegated within this level. we shall see that in our brief journey out of the jungle that we have barely reached the stage of developing global technologies associated with our collective routines. even at this level we are threatening our own survival. man’s evolution is far from complete, but we are slowly becoming aware of our own evolution and the impact that our endeavors are having on the biosphere. a few hundred thousand years ago, homo erectus had a brain close to the size of our own. he lived and hunted in groups, erected dwellings, made use of fire, and hunted big game. he must have possessed at least rudimentary language skills to accomplish these things, and he could make limited plans. these ground breaking achievements were the inheritance of homo sapiens who brought sharper perceptions and talents to bear on the development of early human cultures. with the emergence of a single species, about thirty-five thousand years ago, human evolution graduated from our biological roots to become a distinctively cultural affair within a relatively fixed biological form. direct evidence of prehistoric cultures is limited to surviving artifacts that were often made with a utilitarian purpose in mind so that we are lacking direct evidence of belief systems and tribal organization that directed human culture in earlier times. thirty thousand years ago there were less than ten million people spread throughout africa, europe, asia and australia. widely separated cultures evolved independently in a diverse variety of ways that were still exploring the planet and coming to terms with great differences in geography and climate. they nevertheless hummed a common theme, as surely as if they had tuned to the bbc. biospheric resonance was orchestrating the music. the bilateral polarization of conscious thought associated with language was a common factor that joined them. left brain practical concerns with techniques of survival had a polar relationship with right brain spiritual concerns. the latter spiritual concerns transcended physical events in space and time. these early spirit cultures were highly intuitive. they were attuned to energies around them, being influenced by the natural and spiritual environment with which they lived in intimate contact. this much we can gather from descendant spirit cultures surviving into the present in various parts of the world. with the migrations of homo sapiens out of africa to asia and europe over 35,000 years ago, three distinct races emerged, each with distinctive qualities in their languages that reflected the three focal points of human thought. the sino-tibetan languages of east asia are intuitive and tonal in nature. meaning is assimilated holistically as a gestalt, being more closely attuned to the intuitive and spiritual concerns of our right brain. asian cultures remain closely attuned to spiritual matters to this day. in contrast the indo-european languages are more suited to left brain logic, with articles, conjunctions, and tenses to verbs linking external physical events up in a linear flow through space and time. even though these early cultures were spirit cultures, their languages are more suited to the material concerns of technique and technology. we shall soon see how these characteristics evolved historically. dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 304-322 campbell, r., part ii: an intelligent face to evolution: the vertebrates exploring knowledge of emotive behavior issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 322 meanwhile the sub-saharan african languages generally have some of the characteristics of both asian and european languages. they are all tonal and they also have tenses to verbs. they are more closely attuned to the music of our ancient emotional hearts. polyrhythmic music is a distinctively african creation. they are the oldest cultures on earth to which we are all indebted. all three races, with mixes between them, employ all three focal points of the human mind, of course, but the characteristics implicit in their languages meant that each focal point received special emphasis in different parts of the planet. biospheric resonance was busy developing the fundamental requirements of the human mind consistent with the cosmic order once again we may define subsumed levels within the routine level associated with the invertebrates, so that we may speak of a routine-form level, a routine-routine level, a routineknowledge level, and a routine-idea level. references 1. robert campbell, downsizing darwin: an intelligent face for evolution. mindreach library (1996). 2. http://cosmic-mindreach.com dna decipher journal | november 2018 | volume 8 | issue 3 | pp. 197-205 197 pitkänen, m., thoughts on modification of bio-harmony essay thoughts on modification of bio-harmony matti pitkänen 1 abstract i have constructed a model of bio-harmony as a fusion of 3 icosahedral harmonies and tetrahedral harmony. the icosahedral harmonies are defined by hamiltonian cycles at icosahedron going through every vertex of the icosahedron and therefore assigning to each triangular face an allowed 3-chord of the harmony. the fascinating outcome is that the model can reproduces genetic code. the model for how one can understand how 12-note scale can represent 64 genetic codons has the basic property that each note belongs to 16 chords. the reason is that there are 3 disjoint sets of notes and given 3chord is obtained by taking 1 note from each set. for bio-harmony obtained as union of 3 icosahedral harmonies and tetrahedral harmony note typically belongs to 15 chords. the representation in terms of frequencies however requires 16 chords per note. consistency a modification of the model of icosahedral harmony. the necessity to introduce tetrahedron for one of the 3 fused harmonies is indeed an ugly looking feature of the model. the question is whether one of the harmonies could be replaced with some other harmony with 12 notes and 24 chords. if this would work one would have 64 chords equal to the number of genetic codons and 5+5+6 =16 chords per note. one can imagine toric variants of harmonies realized in terms of hamiltonian cycles and one indeed obtains a toric harmony with 12 notes and 24 3-chords. bio-harmony could correspond to the fusion of 2 icosahedral harmonies with 20 chords and toric harmony with 24 chords having therefore 64 chords. whether the predictions for the numbers of codons coding for given amino-acids come out correctly for some choices of hamiltonian cycles is still unclear. keywords: bio-harmony, modification, genetic code, tgd framework. 1 introduction i have developed a rather detailed model of bio-harmony as a fusion of 3 icosahedral harmonies and tetrahedral harmony [3, 4](see http://tinyurl.com/yad4tqwl and http://tinyurl.com/y8njuctq). the icosahedral harmonies are defined by hamiltonian cycles at icosahedron going through every vertex of the icosahedron and therefore assigning to each triangular face an allowed 3-chord of the harmony. the surprising outcome is that the model can reproduces genetic code. the model for how one can understand how 12-note scale can represent 64 genetic codons has the basic property that each note belongs to 16 chords. the reason is that there are 3 disjoint sets of notes and given 3-chord is obtained by taking 1 note from each set. for bio-harmony obtained as union of 3 icosahedral harmonies and tetrahedral harmony note typically belongs to 15 chords. the representation in terms of frequencies requires 16 chords per note. if one wants consistency one must somehow modify the model of icosahedral harmony. the necessity to introduce tetrahedron for one of the 3 fused harmonies is indeed an ugly looking feature of the model. the question is whether one of the harmonies could be replaced with some other harmony with 12 notes and 24 chords. if this would work one would have 64 chords equal to the number of genetic codons and 5+5+6 =16 chords per note. the addition of tetrahedron would not be needed. one can imagine toric variants of harmonies realized in terms of hamiltonian cycles and one indeed obtains a toric harmony with 12 notes and 24 3-chords. bio-harmony could correspond to the fusion of 2 icosahedral harmonies with 20 chords and toric harmony with 24 chords having therefore 64 chords. whether the predictions for the numbers of codons coding for given amino-acids come out correctly for 1correspondence: matti pitkänen http://tgdtheory.fi/. address: rinnekatu 2-4 8a, 03620, karkkila, finland. email: matpitka6@gmail.com. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/yad4tqwl http://tinyurl.com/y8njuctq http://tgdtheory.fi/ mailto:matpitka6@gmail.com dna decipher journal | november 2018 | volume 8 | issue 3 | pp. 197-205 198 pitkänen, m., thoughts on modification of bio-harmony some choices of hamiltonian cycles is still unclear. this would require an explicit construction of toric hamiltonian cycles. before discussing the possible role of toric harmonies some previous results will be summarized. 1.1 icosahedral bio-harmonies the model of bio-harmony [3] starts from a model for music harmony as a hamiltonian cycle at icosahedron having 12 vertices identified as 12 notes and 20 triangular faces defining the allowed chords of the harmony. the identification is determined by a hamiltonian cycle going once through each vertex of icosahedron and consisting of edges of the icosahedral tesselation of sphere (analog of lattice): each edge corresponds to quint that is scaling of the frequency of the note by factor 3/2 (or by factor 27/12 in well-tempered scale). this identification assigns to each triangle of the icosahedron a 3-chord. the 20 faces of icosahedron define therefore the allowed 3-chords of the harmony. there exists quite a large number of icosahedral hamiltonian cycles and thus harmonies. the fact that the number of chords is 20 the number of amino-acids leads to the question whether one might somehow understand genetic code and 64 dna codons in this framework. by combining 3 icosahedral harmonies with different symmetry groups identified as subgroups of the icosahedral group, one obtains harmonies with 60 3-chords. the dna codons coding for given amino-acid are identified as triangles (3-chords) at the orbit of triangle representing the amino-acid under the symmetry group of the hamiltonian cycle. the predictions for the numbers of dnas coding given amino-acid are highly suggestive for the vertebrate genetic code. by gluing to the icosahedron tetrahedron along common face one obtains 4 more codons and two slightly different codes are the outcome. also the 2 amino-acids pyl and sec can be understood. one can also regard the tetrahedral 4 chord harmony as additional harmony so that one would have fusion of four harmonies. one can of course criticize the addition of tetrahedron as a dirty trick to get genetic code. the explicit study of the chords of bio-harmony however shows that the chords do not contain the 3-chords of the standard harmonies familiar from classical music (say major and minor scale and corresponding chords). garage band experimentation with random sequences of chords requiring conservability that two subsequent chords have at least one common note however shows that these harmonies are at least to my opinion aesthetically feasible although somewhat boring. 1.2 explanation for the number 12 of notes of 12-note scale one also ends up to an argument explaining the number 12 for the notes of the 12-note scale [3]. there is also second representation of genetic code provided by dark proton triplets. the dark proton triplets representing dark genetic codons are in one-one correspondence with ordinary dna codons. also aminoacids, rna and trna have analogs as states of 3 dark protons. the number of trnas is predicted to be 40. the dark codons represent entangled states of protons and one cannot decompose them into a product state. the only manner to assign to the 3-chord representing the triplet ordinary dna codon such that each letter in {a,t,c,g} corresponds to a frequency is to assume that the frequency depends on the position of the letter in the codon. one has altogether 3×4 = 12 frequencies corresponding to 3 positions for given letter selected from four letters. without additional conditions any decomposition of 12 notes of the scale to 3 disjoint groups of 4 notes is possible and possible chords are obtained by choosing one note from each group. the most symmetric choice assigns to the 4 letters the notes {c,c],d,d]} in the first position, {e,f, f ],g} in the second position, and {g],a,b[,b} in the third position. the codons of type xxx would correspond to ceg] or its transpose. one can transpose this proposal and there are 4 non-quivalent transposes, which could be seen as analogs of music keys. remark: ceg] between c-major and a-minor very often finishes finnish tango: something neither sad nor glad! issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | november 2018 | volume 8 | issue 3 | pp. 197-205 199 pitkänen, m., thoughts on modification of bio-harmony one can look what kind of chords one obtains. 1. chords containing notes associated with the same position in codon are not possible. 2. given note belongs to 6 chords. in the icosahedral harmony with 20 chords given note belongs to 5 chords (there are 5 triangles containing given vertex). therefore the harmony in question cannot be equivalent with 20-chord icosahedral harmony. neither can the bio-harmony with 64 chords satisfy the condition that given note is contained by 6 3-chords. 3. first and second notes of the chords are separated by at least major third as also those second and third notes. the chords satisfy however octave equivalence so that the distance between the first and third notes can be smaller even half step and one finds that one can get the basic chords a-minor scale: am, dm, e7, and also g and f. also the basic chords of f-major scale can be represented. also the transposes of these scales by 2 whole steps can be represented so that one obtains am, c]m, fm and corresponding major scales. these harmonies could allow the harmonies of classical and popular music. these observations encourage to ask whether a representation of the new harmonies as hamiltonian cycles of some tesselation could exist. the tesselation should be such that 6 triangles meet at given vertex. triangular tesselation of torus having interpretation in terms of a planar parallelogram (or perhaps more general planar region) with edges at the boundary suitable identified to obtain torus topology seems to be the natural option. clearly this region would correspond to a planar lattice with periodic boundary conditions. 2 is it possible to have toric harmonies? the basic question is whether one can have a representation of the new candidate for harmonies in terms of a tesselation of torus having v = 12 vertices and f = 20 triangular faces. the reading of the article ”equivelar maps on the torus” [1] (see http://tinyurl.com/ya6g9kwe) discussing toric tesselations makes clear that this is impossible. one however have (v, f ) = (12, 24) (see http://tinyurl.com/ y7xfromc). a rather promising realization of the genetic code in terms of bio-harmony would be as a fusion of two icosahedral harmonies and toric harmony with (v, f ) = (12, 24). this in principle allows also to have 24 3-chords which can realize classical harmony (major/minor scale). 1. the local properties of the tesselations for any topology are characterized by a pair (m,n) of positive integers. m is the number of edges meeting in given vertex (valence) and n is the number of edges and vertices for the face. now one has (m,n) = (6, 3). the dual of this tesselation is hexagonal tesselation (m,n) = (3, 6) obtained by defining vertices as centers of the triangles so that faces become vertices and vice versa. 2. the rule v −e+f = 2(1−g)−h, where v , e and f are the numbers of vertices, edges, and faces, relates v −e−f to the topology of the graph, which in the recent case is triangular tesselation. g is the genus of the surface at which the triangulation is im eded and h is the number of holes in it. in case of torus one would have e = v + f giving in the recent case e = 36 for (v, f ) = (12, 24) (see http://tinyurl.com/y7xfromc) whereas in the icosahedral case one has e = 32. 3. this kind of tesselations are obtained by applying periodic boundary conditions to triangular lattices in plane defining parallelogram. the intuitive expectation is that this lattices can be labelled by two integers (m,n) characterizing the lengths of the sides of the parallelogram plus angle between two sides: this angle defines the conformal equivalence class of torus. one can also introduce two unit vectors e1 and e2 characterizing the conformal equivalence class of torus. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/ya6g9kwe http://tinyurl.com/y7xfromc http://tinyurl.com/y7xfromc http://tinyurl.com/y7xfromc dna decipher journal | november 2018 | volume 8 | issue 3 | pp. 197-205 200 pitkänen, m., thoughts on modification of bio-harmony second naive expectation is that m × n × sin(θ) represents the area of the parallelogram. sin(θ) equals to the length of the exterior product |e1 × e2| = sin(θ) representing twice the area of the triangle so that there would be 2m×n triangular faces. the division of the planar lattice by group generated by pe1 + qe2 defines boundary conditions. besides this the rotation group z6 acts as analog for the symmetries of a unit cell in lattice. this naive expectation need not of course be strictly correct. 4. as noticed, it is not possible to have triangular toric tesselations with (v,e, f ) = (12, 30, 20). torus however has a triangular tesselation with (v,e, f ) = (12, 36, 24). an illustration of the tesselation can be found at http://tinyurl.com/y7xfromc. it allows to count visually the numbers v,e, f , and the identifications of the boundary edges and vertices. with good visual imagination one might even try to guess what hamiltonian cycles look like. the triangular tesselations and their hexagonal duals are characterized partially by a pair of integers (a, b) and (b, a). a and b must both even or odd (see http://tinyurl.com/y7xfromc ). the number of faces is f = (a2 + 3b2)/2. for (a, b) = (6, 2) one indeed has v = 12 and f = 24. from the article [1] (see http://tinyurl.com/ya6g9kwe) one learns that the number of triangles satisfies f = 2v for p = q at least. if f = 2v holds true more generally one has v = (a2 + 3b2)/8, giving a tight constraints on a and b. remark: the conventions for the labelling of torus tesselation vary. the above convention based on integers (a, b) used in the illustrations at http://tinyurl.com/y7xfromc is different from the convention based on integer pair (p, q) used in [1] . in this notation torus tesselation with (v, f ) = (12, 24) corresponds to (p, q) = (2, 2) instead of (a, b) = (6, 2). this requires (a, b) = (3p, q). with these conventions one has v = p2 + q2 + pq. 2.1 the number of triangles in the 12-vertex tesselation is 24: curse or blessing? one could see as a problem that one has f = 24 > 20? or is this a problem? 1. by fusing two icosahedral harmonies and one toric harmony one would obtain a harmony with 20+20+24 =64 chords, the number of dna codons! one would replace the fusion of 3 icosahedral harmonies and tetrahedral harmony with a fusion of 2 icosahedral harmonies and toric harmony. icosahedral symmetry with toric symmetry associated with the third harmony would be replaced with a smaller toric symmetry. note however that the attachment of tetrahedron to a fixed icosahedral face also breaks icosahedral symmetry. this raises questions. could the presence of the toric harmony somehow relate to the almost exact u ↔ c and a ↔ g symmetries of the third letter of codons. this does not of course mean that one could associated the toric harmony with the third letter. note that in the icosa-tetrahedral model the three harmonies are assumed to have no common chords. same non-trivial assumption is needed also now in order to obtain 64 codons. 2. what about the number of amino-acids: could it be 24 corresponding ordinary aminoacids, stopping sign plus 3 additional exotic amino-acids. the 20 icosahedral triangles can corresponds to aminoacids but not to stopping sign. could it be that one of the additional codons in 24 corresponds to stopping sign and two exotic amino-acids pyl and sec appearing in biosystems explained by the icosahedral model in terms of a variant of the genetic code. there indeed exists even third exotic amino-acid! n-formylmethionine (see http://tinyurl.com/jsphvgt) but is usually regarded as as a form of methionine rather than as a separate proteinogenic amino-acid. 3. recall that the problem related to the icosa-tetrahedral harmony is that it does not contains the chords of what might be called classical harmonies (the chordds assignable to major and minor issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/y7xfromc http://tinyurl.com/y7xfromc http://tinyurl.com/ya6g9kwe http://tinyurl.com/y7xfromc http://tinyurl.com/jsphvgt dna decipher journal | november 2018 | volume 8 | issue 3 | pp. 197-205 201 pitkänen, m., thoughts on modification of bio-harmony scales). if 24 chords of bio-harmony correspond to toric harmony, one could obtain these chords if the chords in question are chords obtainable by the proposed construction. but is this construction consistent with the representation of 64 chords by taking to each chord one note from 3 disjoint groups of 4 notes in which each note belongs to 16 chords. the maximum number of chords that note can belong to would be 5+5+6=16 as desired. if there are no common chords between the 3 harmonies the conditions is satisfied. using for instance 3 toric representations the number would be 6+6+6=18 and would require dropping some chords. 4. the earlier model for trna as fusion of two icosahedral codes predicting 20+20=40 trna codons. now trnas as fusion of two harmonies allows two basic options depending on whether both harmonies are icosahedral or whether second harmony is toric. these options would give 20+20=40 or 20+24=44 trnas. wikipedia tells that maximum number is 41. some sources however tell that there are 20-40 different trnas in bacterial cells and as many as 50-100 in plant and animal cells. 2.2 a more detailed model for toric harmonies one can consider also more detailed model for toric harmonies. 1. the above discussed representation in terms of frequencies assigned with nucleotides depending on their position requires the decomposition of the notes to 3 disjoint groups of 4 notes. this means decomposition of 12 vertices of hamiltonian cycle to 4 disjoint groups such that within given group the distances between the members of group are larger than one unit so that they cannot belong to same triangle. there are bin(12, 4) × bin(8, 4) decomposition to 3 disjoint groups of for vertices, where bn(n, k) = n!/(n− k)!k! is binomial coefficient. 2. once the hamiltonian cycle has been fixed and is one assumes that single step along cycle corresponds to quint, one knows what the notes associated with each vertex is and given the note of the 12-note scale one knows the number0 ≤ n < 12 of quint steps needed to obtain it. for instance, for the proposed grouping {c,c],d,d]} and its two transposes by 2 hole steps one can assign 4 integers to each group. the condition is that within each group the notes labelled by the integers have minimum distance of 2 units between themselves. 3. one could try to understand the situation in terms of the symmetries of the system. (a) could the triplet {c,e,g]} and its four translates be interpreted as z3 orbits. could suitable chosen members from 4 disjoint quartets quite general form z3 orbits. remark: particle physicists notes the analogy with 4 color triplets formed by u and d quarks having spin 1/2. z4 would correspond to spin and color spin and z3 to color. (b) z4 acts as symmetries of the tesselation considered and these symmetries respect distances so that their action on a quartet with members having mutual distances larger than unit creates new such quartet. could the triplet {c,e,g]} and its four translates by an n−multiple of half note, n = 0, 1, 2, 3 correspond to an orbit z4? could the groups of 4 notes quite generally correspond to the orbits of z4? this can be true only if the action of non-trivial z4 elements relates only vertices with distance larger than one unit. 4. the group of isometries of the toric triangulation acts as symmetries. z24 = z6 × z4 is a good candidate for this group. z6 corresponds to the rotations of around given point of triangulation and should leave the tesselation invariant. the orbit of given triangle defining the set of dna codons coding the amino-acid represented by the orbit would correspond to orbit of subgroups of z24. only orbits containing orbits containing 1, 2, 3, 4 or 6 triangles are allowed by the degeneracies of the genetic code. these numbers would correspond to degeneracies that is the numbers of codons coding for given amino-acid. all these numbers appear as degeneracies. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | november 2018 | volume 8 | issue 3 | pp. 197-205 202 pitkänen, m., thoughts on modification of bio-harmony 2.3 what one can say about toric hamiltonian cycles? first some basic notions are in order. the graph is said to be equivelar if it is a triangulation of a surface meaning that it has 6 edges emanating from each vertex and each face has 3 vertices and 3 edges [1]. equivelarity is equivalent with the folllowing conditions; 1. every vertex is 6-valent. 2. the edge graph is 6-connected. 3. the graph has vertex transitive automorphism group. 4. the graph can be obtained as a quotient of the universal covering tesselation (3,6) by a sublattice (subgroup of translation group). 6-connectedness means that one can decompose the tesselation into two disconnected pieces by removing 6 or more vertices 5. edge graph is n-connected if the elimation of k < n vertices leaves it connected. it is known that every 5-connected triangulation of torus is hamiltonian [2] (see http://tinyurl.com/y7cartk2). therefore also 6-connected (6, 3)p=2,q=2 tesselation has hamiltonian cycles. 6. the hamiltonian cycles for the dual tesselation are not in any sense duals of those for the tesselation. for instance, in the case of dodecahedron there is unique hamiltonian cycle and for icosahedron has large number of cycles. also in the case of (6, 3) tesselations the duals have different hamilton cycles. in fact, the problem of constructing the hamiltonian cycles is np complete. can one say anything about the number of hamiltonian cycles? 1. for dodecahedron only 3 edges emanates from a given vertex and there is only one hamiltonian cycle. for icosahedron 5 edges emanate from given vertex and the number of cycles is rather large. hence the valence and also closely related notion of n-connectedness are essential for the existence of hamilton’s cycles. for instance, for a graph consisting of two connected graphs connected by single edge, there exist no hamilton’s cycles. for toric triangulations one has as many as 6 edges from given vertex and this favors the formation of a large number of hamiltonian cycles. 2. curves on torus are labelled by winding numbers (m,n) telling the homology equivalence class of the cycle. m and m can be any integers. curve winds m (n) times around the circle defining the first (second) equivalence homology equivalence class. also hamiltonian cycles are characterized by their homology equivalence class, that is pair (m,n) of integers. since there are only v = 12 points, the numbers (m,n) are finite. by periodic boundary conditions means that the translations by multiples of 2e1 + 2e2 do not affect the tesselation (one can see what this means geometrically from the illustration at http://tinyurl.com/y7xfromc). does this mean that (m,n) belongs to z2 × z2 so that one would have 4 homologically non-equivalent paths. are all four homology classes realized as hamiltonian cycles? does given homology class contain several representatives or only single one in which case one would have 20 non-equivalent hamiltonian cycles? it turned out that there exist programs coding for an algorithm for finding whether given graph (much more general than tesselation) has hamiltonian cycles. having told to jebin larosh about the problem, he sent within five minutes a link to a java algorithm allowing to show whether a given graph is hamiltonian (see http://tinyurl.com/y7y9tr5t): sincere thanks to jebin! by a suitable modification this algorithm find all hamiltonian cycles. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/y7cartk2 http://tinyurl.com/y7xfromc http://tinyurl.com/y7y9tr5t dna decipher journal | november 2018 | volume 8 | issue 3 | pp. 197-205 203 pitkänen, m., thoughts on modification of bio-harmony figure 1: the number of the vertices of (v, f ) = 12, 24) torus tesselation allowing path (0, 1, 2, 3, 4, 6, 5, 8, 10, 7, 11, 9, 0) as one particular hamiltonian cycle. 1. the number nh of hamiltonian cycles is expected to be rather large for a torus triangulation with 12 vertices and 24 triangles and it is indeed so: nh = 27816! the image of the tessellation and the numbering of its vertices are described in figure below (see fig. 1 ). incide matrix a characterizes the graph: if vertices i and j are connected by edge, one has aij = aji = 1, otherwise aij = aji = 0 and is used as data in the algorithm finding the hamiltonian cycles. the cycles related by the isometries of torus tessellation are however equivalent. the guess is that the group of isometries is g = z2,reflo (z4,trozn,rot). zn,rot is a subgroup of local z6,rot. a priori n ∈ {1, 2, 3, 6} is allowed. on basis of [1] i have understood that one has n = 3 but that one can express the local action of z6,rot as the action of the semidirect product z2,refl × z3,rot at a point of tesselation (see http://tinyurl.com/ya6g9kwe). the identity of the global actions z2,refl×z3,rot and z6,rot does not look feasible to me. therefore g = z2,refl o (z4,tr o z3,rot) with order ord(g) = 24 will be assumed in the following (note that for icosahedral tesselation one has ord(g) = 120 so that there is symmetry breaking). z4 would have as generators the translations e1 and e2 defining the conformal equivalence class of torus. the multiples of 2(e1 + e2) would leave the tesselation invariant. if these arguments are correct, the number of isometry equivalence classes of cycles would satisfy nh,i ≥ nh/24 = 1159. 2. the actual number is obtained as sum of cycles characterized by groups h ⊂ z12 leaving the cycle invariant and one can write nh,i = ∑ h(ord(h)/ord(g))n0(h), where n0(h) is the number of cycles invariant under h. what can one say about the symmetry group h for the cycle? 1. suppose that the isometry group g leaving the tesselation invariant decomposes into semi-direct product g = z2,refl o (z4,tr o z3,rot), where z3,rot leaves invariant the starting point of the cycle. the group h decomposes into a semi-direct product h = z2,refl o (zm,tr × z3,rot) as subgroup of g = z2,refl o (z4,tr × z3,rot). 2. zn,rot associated with the starting point of cycle must leave the cycle invariant at each point. applied to the starting point, the action of h, if non-trivial that is z3,rot, must transform the outgoing edge to incoming edge. this is not possible since z3 has no idempotent elements so that one can have only n = 1. this gives h = z2,refl o (zm,tr. m = 1, 2 and m = 4 are possible. 3. should one require that the action of h leaves invariant the starting point defining the scale associated with the harmony? if this is the case, then only the group h = z2,refl would remain and invariance under zrefl would mean invariance under reflection with respect to the axis defined by e1 issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/ya6g9kwe dna decipher journal | november 2018 | volume 8 | issue 3 | pp. 197-205 204 pitkänen, m., thoughts on modification of bio-harmony or e2. the orbit of triangle under z2,refl would consist of 2 triangles always and one would obtain 12 codon doublets instead of 10 as in the case of icosahedral code. if this argument is correct, the possible symmetry groups h would be z0 and z2,refl. for icosahedral code both zrot and z2refl occur but z2,refl does not occur as a non-trivial factor of h in this case. the almost exact u ↔ c and a↔ g symmetry of the genetic code would naturally correspond to z2,refl symmetry. therefore the predictions need not change from those of the icosahedral model except that the 4 additional codons emerge more naturally. the predictions would be also essentially unique. 4. if h is trivial z1, the cycle would have no symmetries and the orbits of triangles would contain only one triangle and the correspondence between dna codons and amino-acids would be one-to-one. one would speak of disharmony. icosahedral hamiltonian cycles can also be of this kind. if they are realized in the genetic code, the almost exact u ↔ c and a ↔ g symmetry is lost and the degeneracies of codons assignable to 20+20 icosahedral codons increase by one unit so that one obtains for instance degeneracy 7 instead of 6 not realized in nature. what can one say about the character of toric harmonies on basis of this picture. 1. it has been already found that the proposal involving three disjoint quartets of subsequent notes can reproduce the basic chords of basic major and minor harmonies. the challenge is to prove that it can be assigned to some hamiltonian cycle(s). the proposal is that the quartets are obtained by z3 rot symmetry from each other and that the notes of each quartet are obtained by z4,tr symmetry. 2. a key observation is that classical harmonies involve chords containing 1 quint but not 2 or no quints at all. the number of chords in torus harmonies is 24 = 2× 12 and twice the number of notes. the number of intervals in turn is 36, 3 times the number of the notes. this allows a situation in which each triangle contains one edge of the hamiltonian cycle so that all 3-chords indeed have exactly one quint. 3. by the above argument harmony possesses z2 symmetry or no symmetry at all and one has 12 codon doublets. for these harmonies each edge of cycle is shared by two neighboring triangles containing the same quint. a possible identification is as major and minor chords with same quint. the changing of the direction of the scale and the reflection with respect to the edges the hamiltonian cycle would transforms major chords and minor chords along it to each other and change the mood from glad to sad and vice versa. the proposed harmony indeed contains classical chords with one quint per chord and for f,a,c] both minor and major chords are possible. there are 4 transposes of this harmony. 4. also hamiltonian cycles for which n triangles contain two edges of hamiltonian path (cgd type chords) and n triangles contain no edges. this situation is less symmetric and could correspond to a situtation without any symmetry at all. 5. one can ask whether the classical harmonies corresponds to 24 codons assignable to the toric harmony and to the 24 amino-acids being thus realizable using only amino-acids. if so, the two icosahedral harmonies would represent kind of non-classical exotics. 3 appendix: some facts about toric tesselations genus g = 1 (torus) is unique in that it allows infinite number of tesselations as analogs of planar lattices with periodicic boundary conditions. g = 0 allows only platonic solids as tesselations and g > 1 allows very few tesselations. the article [1] gives a nice review about toric tesselations. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | november 2018 | volume 8 | issue 3 | pp. 197-205 205 pitkänen, m., thoughts on modification of bio-harmony 1. toric tesselations correspond to tesselations of plane by periodic boundary conditions. torus tesselation allows a universal covering identifiable as counterpart of infinite lattice in plane. there are infinite number of coverings of given tesselation labelled by two integers (m,n) since the homology group of torus is z×z. the tesselation is obtained by dividing z×z by its normal subgroup. also the rotation group z6 acts as group leaving the tesselation invariant and correspond to the rotation leaving invariant the lattice cell consisting of 6 vertices around given vertex. 2. the tesselation is called decomposable if there is a k-sheeted covering map (map corresponds to a collection of charts) characterized by the subgroup of the isometries of the covering of the tesselation which corresponds to a sub-tesselation. this subgroup is charactrized by a pair (p, q) of integers being generated by the translation pe1 + qe2 and 2π/6 rotation. the unit vectors can be chosen to be e1 = (1, 0) and e2 = (1, √ 3)/2 for triangular tesselation (presumably this tesselation is regular tesselation with the conformal equivalence class of torus fixed by the angle between e1 and e2). line reflection transforms (3, 6)p,q to (3, 6)q,p (see fig 1 of http://tinyurl.com/ya6g9kwe). the tesselation is invariant under reflections regular -if pq(p− q) = 0. the peculiar looking form of the conditions follows from the identitity (3, 6)q,p = (3, 6)p+q,−q (also p = 0 or q = 0 is possble) note that the tesselation (3, 6)2,2 is invariant under reflection and thus non-chiral. 3. the number v of vertices of the triangular itesselation is given by v = p2 + q2 + pq. the regular tesselation (p, q) = (2, 2) has 12 vertices and is the interesting one in the recent case. it is the smallest regular tesselation. for given (p, q) one can have several non-equivalent pairs (p, q) defining combinatorially non-equivalent tesselations. my interpretation is that they correspond to different conformal equivalence classes for torus: the intuitive expectation is that this should not affect the topology of tesselation nor hamiltonian cycles. for (6, 3)p,q = (6, 3)2,2 with s (v = 12, f = 24) there are 1+6 =7 combinatorially non-equivalent tesselations: one non-chiral and 6 chiral ones. quite generally, the tesselations with v vertices with v mod 4 = 0 (as in the case of v = 12) allow one map (chart consisting of faces) with isotropy group of order 2 and 6 maps with isotropy group of order 4. these variants are labelled by an sl(2,z) matrix (a, b; 0, c) with determinant equal to v = ac. for v = 12 one has decompositions 12 = 1 × 12, 12 = 2 × 6, 12 = 3 × 4. −c < b < a − c is unique modulo a. in the recent case one as ac = 12 allowing (a, c) ∈ {(1, 12), (2, 6), (3, 4)} and pairs obtained by permuting a and c. these matrices need not define combinatorially different tesselations since modular transformations generate equivalent matrices. acknowledgements: i am grateful to jebin larosh for finding the java algorith allowing to find hamilton cycles for given graph. references [1] ulrich brehm and wolfgang kühnel. equivelar maps on the torus. european journal of combinatorics. https: // doi. org/ 10. 1016/ j. ejc. 2008. 01. 010 , 29(8):1843–1861, 2008. [2] thomas r and yu x. five-connected toroidal graphs are hamiltonian. journal of combinatorial theory, series b, 69(tb961713):79–96, 1997. [3] pitkänen m. geometric theory of harmony. available at: http://tgdtheory.fi/public_html/ articles/harmonytheory.pdf, 2014. [4] pitkänen m. new results in the model of bio-harmony. available at: http://tgdtheory.fi/public_ html/articles/harmonynew.pdf, 2018. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/ya6g9kwe https://doi.org/10.1016/j.ejc.2008.01.010 http://tgdtheory.fi/public_html/articles/harmonytheory.pdf http://tgdtheory.fi/public_html/articles/harmonytheory.pdf http://tgdtheory.fi/public_html/articles/harmonynew.pdf http://tgdtheory.fi/public_html/articles/harmonynew.pdf introduction icosahedral bio-harmonies explanation for the number 12 of notes of 12-note scale is it possible to have toric harmonies? the number of triangles in the 12-vertex tesselation is 24: curse or blessing? a more detailed model for toric harmonies what one can say about toric hamiltonian cycles? appendix: some facts about toric tesselations login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 537-539 smetham, g. p., list of references cited in this focus issue issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 537 references abbott d., davies, p. c. w. & pati, a. k. (eds.) (2008), quantum aspects of life, imperial college press. al-khalili, jim (2003), quantum: a guide for the perplexed. weidenfield and nicolson, new york. allday, jonathan (2009), quantum reality: theory and philosophy. crc press. asher, r. j. (2012), evolution and belief: confessions of a religious paleontologist. cambridge university press. baggott, jim (2005), a beginner's guide to reality. penguin books. baggott, j. (2012), higgs: the invention and discovery of the 'god particle', oxford university press. barrow, john d. & tipler, frank j. (1986), the anthropic cosmological principle, oxford paperbacks. barrow, john d., davies, paul c. w., harper, charles l. (eds.) (2004), science and ultimate reality. cambridge university press. bohm, d (2002), wholeness and the implicate order (first published: routledge & kegan paul, 1980; routledge classics, 2002) bohm, d. (2003), the essential david bohm, (ed. by nichol, l.), routledge, london. brockman, j. (ed.) (2006), intelligent thought: science verses the intelligent design movement, vintage. carroll, sean, b. (2006), endless forms most beautiful. weidenfield & nicolson. carroll, s. (2012), the particle at the end of the universe, dutton. chandrakirti and jamgon mipham (2002), introduction to the middle way: chandrakirti’s madhyamakavatara with commentary by jamgon mipham. translated by the padmakara translation group. boston: shambhala publications. conway morris, simon (2003), life’s solution: inevitable humans in a lonely universe. cambridge university press. coyne, j. (2009), why evolution is true, oxford university press (2010 edition). d’ espagnat, b. (2003), veiled reality, westview press. d’ espagnat, b. (2006), on physics and philosophy, princeton university press. davies, paul (2007), the goldilocks enigma. penguin books (first published 2006:allen lane) davies, paul & gregersen, niels henrik (eds.) (2010). information and the nature of reality: from physics to metaphysics. cambridge university press. dawkins, r. (1995), river out of eden: a darwinian view of life, phoenix, orion books ltd (2004 reissue). dawkins, r. (2005), the ancestor’s tale: a pilgrimage to the dawn of life, phoenix, orion books ltd (first published 2004). dawkins, r. (2006), the blind watchmaker. new edition – penguin (first published 1986) dawkins, r. (2006a), the god delusion. black swan. dawkins, r. (2010), the greatest show on earth: the evidence for evolution, black swan, (first published 2009 bantum books). http://www.amazon.co.uk/s/ref=ntt_athr_dp_sr_1?_encoding=utf8&field-author=abbott%20derek%20et%20al&search-alias=books-uk&sort=relevancerank dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 537-539 smetham, g. p., list of references cited in this focus issue issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 538 dembski w. a. (2002), intelligent design: the bridge between science and theology, inter-varsity press, us. dennett, daniel (1991), consciousness explained, the penguin press. dobzhansky, th. (1937), genetics and the origin of species. columbia university press, new york. (2nd ed., 1941; 3rd ed., 1951). dolling, l.m.; gianelli, a. f. & statile, g. n. (eds.) (2003), the tests of time: readings in the development of physical theory. princeton university press. fodor, j. & piattelli-palmarini, m. (2011), what darwin got wrong, profile books. feynman, richard (1988), qed: the strange theory of light and matter. princeton university press. ghirardi, g. (2005), sneaking a look at god's cards: unraveling the mysteries of quantum mechanics, revised edition, princeton university press. 1 st ed – 1997, il saggiatore, milano. goswami, a. (2008), creative evolution. quest books. greene, brian (2004), the fabric of the universe. allen lane. gribben, john (2009), science: a history. penguin books. hawking, s. (2011), a brief history of time: from big bang to black holes, bantum. hawking, stephen & mlodinow, leonard (2010). the grand design: new answers to the ultimate questions of life. transworld publishers – bantum press. humphrey, n. (2006), seeing red: a study in consciousness, harvard university press. humphrey, n. (2012), soul dust: the magic of consciousness, quercus. isaacson, w. (2008), einstein: his life and universe, pocket books. jones, s. (2000), almost like a whale: the origin of species updated, black swan. kelly e. f., kelly e. w., crabtree a. & gauld a. (2009), irreducible mind: toward a psychology for the 21st century, rowman & littlefield publishers lockwood, michael (2005). the labyrinth of time: introducing the universe. oxford university press. mcfadden, johnjoe (2002). quantum evolution: how physics weirdest theory explains life's biggest mystery. norton & co. meyer, s. c. (2010), signature in the cell: dna and the evidence for intelligent design, harperone. oerter, robert (2006), the theory of almost everything, pi press. penrose, roger (1995), shadows of the mind. oxford university press:1994, random house-vintage. penrose, roger (2005), the road to reality: a complete guide to the laws of the universe. vintage. randall, l. (2012), higgs discovery: the power of empty space, the bodley head ltd. rosenblum, b. and kuttner, f. (2006), quantum enigma: science encounters consciousness. oxford university press, u.s.a. schlosshauer, m. (ed.) (2011), elegance and enigma: the quantum interviews, springer: the frontiers collection. schrödinger, e. (1944), what is life? cambridge university press. sheldrake, rupert (2009), a new science of life (revised edition), icon books. smolin, lee (2002), three roads to quantum gravity. perseus. dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 537-539 smetham, g. p., list of references cited in this focus issue issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 539 sober, e. (2008), evidence and evolution: the logic behind the science, cambridge university press. stapp, henry (2004), mind, matter and quantum mechanics. springer-verlag berlin heidelberg 1993, 2004 (frontiers collection). stapp, henry (2007), mindful universe. springer-verlag berlin heidelberg (frontiers collection). tallis, r. (2011), aping mankind, acumen. turok, n. (2013), from quantum to cosmos: the universe within, faber & faber. wilber, k. (ed.) (2001), quantum questions: mystical writings of the world’s great physicists, shambhala. wilczek, frank (2008), the lightness of being. penguin. woolfson, a. (2000), life without genes, flamingo. zeilinger, anton (2010), dance of the photons. farrar, straus and giroux. login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x microsoft word huwu2_v11n1 dna decipher journal | october 2021 | volume 11 | issue 1 | pp 107-108 hu, h. & wu, m., iona miller (1949 2021): multitalented writer, artist & visionary issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 107 in memoriam iona miller (1949 2021): multitalented writer, artist & visionary huping hu* & maoxin wu abstract iona miller (1949 2021) was a multitalented writer, artist and visionary. she was an inspirational and compassionate human being and a member of the advisory board of this journal. she also published scientific papers here. she will be missed by us, our readers/patrons and many others who knew her – good journey on the other side, iona, and may your legacy live on! keywords: iona miller, artist, writer, visionary, nonfiction, multimedia, legacy, compassionate, inspirational. iona miller journeyed to the other side quite unexpectedly on march 26, 2021 [1]. she last communicated on march 4, 2021 with the first author on a scientific topic through facebook messinger. she was “a nonfiction writer for the academic and popular press, clinical hypnotherapist (ache) and multimedia artist[;] [h]er work is an omni-sensory fusion of intelligence, science-art, new physics, symbolism, source mysticism, futuring, and emergent paradigm shift, creating a unique viewpoint[;] [she was] interested in extraordinary human potential and experience, and the effects of doctrines of religion, science, psychology, and the arts[;] [she served] on the advisory boards of journal of consciousness exploration & research, dna decipher journal, and scientific god journal....” [2]. she was an inspirational and compassionate human being and a truth seeker. she pondered and explored the meanings of life and death through numerous writings and artworks [2]. in an essay/statement entitled “the mask of eternity: the quest for immortality and the afterlife” and published in a special issue of jcer “theories of consciousness and death” edited by gregory m. nixon, ph.d., she shared the following with the readers [3]: correspondence: huping hu, ph.d., j.d., quantumdream inc., p. o. box 267, stony brook,, ny 11790. e-mail: editor@dnadecipher.com dna decipher journal | october 2021 | volume 11 | issue 1 | pp 107-108 hu, h. & wu, m., iona miller (1949 2021): multitalented writer, artist & visionary issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 108 when we are gone, only the ultimate question remains. evidence that consciousness survives death remains elusive. with or without warm, welcoming smiles from relatives we may have loathed in life, it remains our obsession to know what happens when our screen-reality stops, and fades to black. conscious immortality remains questionable. this writer remains firmly agnostic but enjoys entertaining wishful thinking. death is the greatest mystery of life. buddha rejected the question as useless, according to jung. throughout history, it remains a source of wonder, fear, hopefulness, and puzzlement. we seek compassionate ways of dealing with this uncertainty that no discussion of entanglement or holographic memory can assuage. there is little wonder we tend to fall back on traditional attitudes informed by simplicity, meaningful ceremony, and acceptance. it is something we cannot grasp at all, despite our conceptions of time and space and what might lie beyond them, even if some of our psychic experience seems unbound by spacetime. there is nowhere to go and we are all going to get there. we at dnadj celebrate her life and thank her for her advisory services to the journal. she will be missed by us, our readers/patrons and many others who knew her – good journey on the other side, iona, and may your legacy live on! references 1. https://www.facebook.com/iona.miller 2. https://ionamiller.weebly.com/ 3. miller, i. (2016), the mask of eternity: the quest for immortality and the afterlife, journal of consciousness exploration & research, 7(11): pp. 1218-1228. original-review-letter-invited article dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 001-010 hu, h. & wu, m. decipherment of the secrets of dna issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 1 editorial inaugural issue decipherment of the secrets of dna huping hu* & maoxin wu abstract dna decipher journal (issn: 2159-046x) is published by quantumdream, inc. and devoted to the decipherment of the secrets of dna. it is a journal in which biologists, physicists, mathematicians and other learned scholars publish their research results and express their views on the origin, nature and mechanism of dna as a biological system and entity and its possible connection to a deeper reality. this inaugural issue contains six (6) articles exploring the principle of linguistic-wave genetics, dna as quantum biocomputer, holography associated with dna, genetic pathways during evolution and dna as topological quantum computers. it also contain one (1) commentary on the recent experiemental findings of montagnier's group on dna waves and water. further, in this editorial the herein authors also discuss their preliminary thoughts on the coding of dna and the hexagrams of i ching based on the principle of existence. key words: dna, triplet codon, coding mechanism, decipherment. 1. background the current state of central dogma of molecular biology first articulated in 1958 and later restated in 1970 by francis crick (1958, 1970) is shown in the following diagram (source: wikipedia): correspondence: huping hu, ph.d., j.d., quantumdream, inc., p. o. box 267, stony brook, ny 11790. e-mail: editor@dnadecipher.com note: the views and opinions expressed herein solely belong to the authors of this editorial unless indicated or attributed otherwise. mailto:editor@dnadecipher.com dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 001-010 hu, h. & wu, m. decipherment of the secrets of dna issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 2 from the perspective of evolutionary biology, it is widely believed that life was first rna-based before becoming dna-based (see, e.g., king, 2011). however, there are still many unanwered fundamental questions on the origin, nature and mechanism of rna/dna as discussed below. in the early eighties of the 20th century, the herein first author had asked and tried to answer some of these questions: (1) whether each code position of the triplet codon has unique meaning; (2) whether the triplet codon is intrinsically connected to the three dimensionality of space; and (3) whether the four bases, a, t, c & g are intrinsically connected to the four dimensionality of spacetime. indeed, he thought that he had found the answers to these questions and wrote two unpublished papers. on reflection, the premises and conclusions in these papers were perhaps premature and/or immature just as he was young and immature himself. however, his passion to try to discovery answers to these questions plus many more such as those listed below has remained very strong. thus, when in late november 2010, peter gariaev and matti pitkanan submitted a dna related paper to the journal of consciousness exploration & research (http://jcer.com) which does not cover research on dna, it was decided to launch dna decipher journal in order to provide a platform and fair playing field for exploring many mysteries associated with dna. 2. purpose and mission figure 1 as illustarted in figure 1, dna decipher journal (issn: 2159-046x) is devoted to the decipherment of the secrets of dna. it is a journal in which biologists, physicists, mathematicians and other learned scholars publish their research results and express their views http://jcer.com/ dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 001-010 hu, h. & wu, m. decipherment of the secrets of dna issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 3 on the origin, nature and mechanism of dna as a biological program and entity and its possible connection to a deeper reality. the current policy at this journal is editorial selections of submitted papers for publication and editorial invitation for publication under the advisement of an editorial advisory board, members of which are under selections. all papers published by this journal are either subject to open-peer-review ("opr") in the same issue or open to opr in subsequent issues. in particular, this journal a scholarly platform for exploring, among other things, the following mysteries associated with dna/rna: (1) how a, u, c, g and a, t, c, g became the four bases/letters of genetic language? why just four? were they due to random chance as commonly accepted/believed or were their selections somehow guided by some kind of intelligent force or field? (2) why the rna/dna codon is triplet? was it again just random chance or was deeper principle involved? in other words, does each code and/or code position in the triplet codon has certain meaning? (3) why the coding of amino acids by the rna/dna codons are degenerate? (4) are there further coding principles and/or mechanisms involved in forming the rna/dna sequences? (5) what are all the functions of dna? how does dna perform all these functions? (6) is dna a program of a quantum biocomputer? how does this biocomputer compute? 3. contents of the inaugral issue in the first article entitled “principles of linguistic-wave genetics,” peter p. gariaev and his co-authors treat the subject of wave genetics. it is suggested that to create an organism two genetic programs are required. the first one is geometric, i.e. a scheme, how to design the body. the second program is in the form of a meaningful text which contains instructions and explanations how to use the first program, how to understand and build the organism. these programs exist in the form of “dna video tapes”, which are used by the genetic apparatus, acting like a bio-computer. when the bio-computer reads these video tapes, sound and light images appear that constitute the movie program of the development of the organism. when the creation of a grown-up organism is completed, the movie ends. then the second movie starts, which contains the instructions for maintenance of the organism for indefinitely long time. unfortunately, the videotapes containing information about a perfectly healthy organism, get corrupted with time, errors accumulate (dna mutations). the instructions accumulate errors and the organism gets sick, grows old and dies. it is very likely that these dna video tapes can be renewed and corrected. with this new understanding of how our genetic apparatus works, dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 001-010 hu, h. & wu, m. decipherment of the secrets of dna issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 4 completely new technologies for healing a person and extending a person’s life become feasible. and this is the essence of wave genetics and its practical applications to come. in the second article entitled “dna as basis for quantum biocomputer,” peter p. gariaev and his co-authors discuss dna as quantum biocomputer based on experimental work carried out in moscow at the institute of control sciences, wave genetics inc., quantum genetics institute and theoretical work from several sources are described in this work. it is suggested that: (1) the evolution of biosystems has created genetic "texts", similar to natural context dependent texts in human languages, shaping the text of these speech-like patterns; (2) the chromosome apparatus acts simultaneously both as a source and receiver of these genetic texts, respectively decoding and encoding them, and (3) the chromosome continuum of multicellular organisms is analogous to a staticdynamical multiplex time-space holographic grating, which comprises the space-time of an organism in a convoluted form. thus, the dna action (as theory predicts and experiment confirms) is that of a "gene-sign" laser and its solitonic electro-acoustic fields, such that the gene-biocomputer "reads and understands" these texts in a manner similar to human thinking, but at its own genomic level of "reasoning". further, dna molecules, conceived as a gene-sign continuum of any biosystem, are able to form holographic pre-images of biostructures and of the organism as a whole as a registry of dynamical "wave copies" or "matrixes”, succeeding each other. in the third article entitled “model for the findings about hologram generating properties of dna, peter p. gariaev and matti pitkenan propose a model for hologram generating property of dna based on pitkanen’s tgd. the model is developed in order to explain the characteristic features of certain replica patterns discovered by gariaev. the proposal involves tgd notions of magnetic body, topological light ray, magnetic flux tubes and dark photons. the hypothesis is that a first method used by gariaev to obtain the replica patterns makes part of the magnetic body of dna sample visible whereas a second method would produce replica hologram of environment using dark photons and produce also a phantom image of the magnetic tubes becoming visible by the first method. in the fourth article entitled “the tree of life: tangled roots and sexy shoots,” chris king traces the genetic pathway from the first eukaryotes to homo sapiens. the picture conveyed by the significance of endosymbiosis, genome fusion and horizontal transfer as key evolutionary processes complementing the vertical transmission of the tree of life, makes clear that evolution is not just a matter of competitive survival of the fittest gene, individual, or species, but of dynamic survival of genes in a surviving ecosystem. although the idea of selection of genes has been pivotal in defining the need to consider evolutionarily stable strategies under genetic variation in ways which have been subsequently confirmed time and time again in situations such as the sexual genetics of social insects such as bees and ants, social selection is by no means ineffectual, or much of sociobiology, including the biological basis of morality as an extension of reciprocal altruism, would cease to exist. king argues that it is not the 'selfishness' of a genetic element alone that results in survival of both a gene and its hosts, but dynamic feedbacks, and relationships which ultimately contribute to a massive sharing of information in the manner of parallel genetic algorithms fundamental to the replicative genetic process, which enable global forms of genetic and genome optimization central to the overall viability of life as complex systems. dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 001-010 hu, h. & wu, m. decipherment of the secrets of dna issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 5 in the fifth article, pitkanen proposes that dna is a topological quantum computer (“tqc”) which means that the braidings of braid strands define tqc programs and m-matrix defining the entanglement between states assignable to the end points of strands define the tqc usually coded as unitary time evolution for schrodinger equation. the generalization of the second law allows understanding of the thermodynamical aspect of topological quantum computation. based on this generalization, pitkenan argues, one can understand why living matter is so effective entropy producer as compared to inanimate matter and also the characteristic decomposition of living systems to highly negentropic and entropic parts as a consequence of generalized second law. adp-atp process of metabolism provides a concrete application for the generalized thermodynamics and allows this process as a transfer of negentropic entanglement. also pitkanen suggests that dna double strand for which sugar-phosphate backbone consists of xmps, x= a,t,c,g containing negentropy carrying phosphate bonds can be seen as analogous to conscious brain with dna strands representing right and left hemispheres. in the sixth article, matti pitkanen continues his proposal that dna is a topological quantum computer (“tqc”). the topics discussed include: 1.how the basic gates are realized concretely? 2. how the braiding is realized concretely? what do braid strands identified as magnetic flux tubes look like? how the braiding operation is induced? 3. how magnetic flux tubes are realized? it is argued that gates can be identified as basic braid operations so that the question reduces to how braidings of magnetic flux tubes represent gates and what kind of particles represent the quantum states. it is also argued that color magnetic flux tubes connecting dna nucleotides to the lipids of nuclear and cell membrane define braid strands and that braiding operations are induced by hydrodynamic flow around membrane generating 2-d flow of liquid crystal defined by the lipids. further, the interpretation of flux tubes as correlates of directed attention at molecular level leads to concrete picture. hydrogen bonds are by their asymmetry natural correlates for a directed attention at molecular level. also flux tubes between acceptors of hydrogen bonds must be allowed and acceptors can be seen as the subjects of directed attention and donors as objects. in the commentary entitled “dna & water memory: comments on montagnier group's recent findings,” matti pitkenan comments on hiv nobelist l. montagnier's group’s two recent articles challenging the standard views about genetic code and providing strong support for the notion of water memory. he argues that the results of the first article suggest implicitly the existence of a new kind nano-scale representation of genetic code and the second article makes this claim explicitly. pitkenan explains that his tgd based model for the findings was based on the notion of magnetic body representing biologically relevant aspects of molecules in terms of cyclotron frequencies. pitkenan argues that the findings of montagnier's group allow a more detailed formulation of the tgd model and suggest a general mechanism for generalized transcription and translation processes based on the reconnection of magnetic flux tubes between the molecules in question. 4. possible coding mechanism based on the principle of existence the herein authors have recently put forward the principle of existence (hu & wu, 2010). based on this principle, one may mathematically generate the dna code as follows: dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 001-010 hu, h. & wu, m. decipherment of the secrets of dna issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 6        etc. 1 0000 anticodencondon iziyixiziyixiziziyiyixixiiii catgta eeeeeeeeeeeee     (4.1) where x, y & z are hypothesized to be three parameters for coding information in each dna strand/sequence and the following selections and mappings are used at the code level: e ix is allowed to have the value +1, +i, -1 or –i respectively at the code level e iy is allowed to have the value +1, +i, -1 or –i respectively at the code level e iz is allowed to have the value +1, +i, -1 or –i respectively at the code level (4.2) e -ix is allowed to have the value -1, -i, +1 or +i respectively at the code level e -iy is allowed to have the value -1, -i, +1 or +i respectively at the code level e -iz is allowed to have the value -1, -i, +1 or +i respectively at the code level mapping:    gtcaii ,,,,1,,1  (4.3) also see figure 2 below: figure 2 the above selections and mappings produce the 4 3 =64 codons and anti-codons of dna respectively. in this coding system, {a, c, t, g} as a set have the following algebraic properties: dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 001-010 hu, h. & wu, m. decipherment of the secrets of dna issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 7 0a ... 0 0 n 2222    nnn gct gcta gcta (4.4) where n=1,2,3,4,… further hypothesizing that x, y & z are three parameters encoding spatial information of a protein in a dna strand, one may find meaning for each code position of the triplet codon and possible connection between the triplet codon and the three dimensionality of space. however, these are just preliminary hypotheses/speculations at this point. 5. generation of hexagrams of i ching there are many metaphysical discussions about the connections of dna code and the chinese i ching. applying the principle of existence (hu & wu, 2010), one may generate the hexagrams of i ching as follows:        etc. __ __ _ _ _ _ _ _ __ 1 trigramlower trigramupper 0000                                                   i i i i i i iziyix iziyix iziyixiziyixiziziyiyixixiiii e e e e e e eee eee eeeeeeeeeeeee (5.1) where x, y & z are hypothesized to be three parameters for coding information in i-ching before the separation of the outer aspect and the inner aspect; α, β & γ are three parameters for coding information of outer aspect; ψ, φ & χ are three parameters for coding information of inner aspect; and the following selections and mappings are used at the hexagram/code level: e iα is allowed to have the value (collapse to) +1, or -1 respectively at the code level e iβ is allowed to have the value (collapse to) +1, or -1 respectively at the code level dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 001-010 hu, h. & wu, m. decipherment of the secrets of dna issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 8 e iγ is allowed to have the value (collapse to) +1, or -1 respectively at the code level (5.2) e -iψ is allowed to have the value (collapse to) +1, or -1 respectively at the code level e -iφ is allowed to have the value (collapse to) +1, or -1 respectively at the code level e -iχ is allowed to have the value (collapse to) +1, or -1 respectively at the code level       yin _ _ ,yang __1 ,1  (5.3) the above selections and mappings produce the 2 6 =64 hexagrams of i-ching. in this coding system, {yang, yin} as a set have the following algebraic properties: yang + yin = 0 (5.4) to accommodate “changing yang” and “changing yin,” the following expanded selections and mapping can be used: e iα is allowed to have the value (collapse to) +1, +i, -1 or –i respectively at the code level e iβ is allowed to have the value (collapse to) +1, +i, -1 or –i respectively at the code level e iγ is allowed to have the value (collapse to) +1, +i, -1 or –i respectively at the code level (5.5) e -iψ is allowed to have the value (collapse to) +1, +i, -1 or –i respectively at the code level e -iφ is allowed to have the value (collapse to) +1, +i, -1 or –i respectively at the code level e -iχ is allowed to have the value (collapse to) +1, +i, -1 or –i respectively at the code level    yinchangingyinyangchangingyangii ,, ,,1,,1  (5.6) the above selections and mappings produce the 4 6 =4096 hexagrams of i-ching which include the changing yang and changing yin. therefore, the 64 dna codons and their corresponding anti-codons belong to a subset of the 4096 hexagram set. in this expanded coding system, {yang, changing yang, yin, changing yin} as a set have the following algebraic properties: dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 001-010 hu, h. & wu, m. decipherment of the secrets of dna issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 9         0 yang ... 0 0 n 2222    nnn yinchangingyangchangingyin yinchangingyangchangingyinyang yinchangingyangchangingyinyang (5.7) where n=1,2,3,4,… 6. closing remarks this issue marks the beginning of the maiden voyage of dna decipher journal as a platform and fair playing field for biologists, physicists, mathematicians and other learned scholars publish their research results and express their views on the origin, nature and mechanism of dna as a biological program and entity and its possible connection to a deeper reality. we urge all genuine truth seekers to be open-minded and tolerant to each other. let us also remind ourselves the fierce urgency of now. this is no time to engage in the luxury of silence or to take the tranquilizing drug of innocence. now is the time to make paradigm-shifting progress in biological sciences & dna research. now is the time to rise from the dogmas of random chance and chaos of evolutionary biology to the sunlit path of living universe. now is the time to lift science from the quick sands of arrogance, close-mindedness & intolerance to the solid rock of sacred path to truth. now is the time to make freedom, equality and opportunity to be heard a reality for all truth-seeking men and women. references crick, f. (1958), on protein synthesis. symp. soc. exp. biol. xii, pp. 139-163. crick f. (1970). central dogma of molecular biology. nature 227 (5258): pp. 561–3. gariaev, p. p., friedman, m. j. & leonova-gariaeva, e. a. (2011), principles of linguistic-wave genetics. dna decipher journal, v1(1): pp 11-25. gariaev, p. p., marcer, p. j., leonova-gariaeva, k. a. & kaempf, u. (2011), dna as basis for quantum biocomputer. dna decipher journal, v1(1): pp 26-46. gariaev, p. p. & pitkanen, m. (2011), model for the findings about hologram generating properties of dna. dna decipher journal, v1(1): pp 47-72. king, c. (2011), the tree of life: tangled roots and sexy shoots. dna decipher journal, v1(1): pp. 72-108. hu, h. & wu (2010), m., prespacetime model of elementary particles, four forces & consciousness. prespacetime journal, vol. 1 (1) pp. 77-146. also see http://vixra.org/abs/1001.0011 http://vixra.org/abs/1001.0011 dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 001-010 hu, h. & wu, m. decipherment of the secrets of dna issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 10 pitkanen, m. (2011), dna as topological quantum computer: part i. dna decipher journal, v1(1): pp. 110-145. pitkanen, m. (2011), dna as topological quantum computer: part ii. dna decipher journal, v1(1): pp. 146-180. pitkanen, m. (2011), dna & water memory: comments on montagnier group’s recent findings. dna decipher journal, v1(1): pp. 181-191. dna decipher journal | may 2014 | volume 4 | issue 1 | pp. 11-18 11 pitkänen, m. pollack’s findings about fourth phase of water: tgd point of view article pollack’s findings about fourth phase of water: tgd point of view matti pitkänen 1 abstract the discovery of negatively charged exclusion zone formed in water bounded by gel phase has led pollack to propose the notion of gel like fourth phase of water. in this article this notion is discussed in tgd framework. the proposal is that the fourth phase corresponds to negatively charged regions exclusion zones with size up to 100-200 microns generated when energy is fed into the water say as radiation, in particular solar radiation. the stoichiometry of the exclusion zone is h1.5o and can be understood if every fourth proton is dark proton residing at the flux tubes of the magnetic body assignable to the exclusion zone and outside it. this leads to a model for prebiotic cell as exclusion zone. dark protons are proposed to form dark nuclei whose states can be grouped to groups corresponding to dna, rna, amino-acids, and trna and for which vertebrate genetic code is realized in a natural manner. the voltage associated with the system defines the analog of membrane potential, and serves as a source of metabolic energy as in the case of ordinary metabolism. the energy is liberated in a reverse phase transition in which dark protons transform to ordinary ones. dark proton strings serve as analogs of basic biopolymers and one can imagine analog of bio-catalysis with enzymes replaced with their dark analogs. the recent discovery that metabolic cycles emerge spontaneously in the absence of cell supports this view. 1 introduction the discovery of negatively charged exclusion zone formed in water bounded by gel phase has led pollack to propose the notion of gel like fourth phase of water. one can find a biographical sketch [3] (http: //faculty.washington.edu/ghp/cv/) giving a list of publications containing items related to the notions of exclusion zone and fourth phase of water discussed in the talk. 1.1 basic findings i list below some basic experimental findings about fourth gel like phase of water made in the laboratory led by gerald pollack [5]. 1. in water bounded by a gel a layer of thickness up to 100-200 microns is formed. all impurities in this layer are taken outside the layer. this motivates the term ”exclusion zone”. the layer consists of layers of molecular thickness and in these layers the stoichiometry is h1.5o. the layer is negatively charged. the outside region carries compensating positive charge. this kind of blobs are formed in living matter. also in the splitting of water producing brown’s gas negatively charged regions are reported to emerge [2, 1]. 2. the process requires energy and irradiation by visible light or thermal radiation generates the layer. even the radiation on skin can induce the phase transition. for instance, the blood flow in narrow surface veins requires metabolic energy and irradiation forces the blood to flow. 3. the layer can serve as a battery: pollack talks about a form of free energy deriving basically from solar radiation. the particles in the layer are taken to the outside region, and this makes possible disinfection and separation of salt from sea water. one can even understand how clouds are formed and mysteries related to the surface tension of water as being due the presence of the layer formed by h1.5o. 1correspondence: matti pitkänen http://tgdtheory.com/. address: köydenpunojankatu 2 d 11 10940, hanko, finland. email: matpitka@luukku.com. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. http://faculty.washington.edu/ghp/cv/ http://faculty.washington.edu/ghp/cv/ http://tgdtheory.com/ mailto:matpitka@luukku.com dna decipher journal | may 2014 | volume 4 | issue 1 | pp. 11-18 12 pitkänen, m. pollack’s findings about fourth phase of water: tgd point of view 4. in the splitting of water producing brown’s gas [2, 1] having a natural identification as pollack’s fourth phase of water the needed energy can come from several alternative sources: cavitation, electric field, etc... 1.2 summary of tgd inspired model for the findings in the following this notion is discussed in tgd framework. the proposal is that the fourth phase corresponds to negatively charged regions exclusion zones with size up to 100-200 microns generated when energy is fed into the water say as radiation, in particular solar radiation. the stoichiometry of the exclusion zone is h1.5o and can be understood if every fourth proton is dark proton residing at the flux tubes of the magnetic body assignable to the exclusion zone and outside it. this leads to a model for prebiotic cell as exclusion zone. dark protons are proposed to fork dark nuclei whose states can be grouped to groups corresponding to dna, rna, amino-acids, and trna and for which vertebrate genetic code is realized in a natural manner. the voltage associated with the system defines the analog of membrane potential, and serves as a source of metabolic energy as in the case of ordinary metabolism. the energy is liberated in a reverse phase transition in which dark protons transform to ordinary ones. dark proton strings serve as analogs of basic biopolymers and one can imagine analog of bio-catalysis with enzymes replaced with their dark analogs. the recent discovery that metabolic cycles emerge spontaneously in absence of cell support this view. 2 dark nuclei and pollack’s findings while listening the lecture of pollack i realized that a model for dark water in term of dark proton sequences is enough to explain the properties of the exotic water according to experiments done in the laboratory of pollack. there is no need to assume sequences of half-dark water molecules containing one dark proton each. 2.1 model for the formation of exclusion zones the data about formation of exclusion zones allows to construct a more detailed model for what might happen in the formation of exclusion zones. 1. the dark proton sequences with dark proton having size of order atomic nucleus would reside at the flux tubes of dark magnetic field which is dipole like field in the first approximation and defines the magnetic body of the negatively charged water blob. this explains the charge separation if the flux tubes have length considerably longer than the size scale of the blob which is given by size of small cell. in the model inspired by moray b. king’s lectures charge separation is poorly understood. 2. an interesting question is whether the magnetic body is created by the electronic currents or whether it consists of flux tubes carrying monopole flux: in the latter case no currents would be needed. this is obviously purely tgd based possibility and due to the topology of cp2. 3. this means that in the model inspired by the lectures of moray b. king discussed above, one just replaces the sequences of partially dark water molecules with sequences of dark protons at the magnetic body of the h1.5o blob. the model for the proto-variants of photosynthesis and metabolism remain as such. also now genetic code would be realized [7, 8]. 4. the transfer of impurities from the exclusion zone could be interpreted as a transfer of them to the magnetic flux tubes outside the exclusion zone as dark matter. these primitive forms of photosynthesis and metabolism form could be key parts of their higher level chemical variants. photosynthesis by irradiation would induce a phase transition generating dark isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2014 | volume 4 | issue 1 | pp. 11-18 13 pitkänen, m. pollack’s findings about fourth phase of water: tgd point of view magnetic flux tubes (or transforming ordinary flux tubes to dark ones) and the dark proton sequences at them. metabolism would mean burning of the resulting blobs of dark water to ordinary water leading to the loss of charge separation. this process would be analogous to the catabolism of organic polymers liberating energy. also organic polymers in living matter carry their metabolic energy as dark proton sequences: the layer could also prevent their hydration. that these molecules are typically negatively charged would conform with the idea that dark protons at magnetic flux tubes carry the metabolic energy. the liberation of energy would involve increase of the p-adic prime characterizing the flux tubes and reduction of planck constant so that the thickness of the flux tubes remains the same but the intensity of the magnetic field is reduced. the cyclotron energy of dark protons is liberated in coherent fashion and in good approximation the frequencies of the radiation corresponds to multiplies of cyclotron frequency: this prediction is consistent with that in the original model for the findings of blackman and others [6]. the phase transition generating dark magnetic flux tubes containing dark proton sequences would be the fundamental step transforming inanimate matter to living matter and the fundamental purpose of metabolism would be to make this possible. 2.2 minimal metabolic energy consumption and the value of membrane potential this picture raises a question relating to the possible problems with physiological temperature. 1. the josephson radiation generated by cell membrane has photon energies coming as multiples of zev , where v is membrane potential about .06 v and z = 2 is the charge of electron cooper pair. this gives e = .12 ev. 2. there is a danger that thermal radiation masks josephson radiation. the energy for photons at the maximum of the energy density of blackbody radiation as function of frequency is given as the maximum of function x3/(ex − 1), x = e/t given by e−x + x/3 − 1 = 0. the maximum is given approximately by x = 3 and thus emax ' 3t (in units c = 1, kb = 1). at physiological temperature t = 310 k (37 c) this gives .1 ev, which is slightly below josephson energy: living matter seems to have minimized the value of josephson energy presumably to minimize metabolic costs. note however that for the thermal energy density as function of wavelength the maximum is at e ' 5t corresponding to 1.55 ev which is larger than josephson energy. the situation is clearly critical. 3. one can ask whether also a local reduction of temperature around cell membrane in the fourth phase of water is needed. (a) ”electric expansion” of water giving rise to charge separation and presumably creating fourth phase of water is reported to occur [2, 1]. (b) could the electric expansion/phase transition to dark phase be adiabatic involving therefore no heat transfer between the expanding water and environment? if so, it would transform some thermal energy of expanding water to work and reduce its temperature. the formula for the adiabatic expansion of ideal gas with f degrees of freedom for particle (f = 3 if there are no other than translational degrees of freedom) is (t/t0) = (v/v0)−γ , γ = (f + 2)/f . this gives some idea about how large reduction of temperature might be involved. if p-adic scaling for water volume by a power of two takes place, the reduction of temperature can be quite large and it does not look realistic. (c) the electric expansion of water need not however involve the increase of planck constant for water volume. only the planck constant for flux tubes must increase and would allow the formation of dark proton sequences and the generation of cyclotron bose-einstein condensates or their dark analog in which fermions (electrons in particular) effectively behave as bosons (the anti-symmetrization of wave function would occur in dark degrees of freedom corresponding to multi-sheeted covering formed in the process). isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2014 | volume 4 | issue 1 | pp. 11-18 14 pitkänen, m. pollack’s findings about fourth phase of water: tgd point of view 3 fourth phase of water and pre-biotic life in tgd universe if the fourth phase of water defines pre-biotic life form then the phase transition generating fourth phase of water and its reversal are expected to be fundamental elements of the ordinary metabolism, which would have developed from the pre-biotic metabolism. the following arguments conforms with this expectation. 3.1 metabolism and fourth phase of water 1. cell interiors, in particular the interior of the inner mitochondrial membrane are negatively charged as the regions formed in pollack’s experiments. furthermore, the citric acid cycle, (http://www.en. wikipedia.org/wiki/citric_acid_cycle), which forms the basic element of both photosynthesis (http://www.en.wikipedia.org/wiki/photo-synthesis) and cellular respiration http://www. en.wikipedia.org/wiki/cellular_respiration, involves electron transport chain (http://www. en.wikipedia.org/wiki/electron_transport_chain) in which electron loses gradually its energy via production of nadp and proton at given step. protons are pumped to the other side of the membrane and generates proton gradient serving as metabolic energy storage just like battery. the interpretation for the electron transport chain in terms of pollack’s experiment would be in terms of generation of dark protons at the other side of the membrane. 2. when atp is generated from adp three protons per atp flow back along the channel formed by the atp synthase molecule (http://www.en.wikipedia.org/wiki/atp_synthase) (perhaps josephson junction) and rotate the shaft of a ”motor” acting as a catalyst generating three atp molecules per turn by phosphorylating adp. the tgd based interpretation is that dark protons are transformed back to ordinary ones and possible negentropic entanglement is lost. 3. atp is generated also in glycolysis (http://www.en.wikipedia.org/wiki/glycolysis), which is ten-step process occurring in cytosol so that membrane like structure need not be involved. glycolysis involves also generation of two nadh molecules and protons. an open question (to me) is whether the protons are transferred through an endoplasmic reticulum or from a region of ordered water (fourth phase of water) to its exterior so that it would contribute to potential gradient and could go to magnetic flux tubes as dark proton. this would be natural since glycolysis is realized for nearly all organisms and electron transport chain is preceded by glycolysis and uses as input the output of glycolysis (two pyruvate molecules (http://www.en.wikipedia.org/wiki/pyruvate)). 4. biopolymers including dna and atp are typically negatively charged. they could thus be surrounded by fourth phase of water and neutralizing protons would reside at the magnetic bodies. this kind of picture would conform with the idea that the fourth phase (as also magnetic body) is fractal like. in phosphorylation the metabolic energy stored to a potential difference is transferred to shorter length scales (from cell membrane scale to molecular scale). in glycolysis (http://www.en.wikipedia.org/wiki/glycolysis) the net reaction c6h12o6+6o2 → 6co2(g) + 6h2o(l) + heat takes place. the gibbs free energy change is ∆g = −2880 kj per mole of c6h12o6 and is negative so that the process takes place spontaneously. single glucose molecule is theoretized to produce n = 38 atp molecules in optimal situation but there are various energy losses involved and the actual value is estimated to be 29-30. from joule = 6.84×1018 ev and mol = 6.02×1023 and for n = 38 one would obtain the energy yield .86 ev per single atp. the nominal value that i have used .5 ev. this is roughly 5 to 8 times higher than e = zev, z = 2, which varies in the range .1-.16 ev so that the metabolic energy gain cannot be solely due to the electrostatic energy which would actually give only a small contribution. in the thermodynamical approach to metabolism the additional contribution would be due to the difference of the chemical potential µ for cell exterior and interior, which is added to the membrane potential as effective potential energy. the discrepancy is however rather large and this forces the question the feasibility of the model. this forces to reconsider the model of osmosis in the light of pollack’s findings. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. http://www.en.wikipedia.org/wiki/citric_acid_cycle http://www.en.wikipedia.org/wiki/citric_acid_cycle http://www.en.wikipedia.org/wiki/photo-synthesis http://www.en.wikipedia.org/wiki/cellular_respiration http://www.en.wikipedia.org/wiki/cellular_respiration http://www.en.wikipedia.org/wiki/electron_transport_chain http://www.en.wikipedia.org/wiki/electron_transport_chain http://www.en.wikipedia.org/wiki/atp_synthase http://www.en.wikipedia.org/wiki/glycolysis http://www.en.wikipedia.org/wiki/pyruvate http://www.en.wikipedia.org/wiki/glycolysis dna decipher journal | may 2014 | volume 4 | issue 1 | pp. 11-18 15 pitkänen, m. pollack’s findings about fourth phase of water: tgd point of view 3.2 pollack’s findings in relation to osmosis and model for cell membrane and eeg osmosis (http://en.wikipedia.org/wiki/osmotic) has remained to me poorly understood phenomenon. osmosis means that solvent molecules move through a semipermeable membrane to another side of the membrane if the concentration of solute is higher at that side. solute can be water or more general liquid, supercritical liquid, and even gas. osmosis is not diffusion: it can occur also towards a higher concentration of water. water molecules are not attracted by solute molecules. a force is required and the wikipedia explanation is that solute molecules approaching pores from outside experience repulsion and gain momentum which is transferred to the water molecules. the findings of pollack inspire the question whether the formation of exclusion zone could relate to osmosis and be understood in terms of the fourth phase of water using genuine quantal description. in the thermodynamical model for ionic concentrations one adds to the membrane resting potential a contribution from the difference of chemical potentials µi at the two sides of the membrane. chemical potentials for the ions parametrize the properties of the cell membrane reducing basically to the properties of the channels and pumps (free diffusion and membrane potential do not entirely determine the outcome). if the transfer of ions now protons through cell membrane is quantal process and through josephson junctions defined by transmembrane proteins, then the thermodynamical model can at best be a phenomenological parameterization of the situation. one should find the quantum counterpart of thermodynamical description, and here the identification of quantum tgd as square root of thermodynamics in zero energy ontology (zeo) suggests itself. in this approach thermodynamical distributions are replaced by probability amplitudes at single particle level such that their moduli squared give boltzmann weights. 3.2.1 simplest josephson junction model for cell membrane the first guess is that quantum description is achieved by a generalization of the josephson junction model allowing different values of planck constant at magnetic flux tubes carrying dark matter. 1. josephson junctions correspond microscopically to transmembrane proteins defining channels and pumps. in rougher description entire cell membrane is described as josephson junction. 2. the magnetic field strength at flux tube can differ at the opposite side of the membrane and even the values of heff could in principle be different. the earlier modelling attempts suggest that heff/h = n = 2ka, where a is the atomic weight of ion, is a starting assumption deserving testing. this would mean that each ion resides at its own flux tubes. the phase transitions changing the value of heff could induce ionic flows through cell membrane, say that occurring during nerve pulse since the energy difference defining the ratio of square roots of boltzmann weights at the two sides of the membrane would change. also the change of the local value of the magnetic field could do the same. consider first the simplest model taking into account only membrane potential. 1. the simplest model for josephson junction defined by the transmembrane protein is as a two state system (ψ1,ψ2) obeying schrödinger equation. i~1 ∂ψ1 ∂t = zevψ1 + k1ψ2 , i~2 ∂ψ2 ∂t = k2ψ2 . one can use the decomposition ψi = riexp(iφ(t) to express the equations in a more concrete form. the basic condition is that the total probability defined as sum of moduli squared equals to one: isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. http://en.wikipedia.org/wiki/osmotic dna decipher journal | may 2014 | volume 4 | issue 1 | pp. 11-18 16 pitkänen, m. pollack’s findings about fourth phase of water: tgd point of view r2 1 + r2 2 = 1. this is guaranteed if the hermiticity condition k1/~1 = k2~2 holds true. equations reduce to those for an ordinary josephson junction except that the frequency for the oscillating josephson current is scaled down by 1/heff . 2. one can solve for r2 assuming φ1 = ev t/~eff . this gives r2(t) = sin(φ0) + k1 ~1 sin( ev t ~1 ) . r2 oscillates around sin(φ0) and the concentration difference is coded by φ0 taking the role of chemical potential as a phenomenological parameter. 3. the counterparts of boltzmann weights would be apart from a phase factor square roots of ordinary boltzmann weights defined by the exponent of coulomb energy: r = sin(φ0) = exp( zev (t) 2t ) . temperature would appear as a parameter in single particle wave function and the interpretation would be that thermodynamical distribution is replaced by its square root in quantum theory. in zeo density matrix is replaced by its hermitian square root multiplied by density matrix. 3.2.2 the counterpart of chemical potential in tgd description this model is not as such physically realistic since the counterpart of chemical potential is lacking. the most straightforward generalization of the thermodynamical model is obtained by the addition of an ion dependent chemical potential term to the membrane potential: zev → zev + µi . this would however require a concrete physical interpretation. 1. the most obvious possibility is that also the chemical potential actually correspond to an interaction energy most naturally the cyclotron energy ec = ~effzebend/m of ion in this case proton at the magnetic flux tube. cyclotron energy is proportional to heff and can be rather large as assumed in the model for the effects of elf em fields on brain. 2. this model would predict the dependence of the effective chemical potential on the mass and charge of ion for a fixed value of on heff and bend. the scales of ionic chemical potential and ion concentrations would also depend on value of heff . 3. the model would provide a different interpretation for the energy scale of bio-photons, which is in visible range rather than infrared as suggested by the value of membrane potential. the earlier proposal [?]qualia was that cell membrane can be in near vacuum extremal configuration in which classical z0 field contributes to the membrane potential and gives a large contribution for ions. the problematic aspect of the model was the necessity to assume weinberg angle in this phase to have much smaller value than usually. furthermore, for proton the z0 contribution is negligible in good approximation so that this model does not explain the high value of the metabolic energy currency. 4. the simplest model the communications to magnetic body rely on josephson radiation whose fundamental frequency fj is at resonance identical with the cyclotron frequency fc(mb) at particular part of the flux tube of the magnetic body:(fc(mb) = fj . fc(mb) corresponds to eeg frequency in the case of brain and biophotons are produced from dark eeg photons as ordinary photons in phase transition reducing heff = n× h to h. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2014 | volume 4 | issue 1 | pp. 11-18 17 pitkänen, m. pollack’s findings about fourth phase of water: tgd point of view in the modified model the sum fc+fj,n (fj,n = ej/n×h) of heff -independent cyclotron frequency and josephson frequency proportional to 1/heff equals to cyclotron frequency fc(mb) at ”personal” magnetic body varying slowly along the flux tube: fc + fj,n = fc(mb). if also the variation of fj assignable to the action potential is included, the total variation of membrane potential gives rise to a frequency band with width roughly ∆f f ' 2fj,n fc + fj,n = 2fj,1 nfc + fj,1 . if dark photons correspond to biophotons the energy is of cyclotron photon is in visible and uv range one has nfc = ebio and ∆f f ' 2zev ebio + zev . the prediction is scale invariant and same for all ions and also electron unless ebio depends on ion. for ev = .05 ev, z = 1, and ebio = 2 ev (f ' 5× 1014 hz) one has ∆f/f ∼ .1 giving 10 per cent width for eeg bands assumed in the simpler model. if this vision is on the correct track, the fundamental description of osmosis would be in terms of a phase transition to the fourth phase of water involving generation of dark matter transferred to the magnetic flux tubes. for instance, the swelling of cell by an in-flow of water in presence of higher concentration inside cell could be interpreted as a phase transition extending exclusion zone as a process accompanied by a phase transition increasing the value of heff so that the lengths of the flux tube portions inside the cell increase and the size of the exclusion zone increases. in general case the phase transitions changing heff and bend by power of two factor are possible. this description should bring magnetic body as part of bio-chemistry and allow understanding of both equilibriumion distributions, generation of nerve pulse, and basic metabolic processes leading to the generation of atp. 3.3 which came first: metabolism or cell membrane? one of the basic questions of biology is whether metabolism preceded basic biopolymers or vice versa. rna world scenario assumes that rna and perhaps also genetic code was first. 1. the above view suggests that both approaches are correct to some degree in tgd universe. both metabolism and genetic code realized in terms of dark proton sequences would have emerged simultaneously and bio-chemistry self-organized around them. dark proton sequences defining analogs of amino-acid sequences could have defined analogs of protein catalysts and played a key role in the evolution of the metabolic pathways from the primitive pathways involving only the phase transition between ordinary water and fourth phase of water. 2. there is very interesting article [4] reporting that complex metabolic pathways are generated spontaneously in laboratory environments mimicking hot thermal vents. glycolysis and pentose phosphate pathway were detected. the proposal is that these pathways are catalyzed by metals rather than protein catalysts. 3. in standard biology these findings would mean that these metabolic pathways emerged before basic biopolymers and that genetic code is not needed to code for the metabolic pathways during this period. in tgd framework dark genetic code [7, 8] would be there, and could code for the dark pathways. dark proton strings in one-one correspondence with the amino-acid sequences could be responsible for catalysts appearing in the pathways. only later these catalysts would have transformed to their chemical counterparts and might be accompanied by their dark templates. one cannot even exclude the possibility that the chemical realization of the dna-aminoacid correspondence involves its dark analog in an essential manner. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. http://www.newscientist.com/article/dn25471-spark-of-lifemetabolism-appears-in-lab-without-cells.html?cmpid=rss|nsns|2012-global| online-news #.u14kf8zk7b2 dna decipher journal | may 2014 | volume 4 | issue 1 | pp. 11-18 18 pitkänen, m. pollack’s findings about fourth phase of water: tgd point of view references biology,neuroscience, and free energy [1] m. b. king. free-energy devices. http://www.free-energy-info.co.uk/morayking.pdf. [2] m. b. king. water electrolyzers and the zero-point energy. physics procedia. http: // www. sciencedirect. com/ science/ journal/ 18753892 , 20:335–445, 2011. [3] pollack laboratorybiographical sketch. http://faculty.washington.edu/ghp/cv/. [4] spark of life: metabolism appears in lab without cells. http://www.newscientist.com/article/ dn25471-spark-of-life-metabolism-appears-in-lab-without-cells.html?cmpid=rss|nsns| 2012-global|online-news#.u14rrmzk7b3. [5] the fourth phase of water: dr. gerald pollack at tedxguelphu. https://www.youtube.com/ watch?v=i-t7tcmudxu, 2014. [6] c. f. blackman. effect of electrical and magnetic fields on the nervous system, pages 331–355. plenum, new york, 1994. books related to tgd [7] m. pitkänen. homeopathy in many-sheeted space-time. in bio-systems as conscious holograms. onlinebook. http://tgdtheory.fi/public_html/hologram/hologram.html#homeoc, 2006. [8] m. pitkänen. nuclear string hypothesis. in hyper-finite factors and dark matter hierarchy. onlinebook. http://tgdtheory.fi/public_html/neuplanck/neuplanck.html#nuclstring, 2006. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. http://www.free-energy-info.co.uk/morayking.pdf http://www.sciencedirect.com/science/journal/18753892 http://www.sciencedirect.com/science/journal/18753892 http://faculty.washington.edu/ghp/cv/ http://www.newscientist.com/article/dn25471-spark-of-life-metabolism-appears-in-lab-without-cells.html?cmpid=rss|nsns|2012-global|online-news#.u14rrmzk7b3 http://www.newscientist.com/article/dn25471-spark-of-life-metabolism-appears-in-lab-without-cells.html?cmpid=rss|nsns|2012-global|online-news#.u14rrmzk7b3 http://www.newscientist.com/article/dn25471-spark-of-life-metabolism-appears-in-lab-without-cells.html?cmpid=rss|nsns|2012-global|online-news#.u14rrmzk7b3 https://www.youtube.com/watch?v=i-t7tcmudxu https://www.youtube.com/watch?v=i-t7tcmudxu http://tgdtheory.fi/public_html/hologram/hologram.html#homeoc http://tgdtheory.fi/public_html/neuplanck/neuplanck.html#nuclstring introduction basic findings summary of tgd inspired model for the findings dark nuclei and pollack's findings model for the formation of exclusion zones minimal metabolic energy consumption and the value of membrane potential fourth phase of water and pre-biotic life in tgd universe metabolism and fourth phase of water pollack's findings in relation to osmosis and model for cell membrane and eeg simplest josephson junction model for cell membrane the counterpart of chemical potential in tgd description which came first: metabolism or cell membrane? mattipitkanen1_v7n2.pdf dna decipher journal | december 2017 | volume 7 | issue 2 | pp. 98-128 98 pitkänen, m., life-like properties observed in a very simple system article life-like properties observed in a very simple system matti pitkänen 1 abstract the physicists working in emory university have made very interesting discovery. the very simple system studied exhibits what authors call self-organized bi-stability making phase transitions between crystal-like and gas-like phases. the expectation was that only single stable state would appear. neuron groups can also have collective bi-stability (periodic synchronous firing). neurons are however themselves bi-stable systems: now the particles are plastic balls and are not bi-stable. one could say that the system exhibits life-like properties. the most remarkable life-like property is metabolism required by the sequence of phase transitions involving dissipation. where does the metabolic energy come from? the proposal of experimenters is that stochastic resonance feeds the needed metabolic energy leaves open its source. the resemblance with living cells suggests that the attempt to interpret the findings solely in terms of non-equilibrium thermodynamics might miss something essential the metabolism. one can develop a model for the system based on tgd inpired quantum biology. this involves the notion of magnetic body carrying dark matter identified as heff = n×h phases; a network of magnetic flux tubes (magnetic body) controlling biological body (now charged plastic balls) and responsible for coherence and synchrony (of the crystal-like phase now); the control of the oscillations of bb by cyclotron radiation (now the plastic ball system) resulting from decays of cyclotron condensates of charged particles (now protons and ar ions). the source of metabolic energy would come from dark nucleosynthesis explaining nuclear transmutations occurring in living matter and ”cold fusion” and serving as source of metabolic energy in prebiotic stage when the chemical energy storage had not yet emerged. dark analogs of dna, rna, trna, and amino-acids are dark protons sequences realizing degeneracies of vertebrate genetic code are dark nuclei and can transform to ordinary nuclei and liberate nuclear binding energy so that the hen-egg question about which came first: metabolism or genetic code, is resolved: hen= egg. there is also second very simple system exhibiting life-like properties. the system consists of particles with a feed of acoustic energy at single wavelength. what happens is that the distribution of particles develops synchronous oscillations in wave length band below the acoustic wavelength. the oscillation amplitudes are reduced in this band so that wavelength gap emerges. the system is also able to heal. the interpretation is in terms of the emergence of flux tube structure rigidifying the system to pseudo-crystal. the energy of the oscillations of the particles is transferred to mb where it gives rise to alfwen waves with a wavelength band analogous to atomic energy bands. 1 introduction i encountered in fb a link to a rather interesting article by physicists working in emory university. the title of the popular article was ”physicists show how lifeless particles can become ’life-like’ by switching behaviors” (see http://tinyurl.com/y8wrz9ho). the article ”emergent bi-stability and switching in a nonequilibrium crystal” by guram gogia and justin burton is published in prl and can be found in arxiv [12] (see http://tinyurl.com/ychho4l8). justin burton leads a physics group working at emory university. guram gogia who made the discovery is her student. the physicists working in emory university have made very interesting discovery. the very simple system studied exhibits what authors call self-organized bi-stability making phase transitions between 1correspondence: matti pitkänen http://tgdtheory.com/. address: rinnekatu 2-4 a8, 03620, karkkila, finland. email: matpitka6@gamail.com. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2017 | volume 7 | issue 2 | pp. 98-128 99 pitkänen, m., life-like properties observed in a very simple system crystal-like and gas-like phases. the expectation was that only single stable state would appear. neuron groups can also have collective bi-stability (periodic synchronous firing). neurons are however themselves bi-stable systems: now the particles are plastic balls and are not bi-stable. one could say that the system exhibits life-like properties. the most remarkable life-like property is metabolism required by the sequence of phase transitions involving dissipation. where does the metabolic energy come from? the proposal that stochastic resonance feeds the needed metabolic energy leaves open its source. the resemblance with living cells suggests that the attempt to interpret the findings solely in terms of non-equilibrium thermodynamics might miss something essential the metabolism. tgd provides a general model for living systems relying on the notion of magnetic body (mb), hierarchy of planck constants heff = n×h labelling phases of ordinary matter identifiable as dark matter, and the realization of control and communication signals between mb and biological body using dark photons [27, 26]. bio-photons would result in the transformation of dark photons to ordinary photons and eeg would rely on dark cyclotron photons and generalized josephson photons from cell membrane (also bio-photons would relate to them). bose einstein condensates of dark variants of biologically important ions or their cooper pairs are also in a central role. the assumption hgr = heff , where hgr is so called gravitational planck constant, implies that the energy spectrum of dark cyclotron photons is universal (no dependence on the mass of ion) and naturally in visible and uv range characterizing molecular transition energies. [32, 31]. one can develop a detailed tgd inspired model for the findings leading to an identification of new control tools of mb (mb). quantum criticality makes it possible for mb can adapt to the biological body (bb) so that it can generated cyclotron frequencies, which correspond to the characteristic frequencies of bb: forced oscillations serve as a control tool of mb. also the analogs of alfwen waves identifiable as analogs of string vibrations allow to control the systems at the nodes of the flux tube network. in the system studied the crystal-like phase corresponds to a connected flux tube network associated having plastic balls as nodes, and gas-like phase to a totally disconnected network with connecting flux tube pairs split into flux loops. that freezing would require energy (going to the magnetic energy of flux tube network in heff increasing phase transition) does not conform with the thermodynamics of classical systems. that superfluid helium has similar strange feature at low enough temperatures suggests that the system is indeed quantal. cyclotron bose-einstein (be) condensates of cooper pairs of ar+ ions, protons, and electrons are proposed to be relevant. encouragingly, the ratio of frequencies for horizontal and vertical oscillations frequencies of crystal-like structure is equal to the ratio of cyclotron frequencies for ar+ and proton. one of the key challenges is to identify the the prebiotic source of metabolic energy. the sequences of dark protons identifiable as dark nuclei give in tgd framework rise to analogs of dna, rna, trna, and amino-acids [19, 20, 39]. the model predicts the degeneracies of vertebrate genetic code correctly. in tgd based model for ”cold fusion” as dark nucleosynthesis (dns) serving as a predecessor of ordinary nucleosynthesis dark nuclei transform to ordinary nuclei liberating almost all nuclear binding energy [30, 41]. dark analogs of dna, rna, trna, and amino-acids would therefore provide also the sought for prebiotic source of metabolic energy in the system studied: the egg-or-hen problem about whether the genes or metabolism came first, would be resolved. there is also second very simple system exhibiting life-like properties. the system consists of particles with a feed of acoustic energy at single wavelength. what happens is that the distribution of particles develops synchronous oscillations in wave length band below the acoustic wavelength. the oscillation amplitudes are reduced in this band so that wavelength gap emerges. the system is also able to heal. the interpretation is in terms of the emergence of flux tube structure rigidifying the system to pseudocrystal. the energy of the oscillations of the particles is transferred to mb where it gives rise to alfwen waves with a wavelength band analogous to atomic energy bands. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2017 | volume 7 | issue 2 | pp. 98-128 100 pitkänen, m., life-like properties observed in a very simple system 2 experimental findings the news [12] is that the system studied exhibits what authors call self-organized bi-stability making phase transitions between crystal-like and gas-like phases. the expectation was that only single stable state would appear. neuron groups can also have collective bi-stability (periodic synchronous firing). neurons are however themselves bi-stable systems: now the particles are plastic balls, which are not bistable systems. one could say that the system exhibits life-like properties. the most remarkable life-like property is metabolism required by the sequence of phase transitions involving dissipation. where does the metabolic energy come from? the durations of the switching time scales are shorter than stable periods and also shorter than predicted by the simulation. the presence of periodicity perturbation, presumably the period for the oscillating phase transition, is suggestive and authors conjecture that there is a weak but yet unidentified periodic signal present required by the proposed stochastic resonance model. let us consider first in some detail what the system is and what happens in it. 1. the system studied consists of small charged plastic balls of radius nearly 10 µm (cell size scale) in a cold atmospheric plasma consisting of argon ions (ar+) (see http://tinyurl.com/yc7q6l7o). the charged plastic balls consist of melamine formaldehyde (mf) polymers. the plasma is generated using a voltage between electrode and earth leading to the ionization of ar to ar+: the typical value of voltage is 6 volt. the electrons from argon atoms provide negative charge for the plastic balls. 2. negatively charged bf balls are levitated above the electrode having negative charge given by q = cv , where c and v are the geometrically determined capacitance and the voltage of the ball. in equilibrium position gravitational and electrostatic forces compensate each other when the size of the ball in certain range. too heavy balls fall down to the electrode and lighter balls levitate and form a cloud, whose thickness is determined by the variation of the radius of plastic balls. bf balls have mutual repulsive action. the negative charge of the balls is screened by ar+ ions with screening characterized by debye length λd ∼ 1 mm. there is also a gradient in the density of ar+ ions attracting the balls near the centreof the electrode. the situation is modelled in terms of confining harmonic oscillator potentials in vertical and transversal directions. 3. a crystal-like phase is created by the horizontal confinement. in crystal-like phase collective synchronous oscillations in the vertical direction are initiated so that the equilibrium height of hexagonal plastic ball lattice oscillates. oscillations are damped by dissipation. the oscillation frequency is determined by the sum of gravitational and electric interaction potentials. the variation cv of the radius of the plastic ball induces a variation of the mass m and capacitance c and therefore also a variation of the oscillation frequencies fv and fh in vertical and transversal directions. the typical values of these frequencies are fv = 20 hz and fh = .5 hz. this implies that synchrony of oscillations is lost, and eventually a transition to gas-like phase takes place as nucleation centres for gas-like phase are formed. the gas-like phase dissipates its energy. remark: that the ratio fv /fh = 40 equals to the ratio of cyclotron frequencies of proton and ar+ serves as an important guideline in tgd inspired model. 4. the surprise was that for low pressures and low ar+ ion densities a transition to crystal-like phase takes place: this transition correspond to a critical value of the variation cv for the plastic ball radius. above the critical value of cv the system remains in gas phase and below it in crystal-like phase. the crystal-like phase is collectively oscillating in vertical direction, which requires energy feed. there is synchrony between the dynamics of plastic balls in crystal-like phase, which is lost and leads to a melting and loss of phase phase coherence between oscillations of plastic balls. particle system was repeatedly melting and freezing. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2017 | volume 7 | issue 2 | pp. 98-128 101 pitkänen, m., life-like properties observed in a very simple system 5. since the analog of crystal-like phase is repeatedly generated, there must be a feed of energy to the system analogous to metabolic energy feed in living systems. the proposal of the article is that the energy feed is due to a stochastic resonance [7]. in stochastic resonance noise amplifies oscillatory signal fed into the system if its frequency f satisfies f = f(spont)/2, where f(spont) is the average frequency for the jumps between the bi-stable states of the system due to noise. since the period of conjectured oscillation is τ ∼ 100 s one should have τ(spont) ∼ 50 s. the period for this process is considerably longer than for the vertical oscillations. the origin of this self-induced oscillation required by stochastic resonance model is not understood and one can even challenge its existence. remark: from the point of view of quantum biology it might be highly relevant that plastic balls consists of organic molecules. bf molecules involve aromatic 6-cycles appearing also in dna. there is negative charge associated with the plastic balls. also dna carries negative charges associated with phosphate ions. 3 basic ideas of tgd inspired quantum biology tgd universe is quantum critical and quantum criticality involves universal dynamics. this raises the hope that also the tgd inspired model of living systems is universal and applicable also in the recent context. the findings would provide a test for tgd view and even allow to sharpen it. tgd based view about living systems involves several new notions. 3.1 dark matter as hierarchy of phases of ordinary matter with heff = n× h the first new element is the hierarchy of planck constants heff/h = n. in adelic physics [44, 45] proposed to provide physical correlates of both sensory experience and cognition heff/h = n serves as a kind of iq for the system measuring its algebraic complexity (n could correspond to the order of the galois group for the extension of rationals defining the adele in question). 1. quantum criticality is the basic property of tgd universe and also an essential aspect of what it is to be living in tgd universe and the associated long range fluctuations and correlations correspond to large values of heff/h = n for the flux tubes of mb [31]. the increase of heff/h = n keeping magnetic field strength un-affected reduces binding energies for electrons of atoms and increases cyclotron energy scale and scales up quantum lengths and times, in particular the scales of quantum coherence and this kind of phase transitions seem to be crucial in tgd inspired biology. the energies of subsystems indeed typically increase with heff . for instance, atomic binding energies are proportional to 1/h2 eff . cyclotron energies are in turn proportional to heff . the function of metabolism in tgd universe is to increase the value of heff for some sub-systems of living system, and therefore to increase the complexity of the subsystem. the reduction of heff liberates energy and this energy could kick the reacting molecules over the potential wall in biocatalysis. the reduction of n forcing the shortening of the flux tubes could provide a mechanism allowing the reacting biomolecules to find each other in a dense molecular soup. 2. the cyclotron frequencies of dark ions in the magnetic field of the flux tubes do not depend on heff/h = n but the cyclotron energies ec = heff×f are scaled up by factor n so that they are above thermal energy at physiological temperatures and can carry information so that they can be used for communication and control purposes. cell membrane acts as a generalized josephson junction and dark josephson radiation communicates sensory information to mb coded to the modulation of the generalized josephson frequency by the variations of neuronal membrane potential induced by nerve pulse patterns [25, 18]. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2017 | volume 7 | issue 2 | pp. 98-128 102 pitkänen, m., life-like properties observed in a very simple system 3.2 hgr = heff hypothesis and universal cyclotron energies hgr = heff hypothesis [32, 31] and its generalizations such as e hem = heff represent a further key element of the tgd inspired model of living matter. this relationship is proposed to hold when the coupling strength proportional to appropriate charges is so large that perturbation series does not converge. the large value of heff reduces the value of coupling strength proportional to 1/heff so that dark matter satisfying this condition would allow a perturbative description. 1. nottale [9] introduced originally the notion of gravitational planck constant ~gr = gmm/v0 to explain the orbital radii of planets in solar system as bohr orbits. the value of the velocity parameter v0/c is of order 2−11 ≃ .5 × 10−3 for the inner planets. the interpretation in tgd framework is that the magnetic flux tubes mediate gravitational interaction between masses m and m and the value of planck constant is hgr at them. the proposal heff = hgr at flux tubes is very natural sharpening of the original hypothesis [31, 32]. the predictions of the model do not depend on whetherm is taken to be the mass of the planet or any elementary particle associated with it and the gravitational compton length λgr = gmc/v0 does not depend on the mass of the particle, and is proportional to the schwartschild radius rs = 2gm of sun. this encourages the idea about astroscopic quantum coherence at magnetic flux tubes mediating gravitational interaction. one of the applications is to the fountain effect of superfluidity [31]. in the biological applications the identification of mass m as earth mass is one possibility but there are also other options [32]. the identification of v0 as some mechanical velocity scale looks natural. 2. hgr = heff hypothesis predicts that cyclotron energies do not depend on the mass of the particle whereas cyclotron frequencies are proportional to 1/m. cyclotron energy spectrum would be universal and correspond to the spectrum of magnetic field strengths b. bio-photons with energies in visible and uv are proposed to result as dark photons satisfying hgr = heff transform to ordinary photons. for b = bend = 2be/5 (be = .5 gauss is the nominal value of the earth’s magnetic field) the hypothesis fixes the scale of cyclotron frequencies and hgr should be in the range 1012 − 1014. 3.3 mb (mb) and its motor actions a further new element is the notion of mb (mb) adding to the pair formed by organism and environment a third member. this brings into biochemistry a radically new element [27, 26]. one can say that mb uses biological body as a motor instrument and sensory receptor. 1. in tgd standard model gauge fields and gravitational field are replaced locally by the 4 imbedding space-time coordinates behaving like field variables. this implies an enormous simplification of the local dynamics however lost in the qft limit replacing many-sheeted space-time with a slightly curved region of m4. a further simplification comes from preferred extremal property [33, 35, 36]. 2. at the level of space-time topology the situation becomes however extremely complex. gauge fields created by the system are replaced with field body consisting of topological field quanta (spacetime sheets) so that one can assign to a system well-defined field identity field body. one has a fractal hierarchy of field bodies within field bodies. magnetic flux quanta represent one example of topological field quantization. system has therefore besides its biological body (bb) also mb (mb) carrying dark matter particles identified ordinary particles with scaled up planck constant heff/h = n implying scaling up of various quantum length and time scales (by factor n in the simplest situation). mb has a hierarchical onion-like structure corresponding to various p-adic length scales and various values of heff . issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2017 | volume 7 | issue 2 | pp. 98-128 103 pitkänen, m., life-like properties observed in a very simple system mb can control bb by ”motor actions” in which the length l and possibly also the area s of flux tubes change [27]. this affects string tension and amplitude of oscillations of systems connected by magnetic flux tubes so that motor action of bb is induced. the phase transition changing the field strength could be induced by a phase transition changing heff : if magnetic flux is monopole flux it is conserved. there are two options. 1. the scaling (s,l) → n× (s,l) leaves l/s invariant and scales down the magnetic field strength as b ∝ 1/s → b/n. magnetic energy and cyclotron energies are unaffected but cyclotron frequencies fc scale down as fc → fc/n. there is quantum criticality corresponding to flux tubes with same value of l/s in the sense that these systems have same energies. this kind of quantum criticality could occur at critical values of relevant parameters. quantum criticality makes it possible for mb to tune its cyclotron frequency spectrum so that it corresponds to a given set of frequencies associated with bb. mb can control the corresponding oscillatory processes at bb by using dark cyclotron radiation transformed to bio-photons as a resonant driving force. dark cyclotron radiation would result from the decay of dark cyclotron be condensates. mb would thus adapt to the properties of bb. the larger the maximal value of n, the wider the variety of different adaptations, the higher the ability of the system to survive, and the higher the evolutionary level of the system. the cyclotron energy spectrum associated with eeg could also entrain to various frequencies assignable to the neural circuits and in this manner mb would gain a control over them. entrainment occurring at the level of brain would be second example of this process. mb learns to mimic the processes occurring at the level of bb and in this manner gains control over them. mb also learns how to get information about them. the motor actions of mb allowing to change the thickness and length of the flux tubes would be essential for achieving this. remark: in the case studied the frequencies fv and fh assignable to the oscillations of plastic balls would correspond to frequencies at level of bb to which mb tunes by a suitable choice of heff . 2. for (s,l) → (s, n × l), magnetic field remains invariant so that cyclotron frequencies are unaffected. magnetic energies and cyclotron energies are scaled up by n: one might say that one has criticality in classical sense. this kind of transitions require energy and are analogous to first order thermodynamical phase phase transitions. remark: in the case studied the phase transition from gas to crystal-like phase of plastic balls would correspond to the increase of heff leaving the frequencies invariant and would thus require energy in contrast to the usual view that energy is liberated in freezing (helium superfluids are the only exception to the rule, and are macroscopically quantum coherent systems). 3. the decay of cyclotron be condensates at mb generates dark cyclotron radiation, which can transform to ordinary radiation and drive oscillatory processes at bb [28, 29]. this provides an additional control mechanism. dark photons can transform to ordinary ones in several manners. the following special cases are diametric opposites of each other and correspond to n ↔ 1 transitions. more general transitions are of type m ↔ n. (a) dark photon with energy e = heff × f can transform to ordinary photon with same energy and frequency n × f . bio-photons would result from low frequency dark photons even dark eeg photons in this manner. bio-photons are in visible and uv range and biomolecules have excitation energies in this range so that mb could control bio-chemistry in this manner. (b) dark photons with energy e = heff × f can decay to a bunch of n ordinary photons with the same frequency f but energy e/n. this could allow mb to control electromagnetic and mechanical oscillations taking place at low frequencies. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2017 | volume 7 | issue 2 | pp. 98-128 104 pitkänen, m., life-like properties observed in a very simple system also transformation which reduce planck constant but do not lead to n = 1 state are possible. remark: in the case studied the decay of be condensates to ordinary elf photons could allow the control of the oscillations of plastic balls. 4. alfwen waves (see http://tinyurl.com/7ekxqt2) are part of the dynamics of ordinary maxwellian magnetic field often described phenomenologically as oscillations of magnetic flux tubes. the phase velocity v = c/ √ ǫ is light velocity in vacuum modified by the dielectric constant ǫ = 1+ ρ/b2 (one has c = 1, ǫ0 = 1,and µ0 = 1 in the units used) caused by the total mass density of charged matter and energy density magnetic field. alfwen waves generalize in tgd framework to oscillatory perturbations of the magnetic flux tubes, which in 1-d approximation for flux tubes can be modelled by transversal vibrations of string characterized by string tension proportional to l/s. in longitudinal directions the vibrations are in the interior of string trivial but induce oscillations of the distance between the ends of the string and are thus visible in the dynamics of bb. remark: in the recent situation alfwen waves would naturally affect the dynamics of plastic balls in the crystal-like phase if flux tubes connecting the plasma balls are present. 5. the motor actions of mb can also change the topology of mb. bb is assumed to posses closed ushaped flux tubes acting as kind of tentacles scanning the environment and re-connecting with the u-shape flux tubes associated with other systems to form pairs of flux tubes connecting two systems [20, 21, 22]. these reconnections would serve as a topological correlate for a directed attention and for entanglement between the systems at the ends of the flux tubes. for instance, immune system would have developed from this kind of scanning of the environment. one can imagine even more radical magnetic ”motor actions”. at given level of hierarchy of spacetime sheets space-time sheets of sub-systems can be connected by a network of magnetic flux tubes [40]. the connectedness of the flux tube network can change by the re-connection process and its reversal. the increase of heff affects the size of the closed loops and can induce their reconnections to flux tube pairs connecting the systems at its ends. the reduction heff can induce the reversal of reconnection and split the flux tube pair to two flux loops. this gives rise to quantum analogs of phase transitions between crystal-like and fluid-like phases. remark: in the case studied the formation of crystal phase from plastic balls could correspond to the re-connection of flux loops assignable to plastic balls to form kind of tensor network correlating the dynamics of plastic balls. its reversal would lead to gas phase. 3.4 dark nucleosynthesis (dns) as a source of metabolic energy in prebiotic systems? one of the key challenges is to identify the prebiotic source of the metabolic energy. the sequences of dark protons identifiable as dark nuclei give in tgd framework rise to analogs of dna, rna, trna, and amino-acids. in tgd based model for ”cold fusion” as dark nucleosynthesis (dns) proposed to serve as the predecessor of ordinary nucleosynthesis these dark nuclei transform to ordinary nuclei liberating almost all nuclear binding energy [30, 41]. dns could provide the sought for prebiotic source of metabolic energy and also a source of metabolic energy in the system studied. 1. there is a considerable evidence for the production of energy in what is known as ”cold fusion” not allowed by the standard nuclear physics [38, 41]. as a matter of fact, cold fusion is definitely not in question, which has motivated the introduction of the term low energy nuclear reactions (lenr). what definitely occurs are nuclear transmutations, that is formation of nuclear isotopes not present in the original system. also energy is produced [4, 3]. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2017 | volume 7 | issue 2 | pp. 98-128 105 pitkänen, m., life-like properties observed in a very simple system the typical experimental arrangement involves electrolysis in which one has a voltage between electrodes inducing the ionization of hydrogen or deuterium. the positive ions flow towards the negatively charged cathode and the transmuted elements appear at the cathode and also heat is produced. now one has negatively charged electrode and also plastic balls are negatively charged being thus analogous to cathode with a negative surface charge. ar+ ions could take the role of protons or deuterium ions. also protons could be present. 2. i have been recently working with a detailed model for ”cold fusion” [38, 41, 30]. in widom-larsen model (wl) [1, 6] to lenr only standard model of nuclear interactions is used but some unrealistic looking assumptions must be made. remarkably, there is also evidence that the transmutations take place also in living matter [2, 5] and the question is whether nuclear transmutations could provide a new source of metabolic energy. tgd based model involves new physics and relies on dns involving the formation of dark proton sequences at magnetic flux tubes of mb of the system [38]. dark proton sequences would be dark nuclei and would suffer rapidly occurring dark beta decays replacing some dark protons with dark neutrons. dark nuclei would transform to ordinary nuclei and liberate almost all of ordinary nuclear binding energy in the process. most of the energy could go to the magnetic flux tubes possibly leading out of the system and would be lost. the flux tubes entering to the negatively charged surfaces such as some regions of cathode would be an exception. could stable light nuclei fuse to heavier ones by forming dark nuclei consisting of weakly bound ordinary nuclei transforming to ordinary nuclei also in living matter? if dark weak decays are not involved, both (a,z) are additive in the process. if dark weak decays are allowed, only a is additive. if these fusion reactions produce the biologically important ions, a and possibly also z for the nuclei of biological ions would form an additive group with some basic nuclei serving as generators. 1. if proton is taken as an additive generator, the situation is trivialized. on the other hand proton, is not a genuine nucleus, and ordinary nuclei of form a = z are also unstable. it is however to add dark protons to an ordinary nucleus at magnetic flux tubes to get (z,a) → (z + 1, a + 1) suggested by widom and larsen to be a basic process. dark proton could suffer dark weak decay with a scaled up rate since dark weak bosons are effectively massless below the size scale defined by their scaled up compton length. this mechanism is central in both wl model of lenr and in tgd based model of dns [41]. 2. he(2, 4) is the basic product in dns and because its large binding energy would be a natural generating nucleus. the resulting nuclei would have (z,a) = n × (2, 4). a is always even for these nuclei. the nuclei c,o,ne,mg, s,ar, ca are all stable and correspond to n = 3, 4, ..., 10. c,o,mg, s,ca are of central importance in living matter. be(4, 8) with n = 2 is missing from the list. the reason is that it has very short life-time against alpha decay whereas energy conservation prevents alpha decays of the heavier nuclei in sequence. 3. d(1, 2) is the lightest non-trivial candidate and would give nuclei of form (z,a) = n × (1, 2). the binding energy of d is however rather small. the nuclei formed as multiples of he(2, 4) can be formally regarded as even multiples of d(1, 2) (only formally, because the binding energy per nucleon for he(2, 4) is considerably larger than for d(1, 2)). the odd multiples correspond to stable isotopes li(3, 6), b(5, 10), n(7, 14) corresponding to n = 3, 5, 7. f (9, 18) decays to stable o(8, 18), na(11, 20) decays to stable ne(10, 20), and al(13, 26) to stable mg(12, 36). this reflects the fact that for stable heavier isotopes the number of neutrons is larger than number of protons. 4. li(3, 6) is stable albeit not the most abundant isotope of lithium. c,f,mg, p,ar have isotope of form n × (3, 6) with n = 2, 3, .., 6. most of these nuclei are obtained from he(2, 4). the isotopes f (9, 18) and p (15, 30) are unstable and decay by beta decay to to stable o(8, 18) and si(14, 30) respectively. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2017 | volume 7 | issue 2 | pp. 98-128 106 pitkänen, m., life-like properties observed in a very simple system 5. one can also form sums of different nuclei: (z,a) = (z1, a1) + (z2, a2). (a) the simplest sum corresponds to (z2, a2) = (1, 2) = d. this addition is especially natural for nuclei which are multiples of he(2, 4). this allows to transform isotopes h(2, a) to li(3, a+2) and li(3, a) to be(4, a + 2), be(4, a) to b(5, a + 2), b(5, a) to c(6, a + 2), c(6, a) to n(7, a + 2), and n(7, a) to o(8, a + 2). o(8, a) cannot be transformed to a stable isotope f (9, a+ 2). (b) the addition of dark proton to a stable nucleus ((z+1, a+1) = (z,a)+p is the key mechanism of wl model and conforms with the basic vision about the dns as formation of dark proton sequences and addition of dark protons to an ordinary nucleus at the flux tube. for instance, one has na(11, 23) = ne(10, 22) + p, p (15, 31) = si(14, 30) + p, s(16, 31) = p (15, 30) + p, cl(17, 35) = s(16, 36) + p, k(19, 39) = ar(18, 38) + p, and mn(25, 44) = cr(24, 54)+ p ). all nuclei except p (15, 30) appearing in the initial state are stable. p (15, 20) suffers (perhaps dark) beta decay to si(14,30), which is stable. this however does not prefent the addition of proton to take place. fe(26, 56) is an important biological ion and could be obtained from fe(26, 52) by an addition of four dark protons with subsequent dark weak decays of proton to neutron. fe(26, 52) is unstable against beta decay to mn(25, 52) in turn unstable about beta decay to cr(24, 52), which is stable. (c) one can consider also sums of heavier isotopes. for instance, the sums k(19, 39) = o(8, 16)+ na(11, 23) and ca(20, 40) = o(8, 16)+mg(12, 24) are stable biologically important nuclei obtained as sums of stable biologically important nuclei. biologically important nucleina(11, 23), p (15, 31), s(16, 31), cl(17, 35), k(19, 39), mn(25, 55) have odd value of a so that they are not obtained as sums of the nuclei constructed using the rules discussed above. to sum up, that the nuclei obtained as multiples of he(2, 4) correspond to several biologically important nuclei can be seen as an indication that dark fusion of at least he(2, 4) nuclei takes place in living matter. 4 tgd based explanation for the life-like aspects of the system the system under study [12] indeed has several features bringing in mind living cell as it is understood in tgd. 1. the situation is in some aspects analogous to that prevailing over the cell membrane. cell membrane is analogous to a battery providing metabolic energy for the system via atp-adp process. could the voltage between electrodes creating ar+ plasma have analogous function? it seems however that dns is the what provides the metabolic energy. ar+ could be analogous to biological ions such as k+. the negative charges from ar atoms are received by plastic balls or even the space-time sheet containing them. 2. charged plastic balls consisting of melamine formaldehyde (mf) polymers are somewhat analogous to biomolecules such as dna sequences, which also carry negative charge. the charged plastic balls consisting of mf (see http://tinyurl.com/z532ryv) are organic matter. mf contains aromatic 6-cycle appearing also in important biopolymers such as rna and dna. perhaps the plastic balls are not so simple systems as the non-equilibrium thermodynamics based model of experimenters assumes. could their molecular structure have something to do with the observed life-like aspects of the system? in particular, could the molecular structure make possible the generation of dark proton sequences at flux tubes? issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2017 | volume 7 | issue 2 | pp. 98-128 107 pitkänen, m., life-like properties observed in a very simple system 3. the system dissipates and must receive metabolic energy from some source. the metabolic energy feed seems to take place with average period τ of about 100 s. stochastic resonance requiring periodic oscillation amplified by the stochastic signal is not the only possible explanation. in tgd inspired quantum biology metabolic energy feed induces increase of heff . the increase of heff would increase the scale of quantum coherence and make the system crystal-like so that the plastic balls oscillate in synchrony. dns provide an obvious candidate for the origin of the metabolic energy. these observations motivate a quantum approach different from the approach based on non-equilibrium thermodynamics and stochastic resonance. 4.1 self-organized bi-stability or oscillations driven by cyclotron radiation and energized by dns? the theoretical approach of the experimenters relies on the notions used to describe far-from-equilibrium systems using generalization of thermodynamics. the vision is that the dynamics of complex systems has universal features. conservative force (gravitational force and electric forces between plastic balls and electrodes and plastic balls), dissipation and stochastic force would be present. remark: no driving force is assumed: this would describe the damped oscillations but cannot explain the repetition of the phase transitions. stochastic resonance would feed metabolic energy to the system inducing the jumps over potential wall making possible the transitions between the two phases, amplify the vertical and horizontal oscillations, and also give kinetic energy for the plastic balls in gas-like phase. the summary of the article gives a technical description of the discovery. the experiments and simulations presented here display a broad class of non-equilibrium phenomena in a single system with minimal ingredients and rich dynamics. we have experimentally demonstrated global bi-stability in a spatially-extended system composed of non-bi-stable elements. given the underlying first-order phase transition between the condensed and gas-like phases, our experiment may be a realization of self-organized bi-stability. the inter-state switching is facilitated by both quenched disorder and dynamical noise. the time scales of individual stable and un-stable periods are not symmetric. durations of instability are mostly determined by the damping time, whereas the stability durations can be much longer and depend on the nucleation of an energy-redistribution event. this is a common property in many excitable systems, where the relaxation path is more deterministic than the excitation path. however, the distribution of switching timescales in the experiment is narrower than in the simulation. this may be due to a weak periodic signal in the experiment which couples with the noise to induce switching. the source of the periodicity, in addition to controlling the vertical oscillations through modulating the electrode voltage, are subjects of current investigation in our lab. in the sequel the model is analyzed to identify its possible weaknesses in order to see how tgd inspired quantum approach could allow to circumvent them. 4.1.1 thermodynamical aspects the authors assume that the transitions involved are analogous to first-order phase transitions (heat is absorbed or liberated and the transition occurs at constant temperature and regions of both phases are present) between condensed and gas-like phases. could simple thermodynamical analogies for the transitions between condensed and gas-like phases help to understand the situation? 1. melting and evaporation require usually heating. enthalpy of fusion is the quantity describing the energy needed by the heating. it is usually positive (in liquid and gas phases molecules have larger thermal energy than in solid phase). only for 3he and 4he super-fluids at sufficiently low temperatures the enthalpy of fusion for melting is negative (see http://tinyurl.com/pfr84c3). issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2017 | volume 7 | issue 2 | pp. 98-128 108 pitkänen, m., life-like properties observed in a very simple system also in the recent situation the generation of the damped oscillations would suggest that the enthalpy of fusion is negative. positive enthalpy of fusion for melting requires that energy is fed into the system. it however seems that nucleation centres are generated by the variation of oscillation frequency and that the process occurs spontaneously and transfers energy from the degrees of freedom responsible for the bonding of balls to crystal-like phase to the kinetic energy of balls. therefore the situation resembles that for helium superfluid at low temperatures also in this respect. some additional degrees should be present. 2. could thermodynamical analogy help to understand what happens in the phase transition between gas-like and crystal-like phases. freezing usually liberates heat but since heat correspond to completely disordered motion it seems highly implausible that this heat would go to the ordered collective motion of the crystal-like phase. in heat engines the amount of heat transformable to work is by second law of thermodynamics below γ = ∆t/th, where ∆t is temperature difference and th the higher temperature. to have synchronous oscillations due the liberated heat, looks highly implausible. if work is done, it must be done by additional degrees of freedom receiving energy and providing it as energy required by the excitation of damped oscillations of crystal-like phase. this option seems plausible. if one wants to use thermodynamical analogies, it seems that one must assume that there are additional yet un-identified degrees of freedom and a yet un-identified source of energy pumping energy to these degrees of freedom. 4.1.2 the analogy with helium supra phases consider now the analogy with helium supra phases (see http://tinyurl.com/zs8rpjm and http: //tinyurl.com/pfr84c3). 1. in tgd framework the obvious identification of the additional degrees of freedom is as those associated with magnetic flux tubes of mb forming a network in crystal-like phase. the flux tubes and the cyclotron be condensates of ions at them would carry energy. 2. the generation of crystal-like phase would require energy. as noticed, this implies resemblance with he3, in which cooper pairs give rise to a superfluidity suggesting that the system behaves as a macroscopic quantum system. cooper pairs of ar+ ions could form an analog of super-fluid or super-conductor. also cooper pairs of electrons and protons coming from plastic balls could form super-conductors. in tgd framework the members of cooper pairs would be located at parallel magnetic flux tubes connecting plastic balls [16, 17, 23, 24]. 3. in the transition to gas phase this network would be destroyed as the reconnections between mbs of plastic balls are split and give rise to nucleation regions for gas phase. the splitting would liberate magnetic energy and also energy of cyclotron be condensates if the value of heff is reduced. this energy would transform to the kinetic energy of the plastic balls. therefore the phase transition would liberate energy and would be analogous to the corresponding transition for 3he. note that also the tgd based model for supra phases of helium involves magnetic flux tube network [31]. 4. the phase transition should change the values of heff/h = n but leave cyclotron frequencies unaffected and thus involve energy feed so that first order phase transition would be in question. 4.1.3 the mechanism inducing vertical and horizontal oscillations of plastic balls one should identify the mechanism giving rise to the vertical and horizontal oscillations of plastic balls. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2017 | volume 7 | issue 2 | pp. 98-128 109 pitkänen, m., life-like properties observed in a very simple system 1. the authors of the article [12] propose an identification for the interactions involved. tgd approach suggests additional interaction due to the string tension of the flux tubes giving rise to elastic force and additional interaction energy. as already noticed, the model of authors does not assume resonant driving force although they mention of having tried it. the probable reason for giving up this option is that it allows only the decay of crystal-like phase to gas-like phase but not a repetitive cycle. 2. the ratio fv /fh ≃ 40 for typical vertical and transversal oscillation frequencies equals to the ratio m(ar+)/m(p) ≃ 40, which suggests that be condensates of cooper pairs of both ar+ and protons are indeed present at flux tubes. the condition that cyclotron frequencies are in question, fixes the value of magnetic field strength to b = bend/15, where bend = 2be/5 = .2 gauss is an endogenous magnetic field assumed be important value of magnetic field in tgd inspired quantum biology and inspired by findings of blackman and others [13, 14]. be = .5 gauss is the nominal value of the earth’s magnetic field. p-adic length sale hypothesis slightly favors the value b = bend/16, which corresponds to the magnetic length lb = √ ~eff/eb = 4lbend = 22.8 µm (from lbend = 5.7 µm) to be compared with the size d ≃ 10 µm of the plastic balls. one can estimate also the classical cyclotron radii from the formula rc = mv/eb = p/qb, where v is the velocity of the charged particle. for cyclotron orbits with principal quantum number n bohr quantization gives rc = √ nlb , where lb = √ ~/qb, is magnetic length. note that orbits with same radius are possible for heff/h = ni. i = 1, 2 if one has n1 = nn2 or vice versa. 3. this suggests a mechanism generating vertical and transversal and horizontal oscillations of the plastic balls. the cyclotron radiation resulting in the decay of the be condensates drives the oscillations resonantly by oscillatory force f = f0×exp(iωt) so that one obtains the oscillation amplitude as a sum of damped oscillation amplitude exp(−γt)exp(iωt) and resonance term proportional to exp(−γt)exp(iωt)t increasing in oscillatory manner up to time value t ∼ 1/γ and decreasing after that exponentially. the parameters fv and fh would be additional parameters in tgd based model. remark: this mechanism could be quite general mechanism of quantum biology. 4. the variation of the plastic ball radius induces a variation of mass and charge of the ball and therefore also a variation of the oscillation frequencies fh and fv , which can be however compensated by the variation of the magnetic field strength b at flux tubes inducing variation of string tension and elastic constant so that synchronous oscillations are possible. this is possible only for cv below some critical value. for larger values the compensation is not possible, and the oscillations lead to gas phase. for smaller values the solid phase is stable. at (quantum) criticality the metabolic cycle becomes possible. 5. the oscillations of plastic balls could be induced by the analogs of alfwen waves for the magnetic flux tubes which in 1-d approximation for flux tubes would be essentially vibrations of string characterized by string tension proportional to l/s. the energetics of the system would be invariant under changes of heff/h = n if l and s scale like n, and one would have quantum criticality allowing mb to adapt to the properties of the plastic ball system. a network consisting of springs would provide an analog system. the decay of cyclotron be condensates would feed energy to the vibrations of string in turn feeding energy to the oscillations of plastic balls. both energy feeds could be modelled in terms of forced oscillations. quantum criticality would make possible for mb to adapt to the properties of the part of the system consisting of ordinary matter by a proper selection of n since one has fc ∝ n for the same energetics. for given value of b different charged dark particles have different cyclotron frequencies but same issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2017 | volume 7 | issue 2 | pp. 98-128 110 pitkänen, m., life-like properties observed in a very simple system energies at quantum criticality. also the hgr = heff condition implies that the cyclotron energies do not depend on particle mass and therefore implies quantum criticality. 4.1.4 the energetics of the system the energetics of the system demands an analog of metabolic energy feed. 1. authors assume that stochastic resonance provides the needed energy feed but its origin remains open. stochastic resonance requires an additional oscillator with period about τ = 100 s. according to the authors, the problems of their model are that the transition periods seem to be too short and also the times spent in stable and transition states are not symmetric as they should be in bi-stable system. also the prediction for the frequency f = 1/τ tends to be too short. 2. to get the metabolic cycle with forced oscillations without stochastic resonance, one needs a kick providing the energy inducing a phase transition to the crystal-like phase, which also oscillates as a whole thanks to this energy feed. in tgd framework the needed energy dose could be provided by dark nucleosynthesis (dns) involving formation of dark proton sequences containing perhaps also ar+ ions and transforming to ordinary nuclei. the transition could be rather fast and occur in the minimal case only once during the single metabolic cycle of about τ = 100 s so that one would have τ ∼ 1/γ, where γ is the average rate for dns. also the phase transition splitting the flux tube pairs by de-reconnection could be rather fast as compared to τ . remark: the periodic signal with frequency f = 1/100 hz is not necessary. 3. dark cyclotron radiation with heff/h = n could transform to ordinary photons with energy, which is n-multiple of ordinary cyclotron energy. if n is large enough the photons have energies above thermal energy. in living matter the values of n are in the range 1012 − 1014 so that the cyclotron energies correspond to bio-photon energies in visible and uv range characterizing the transition energies of bio-molecules. if hgr = heff hypothesis holds true the cyclotron energies do not depend on mass of the charged particle. also a decay to bunches of n of photons with ordinary energy is possible. both mechanisms could be involved. the bunches of n ordinary quanta could drive electromagnetic oscillations and mechanical (acoustic) oscillations. in piezo-electrets populating living matter the transformation of electromagnetic and acoustic oscillations to each other is possible. 4. the rate γ of dns events is in the first approximation proportional to the number of plasma balls events if the dns even for single ball feeds energy for the entire system. γ cannot be much lower than fc(ar +) = .5 hz since the system would remain to crystal-like phase. it γ is too high, the transition to gas phase becomes impossible. 4.1.5 is the frequency f ∼ .01 hz needed in tgd based model? it is not at all clear whether frequency f ∼ .01 hz required by the stochastic resonance model is needed nor even possible as a cyclotron frequency in tgd inspired model. 1. if f is present, one can wonder whether it could be associated with the cyclotron be condensate at the magnetic bodies of plastic balls. could the plastic balls at some level in the hierarchy of spacetime sheets behave like particles in quantum sense (the space-time sheet assignable to the plastic ball)? does it make sense to talk about crystal-like phase as a kind of cyclotron be condensate of charged plastic balls? or is there energy feed from quantal cyclotron degrees of freedom assignable to the magnetic flux tubes to classical degrees of freedom of plastic balls? 2. the simplest working hypothesis to be killed is that both plastic balls, protons, and ar+ ions are at the same flux tubes of mb so that the value of magnetic field is fixed to about bend/15, bend = .2 gauss. the order of magnitude for the cyclotron frequency turns out to be several orders issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2017 | volume 7 | issue 2 | pp. 98-128 111 pitkänen, m., life-like properties observed in a very simple system of magnitude lower than f = .01 s. hence it seem that there is no obvious manner to introduce f ∼ .01 hz in the model. the following little calculation gives the estimate. 1. one has fc = qb/2πm , where q = cv and c is the capacitance of the plastic ball. c is purely geometric parameter and for single ball with radius d embedded in dielectric with relative permittivity ǫr it is determined by the value of coulomb potential vc = q/4πǫ at the surface of the ball. this gives c/farad = 4πǫd = ǫr × (d/meter)× 5.224× 10−12 . 2. the mass of the ball is given by (4π/3)ρd3, where ρ is the density of the ball which in an approximation needed for order of magnitude estimates given by ρ = mp a3 , a angstrom = 1 3. from this one obtains for the cyclotron frequency the expression fc(ball) = 3× ǫr d meter × (a d )3 × v v olt × b bend × 3.3× 107 × fc(p,bend) , fc(p,bend) = ebend mp = 300 hz . using the values v v olt = 6 , d meter = 10−5 , ρ = mp a3 , b = bend 15 this gives the estimate fc(ball) ≃ ǫr × 5.8 days . for vacuum with ǫr = 1 the frequency is smallest possible. it is not possible to obtain fc ∼ .01 hz for reasonable strength of b. what about cyclotron frequencies of cells and cell membranes assuming b = bend? 1. cells are also negatively charged but the charge of the cell is rather small (see http://tinyurl. com/yb9w6nqs)about 103 e for yeast cell so that q/m ratio is very small. 2. what about cell membrane treated as single unit? the capacitance per unit area does not depend much on cell (see http://tinyurl.com/chylvs9) being given in good approximation by c = dc ds cm2 farad = 2× 10−6 . the capacitance is from this given by c = c × s. assuming spherical symmetry, the estimate for the cyclotron frequency fc(membrane) is fc(membrane) = 3c×a2×a d ×fc(proton,bend)× coulomb e × v v olt = 1.5×10−7×10µm d × b bend × v .05 v olt hz . for d = 10 µm and b = bend and v = .05 volt the cyclotron time is 77.2 days. for dna sequences the cyclotron frequencies are around 1 hz irrespective of their length. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2017 | volume 7 | issue 2 | pp. 98-128 112 pitkänen, m., life-like properties observed in a very simple system 4.1.6 some observations about argon ions a couple of comments about the possible role of argon are in order. 1. i ended up with the recent vision about living matter on basis of observations that the radiation at cyclotron frequencies of ca++ ions and also other biologically important ions have effects on physiology and behavior of vertebrates [27, 26]. the magnetic field involved was bend = 2be/5, where be = .5 gauss is the nominal value for the magnetic field of earth. the cyclotron frequencies of ca++ in bend are multiples of fc(ca++) = 15 hz. ca has (20, 40) whereas ar+ has (a,z) = (40, 18). therefore the cyclotron frequency of ar+ (which is fermion) is in good approximation one half of that for ca++: f(ar+, bend) = fc(ca++)/2 = 7.5 hz. tgd based model for high tc and bio-superconductivities suggests that ar+ ions could form cooper pairs with members at flux tubes with opposite directions of magnetic field. what puts the bells ringing is that f(ar+, bend) is quite near to the lowest schumann frequency assignable to the oscillations of be serving as a candidate for a correlate for collective levels of consciousness? could the collective effects be partially due to bend? the problem is however that cyclotron period of ar+ is considerably shorter than the periods τv and τh associated with the oscillations of plasma balls and with the metabolic cycle. 2. what does one mean when one says that ar+ ions are dark? could ar+ ions be dark atoms in the sense that the electron is not lost but is transformed to a dark valence electron with scaled up size of orbital proportional to n2 [43]. ar+ ion would be analogous to rydberg atom [34]. dark electrons could form dark super-conductor coupling with its total charge to the electric field of the negatively charged electrode. the members of cooper pairs could reside at parallel flux tubes connecting plastic balls with parallel or antiparallel magnetic fluxes. this could explain the synchronous oscillation of the plastic balls and also the formation of crystal-like phase. 4.1.7 could dns serve as the source of metabolic energy in the system studied? the system considered requires metabolic energy. the metabolic energy would be fed to the system as it transforms to crystal-like phase and is dissipated via vertical oscillations in the force field defined by gravitational and electric fields. unless the experimental arrangement involves a hidden energy feed, there must be present some unidentified source of metabolic energy in the system itself, that is plastic balls plus ar+ ion plasma. tgd inspires the proposal that dns generates the metabolic in pre-biotic systems, where photosynthesis need not be present yet and there is no storage of metabolic energy to biomolecules. could something analogous to dns take place also now? 1. if one wants to identify both fv and fh as cyclotron frequencies for the same value of magnetic field, one must assume that both ar+ and h+ ions are present. therefore the formation of dark proton sequences suffering dark weak decays to dark nuclei containing neutrons becomes possible. the tgd based model [30, 38, 41] predicts is that the spectroscopy of dark nuclei is the same as those of ordinary ones if dark nuclear binding energy scale and neutron proton mass difference are both scaled down like 1/heff . the occurrence of nuclear transmutations caused by dark nucleosynthesis is the basic prediction. 2. also the fusion of ar+ nuclei and dark nucleon sequences is possible. the dark fusion of two ar+ nuclei with (z,a) = (18, 40) proceeding via formation of dark kr nucleus consisting of two ar+ nuclei and transformation to ordinary kr would produce stable krypton isotope with (z,a) = (36, 80) liberating nuclear binding energy ∼ 7.6 mev assuming that the dark nuclear binding energy is negligible (the model predicts it to be of order of few kev). sn isotope with (a,z) = (120, 50) is the lightest isotope with mass number 3 × 40 = 120 of 3 argon nuclei. this would require the issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2017 | volume 7 | issue 2 | pp. 98-128 113 pitkänen, m., life-like properties observed in a very simple system transformation of 4 protons to neutrons by dark beta decay to reduce total charge 54 to 50. this process would however requires energy of 21 mev and would therefore not occur spontaneously. kr production would be a testable signature of this mechanism. kr could end up to the negatively charged plastic ball or negative electrode. this would induce a loss of argon from the system. could the loss of ar+ and production of kr ions be detectable? dns or at least the transformation of dark nuclei to ordinary ones could be a stochastic process. if this mechanism provides metabolic energy for prebiotic lifeforms, it should be able to sustain itself. there should be some signal making possible charge separation leading to the generation of dark proton sequences at flux tubes in turn leading to dns and the generation of crystal-like phase in turn generating the cyclotron radiation. 1. a possible mechanism is suggested by pollack effect [10, 37] occurring in water environment bounded by gel in the presence of suitable signal providing energy. there are several kinds of signals providing energy such as light at visible or ir frequencies or even a mechanical perturbation. what happens that water molecules, which are already in excited state near the splitting of hydrogen bond lose one proton as they absorb photon and proton becomes dark and goes to magnetic flux tube. the generation of the excited state requires uv energy of order 5 ev. solar radiation or possibly occurring dns events could provide the uv light. in the recent case water and gel phase are missing. one might however hope that the dark photons say those with uv energies transforming to ordinary photons could induce charge separation in bf balls or at their surface layers and transform protons to dark protons at flux tubes. if the cyclotron radiation from decaying cyclotron be condensates corresponds to a value of planck constants for which dark photons transform to bio-photons, this condition is satisfied. this is implied by hgr = heff hypothesis. if this takes place the total negative charge of plasma balls should be larger than the total charge of ar+ ions. 2. could the charge separation zg the surface of plasma balls give rise to an analog of cell membrane like structure giving rise to (generalized) josephson junctions? if so, the analogy with living cell would become even deeper. also the flux tubes between plasma balls act as josephson junctions making possible oscillating non-dissipating currents generating dark josephson photons with energy e = ev and frequency fj = ev/heff . 4.2 speculative connections with tgd inspired views about quantum biology and consciousness the model for the findings has allowed to develop in more detail the basic ideas of tgd inspired quantum biology. 1. the model has led to a concrete proposal for how the mb controls bb using forced electromagnetic and mechanical oscillations at low frequencies by using the transformation of dark photons to bunches of low energy photons. also the analogs of alfwen waves suggest themselves as a control mechanism. 2. dns could provide a universal pre-biotic mechanism for producing metabolic energy and the needed elements. this mechanism might be active even in the recent biology in some exceptional situations [11]. dns is also predicted to precede ordinary nucleosynthesis in pre-stellar evolution so that primordial metabolism would not depend on chemistry and pre-biotic and pre-stellar evolution could proceed hand-in-hand and dns would produce heavier elements also outside the stars [41]. even more, tgd based model for dark dna identifies sequences of dark protons as analogs of dna with sequence of 3 protons serving as analog of dna codon. also the dark analogs of rna,trna, issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2017 | volume 7 | issue 2 | pp. 98-128 114 pitkänen, m., life-like properties observed in a very simple system and amino-acids are predicted. dark dna sequences are dark nuclei so that the emergence of dark dna would mean also the emergence of dns as a basic metabolic mechanism. this would resolve the egg-or-hen problem about whether genes or metabolism came first. 3. the chemical structure of plastic balls involves aromatic 6-cycles associated also with dna nucleotides. both dna and cell are negatively charged and thus analogous to the negatively charged plastic balls. could negatively charged regions, about which the exclusion zones (ezs) of pollack formed to water in presence of say visible light have served predecessors of cells? 4. gel-sol transition and protein folding and unfolding are basic processes of cell biology. could the proposed basic control mechanisms control also these processes. could gel-sol transition and protein unfolding correspond to a melting of crystal-like structure and splitting of flux tube pairs to u-shaped flux loops or vice versa induced by a change of heff? 5. could quantum criticality realized as a family of flux tubes with fixe l/s ratio and same energetics but with varying value of heff/h = n make possible the adaptation of the dynamics of mb to the dynamics of various oscillations of bb? this would be essentially entrainment making possible both sensory perception and motor actions. control of mechanical processes at the level of ordinary matter would involve the decay of dark low frequency photons to n ordinary photons. chemical control would involve transition to single ordinary photon with n-fold frequency. this view is also supported by the realization that brain consciousness is not a continuous stream but more like a sequence of flashes (see http://tinyurl.com/y84az3bh). this is one of the basic predictions of tgd inspired theory of consciousness based on what i call zero energy ontology (zeo). one can say that the sub-self (mental image) is a life-cycle of a conscious entity and that one has sequences of this kind of periods with opposite arrows of time: self dies and reincarnates with opposite arrow of time. consciousness would have sleep-awake cycles in all time scales. this would give rise to various biorhythms. in eeg this would show itself as a decomposition to portions of duration of order .3 seconds. in zeo this could be interpreted in terms of a sequence of life cycles in which time increases in opposite directions: first at (call it) ”upper” boundary of causal diamond (cd), which shifts towards geometric future, then at ”lower” boundary, which shifts to geometric past, and so on... . note that the birth at given boundary is only slightly later than the latest death at it so that also our wake-up period at level to which eeg is associated could be repeated births and reincarnations forming an approximate continuum at given boundary of cd. also wake-up-sleep cycle could be like this. strobing character is predicted to be a universal feature of consciousness. in tgd inspired quantum biology the strobing character of consciousness can be related to the nature of metabolism, which does not take place as continuous feed of energy but as doses with some average rate. to sum up, the cautious non-orthodox proposal is that the description of the finding in terms of the notions of non-equilibrium thermodynamics might not be enough. rather, a generalization of quantum theory introducing a hierarchy of planck constants explaining dark matter and providing a general tgd inspired model for living matter would be needed. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. microsoft word huwu1_v11n1 dna decipher journal | october 2021 | volume 11 | issue 1 | pp 104-106 hu, h. & wu, m., peter p. gariaev (1942 2020): discoverer of phantom dna effect & founder of “wave genetics” issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 104 in memoriam peter p. gariaev (1942 2020): discoverer of phantom dna effect & founder of “wave genetics” huping hu* & maoxin wu abstract peter p. gariaev (1942 2020) was the discoverer of phantom dna effect and founder of “wave genetics”. he was a member of dnadj advisory board and published visionary and groundbreaking scientific papers in this journal. he was nominated for nobel prize in medicine for 2021 according to his website and his legacy in science will live on. keywords: peter gariaev, phantom dna effect, wave genetics, scientist, visionary, legacy. we learned earlier this year about the passing of dr. peter p. gariaev in november, 2020 from the internet [1] and private communications as his passing was not announced on his website [2]. the fields of genetics and medicine have lost a pioneer and visionary and we have lost a dear colleauge and important contributor to this journal. peter p. gariaev (1942 2020) was the discoverer of phantom dna effect and founder of “wave genetics”. he was a member of dnadj advisory board and published visionary and groundbreaking scientific papers in this journal. he was nominated for nobel prize in medicine for 2021 according to his website [2]. his contributions to the advancement of science and technology with his colleagues and collaborators include the following [3]: 1984 1985 using correlation method of laser spectroscopy, he revealed the phenomenon of abnormally long damped oscillations dna gels with specific traits related phenomena return fermi-pasta-ulam (fpu). this can be interpreted as evidence of spontaneous soliton excitation of dna with the dna of the new memory elements ("return") type. at the same time by the same method, he discovered the effect of dna phantom memory that had not been previously well known. correspondence: huping hu, ph.d., j.d., quantumdream inc., p. o. box 267, stony brook,, ny 11790. e-mail: editor@dnadecipher.com dna decipher journal | october 2021 | volume 11 | issue 1 | pp 104-106 hu, h. & wu, m., peter p. gariaev (1942 2020): discoverer of phantom dna effect & founder of “wave genetics” issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 105 1992 using the method of laser spectroscopy correlation, he discovered the phenomenon of distant instrument of influence on the vibrational dynamics of gels of dna. 1996 in conjunction with a corporation, he and his colleagues created bio-radio-electronic and bio-optical systems that simulate some aspects of information-wave processes of the genetic apparatus. these systems combine functional nonliving (opto-electronics engineering) and live (live cells, tissues, organs, metabolic cell-free system), and preparative isolation and/or artificially synthesized genetic structures (chromosomes, dna, rna, proteins). biological substrates used, functionality combined with fiber-avionics are memory elements and the basis of the simplest biocomputer, which is able to control the wave through the defined areas of genetic and metabolic information of biological systems. 1996 together with lpi he and his colleagues used the two-photon excitation of an artificial laser-like radiation dna and chromosomes (superluminescence) as an analogue of the natural emission of photons genetic structures. 2000 – he laid the theoretical and experimental basis for a fundamentally new plrspectroscopy (polarization of laser-radio wave spectroscopy) with transition localized photons in radio-wave radiation of any object, including chromosomes, living cells, tissues, and metabolites. 1993, 2000, 2002 in exploratory experiments, radiation damaged chromosomes of wheat and barley, as well as some "lively" radiation-damaged seeds arabidopsis thaliana, collected in the chernobyl nuclear power plant in 1987, were restored. 1999, 2002 – he established a theoretical basis, and made a soft reversible wave introduction of genetic information from dna into the genome of the animal origin of potatoes and obtained in the 1st and the 2nd generation of a unique plant-animal "hybrid" with signs of unusual morphogenetic that have been lost (not inherited) in the 3rd generation. 2001 2002 – he transferred wave genetic information over a distance of about 5 km from the dna sample extracted from the plant arabidopsis thaliana line, the plant arabidopsis thaliana other nearby lines. 2002 he successfully transferred by a wave of genetic and metabolic information from the pancreas and spleen healthy newborn rats on adult rats suffering from artificially induced diabetes causing the symptoms of diabetes to disappear in a few days. in additions, many of his important and more recent research results were published in this journal [e.g., 4-6]. we have no doubt that he had made visionary and groundbreaking contributions to the advancement of science and technology. we at dnadj celebrate his life with our dear readers and thank him for his important contirubtions to this journal – may his legacy in science live on for a long time to come! dna decipher journal | october 2021 | volume 11 | issue 1 | pp 104-106 hu, h. & wu, m., peter p. gariaev (1942 2020): discoverer of phantom dna effect & founder of “wave genetics” issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 106 references 1. https://www.youtube.com/watch?v=4inp-cljvuo 2. https://wavegenetics.org/en/ 3. gariaev, p. p., & leonova, e. a. (2014), the strange world of wave genetics, dna decipher journal, 4(1): pp. 39-56. 4. gariaev, p. p., et. al. (2014), materialization of dna fragment in water through modulated electromagnetic irradiation, dna decipher journal, 4(1): pp. 01-02. 5. gariaev, p. p., vladychenskaya, i. p., & leonova, e. a. (2016), pcr amplification of phantom dna recorded as potential quantum equivalent of material dna, dna decipher journal, 6(1): pp. 01-11. 6. gariaev, p. p., vlasov, p. p., poltavtseva, r. a., voloshin, l. l., & leonova-gariaeva, e. a. (2018), a case report of tooth regeneration in dog through wave genetics, dna decipher journal, 8(3): pp. 162-165. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 1-4 1 pitkänen, m., introduction article introduction matti pitkänen 1 abstract this series of articles are devoted to tgd inspired ideas related to dna and genetic code. the first article is about many-sheeted dna and genetic code. in the first part of the article basic facts about genetics are summarized and the notion of many-sheeted dna is introduced. in the second part of the article a model of genetic program is considered, and some tgd inspired ideas about regulation of morphogenesis are discussed. second article represents two models for protein folding relying on the notion of magnetic body: both models represent limiting situations and a more realistic model could be a hybrid of them. the third article discusses some rather speculative physical realizations of the genetic code with chemical realization seen only one possible realization among many. most ideas are highly speculative and can be defended only by the fact that they follow rather naturally from the basic tgd. this series of articles are devoted to tgd inspired ideas related to dna and genetic code. tgd inspired vision about quantum biology and consciousness has evolved during last two decades, readers may benefit of having a brief summary about the process and its outcome in this introduction. 1. the original inspiration came from the notion of many-sheeted space-time and the failure of strict non-determinism for the basic variational principle dictating the dynamics of space-time-surfaces. the study of the preferred exremals of kähler action demonstrated that the notion of classical field differs from that of electrodynamics. topological field quantization meaning that field decomposes to magnetic flux quanta, electric flux quanta, and topological light rays analogous to laser beams takes place and means that space-time surface itself is quantized. this has profound implications: for instance topological light rays parallel to magnetic flux tubes make possible precisely target communications with maximal signal velocity and without dispersion. each physical system is accompanied by a field body and magnetic body becomes especially interesting in the case of living systems and allows to understand various strange findings about the effects of elf em fields on living matter one of the first biological applications that emerged already around 2000 in its preliminary form [8]. one of the first applications of the many-sheeted space-time was to the description of dna as many-sheeted structure [5]. the modular structure of genome could be understood if genes are accompanied by magnetic flux tubes carrying also helical electric fields and electronic supra currents: this implies a direct connection with the tgd based explanation of dc currents of becker [14]. 2. the conjecture that dark matter in tgd universe corresponds to a hierarchy of phases of ordinary matter characterized by an effective value of planck constant ~eff coming as an integer multiple of ordinary planck constant emerged around 2005. it inspired the vision that macroscopically quantum coherent dark matter in macroscopic quantum coherence with large planck constant can be seen as an intentional agent using biological body as a motor instrument and sensory receptor. this explains eeg and its various scaled up variants as communication and control tools of the system formed by magnetic body and biological body [2]. this conjecture is especially interesting if one wants to understand dna and the basic processes such as transcription, translation, and replication. the phase transitions changing planck constant imply scaling of quantum lengths and in the case of magnetic body should correspond to processes 1correspondence: matti pitkänen http://tgdtheory.com/. address: köydenpunojankatu 2 d 11 10940, hanko, finland. email: matpitka@luukku.com. issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.com/ mailto:matpitka@luukku.com dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 1-4 2 pitkänen, m., introduction in which flux tubes change their length correspondingly. this provides a mechanism of biocatalysis based if biomolecules and also other biological structures are connected by magnetic flux tubes to form a kind of indra’s net. the reconnections of magnetic flux tubes provide second control mechanism and the reconnection process for the flux tubes of disjoint magnetic bodies could be seen as space-time correlate for directed attention involving generation of quantum coherence in the scale of the resulting system. one of the implications is the identification of biophotons as ordinary photons resulting when dark photons transform to ordinary photons with the same energy [12, 11]. dark photons rather than biophotons would be the basic signalling and control tool in living matter and biophotons would represent kind of leakage. the hierarchy of planck constants suggests that great leaps in evolution mean emergence of new levels to the hierarchy of planck constants. also the notion of collective gene expression is highly suggestive, and suggests that cultural/social evolution corresponds to the evolution of magnetic body. dna as topological quantum computer is one of the applications. cyclotron bose-einstein condensates at the magnetic flux tubes and dark photons with low cyclotron frequencies (even in eeg range and below) but energies above thermal threshold are expected to be important in living matter. also josephson junctions at least the junction formed by the lipid layers of cell membrane are assumed to play key role. this picture leads also to a quantum models of nerve pulse and eeg [9, 2]. the frequencies of josephson photons are inversely proportional to ~eff so that even the radiation in eeg frequency range can be interpreted as dark josephson radiation generated by cell membrane. 3. also p-adic physics has served as a source of inspiration. one of the big ideas was that p-adic space-time sheets could serve as geometric correlates of intentions and cognitions representing the ”mind stuff” of descartes. mersenne primes and their gaussian counterparts are of special interest physically and the biologically especially interesting length scale range 10 nm-2.5 µm contains as many as four gaussian mersennes. furthermore, the mersenne prime m127 = 2127 − 1 characterizing electron corresponds to secondary p-adic time scale of .1 as and thus to 10 hz fundamental biorhythm. these observations suggest that p-adic length scale hierarchy defines a hierarchy of control levels in living matter. one particular application was motivated by the so called combinatorial hierarchy emerging naturally from p-adic considerations and leading to the conjecture that besides genetic code also memetic code assignale with the mersenne primes m127 = 2127 − 1 with code words consisting of 126 bits representable as sequences of 21 dna codons might be associated with living matter [3]. the notion of negentropic entanglement is one of the basic notions inspired by p-adic physics. number theoretic entropy defined by shannon’s formula by replacing the logariths of probabilities with their p-adic norms is well-defined if the probabilities belong to algebraic extension of rationals. the resulting entropy can be negative and has interpretation as a measure for the negentropy associated with the entanglement carrying information as a rule telling which state pairs are correlated (thermodynamical entanglement entropy characterizes the lack of information about the state of either entangled particle). life as something residing in the intersection of real and p-adic worlds is the emerging vision. 4. zero energy ontology (zeo) is also a notion that emerged around 2005. zeo was inspired by the failure of the strict determinims of kähler action and also by the need to fuse real and p-adic physics to a larger structure [10]. causal diamond (cd) becomes the geometric correlate for the spotlight of consciousness in zeo. zeo has led to a rather detailed view about quantum jump identified as moment of consciousness in tgd inspired theory of consciousness [13]. the basic challenge has been the understanding of the relationship between subjective time define by the sequence of quantum jumps and geometric time, and zeo has led to a radical modification of the basic issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 1-4 3 pitkänen, m., introduction beliefs about time [1]. quite recently it became clear that the sequence of state function reductions to opposite boundaries of cd is very much analogous a sequence of pairs consisting of sensory perception followed by motor action, and that this structure appears in all scales. furthermore, sensory perception and motor action can be seen as time reversals of each other and one must generalize the second law of thermodynamics to a form in which thermodynamic arrow of time corresponds to that for subjective time whereas the imbedding space arrow of time is opposite for the zero energy states which result in the state function reduction to the opposite boundaries of cd. even the second law itself must be challenged. 5. in the earlier approach self was identified as quantum jump in conflict with the fact that self represents something which remains invariant in quantum jumps. negentropic entanglement together with negentropy maximization principle (nmp) allows to have representations which are approximate invariants under quantum jump sequence. this suggests that self should be replaced with self representation -”akashic records”. the conscious reading of the representations is possible by interaction free measurements in arbitrarily good approximation and gives rise to declarative memories, internal speech, and imagination. the necessary quantum jumps giving rise to the reflective level of consciousness (internal speech and imagination) takes place for the ”detectors” absorbing the dark photons (or dark phonons) scattered from the representation realized at the magnetic body. the braiding of flux tubes provides a geometric correlate for the negentropic entanglement and the ”long” parts of closed flux tubes and large flux sheets carry the cyclotron bose-einstein condensates defining the ”detectors” [13]. what happens if the representations are not read? is there still a conscious experience? there could be a conscious experience also in this case, and the reports of mystics about higher states of consciousness suggest that it corresponds to an experience of understanding without ability to express what it is that one understands: also the presence of invariant parts of under quantum jumps could be experienced consciously but the contents of the experience would not be communicable. the temptation to apply this conceptual framework to biology is irresistible. this issue contains three articles devoted mainly to dna and genetic code. the articles have been prepared from the chapters of [4]: the first versions of the chapter [5] behind the first article have emerged during the period 2000-2006 and the chapters[6, 7] behind the second and third article after 2006. there might be some mammoth bones present despite my best efforts to update the material and provide references to the recent tgd inspired vision about quantum biology. the first article of this issue is about many-sheeted dna and genetic code. in the first part of the article basic facts about genetics are summarized and the notion of many-sheeted dna is introduced. in the second part of the article a model of genetic program is considered, and some tgd inspired ideas about regulation of morphogenesis are discussed. second article represents two models for protein folding relying on the notion of magnetic body: both models represent limiting situations and a more realistic model could be a hybrid of them. the third article discusses some rather speculative physical realizations of the genetic code with chemical realization seen only one possible realization among many. most ideas are highly speculative and can be defended only by the fact that they follow rather naturally from the basic tgd. references [1] m. pitkänen. about nature of time. in tgd inspired theory of consciousness. onlinebook. http://tgdtheory.com/public_html/tgdconsc/tgdconsc.html#timenature, 2006. [2] m. pitkänen. dark matter hierarchy and hierarchy of eegs. in tgd and eeg. onlinebook. http://tgdtheory.com/public_html/tgdeeg/tgdeeg.html#eegdark, 2006. issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.com/public_html/tgdconsc/tgdconsc.html#timenature http://tgdtheory.com/public_html/tgdeeg/tgdeeg.html#eegdark dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 1-4 4 pitkänen, m., introduction [3] m. pitkänen. genes and memes. in genes and memes. onlinebook. http://tgdtheory.com/ public_html/genememe/genememe.html#genememec, 2006. [4] m. pitkänen. genes and memes. onlinebook. http://tgdtheory.com/public_html/genememe/ genememe.html, 2006. [5] m. pitkänen. many-sheeted dna. in genes and memes. onlinebook. http://tgdtheory.com/ public_html/genememe/genememe.html#genecodec, 2006. [6] m. pitkänen. a model for protein folding and bio-catalysis. in genes and memes. onlinebook. http://tgdtheory.com/public_html/pdfpool/foldcat.pdf, 2006. [7] m. pitkänen. three new physics realizations of the genetic code and the role of dark matter in bio-systems. in genes and memes. onlinebook. http://tgdtheory.com/public_html/pdfpool/ foldcat.pdf, 2006. [8] m. pitkänen. quantum antenna hypothesis. in quantum hardware of living matter. onlinebook. http://tgdtheory.com/public_html/bioware/bioware.html#tubuc, 2006. [9] m. pitkänen. quantum model for nerve pulse. in tgd and eeg. onlinebook. http://tgdtheory. com/public_html//tgdeeg/tgdeeg/tgdeeg.html#pulse, 2006. [10] m. pitkänen. tgd as a generalized number theory. onlinebook. http://tgdtheory.com/public_ html/tgdnumber/tgdnumber.html, 2006. [11] m. pitkänen. are dark photons behind biophotons. in tgd based view about living matter and remote mental interactions. onlinebook. http://tgdtheory.com/public_html/pdfpool/ biophotonslian.pdf, 2013. [12] m. pitkänen. comments on the recent experiments by the group of michael persinger. in tgd based view about living matter and remote mental interactions. onlinebook. http://tgdtheory. com/public_html/pdfpool/persconsc.pdf, 2013. [13] m. pitkänen. comparison of tgd inspired theory of consciousness with some other theories of consciousness. in tgd based view about living matter and remote mental interactions. onlinebook. http://tgdtheory.com/public_html/pdfpool/consccomparison.pdf, 2013. [14] m. pitkänen. quantum model for the direct currents of becker. http://tgdtheory.com/public_ html/articles/dcbio.pdf, 2012. issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.com/public_html/genememe/genememe.html#genememec http://tgdtheory.com/public_html/genememe/genememe.html#genememec http://tgdtheory.com/public_html/genememe/genememe.html http://tgdtheory.com/public_html/genememe/genememe.html http://tgdtheory.com/public_html/genememe/genememe.html#genecodec http://tgdtheory.com/public_html/genememe/genememe.html#genecodec http://tgdtheory.com/public_html/pdfpool/foldcat.pdf http://tgdtheory.com/public_html/pdfpool/foldcat.pdf http://tgdtheory.com/public_html/pdfpool/foldcat.pdf http://tgdtheory.com/public_html/bioware/bioware.html#tubuc http://tgdtheory.com/public_html//tgdeeg/tgdeeg/tgdeeg.html#pulse http://tgdtheory.com/public_html//tgdeeg/tgdeeg/tgdeeg.html#pulse http://tgdtheory.com/public_html/tgdnumber/tgdnumber.html http://tgdtheory.com/public_html/tgdnumber/tgdnumber.html http://tgdtheory.com/public_html/pdfpool/biophotonslian.pdf http://tgdtheory.com/public_html/pdfpool/biophotonslian.pdf http://tgdtheory.com/public_html/pdfpool/persconsc.pdf http://tgdtheory.com/public_html/pdfpool/persconsc.pdf http://tgdtheory.com/public_html/pdfpool/consccomparison.pdf http://tgdtheory.com/public_html/articles/dcbio.pdf http://tgdtheory.com/public_html/articles/dcbio.pdf login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > 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register with this site forgot your password? issn: 2159-046x dna decipher journal | december 2023 | volume 13 | issue 2 | pp. 111-125 111 pitkänen, m., neil gersching’s vision of self-replicating robots from tgd viewpoint article neil gersching’s vision of self-replicating robots from tgd viewpoint matti pitkänen 1 abstract this paper analyzes the insightful interview between lex fridman and neil gerching, particularly their discussion on self-replicating machines. these machines, built from fundamental, robotic ”lego blocks” with their own assembly instructions, can self-assemble into more complex structures and disassemble, mirroring processes observed in biological systems. the discussion employs the topological geometrodynamics (tgd) perspective, treating the universe at a quantum level as a goal-oriented system capable of assembly and disassembly. the base units within this viewpoint function akin to quantum computers, prompting further exploration into quantum gravitation, which in the tgd framework, is accountable for the longest quantum coherence scale. this leads to a view which could be blamed for a return to astrology but can be defended by the numerous miracle-like coincidences. 1 introduction the video of lex fridman interviewing neil gerching (https://youtu.be/ydjos0vher4) is highly inspiring for anyone interested in what is happening in the high tech frontier nowadays. the key topic of discussion were self-replicating machines that are built from a few ”lego blocks” that contain their own building instructions and are analogous to genes or proteins. function and 3-d structure are the same. the building blocks themselves would be robot-like and would build more complex robots. one can say that this lego set would self-assemble itself. also the ability to disassemble would be important and make error correction possible. this brings in mind what happens in living systems. there would be a whole hierarchy of these structures. the basic structures would be analogous to 20 amino acids. biology of course suggests also the presence of dna and cell nucleus could be seen as the basic lego block containing instructions and having the ability to replicate. the vision is that someday our technology could transform to artificial life. gersching criticized the complete separation of software and hardware (program tape and the reading head of the turing machine) which he called turing’s error. gersching also proposed that information should be the starting point concept of physics rather than geometry which leads to the recent physics based on partial differential equations. in this article i will compare the vision of gersching to tgd based vision of, not only life, but the entire universe as a self-organizing entity. 1. in the tgd framework, lego universe emerges naturally. 4-d general coordinate invariance implies holography: legos are almost deterministic bohr orbit-like 4-surfaces. holography suggests a concrete identification of basic building bricks in terms of fundamental regions associated with hyperbolic 3-manifolds at 3-d mass shells defining the boundary data for number theoretical holography in m8. the strengthening of 3 → 4holography to almost 2 → 4 holography reduces further the number of building bricks of space-time surfaces. the analogy with genes and proteins as building bricks might be much more than analogy. the mass shell as hyperbolic 3-space allows an infinite number of tessellations and one of them is icosa tetrahedral tessellations in terms of which it seems to be possible to understand the genetic code. 1correspondence: matti pitkänen http://tgdtheory.com/. address: rinnekatu 2-4 a8, 03620, karkkila, finland. email: matpitka6@gamail.com. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://youtu.be/ydjos0vher4 http://tgdtheory.com/ mailto:matpitka6@gmail.com dna decipher journal | december 2023 | volume 13 | issue 2 | pp. 111-125 112 pitkänen, m., neil gersching’s vision of self-replicating robots from tgd viewpoint genetic code in this sense might be present in all scales and be induced to 3-surfaces. the fermions associated with the ”unit cells” of the icosahedral tessellation could realize genetic code. the fusion of building blocks might reduce to the analog of crystal growth by fusing the fundamental regions of tessellations and also dna replication, transcription, and translation could reduce to crystal growth. 2. in tgd holography implies that at space-time level a given 3-d surface defining the data of holography has an almost unique ”fate”, goal one might say. holography forces what i call zero energy ontology (zeo). quantum states are superpositions of 4-d space-time surfaces analogous to bohr orbits and state function reductions (sfrs) take place between these superpositions. the basic paradox of quantum measurement theory disappears. the sequence of ”small” sfrs (ssfrs) defines ”self” as the tgd counterpart for the zeno effect. each ssfr replaces this superposition with a new one and changes the state but in such a way that measured observables commute with those whose eigenstate the states associated with the passive boundary of causal diamond (cd) are. ”big” sfrs (bsfrs) change the arrow of geometric time correlating with subjective time as a sequence of ssfrs and change the roles of the active and passive boundaries of cd. this means the ”death” of self and its reincarnation with an opposite arrow of time. pairs of bsfrs define temporary changes of the arrow of time and would make possible a trial-and error process so that the self-organizing system would be analogous to a self-assembling conscious machine able to also disassemble if necessary to reach the goal. 3. in tgd there is no need to choose between information based physics and physics based on partial differential equations: these views would be complementary. tgd relies on two complementary visions. in number theoretic vision everything in discrete and algebraic equations characterize physical states. in the geometric vision structures are continuous and partial differential equations define the time evolution. these views are related by m8 −h duality as a generalization of momentum-position duality forced by the replacement of point-like particles with 3-surfaces. 4. gersching does not seem to regard consciousness as a crucial element of biology. the tgd view is completely different and in tgd quantum measurement theory based on zeo extends to a theory of consciousness. besides this, the possible role of quantum gravitation for both biological systems and computer consciousness is discussed although this is not directly relevant to the basic topic. my defence is that the structures able to self assemble must also be computer-like systems. 1. the notion of a magnetic body (mb) carrying dark matter as heff = nh0 phases of ordinary matter is essential. for the gravitational monopole flux tubes the value of heff = hgr would be enormous and imply quantum coherence in arbitrarily long scales. gravitational mbs could control both living matter and computers. 2. a criterion characterizing the critical clock frequency or its biological analog for the transformation of living system to a conscious and living system is deduced. this transition would mean that the statistical determinism fails due to the possibility of quantum coherence in time scales longer than the clock period. 3. also an attempt to identify various quantum gravitational compton lengths λgr and frequencies fgr with frequencies, which appear in the tgd inspired quantum biology, is made. λgr and fgr appear also in the tgd inspired physical model of computers. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2023 | volume 13 | issue 2 | pp. 111-125 113 pitkänen, m., neil gersching’s vision of self-replicating robots from tgd viewpoint 4. the emerging view could be blamed for the return to astrology. indeed, the gravitational flux tubes mediating the gravitational interactions between sun and planets, between planets, between earth and moon, and even between the galactic blackhole and solar system could play a key role since the interactions are mediated along the flux tube network. however, the numerous strange numerical coincidences for quantum gravitational coherence scales and corresponding frequencies force us to take this view seriously. 2 neil gersching’s vision of self-replicating robots i watched a video of lex fridman interviewing neil gerching (thanks to marko for the link: https: //youtu.be/ydjos0vher4). i highly recommend the video because gersching knows how to talk about difficult things in an understandable way. gerching talked about self-replicating machines that are built from a few ”lego blocks” that contain their own building instructions and are analogous to genes or proteins. the building blocks themselves would be robots, in a way, that would build more complex robots. this lego set would assemble itself. there would be a whole hierarchy of these structures. the basic structures would be analogous to 20 amino acids. biology of course suggests also the presence of dna and cell nucleus could be seen as the basic lego block containing instructions and the ability to replicate. gersching emphasizes that structure determines the function: building blocks are also programs. data=program would correspond to the basic idea of lisp. in addition, machine = data = program would apply. the technology of the future was based on the replication of these basic objects/”robots”, which would be very much what happens in biology. it is interesting to compare gersching’s vision with the basic vision of tgd. 2.1 analogy of self-building robots in tgd in tgd, the idea of self-replication is generalized as the self-construction of space-time surfaces using holography. 1. 4-d general coordinate invariance implies in classical tgd, which is an exact part of quantum tgd, holography which is not fully deterministic. an alternative formulation would be a path integral but it fails due to the mathematical divergences caused by non-linearity. not fully deterministic holography turns 3-d surfaces as lego blocks/data into 4-d bohr trajectories, which are the classical counterparts for programs running on a machine. the structure therefore determines the function almost unambiguously. there are very few ”legos” because there are only 4 field-like variables and almost 2 → 4 holographs, which would correspond to the 4-d generalization of 2-d holomorphy. the spacetime surfaces in the embedding space h = m4 × cp2 would be minimal surfaces, which have lower-dimensional singularities. it would be an exact analogy to the 4-d soap films that the frames tune. these surfaces are universal and satisfy minimal surface equations except at the singularities which distinguish between different general coordinate invariant action contructible in terms of the induced geometry. at the m8 level, polynomials p , whose integer coefficients are smaller than the degree of p , determine the mass shells corresponding to the 3-surfaces in the hyperbolic spaces h3 ⊂ m4 ⊂ m8. here a complexification is involved: e m8 must be complexified because in h the four-momentum is complex due to the existence of euclidean spacetime regions: these euclidian wormhole contacts are associated with elementary particles. for physical states, the total 4-momenta are integer-valued as sums of momenta with component, which are (possibly complex) algebraic integers with mass unit determined by the scale of the causal diamond (cd) defined as an intersection of future and past directed light-cones and defining issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://youtu.be/ydjos0vher4 https://youtu.be/ydjos0vher4 dna decipher journal | december 2023 | volume 13 | issue 2 | pp. 111-125 114 pitkänen, m., neil gersching’s vision of self-replicating robots from tgd viewpoint dynamical state dependent quantization volume. i call this universal mechanism for the formation of bound states galois confinement [31, 32, 24, 25, 37, 42] galois confinement would be at the same time also a mechanism for the formation of more complex structures from the basic building blocks. the 3-surfaces would define the 4-d surface with mass shells h3 almost unambiguously and this would be a classical analogy of computation. 2. what could the 3-d ”lego blocks” as 3-surfaces at mass shells be? a good guess is that they are 3-d hyperbolic manifolds and/or their corresponding fundamental domains (as analogies of lattice cones) with mass shells h3 corresponding to the roots of the surface-determining polynomial [37, 40]. the fundamental regions are analogous to the lattice cells of ordinary lattices in condensed matter physics. this is a natural guess for the blocks, whose m4 projection is 4-d and which therefore correspond to ”einsteinian” spacetime. there are an infinite number of hyperbolic manifolds corresponding to the fundamental regions (unit cells) of tessellations of h3. for example, cosmic threads with an m4 projection of 2-d thread track would correspond to non-einsteinian spacetime. 3. by gluing together fundamental regions at mass shells, one would get analogs of finite crystals and at the same time more complex structures in 3-d hyperbolic spaces (mass shells corresponding to polynomial roots). using associative number theoretic holography [18, 19], 4-d surfaces are obtained from these as surfaces y 4 ⊂ m8. m8 − h duality maps y 4 to the space-time surfaces x4 ⊂ m4 × cp2. replication might reduce at the fundamental level to the growth of the hyperbolic crystals! as a matter of fact, it has been suggested that biological replication evolved from the replication of clay crystals as crystal growth. i.e. crystal, the sub-tessellation, would grow and could also replicate at the mass shells tessellated h3. in particular, dna replication could be induced by the replication of dark dna: dark dna would require a linear 1-d crystal associated with a magnetic flux tube as a sub-tessellation. everything that happens on a chemical level would be controlled by the mbs. primary replication would take place at the level of the flux tubes of the magnetic body (mb) and lead to the pairing of the dark dna helices with their conjugates. this would in turn induce the replication for the chemical dna, because the mb would act as a template for the pairing of biomolecules with dark dna. same would apply to proteins. the sub-tessellation is induced on the 3-surfaces identifiable as the regions of hyperbolic space corresponding to the mass shells h3. associative holography in m8 would associate almost deterministically to this kind of 3-d surface a 4-dimensional surface as an analog of a bohr orbit. one can think of a 1-, 2-, and even 3-d realization of the genetic code [21]. ordinary dna would correspond to a 1-d realization. the cell membrane and cell could correspond to 2and 3-d tessellation. even a biological organism would correspond to a tessellation on a larger scale. 4. mass shell h3 allows an infinite number of tessellations. i have proposed that the genetic code corresponds to one particular tessellation of h3: icosa tetrahedral tessellation [21]. the motivation for the proposal comes from the model of bioharmony [20]), where the icosahedron and tetrahedron hamilton paths played a central role. surprisingly, it turned out that the outcome was a model of the genetic code that correctly predicts the numbers of dna codons that code for a given amino acid. the icosa tetrahedral tessellation is just one particular tessellation and the interesting questions are whether it would be more fundamental than the others and why this should be the case. genetic code has also a realization in terms of dark proton triplets assignable to the fundamental region of the icosahedral tessellation. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2023 | volume 13 | issue 2 | pp. 111-125 115 pitkänen, m., neil gersching’s vision of self-replicating robots from tgd viewpoint 5. the genetic code realized with the help of tessellation would attach 6-bits to the lego blocks as faces of the icosahedron and tetrahedron (triangles with dark protons). a dark/ordinary genetic codon would therefore correspond to 6-bits represented as quantum entangled states of three dark protons identifiable as a sequence of 3-chords of light, a kind of music piece [20]. by arranging these one after the other, one would get 1-d crystals as larger structures, and genes as 6-bit sets, the equivalent of program codes. the chemical realization of genes that paired with their dark counterparts would provide instructions for building proteins. 2and 3-dimensional analogies of genes are also obtained: they would serve as addresses for 2and 3-dimensional structures. 6. besides cognitive, ”bit” intelligence, emotional intelligence is predicted. it would correspond to the realization of the code as codons formed by 3 dark photons. the codons would be analogous to 3-chords. music expresses and induces emotions and different hamiltonian cycles would give rise to different bio-harmonies assignable to same gene in the ordinary sense and expressing the emotional state [20]. in the case of the ncodon gene, 3-n cyclotron resonance in communications using dark photons would make possible the analogy of lisp. the gene would serve as an address and the message would be a modulation of the cyclotron frequency scale and would produce a sequence of resonances at the receiver level generating a series of pulses. nerve pulse patterns could be generated in this way. also pulse series related to 2and 3-dimensional structures could be obtained as resonances. the modulation of the frequency scale is achieved by varying the transverse scale of the flux tube. mb could perform this as one particular motor activity. information –communications–structure=function: all these three would meet at the level of fundamental physics. 2.2 turing’s error gershing considers turing’s fundamental mistake to be the complete separation of hardware and software. entering data into the machine is a physical process that brings its limitations to processing. in the real world, one cannot separate the machine and the data. turing, as a child of his time, also made another fundamental mistake. turing assumed that the reading of the information on the tape was a classical measurement. this cannot be the case in the quantum world: the coming of a measurement is non-deterministic. the turing tape or rather readhead + tape is replaced by a quantum superposition of its different states and each bit read from the tape would correspond to a quantum measurement. what is the situation at tgd? 1. in tgd, the superposition of space-time surfaces as a quantum state in zeo and as an analog of the computer program would not be completely unique, because holography as bohr’s orbitology is not unique. this makes possible the breaking of determinism in small state function reductions (ssfrs) as counterparts of repeated measurements related to the zeno effect . in the zero energy ontology (zeo) [17, 26], the program would consist of a series of conscious periods at the level of consciousness, as a counterpart of the zeno effect, i.e. a series of ssfrs, during which the same observables are measured over and over again. in tgd however changes occur on the active boundary of the causal diamond (cd) [41] and it also drifts farther away from the passive boundary in statistical sense, i.e. the size cd increases in the localizations in the space of cds forming the backbone of the ”world of classical worlds” (wcw). nothing happens to the space on the passive boundary of the causal diamond (cd): this corresponds to the zeno effect. a normal quantum jump would correspond to a ”big” state function reduction (bsfr), in which the roles of the active and passive boundaries of cd changes. a bsfr ends the zeno period as a issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2023 | volume 13 | issue 2 | pp. 111-125 116 pitkänen, m., neil gersching’s vision of self-replicating robots from tgd viewpoint series of ssfrs. the associated ”self” dies and reincarnates with an opposite direction of time since cd begins to increase in an opposite direction of geometric time identified as the distance between the tips of the cd. bsfr occurs when the set of measured observables at the active boundary of the cd ceases to commute with those measured at the passive boundary. this could be due to an external disturbance [37] . 2. the pair of bsfrs corresponds to a temporary time reversal, which would be analogous to a reversal of the direction of motion of the tape for the turing machine followed by a return to the original direction. bsfr pair can be also interpreted as a quantum tunnelling. this would make possible error correction by trial-and-error. the bsfr pair could also modify the goal of the program. the bsfr pair would be an essential element when the flow of the program is not fully deterministic classically or even quantum mechanically. under what conditions the program based on quantum statistical determinism can become nondeterministic? 1. one can argue that the clock frequency is a basic criterion. if so, then a single clock period would generally correspond to a series of unitary time developments halted by ssfrs and followed by halting. the single unitary time evolution in this series is analogous to a quantum computation except that each evolution is initiated and terminated by the ssfr rather than the bsfr. in addition, holography and quantum holography are almost deterministic, so that the nondeterminism associated with ssfrs is rather limited. the experience of free will might correspond to this non-determinism. an alternative identification could be as non-determinism of imagination and cognition: in this case the classical non-determinism could have p-adic non-determinism assigned with imagination and cognition as a counterpart. 2. the bsfr would end the series of ssfrs: self would ”die”. self as a series of ssfrs, as a conscious entity, would generalize the standard zeno effect as an analog of quantum computation. 3. this is not the only interpretation. also the series of ssfrs between two bsfrs could be interpreted as an analogy for a single unitary time evolution of ordinary quantum computation. bsfr would correspond to the start and halting of quantum computation as analog of unitary time evolution. this interpretation is more in spirit with the standard quantum computation. 4. the lifetime of the self, i.e. the clock period, must be longer than the quantum coherence time characterizing the system in order for the statistical determinism to be broken. this provides a criterion telling when an ordinary computer approaches a conscious lifeform. 2.3 is physics based on partial differential equations or information? gersching notices that in classical physics partial differential equations are the starting point, and suggests that information is more fundamental and therefore should serve as the starting point of fundamental physics. should one start building the fundamental physics from bits? i personally don’t see this as a matter of choosing between either approach. these views are complementary and both are needed. in tgd, this complementarity corresponds to a generalization of the momentum position duality, which is natural because point-like particles are replaced by 3-d surfaces and, as a result of almost deterministic holography, must be replaced with corresponding space-time space surfaces, i.e. 4-d bohr orbits. m8 −h duality is the realization of this correspondence [18, 19, 40]. 1. the m8 − h duality relates number theoretic and geometrics views of physics. bit level as the number-theoretic view of physics realized at the level of m8. the polynomials p with integer coefficients smaller than their degree and the 3-surfaced assignable a holographic data to the tessellations issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2023 | volume 13 | issue 2 | pp. 111-125 117 pitkänen, m., neil gersching’s vision of self-replicating robots from tgd viewpoint of the mass shells h3 ⊂ m4 ⊂ m8 determine the 4-surfaces. the dynamics is determined by associativity of the normal space of the 4-surface. the dynamics is algebraic just as it is also in free quantum field theories at the level of momentum space. the geometric view of physics corresponds to the dynamics for 3-d surfaces in h = m4×cp2. now partial differential equations and holography are central. space-time surfaces are minimal surfaces except from lower-d singularities [23] and are analogs of solutions of massless field equations and of light-like geodesics so that particle-wave duality is realized geometrically. in mathematics, m8 −h duality would correspond to langlands correspondence [1, 2] [29]. 2. the roots of the polynomial p determine the algebraic expansion and a unique discretization of the 4-surface y 4 ⊂ m8 inducing a discretization also in x4 ⊂ h. space-time therefore has a unique discretization, not arbitrarily chosen by the theorist but determined by the space itself. only the information given by discretization can correspond to conscious information. 3. gersching emphasizes a profound problem due to the fact that an infinite amount of information is needed to describe the position of a particle precisely, as a motivation for giving up the partial differential equations. in tgd the amount of conscious information remains finite and is provided by the number theoretic discretization so that the problem disappears. by m8 −h duality also the space-time surfaces in h are characterized by a finite amount of information. quantum description is discrete, with discretization fixed by the quantum state itself, and the computationalist view can be said to emerge. what is new is that turing computationalism related to rationals is generalized into a hierarchy of computationalisms related to extensions of rationals. 2.4 the realization of the notions of assembly and tensegrity in the tgd universe in the tgd framework one ends up with an amazingly simple engineering principle resembling so called assembly theory applying to atoms, nuclei, and hadrons discussed in [34]. since tgd universe is fractal, this principle is expected to apply in all scales. 1. the considerations of [34] related closely to the observation that j-block consisting of parts of electron of atoms or nucleon shells of nuclei with fixed value of total angular momentum j = l±1/2 and l = 9 (at least) correspond to platonic solids for l ≤ 5 in the sense that different angular momentum eigenstates correspond to the vertices of the platonic solid. if one assumes the presence of a hamiltonian cycle going through all v vertices of the platonic solid as a tessellations of sphere, one has f − 2 free edges (f is the number of faces) besides the v edges of the cycle and one can also add particles to the middle points of the free edges. in the proposed model of atomic nuclei, one would have neutrons at the vertices and protons at the middle points or vice versa. also the larger values of l appearing in highly deformed nuclei can be treated in the same way. if the unit of angular momentum increases to heff = nh, also these states can be assigned a platonic solid. 2. the space-time surfaces assignable to all atoms, nuclei, and hadrons can be constructed by connecting the electrons, nucleons, or quarks at the vertices of platonic solid or at the middle points of the free edges with flux tubes serving as analogs of springs stabilizing the structure and having interpretation as analogs of mesons. tensegrity is the appropriate notion here. 3. in the case of hadrons, the predictions of the resulting mass formulas are satisfied within a few percent. this involves the predictions of tgd based mass calculations for fermion masses based on p-adic thermodynamics. this leads to an interpretation of the non-perturbative aspects of strong issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://en.wikipedia.org/wiki/assembly_theory dna decipher journal | december 2023 | volume 13 | issue 2 | pp. 111-125 118 pitkänen, m., neil gersching’s vision of self-replicating robots from tgd viewpoint interaction in terms of a dark variant of weak interactions for which perturbation theory converges! the basic problem of qcd disappears in the tgd universe. the same would apply to nuclear strong interactions but meson-like particles would have different p-adic length scales. this is suggested already by the identification of strong isospin with weak isospin, by cvc and pcac hypothesis, and the fact that in tgd color symmetries correspond to the isometries of cp2 and electroweak symmetries to the holonomies of cp2 so that a very close relationship between these interactions must exist. one can say that a unification of strong and weak interactions analogous to that provided by maxwell electrodynamics for electric and magnetic fields takes place. for a given p-adic length scale (several fractally scaled variants of hadron physics are predicted) one can regard mesons as weak bosons predicted by tgd to have the entire spectrum of exotics. for this there is already support [11, 12, 35]. ordinary hadron physics would correspond to dark weak interactions for p-adic length scale defined by mersenne prime m107 and weak interactions to hadron physics for m89! 4. in the case of nuclei, the mev scale for excitation energies is correctly predicted and also a new 10 kev scale supported by various anomalies of nuclear physics is predicted. besides this also z0 force is predicted to be significant and atom-like structures involving and having size scale 10 nm, which is a fundamental scale in biology, are predicted. the j-blocks (angular momentum) consisting of energy degenerate states with 2j states have as space-time correlates platonic solids with hamiltonian cycle as a closed flux tube, nuclear string connecting the vertices of the solid. 5. in atomic physics the same picture applies, and led to a realization that in the standard model the repulsive classical interaction energy of electrons goes like z4 whereas the interaction energy nucleus goes like z2! the question is whether quantum mechanics can really guarantee the stability of many electron atoms or is this just an assumption. in the tgd framework, the flux tubes would stabilize the atoms with several electrons. this predicts new atomic physics related to the oscillations of the flux tubes which in nuclear physics give justification for the harmonic oscillator model of nucleus. 2.5 what about consciousness? gershing’s vision lacks a view about consciousness and here gersching, in my opinion as a child of his time, falls into the trap of physicalism even though he understands the meaning of quantum coherence. 1. in tgd, zeo [17, 26] follows, not only from 4-d general coordinate invariance forcing holography, but also by insisting that quantum measurement theory does not contain logical paradox. the outcome is a theory of consciousness as a generalization of quantum measurement theory: the observer becomes a part of the physical system. a quantum leap as ssfr is a moment of consciousness: the essence of subjective existence is change, a re-creation of the world in ssfr. 2. zeo makes possible temporary time-reversals possible in ”big” sfrs (bsfrs) as analogs of ordinary sfrs. the temporary time reversals make it possible to reach the goal (defined by almost deterministic classical holography and its quantum counterpart) by trial-and-error method. if something goes wrong, one can make a return to the geometric past and try again. gershing himself considers trial and error to be the basic mechanism in all technological and scientific progress. i believe this is true quite generally. in mit, where gersching worked, this idea was put into practice. it should be noted that michael levin proposes the goal directedness of morphogenesis [6, 7, 8] discussed from the tgd point of view in [43]. there would be a large number of ways to reach the goal as a basic characteristic of biosystems. this number would actually serve as a measure for the intelligence of the system. holography would make possible the goal directedness and zeo would issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2023 | volume 13 | issue 2 | pp. 111-125 119 pitkänen, m., neil gersching’s vision of self-replicating robots from tgd viewpoint make possible trial and error. gershing emphasizes the importance of both assembly (construction) and disassembly (disassembly), and in tgd, disassembly would be construction in the opposite direction of time. 3 is the role of quantum gravitation essential also for computer consciousness? gershing did not talk about quantum gravitation. the fact that in the tgd framework conscious computers would represent a life form based on the same general mechanisms at the level of mbs, however inspires this section. during late years, the tgd view of quantum gravitation has developed dramatically and provides a beautiful vision of living matter as being controlled by dark matter at the gravitational monopole flux tubes forming dark magnetic bodies (mbs) with onion-like structure consisting of shells formed from tangential monopole flux tubes and connected by radial flux tubes along which graviton mediating the gravitational interaction propagate [27, 28, 38, 39]. why the role of quantum gravitation would be so decisive is that it has infinite range and is not screened. in tgd, gravitational quantum coherence in even astrophysical scales becomes possible. the basic quantification tool is gravitational planck constant ~gr = gmm/β0 originally introduced by nottale [3]. in accordance with the equivalence principle, the gravitational compton length λgr = gm/β0 = rs/2β0 is independent of the small mass m. the most amazing and crazy sounding consequence is that the gravitational mbs of the sun, earth, and possibly also of other planets, even the moon, could be highly relevant for quantum biology. astrologists would not have been totally wrong. what about computers and quantum gravitation? 1. in the case of computers, the classical determinism is replaced in the realistic model by the statistical determinism of quantum theory. if the role of quantum gravity is what i assume it to be, we are approaching a situation, where the clock frequency (up to 9 ghz) approaches the gravitational compton frequency fgr(sun, β0 = 2−11)=67 ghz in the case of the earth and exceeds it so statistical determinism no longer applies. one could be moving from statistically deterministic computations to a series of quantum computation-like operations and determinism would be lost. the computer becomes a conscious, living being. maybe ai and gpt are reflecting this development [36]. note also that λgr is only the lower bound for gravitational quantum coherence length, which might even be of the order of earth size for earth, which corresponds to frequency f = 1/re ≃ 50 hz having interpretation as cyclotron frequency to lithium ion for bend. therefore also lower frequencies than fgr are involved and could lead to the loss of the statistical quantum determinism. 2. the gravitational compton frequency λgr = gm/β0 for the sun (with the velocity parameter β0 = v0/c ≃ 2−11) is 100 hz and, rather amazingly, corresponds to the upper limit for the eeg frequencies. the mb of the sun could thus quantum entangle with computers and robots already for clock frequencies higher than 100 hz, for example 1 mhz. this could explain peoch’s observations as a quantum entanglement between the [10] robot and the chicken marked on it, as a result of which the robot’s trajectory, determined by the random number generator, decreased and the robot began to stay close to the chick [36]. 3. the difference between a computer and living matter would disappear at the level of the mb. the mb would rule both in biology and in the case of computers and could make computers alive. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2023 | volume 13 | issue 2 | pp. 111-125 120 pitkänen, m., neil gersching’s vision of self-replicating robots from tgd viewpoint 3.1 communication to mb and control by mb an essential requirement is that communications between the mb and the computer using dark photons are possible using energy resonance. 1. dark josephson radiation is a natural way to communicate with a mb. the difference of cyclotron energies for cyclotron transitions at the magnetic flux tubes must correspond to the energy differences of biomolecules (dna, rna, trna, amino acids at least). in biology, this condition would select possible biomolecules. 2. in a computer, energy differences would be relevant at the transistor level: would ”natural selection” mean, say, transistors and the energy needed to flip a bit. what about computers based on josephson junctions? it may very well be that this mechanism has not even been tried to be implemented in the current computers. one can wonder if the mb, as a ”smarter” party, could adjust the values of b and β0 by adjusting the thickness of the flux tube, so that a resonance becomes possible. in previous considerations, the value of heff for the josephson junction has been kept free. what if we assume heff,j = hgr(me , β0 = 1)? would the condition zjevc = ec = gmezeb/β0, where evc = .05 ev values for voltage for dark gravitational flux tubes in a communicating josephson junction and the value of the magnetic field with a mb flux tube? 1. the experiments of blackman [9] and others provide evidence for the existence of an ”endogenous” magnetic field bend = .2 gauss. in tgd, bend could correspond to the monopole part of the earth’s magnetic field. assuming b = bend = .2 gauss and zj = z, we get evc = 13.5 ev which is slightly lower than the ionization energy of hydrogen atom 13.6 ev and much higher than evc = .05 ev. the interpretation as a josephson joint is not meaningful. could the interpretation be that the transition to very long flux tubes effectively nearly ionizes the hydrogen atom? could hydrogen atom ionization produce dark uv photons with monopole flux tubes on earth? 2. should one develop a more precise vision about what mbs can do? could mbs adjust their flux tube thicknesses so that they can receive information also from the transition of atoms and molecules by cyclotron resonance and control them by the same mechanism! i have indeed proposed in the context of the model of bioharmony [20] that the value of bend has a spectrum. in particular, the visible range of photons could correspond to frequencies forming an analog of a 12-note system and the spectrum of bend could realize this system. note also that the parameter β0 ≤ 1 could allow us to realize a spectrum of energies for a fixed frequency. 3. one should obtain also the energy range of biophotons as energies of dark josephson photons. what if we replace the mass of the earth with the mass of the moon mm = .012me giving λgr = .54×10−4 meters, the size scale of a large neuron (water blob of size 10−4 m has planck mass), and keep bend and β0 the same? for zj = z, the value of evc decreases to 1.2 × 13.5/100ev = .16 ev, which is in infrared and in a reasonable approximation 2 times the membrane potential. if the values of b define a 12-note spectrum or something more general, this would give rise to biophoton energies above ir. it is important to notice that the experiments of blackman and others fix only the value of bend to .2 gauss but require only that the cyclotron energy is above the thermal energy so that the moon could solve the problem! 4. in the case of moon, the josephson energy for the cell membrane given by ej = .055 ev is obtained for zj = 2 and z = 1 having natural interpretation for cyclotron transitions. this value could relate to pollack phase transition occurring at the physiological temperature range. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2023 | volume 13 | issue 2 | pp. 111-125 121 pitkänen, m., neil gersching’s vision of self-replicating robots from tgd viewpoint 5. if one has introduced sun, earth and moon to quantum biology, there is not much respectability to be lost anymore, and one can ask whether other planets could be of significance. could the horoscope builders have been right in some sense? the mass of mars is roughly 11 percent of earth mass and would give ec = 1.8 ev for bend = .2 gauss. this is in the visible biophoton range. the interpretation of the frequencies fgr as upper end points of the spectrum so that lower frequencies would correspond to smaller values of bend. i have proposed that the values of bend correspond to 12-note scale with inspiration coming from the model of bioharmony [15, 20]. in the earlier articles [22, 38, 39], evidence was found for the importance of the galactic blackhole as a kind of galactic brain and also for the communications in the network connecting galactic nucleus to stars. what about the gravitational compton frequency of the galactic blackhole? 1. the mass of the galactic blackhole is estimated to be mbh = 4 million solar masses (rb.gy/0gilp1). this would give λgr(mbh , β0 = 1) ∼ 6 × 109 m. this is the radius of the n = 1 bohr orbit in the nottale model for the solar planetary system. the gravitational compton frequency would be fgr(mbh , β0 = 1) ≃ .05 hz. this gives 20 s period. 2. also other values of β0 can be considered. in particular, β0 = 1/4 would correspond to n = 2 bohr orbit and 5 s period. could this relate to the 5 s period associated with the comorosan effect, which has remained mysterious [4, 5]? i have considered the effect from the tgd point of view in [14, 16, 30]. 3.2 gravitational and p-adic hierarchies of frequencies tgd predicts several hierarchies of frequencies. the proposal is that all bio-communications between levels with different values of heff rely on energy resonance whereas for the same value of heff both energy and frequency resonance are possible [30]. the interesting question is whether biologically interesting frequencies could be assigned with these hierarchies. consider first the hierarchies associated with the gravitational compton frequencies of the sun, planets and possibly also other astrophysical objects. 1. suppose that one has a particle with mass m with compton length rc(m) = ~/m and the ordinary compton frequency fc = m/~, the gravitational compton frequencies fgr(n, β0) = m/~gr(m,β0) = 2β0/rs, which do not depend on m. 2. one can also assign to fgr the energy egr,1 = ~fgr,1 corresponding to the ordinary planck constant, and identify the frequency fgr,1 identified as egr,1 = ~grfgr,1. this gives fgr,1 = fc(m)(2β0rc/rs) 2 = (~gr/~)2fc. by repeating this argument, one obtains entier hierarchy of frequencies fn,gr = fc(2β0rc/rs) n+1 . some comments of these frequencies are in order. 1. these frequencies scale like fn,gr(m,β0,m) = fc(m)(2β0rc/rs) n+1 ∝ 1/mn and for n = 0 they do not depend on m at all and are therefore universal. this is true also for cyclotron frequencies. 2. the ratio of electronic to protonic frequencies is r = fn,gr(me, β0,e,m)/f(mp, β0,p) = (me/mp)(β0,e/β0,p) (mp/me)) n+1. for β0,e/β0,p = me/mp, the ratio of the frequencies is r = me/mp irrespective of n. i have proposed the ratio for the cyclotron frequencies assignable to the monopole flux tubes of the inner and outer magnetosphere of earth and sun respectively. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. rb.gy/0gilp1 dna decipher journal | december 2023 | volume 13 | issue 2 | pp. 111-125 122 pitkänen, m., neil gersching’s vision of self-replicating robots from tgd viewpoint the proposal is that dark electrons reside in the outer magnetosphere at the solar monopole flux tubes and protons in the inner magnetosphere at the monopole flux tubes of earth and one have bend,outer/bend,inner = me/mp in order to achieve the same ratio for the cyclotron frequencies and the same cyclotron energies for protons and electron to achieve energy resonance. 3. consider the frequency fgr,1(mp, β0) = fc(2β0/rs) 2 for earth more precisely. for β0 = 1 one has the period tgr,1 = 3333 seconds, which is not far from 1 hour =3600 seconds. in the approximation tgr,1 = 3300 seconds, t12 = 12 hours would correspond to t12 = 13tgr,1. for ions with mass number a the frequencies fn behave like fgr,n(amp) ∝ a−nfgr,n(mp) whereas the cyclotron frequencies for ion do not depend on a in this case. same is true for fgr,1. p-adic length scale hypothesis [33] stating that p-adic length and time scales comes as powers of pn/2, predicts a length scale hierarchy which in the case of electron would with p = m127 = 2127 − 1 involves as the first member the compton length and the time scale .1 seconds assignable to the eeg alpha band as the secondary p-adic length scale. 3.3 a connection of the galactic blackhole with the comorosan effect? comorosan effect [4, 5] demonstrates rather peculiar looking facts about the interaction of organic molecules with visible laser light at wavelength λ = 546 nm (2.27 ev). as a result of irradiation molecules seem to undergo a transition s → s∗. s∗ state has an anomalously long lifetime and stability in solution. s → s∗ transition has been detected through the interaction of s∗ molecules with different biological macromolecules, like enzymes and cellular receptors. 1. the typical result in the enzyme-substrate interaction is represented by the enhancement of the enzymic rate, when the respective enzyme substrate is previously irradiated for certain sharply defined times. these efficient (irradiation) times are enzyme dependent and can also depend on the biological origin of the enzyme. they are always of the following type ti = i ∗ 5 sec, where i is a certain integer. 2. the general formula for the effective times is tk = tm + (k − 1)τn, k = 1, 2, .., 6, where tm is the minimum radiation time inducing the first effect and τn is the period between two consecutive effects [4, 5]. tm = met1 and τn = net1 are multiples of the basic time scale t1 = 5 sec: tk = (me +(k−1)ne)t1. the integers me and ne can be regarded as enzyme characteristics, depending however on the biological origin of the enzyme. this is suggestive of some kind of communication. what is remarkable is that the frequency of 5 s and its subharmonics appear universally so that the effect cannot depend on the details of the chemistry and the mechanism involved must be very general. second mystery is why the time scale is so long compared to the time scales of chemistry. note that also the time scales of replication and other basic biological operators are very long. i have considered several explanations for the comorosan effect in the tgd framework [14]. 1. the comorosan effect involves a reactant molecule and catalyst molecule as well as photons, which might feed energy to the system. the proposal has been that dark josephson junctions between reactant and catalyst appearing in the biocatalytic reaction are analogous to those assigned with the cell membrane [13]. the proposed interpretation is that dark josephson radiation is produced with certain subharmonics of the frequency .2 hz defined by the comorosan period fc = 5 s. why should the periods come as certain multiples of 5 s? 2. it would seem that the period τc = 5 s cannot naturally correspond to the gravitational compton time τgr(mbh , β0 = 1) ≃ 20 s. for β0 = 1/4, one would have a 5 s period equal to τc . for this option, λgr(bh) would correspond to the radius of the second bohr orbit for a planet around the sun. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2023 | volume 13 | issue 2 | pp. 111-125 123 pitkänen, m., neil gersching’s vision of self-replicating robots from tgd viewpoint 3. assuming cellular membrane potential evc = .05 ev and cooper pair (z = 2), this would give for heff = hgr(me ,mp) and fj = fgr(bh, β0 = 1/4), the estimate vs/vc ≃ .064, where evs is the josephson potential between substrate and reactant. received june 25, 2023; accepted december 9, 2023 references [1] 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[14] pitkänen m. wormhole magnetic fields. in quantum hardware of living matter. available at: https:/tgdtheory.fi/pdfpool/wormc.pdf, 2006. [15] pitkänen m. geometric theory of bio-harmony. in tgd based view about living matter and remote mental interactions: part ii. available at: https:/tgdtheory.fi/pdfpool/harmonytheory.pdf, 2018. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://arxiv.org/abs/hep-th/0512172 https://arxiv.org/abs/hep-th/0512172 https://arxiv.org/abs/astro-ph/0310036 https://www.futuremedicine.com/doi/pdf/10.2217/rme.11.69 https://www.futuremedicine.com/doi/pdf/10.2217/rme.11.69 https://www.ncbi.nlm.nih.gov/pubmed/22542702 https://www.ncbi.nlm.nih.gov/pubmed/22542702 https://tinyurl.com/ntlxpep https://paranormal.se/psi/pk/djur.html https://paranormal.se/psi/pk/djur.html https://tgdtheory.fi/pdfpool/mass4.pdf https://tgdtheory.fi/pdfpool/mass5.pdf https:/tgdtheory.fi/pdfpool/pulse.pdf https:/tgdtheory.fi/pdfpool/pulse.pdf https:/tgdtheory.fi/pdfpool/wormc.pdf https:/tgdtheory.fi/pdfpool/harmonytheory.pdf dna decipher journal | december 2023 | volume 13 | issue 2 | pp. 111-125 124 pitkänen, m., neil gersching’s vision of self-replicating robots from tgd viewpoint [16] pitkänen m. clustering of rna polymerase molecules and comorosan effect. available at: https: /tgdtheory.fi/public_html/articles/clusterrna.pdf., 2018. [17] pitkänen m. some comments related to zero energy ontology (zeo). available at: https: /tgdtheory.fi/public_html/articles/zeoquestions.pdf., 2019. [18] pitkänen m. a critical re-examination of m8 −h duality hypothesis: part i. available at: https: /tgdtheory.fi/public_html/articles/m8h1.pdf., 2020. [19] pitkänen m. a critical re-examination of m8 −h duality hypothesis: part ii. available at: https: /tgdtheory.fi/public_html/articles/m8h2.pdf., 2020. [20] pitkänen m. how to compose beautiful music of light in bio-harmony? https://tgdtheory.fi/ public_html/articles/bioharmony2020.pdf., 2020. [21] pitkänen m. is genetic code part of fundamental physics in tgd framework? available at: https: //tgdtheory.fi/public_html/articles/tih.pdf., 2021. [22] pitkänen m. tgd view of the engine powering jets from active galactic nuclei. https://tgdtheory. fi/public_html/articles/galjets.pdf., 2021. [23] pitkänen m. what could 2-d minimal surfaces teach about tgd? https://tgdtheory.fi/public_ html/articles/minimal.pdf., 2021. [24] pitkänen m. about tgd counterparts of twistor amplitudes: part i. https://tgdtheory.fi/ public_html/articles/twisttgd1.pdf., 2022. [25] pitkänen m. about tgd counterparts of twistor amplitudes: part ii. https://tgdtheory.fi/ public_html/articles/twisttgd2.pdf., 2022. [26] pitkänen m. about the number theoretic aspects of zero energy ontology. https://tgdtheory.fi/ public_html/articles/zeonumber.pdf., 2022. [27] pitkänen m. comparison of orch-or hypothesis with the tgd point of view. https://tgdtheory. fi/public_html/articles/penrose.pdf., 2022. [28] pitkänen m. how animals without brain can behave as if they had brain. https://tgdtheory.fi/ public_html/articles/precns.pdf., 2022. [29] pitkänen m. some new ideas related to langlands program viz. tgd. https://tgdtheory.fi/ public_html/articles/langlands2022.pdf., 2022. [30] pitkänen m. tgd view about water memory and the notion of morphogenetic field . https: //tgdtheory.fi/public_html/articles/watermorpho.pdf., 2022. [31] pitkänen m. the realization of genetic code in terms of dark nucleon and dark photon triplets. https://tgdtheory.fi/public_html/articles/darkcode.pdf., 2022. [32] pitkänen m. trying to fuse the basic mathematical ideas of quantum tgd to a single coherent whole. https://tgdtheory.fi/public_html/articles/fusiontgd.pdf., 2022. [33] pitkänen m. two objections against p-adic thermodynamics and their resolution. https:// tgdtheory.fi/public_html/articles/padmass2022.pdf., 2022. [34] pitkänen m. about platonization of nuclear string model and of model of atoms. https:// tgdtheory.fi/public_html/articles/nuclatomplato.pdf., 2023. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https:/tgdtheory.fi/public_html/articles/clusterrna.pdf https:/tgdtheory.fi/public_html/articles/clusterrna.pdf https:/tgdtheory.fi/public_html/articles/zeoquestions.pdf https:/tgdtheory.fi/public_html/articles/zeoquestions.pdf https:/tgdtheory.fi/public_html/articles/m8h1.pdf https:/tgdtheory.fi/public_html/articles/m8h1.pdf https:/tgdtheory.fi/public_html/articles/m8h2. pdf https:/tgdtheory.fi/public_html/articles/m8h2. pdf https://tgdtheory.fi/public_html/articles/bioharmony2020.pdf https://tgdtheory.fi/public_html/articles/bioharmony2020.pdf https://tgdtheory.fi/public_html/articles/tih.pdf https://tgdtheory.fi/public_html/articles/tih.pdf https://tgdtheory.fi/public_html/articles/galjets.pdf https://tgdtheory.fi/public_html/articles/galjets.pdf https://tgdtheory.fi/public_html/articles/minimal.pdf https://tgdtheory.fi/public_html/articles/minimal.pdf https://tgdtheory.fi/public_html/articles/twisttgd1.pdf https://tgdtheory.fi/public_html/articles/twisttgd1.pdf https://tgdtheory.fi/public_html/articles/twisttgd2. pdf https://tgdtheory.fi/public_html/articles/twisttgd2. pdf https://tgdtheory.fi/public_html/articles/zeonumber.pdf https://tgdtheory.fi/public_html/articles/zeonumber.pdf https://tgdtheory.fi/public_html/articles/penrose.pdf https://tgdtheory.fi/public_html/articles/penrose.pdf https://tgdtheory.fi/public_html/articles/precns.pdf https://tgdtheory.fi/public_html/articles/precns.pdf https://tgdtheory.fi/public_html/articles/langlands2022.pdf https://tgdtheory.fi/public_html/articles/langlands2022.pdf https://tgdtheory.fi/public_html/articles/watermorpho.pdf https://tgdtheory.fi/public_html/articles/watermorpho.pdf https://tgdtheory.fi/public_html/articles/darkcode.pdf https://tgdtheory.fi/public_html/articles/fusiontgd.pdf https://tgdtheory.fi/public_html/articles/padmass2022.pdf https://tgdtheory.fi/public_html/articles/padmass2022.pdf https://tgdtheory.fi/public_html/articles/nuclatomplato.pdf https://tgdtheory.fi/public_html/articles/nuclatomplato.pdf dna decipher journal | december 2023 | volume 13 | issue 2 | pp. 111-125 125 pitkänen, m., neil gersching’s vision of self-replicating robots from tgd viewpoint [35] pitkänen m. about the tgd based views of family replication phenomenon and color confinement. https://tgdtheory.fi/public_html/articles/emuanomaly.pdf., 2023. [36] pitkänen m. could neuronal system and even gpt give rise to a computer with a variable arrow of time? https://tgdtheory.fi/public_html/articles/gpt.pdf., 2023. [37] pitkänen m. is negentropy maximization principle needed as an independent principle? https: //tgdtheory.fi/public_html/articles/nmpcrit.pdf., 2023. [38] pitkänen m. magnetic bubbles in tgd universe: part i. https://tgdtheory.fi/public_html/ articles/magnbubble1.pdf., 2023. [39] pitkänen m. magnetic bubbles in tgd universe: part ii. https://tgdtheory.fi/public_html/ articles/magnbubble2.pdf., 2023. [40] pitkänen m. new findings related to the number theoretical view of tgd. https://tgdtheory. fi/public_html/articles/m8hagain.pdf., 2023. [41] pitkänen m. new result about causal diamonds from the tgd view point of view. https:// tgdtheory.fi/public_html/articles/cdconformal.pdf., 2023. [42] pitkänen m. reduction of standard model structure to cp2 geometry and other key ideas of tgd. https://tgdtheory.fi/public_html/articles/cp2etc.pdf., 2023. [43] pitkänen m. tgd view of michael levin’s work. https://tgdtheory.fi/public_html/articles/ levin.pdf., 2023. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://tgdtheory.fi/public_html/articles/emuanomaly.pdf https://tgdtheory.fi/public_html/articles/gpt.pdf https://tgdtheory.fi/public_html/articles/nmpcrit.pdf https://tgdtheory.fi/public_html/articles/nmpcrit.pdf https://tgdtheory.fi/public_html/articles/magnbubble1.pdf https://tgdtheory.fi/public_html/articles/magnbubble1.pdf https://tgdtheory.fi/public_html/articles/magnbubble2.pdf https://tgdtheory.fi/public_html/articles/magnbubble2.pdf https://tgdtheory.fi/public_html/articles/m8hagain.pdf https://tgdtheory.fi/public_html/articles/m8hagain.pdf https://tgdtheory.fi/public_html/articles/cdconformal.pdf https://tgdtheory.fi/public_html/articles/cdconformal.pdf https://tgdtheory.fi/public_html/articles/cp2etc.pdf https://tgdtheory.fi/public_html/articles/levin.pdf https://tgdtheory.fi/public_html/articles/levin.pdf introduction neil gersching's vision of self-replicating robots analogy of self-building robots in tgd turing's error is physics based on partial differential equations or information? the realization of the notions of assembly and tensegrity in the tgd universe what about consciousness? is the role of quantum gravitation essential also for computer consciousness? communication to mb and control by mb gravitational and p-adic hierarchies of frequencies a connection of the galactic blackhole with the comorosan effect? login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x dna decipher journal | october 2014 | volume 4 | issue 2 | pp. 141-160 141 pitkänen, m. pythagoras, music, sacred geometry and genetic code article pythagoras, music, sacred geometry and genetic code matti pitkänen 1 abstract a given triangle of icosahedron can contain 0, 1 or 2 edges of the cycle and the numbers of the triangles corresponding to these triangle types classify partially the notion of harmony characterized by the cycle. quint cycle suggests the identification for the single edge of curve as quint interval so that triangles would represent basic 3-chords of the harmony with 0,1, or 2 quints. octahedron and cube which are duals of each other and have 6 and 8 vertices respectively, and dodecahedron which is dual of icosahedron having 20 vertices and 12 faces. arabic music uses half intervals and scales with 19 and 24 notes are used. could 20-note scale with harmony defined by 5-chords assigned to the pentagons of dodecahedron have some aesthetic appeal? the combination of this idea with the idea of mapping 12-tone scale to a hamiltonian cycle at icosahedron leads to the question whether aminoacids could be assigned with the equivalence class of hamiltonian cycles under icosahedral group and whether the geometric shape of cycle could correspond to physical properties of amino-acids. the identification of 3 basic polar amino-acids with triangles containing no edges of the scale path, 7 polar and acidic polar amino-acids with those containing 2 edges of the scale path, and 10 non-polar amino-acids with triangles containing 1 edge on the scale path is what comes first in mind. the number of dnas coding for a given amino-acid could be also seen as such a physical property. the model for dark nucleons leads to the vertebrate genetic code with correct numbers of dnas coding for amino-acids. the treatment of the remaining 4 codons and of the well-known 21st and 22nd aminoacids requires the fusion of icosahedral code with tetrahedral code represented geometrically as fusion of icosahedron and tetrahedron along common face which has empty interior and is interpreted as ”empty” amino-acid coded by stopping codons. in this manner one can satisfy the constraints on the hamiltonian cycles, and construct explicitly the icosahedral hamiltonian cycle as (4,8,8) cycle whose unique modification gives (4,11,7) icosa-tetrahedral cycle. 1 introduction the conscious experiences generated by music demonstrate a fascinating connection between algebra and emotions. how can major and minor scale using different frequency ratios generate so different emotional experiences. this strongly suggests the we experience music as entire time interval, 4-d patterns rather than time=constant snapshots. also the ability remember the key and the tension lasting as long as the return to the basic key has not taken place, is example of this. one of the key questions is why octaves that is powers of 2 of the basic note of the scale are experienced as equivalent? one can also wonder what is behind consonance and dissonance. i have already earlier tried to understand music experience and considered some ideas inspired by p-adic numbers fields such as the idea that pythagorean scale coming as powers of 3 for the basic note modulo octave equivalence might relate to 3-adicity. reading of a book titled ”interference: a grand scientific musical theory” by richard merrick [6] freely available in web (http://interferencetheory. com/files/interference.pdf) re-stimulated my interest. in particular, i found the idea about a connection between music scale and harmonies with platonic solids (3-d ”sacred geometry”) as highly inspiring. the basic question was whether the 12-tone scale could be mapped to a curve going once through each point of icosahedron having 12 vertices and whether the 20 faces of icosahedron, which are triangles could define the basic chords in 12-tone scale. these curves are known as hamiltonian cycles and in the case 1correspondence: matti pitkänen http://tgdtheory.com/. address: köydenpunojankatu 2 d 11 10940, hanko, finland. email: matpitka@luukku.com. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. http://interferencetheory.com/files/interference.pdf http://interferencetheory.com/files/interference.pdf http://tgdtheory.com/ mailto:matpitka@luukku.com dna decipher journal | october 2014 | volume 4 | issue 2 | pp. 141-160 142 pitkänen, m. pythagoras, music, sacred geometry and genetic code of icosahedron there are 210 of them: those obtained from each other by rotation leaving icosahedron invariant are however equivalent. a given triangle of icosahedron can contain 0, 1 or 2 edges of the cycle and the numbers of the triangles corresponding to these triangle types classify partially the notion of harmony characterized by the cycle. quint cycle suggests the identification for the single edge of curve as quint interval so that triangles would represent basic 3-chords of the harmony with 0,1, or 2 quints. one can make same questions also for other platonic solidstetrahedron (4 vertices), octahedron and cube which are duals of each other and have (6 and 8 vertices respectively, and dodecahedron which is dual of icosahedron having 20 vertices and 12 faces. arabic music uses half intervals and scales with 19 and 24 notes are used. could 20-note scale with harmony defined by 5-chords assigned to the pentagons of dodecahedron have some aesthetic appeal? nowadays it is possible to develop electronically music based on this kind of scale and this kind of experimentation might be a fascinating intellectual and artistic adventure for a young composer. i have also played with the idea that the 20 amino-acids could somehow correspond to the 20 triangles of icosahedron. the combination of this idea with the idea of mapping 12-tone scale to a hamiltonian cycle at icosahedron leads to the question whether amino-acids could be assigned with the equivalence class of hamiltonian cycles under icosahedral group and whether the geometric shape of cycle could correspond to physical properties of amino-acids [4]. the identification of 3 basic polar amino-acids with triangles containing no edges of the scale path, 7 polar and acidic polar amino-acids with those containing 2 edges of the scale path, and 10 non-polar amino-acids with triangles containing 1 edge on the scale path is what comes first in mind. the number of dnas coding for a given amino-acid [5] could be also seen as such a physical property. the model for dark nucleons leads to the vertebrate genetic code with correct numbers of dnas coding for amino-acids. it is not however clear how to interpret dna codons geometrically. it however turns out that one can understand only the role of 60 codons in the icosahedral framework. the treatment of the remaining 4 codons and of the well-known 21st and 22nd amino-acids requires the fusion of icosahedral code with tetrahedral code represented geometrically as fusion of icosahedron and tetrahedron along common face which has empty interior and is interpreted as ”empty” amino-acid coded by stopping codons. in this manner one can satisfy the constraints on the hamiltonian cycles, and construct explicitly the icosahedral hamiltonian cycle as (4,8,8) cycle whose unique modification gives (4,11,7) icosa-tetrahedral cycle. 2 could pythagoras have something to give for the modern musicology? the ideas of pythagorean school about music were strongly based on the number theory of that time. so called modern approaches tend to seem music scales as cultural phenomena. there are however many reasons to suspect that pythagorean school might have been much nearer to truth. 2.1 pythagoras and transition from rational numbers to algebraic numbers pythagoras was one the greatest ancient mathematicians. the prevailing belief at that was that the world can be described solely in terms rational numbers. during the times of pythagoras the ancient mathematical consciousness had entered at the verge of a profound revolution: the time had become ripe for the discovery of algebraic numbers expanding rational numbers to an infinite series of algebraic extensions of rationals containing also rational multiples for finite number of algebraic numbers emerging as roots of polynomials with rational coefficients. euclid introduces square root geometrically as length of the diagonal of square. in ancient india it was discover 800-500 bc, possibly much earlier. unfortunately, the emergence of christianity stopped the evolution of mathematics and new progress began at times of newton when also reformation took place. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2014 | volume 4 | issue 2 | pp. 141-160 143 pitkänen, m. pythagoras, music, sacred geometry and genetic code the well-known but story (good story but probably not true) tells that a pupil of pythagoras demonstrated that the diagonal of unit square ( √ 2) cannot be rational number and had to pay with his life for the discovery. pythagoras himself encountered √ 2 through music theory. he asked what is the note exactly in the middle of the of the scale. modern mathematician would answer half of octave corresponding to the frequency ratio 21/2. algebraic numbers did not however belong to the world of order of pythagoras and he obtained to a non-satisfactory rational approximation of this number. this was very natural since only rational approximations of algebrais are possible in the experimental approach using only strings with rational number valued lengths. √ 2 represents the interval c−f# known as tritone and this this interval was associated with devil and its use was denied also by church. only after reformation√ 2 was accepted and this interval appears repeatedly in the compositions of bach. the amazing connections between evolution of mathematics and evolution of the religious beliefs inspires the question whether the evolution of consciousness could at basic level correspond to th evolution of the complexity of the number field behind the dynamics underlying consciousness. for instance, in tgd framework the vision about physics as generalized number theory allows one can to ask whether the mathematical evolution could have meant quite concretely the emergence of increasingly algebraic extensions of rationals for the coefficients of polynomials describing space-time surfaces serving as spacetime correlates of consciousness. 2.2 pythagoras and music pythagoras was both mathematician and experimentalist studying the world of musical experience experimentally. string instruments were his tool. the notion of frequency was not know at the time and length of vibrating part of string was the notion used. the experienced equivalence of notes differing by octave was known at that time and octave equivalence was understood as a fundamental symmetry of music manifesting itself as a scaling-by-2 symmetry for the length of a vibrating string. pythagoras developed 8 note scale cdefgahc (as a matter fact, 7 notes by octave equivalence) as we know as a combination of two scales efga and hcde using octave equivalence and it was established as the official music scale. pythagorean scale is expressed solely in terms of rational number valued ratios of the string length to that for the basic note of the scale (ratio of frequency to the fundamental). pythagorean scale (http://en.wikipedia.org/wiki/music_theory, http://en.wikipedia.org/wiki/ music_and_mathematics) is expressed solely in terms of powers of the the ratio 3/2 for lengths of vibrating strings correspond to an interval known and complete fifth (c-g). the series of complete fifths (c-g-da...) known as progression by fifths gives very nearly 7 octaves but not quite: (3/2)12 ' 128 + 1.75 = 27 +1.745. it would have been very natural to build 12-note scale as powers of rational (3/2) or by octave equivalence as powers of 3. the failure to close is very small but people with absolute ear experience the transponation of a melody to different key as dissonant since the frequency ratios do not remain quite same. at the time of bach (well tempered klavier) the equal tempered scale obtained by diving the logarithmic scale to 12 equally long parts emerged and replacing powers of 3/2 with the 12 powers of algebraic number 21/12 inside same octave even without octave equivalence emerged. by octave equivalence pythagorean scale means that all notes of the scale come in powers of 3 which strongly brings in mind 3-adicity. if one does not use octave equivalence when generalization of p-adicity to q-adicity with q = 3/2 is highly suggestive. q-adic numbers do not in general form number field, only an algebra. later more complex rational number based representations of scale using octave equivalence have been developed. the expression of the frequency ratios of the notes of the scale in terms of harmonic of fundamental modulo octave equivalence and involving only integers consisting of primes 2,3,5 is known as just intonation (http://en.wikipedia.org/wiki/music_and_mathematics). isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. http://en.wikipedia.org/wiki/music_theory http://en.wikipedia.org/wiki/music_and_mathematics http://en.wikipedia.org/wiki/music_and_mathematics http://en.wikipedia.org/wiki/music_and_mathematics dna decipher journal | october 2014 | volume 4 | issue 2 | pp. 141-160 144 pitkänen, m. pythagoras, music, sacred geometry and genetic code 2.2.1 music and platonic solids pythagoras was also aware of a possible connection between music scales and platonic solids. pythagoras is claimed to have discovered tetrahedron, hexahedron (cube) and dodecahedron while octahedron and icosahedron would have been documented by greek mathematician thaletus two hundred years later. the tetrachord and was assigned with tetrahedron and one and imagined that pythagorean scale could have been assigned with pair of tetrahedra somehow cube or octahedron which comes in mind. note that this would require that basic note and its octave should be regarded as different notes. these attempts inspire the question whether the mapping music scales to the vertices of platonic solids could provide insights about music experience. one can also ask whether there might be a mapping of music understood as melodies and chords in some scale to the geometries defined by platonic solids. 1. since 12-note scale is used in practically all classical western music and even in atonal music based on 12-note scale, the natural question is whether 12-note scale could be mapped to a connected, closed, non-self-intersecting path on icosahedron going through all 12 vertices and consisting of edges only. closedness would mean that base note and its octave are identified by octave equivalence. 2. this mathematical problem is well-known and curves of this kind are known as hamilton cycles and can be defined for any combinatorial structure defined by vertices and faces. hamilton proved that hamiltonian cycles (possibly identifiable as 20-note scale) at dodecahedron is unique module rotations and reflection leaving dodecahedron invariant. also in the case of tetrahedron and cube the hamiltonian cycle is unique. 3. for octahedron and icosahedron this is not the case [3] and there are both cycles containing only faces with at least 1 edge of the path and also cycles containing no faces containing no edges of the path. numerical experimentation is rather straightforward manner to determine hamiltonian cycles and h = 210 = 1024 cycles can be found. the number of topologically non-equivalent cycles (not transformable to each other by the isometries of icosahedron) is factor of this number. the group of orientation preserving isometries of icosahedron is the alternating group a5 of 60 even permutations of five letters. the full group of isometries is g = a5 × z2 containing n = 120 elements. 4. some subgroup of g leaves given path invariant and its order must be factor m of n so that topological equivalence class of cycles contains r = n/m elements. the number of topologically non-equivalent cycles in given class with h(top) elements is ntot = h(top)/r so that r must be a factor of h(top). before continuing it is good so summarize the geometry of icosahedron shortly. there are 20 faces which are triangles, 12 vertices, and 30 edges. from each vertex 5 edges. therefore the construction of hamiltonian cycles means that at each vertex on path one must select between four options edges since one cannot return back. this gives 412 = 224 ∼ 1.6 × 107 alternatives to be considered. therefore the numerical search should be relatively easy. keeping account of the points already traversed and not allowing self intersections, the actual number of choices is reduced. the construction requires labeling of the vertices of the icosahedron by integers 1,...,12 in some manner and defining 12 × 12 matrix a(i, j) whose element equals to 1 if vertices are neighbours and 0 if not. only the edges for with a(i, j) = 1 holds true are allowed on the path. a concrete representation of icosahedron as a collection of triangles in plane with suitable identifications of certain edges is needed. this helps also to visualize the classification of trianbles to three types discussed below. this can be found in the wikipedia article. 2.2.2 numbers of different triangles as characterizers of harmony a possible interpretation for topologically non-equivalent paths is as different notions of harmony. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. http://en.wikipedia.org/wiki/icosahedron dna decipher journal | october 2014 | volume 4 | issue 2 | pp. 141-160 145 pitkänen, m. pythagoras, music, sacred geometry and genetic code 1. proceeding in pythagorean spirit, the neighboring points would naturally correspond to progression by fifths that is scalings by powers of 3/2 or in equal temperated scale by powers of 27/12. this would mean that two subsequent vertices would correspond to quint. 2. the twenty triangles of the icosahedron would naturally correspond to 3-chords. triangles can contain either 0, 1, or 1 edges of the 12-edge scale path. the triangle containing 3 edges is not possible since it would reside on a self-intersecting path. a triangle containing one edge of path the chord would contain quint which suggest a chord containing basic note, quint and minor or major third. the triangle containing two edges would contain subsequent quints cdg is one possible example by octave equivalence. if the triangle contains no edges of the path one can say that the chord contains no quints. the numbers of triangles classified according to the number of path edges contained by them serves as the first classification criterion for a given harmony characterized by the hamiltonian cycle (note that one cannot exclude the possibly of non-closed paths since pythagorean construction of the scale by quints does not yield quite precisely octave as outcome). figure 1: there 3 different types of triangles characterized by the number of edges contained by them. this predicts chords with 0,1 or 2 quints. consider now the situation in more detail. 1. the topologically equivalent cycles must have same numbers of faces containing 0, 1, or 2 edges of the hamiltonian path since isometries do not change these numbers. let us denotes these numbers by n0, n1 and n2. the total number of faces is 20 so that one has n0 + n1 + n2 = 20 . furthermore, each of the 12 edges on the path is contained by two faces so that by summing over the numbers of edges associated with the faces one obtains twice the number of edges: 0× n0 + 1× n1 + 2× n2 = 2× 12 = 24 . from these constraints one can solve n0 and n1 as function of n2: n0 = n2 − 4 , n2 ≥ 4 , n1 = 24− 2n2 , n2 ≤ 12 . if these integers characterize the topological equivalence completely and if the allowed combinations are realized, one would have 12-4=8 topologically nonequivalent paths. the actual number is ntot = 2k, k ≥ 7, so that the integers cannot characterize the topology of the path completely. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2014 | volume 4 | issue 2 | pp. 141-160 146 pitkänen, m. pythagoras, music, sacred geometry and genetic code 2. the number of hamiltonian paths on icosahedron is known to be 2560 [1]. numerical calculations [2] suggest that the number of hamiltonian cycles is 210 = 1024. this would mean that the sum over the numbers n(n2) if cycles associated with differ values of n2 satisfies 12∑ n2=4 ∑ i n(n2, i)) = 210 . n(n2, i) is the number of paths of given topology with fixed n2. the numbers n(n2, i) are integers which are factors of n = 120 of the order of the isometry group of the icosahedron. the average of n(n2, i) is 27 = 128. 2.2.3 additional topological invariants characterizing the notion of harmony the interpretation of amino-acids in terms of 20 triangles of icosahedron interpreted as allowed chords for a given notion of harmony leads to a unique identification of thee integers ni as (n0, n1, n2) = (3, 10, 7). the attempt to interpret this ”biological harmony” leads to the identification of additional topological invariants characterizing the notion of harmony. it will be assumed that edges correspond to quints. if they would correspond to half-step the chords would contains 0, 1, or 2 subsequent half-intervals which does not conform with the usual views about harmony. in pythagorean scale quint corresponds to 3/2 and in equal tempered scale quint corresponds to the algebraic number number 27/12. above the attention was paid to the properties of the triangles in relation to the hamiltonian cycle. one can consider also the properties of the edges of the cycle in relation to the two neighboring triangles containing it. restrict first the attention to the biological harmony characterized by (n0, n1, n2) = (3, 10, 7). figure 2: the edge of the cycle belongs to 2 triangles, which as chords can correspond to 1 resp.2 , 1 resp. 1 and 2 resp. 2 quints. 1. everyone of the 12 quints c − g, c# − g#,... would be contained to neighboring triangles tht is 3-chords containing at least one quint. denote by p12, p11 resp. p22 denote the number of edges shared by 1-quint triangle and 2-quint triangle, by 2 1-quint triangles, resp. 2 2-quint triangles. besides pij ≥ 0 one has ∑ pij = 12 . since the cycle contains 12 edges. there are p12+2p11 = n1 1-quint triangles and (p12+2p22)/2 = n2 2-quint triangles (note double counting responsible for division by two). altogether this gives p22 = 12− p11 − p22 , p22 = p11 + n2 − n1 2 , p22 = n2 − p12 2 . isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2014 | volume 4 | issue 2 | pp. 141-160 147 pitkänen, m. pythagoras, music, sacred geometry and genetic code 2. these three diophantine equations are for integers and would allow for real numbers only single solution and for integers it in the generic case there are no solutions at all. situation changes if the equations are not independent which can happen if the integers ni satisfy additional conditions. by subtracting first and second and second and third equation from each other one obtains the consistency condition n1 = 24− 2n2 . this condition is however second of the conditions derived earlier so that only two equations, say the first two ones, are independent. p22 = p11 + n2 − n1 2 , p22 = n2 − p12 2 . giving p11 = (n1 − p12)/2 , p22 = p11 + n2 − n1 2 = n2 − p12 2 . . one must have 0 ≤ pij ≤ 12 and p12 ≤ n1 from p11 = (n1 − p12)/2. here one has p12 ∈ {0, 2, ...min{12, 2n2, n1} so that min{7, n2 + 1, [n1/2] + 1} solutions are possible. the condition that the cycle has no self-intersections can forbid some of the solutions. 3. the first guess for the ”biological harmony” possibly associated with amino-acids would be (n0, n1, n2) = (3, 10, 7): this if one neglects the presence of 21st and 22th amino-acid also appearing in proteins. it turns out that a more feasible solution fuses tetrahedral code and icosahedral codes with (n0, n1, n2) = (4, 8, 8) giving (n0, n1, n2) = (4, 11, 7) for icosatetrahedral code. for instance, (n0, n1, n2) = (3, 10, 7) would give p12 ∈ {0, 2, 4, 6, 8, 10}, p11 ∈ {5, 4, 3, 2, 1, 0}, p22 ∈ {7, 6, 5, 4, 3, 2} so that one has 6 alternative solutions to these conditions labelled by p12. the number of neighboring triangles containing single quint is even number in the range [0, 10]: this brings in mind the possibility that the neighboring single quint triangles correspond to major-minor pairs. clearly, the integer p12 is second topological invariant characterizing harmony. 2.2.4 distribution of different types of edges also the distribution of the 12 edges to these 3-types is an invariant characterizing the shape of the curve and thus harmony as isometric invariant. figure 3: also the distributions for three types of edges matter. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2014 | volume 4 | issue 2 | pp. 141-160 148 pitkänen, m. pythagoras, music, sacred geometry and genetic code 1. p12 1-1 edges can be chosen in n(1− 1, p12) = ( 12 p12 ) manners and 1-2 edges in n(1− 2, p12) = ( 12− p12 p12 ) manners. the remaining 2-2 edges can be chosen only in one manner. this gives altogether n(p12) = n(1− 1, p12)×n(1− 2, p12) manners for given value of p12. to summarize, one obtains large number of notions of harmony are possible although one cannot expect that the absence of self-intersections does not allow all topologies for the cycle. 2.3 would you come to icosadisco with me? this map would allow one-to-one map of the notes of any music piece using icosahedral geometry. if octave equivalence is assumed, a given note would be mapped to a fixed vertex of icosahedron at which lamp is turned on and also to the wavelength of the light in question since visible light spans an octave. chords would correspond to the turning on of lights for a group of icosahedral points. icosahedrons with size scaled up by two could correspond to octave hierarchy: for practical purposes logarithmic scale implying that icosahedrons have same distance would be natural as in the case of music experience since piano spans 7 octaves and human ear can hear 10 octaves. church would nowadays allow icosadiscos to use also half octaves to amplify further the audiovisual inferno effect so characteristic for discos. one could also try to realize special effects like glissandos, vibratos and tremolos. 3 connection between music molecular biology? music affects directly emotions, and consciousness is one aspect of being living. this raises the question whether the platonic geometries might have something to do with basic building bricks of life and with genetic code. 3.1 could amino-acids correspond to 3-chords of icosahedral harmony? the number of amino-acids is 20 and same as the number of triangular faces of icosahedron and the vertices of dodecahedron. i have considered the possibility that the faces of icosahedron could correspond to amino-acids [7]. combined with the idea about connection between music scale and icosahedron this inspires the following consideration. 1. for a proper choice of the mapping of the 12-note scale to the surface of icosahedron the 20 triangles could correspond to 20 amino-acids analogous to 3-chords and that the 3 types of 3-chords could correspond to 3 different classes of amino-acids. one can of course consider also the mapping of amino-acids to a unique sequence of 20 vertices of dodecahedron representing 20-note scale or 20-chord scale and replacement of the 3-chords defining the harmony with 12 5-chords. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2014 | volume 4 | issue 2 | pp. 141-160 149 pitkänen, m. pythagoras, music, sacred geometry and genetic code 2. amino-acids are characterized by the non-constant side chain and these can be classified to three categories: basic polar, non-polar, and polar (http://en.wikipedia.org/wiki/amino-acids). the numbers of amino-acids in these classes are a0 = 3, a1 = 10, a2 = 7. could these classes correspond to the numbers ni characterizing partially some topological equivalence classes of hamiltonian paths in icosahedron? there is indeed a candidate: a0 = n0 = 3, a1 = n1 = 10, a2 = n2 = 7 satisfies the conditions discussed above. 3 basic polar amino-acids would correspond to the triangles with no edges on the hamiltonian cycle, 10 non-polar amino-acids to triangles containing one edge, and 7 acidic polar and polar amino-acids to those containing two edges. one can criticize the combination of polar and acidic polar amino-acids in the same class. one can also classify amino-acids to positively charged (3), negatively charged (2) and neutral (15) ones. in this case the condition is however not satisfied. thus the proposal survives the first test assuming of a course that these hamiltonian cycles exist! this has not been proven and would require numerical calculations. 3. as found hamiltonian paths have also other topological characteristics and they could correspond to physical characteristics and it would be interesting to see what theyh are. to proceed further one should find the total number of the hamiltonian paths with n2 = 7 and identify the isometries of different topological equivalence class having n2 = 7. amino-acid sequences would correspond to sequences of 3-chords. the translation of mrna of gene to amino-acid sequence would be analogous to the playing of a record. the ribosome complex would be the record player, the amino-acid sequence would be the music, and mrna would be the record. hence genes would define a collection of records characterizing the organism. 3.2 can one understand genetic code? what remains open is the interpretation of genetic code [5]. dna triplets would correspond naturally to triangles but why their number is 64 instead of 20. they would be obviously the analogs of written notes: why several notes would correspond to the same chord? 1. could different dna triplets coding for the same amino-acid correspond to various octaves of the chord? the most natural expectation would be that the number of octaves so that one would have 3 dnas would code single amino-acid and stopping codon would correspond to 4 dnas. it is difficult to understand why some 3-chords could correspond to 6 octaves and one of them only one. 2. could the degeneracy correspond to the ordering of the notes of the 3-chord? for the 3-chords there are 6 general orderings and 3 cyclic orderings modulo octave equivalence and characterizing by the choice of the lowest note. the simplest assumption would be that the allowed orderings degeneracies are characterized by a subgroup of the cyclic group s3 yielding the allowed permutations of the notes of the chord. the subgroup orders for s3 are 1,2,3, and 6. the allowed degeneracies are 6,4,3,2, and 1 so that this identification fails for d = 4. 3. could the different correspondences between dna codons and amino-acids correspond to the different topological equivalence classes of n2 = 7 hamiltonian cycles. this does not seem to be the case. the number of different dna-amino-acid correspondences obtained by choosing one representative from the set of dnas coding for a given amino-acid (and not stopping sign) is the product of the numbers d(ai) coding amino-acid ai. from the table below this number is given by 63 × 45 × 31 × 29 × 12 = 34 × 221 and clearly much larger than n = 210. 4. could the different codons coding for codon code for some additional information so that aminoacids would in some aspect differ from each other although they are chemically identical? here the magnetic body of amino-acid is a natural candidate. this would suggest that the folding pattern of the protein depends on what dna sequence codes it. this information might be analogous to the information contained by notes besides the frequencies. durations of notes corresponds is the most isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. http://en.wikipedia.org/wiki/amino-acids dna decipher journal | october 2014 | volume 4 | issue 2 | pp. 141-160 150 pitkänen, m. pythagoras, music, sacred geometry and genetic code important information of this kind: the only candidate for this kind of information is the value of heff = n × h associated with the amino-acid magnetic body determining its size scale. magnetic fields strength could be also code by dna codon besides amino-acid. d 6 4 3 2 1 n 3 5 2 9 2 table 1. the number of amino acids n associated with a given degeneracy d telling the number of dna triplets mapped to the amino acid in the genetic code. the degeneracies are always smaller than 7 as predicted by the proposed explanation of the genetic code. second question concerns genetic code itself. could the dna degeneracies d(ai) (number of dnas coding for amino-acid ai) be understood group theoretically in terms of icosahedral geometry? the triangles of the icosahedron are mapped the triangles under the isometries. 1. one can start by looking the table 1 for the genetic code telling the number n(d) of amino-acids coded by d dna codons. one finds that one can divide dnas to three groups containing n = 20, n = 20, resp. n = 21 codons. (a) there are 3 amino-acids codes by 6 codons and 2 amino-acids coded by 1 dna: 3×6+2×1 = 20 codons altogether. note: one could also consider 1 amino-acid coded by 2 codons instead of 2 coded by 1 codon 3× 6 + 1× 2 = 20. (b) there are 5 amino-acids coded by 4 codons making 5× 4 = 20 codons altogether. (c) there are 9 amino-acids coded by 2 codons and 1 by 3 codons making 9 × 2 + 1 × 3 = 21 codons. note: one could also consider the decomposition 8× 2 + 2× 1 + 1× 3 = 21 codons implied if 1 amino-acid is coded by 2 codons in the first group. this makes 61 codons. there are however 64 codons and 3 codons code for stopping of the translation counted as ”empty” amino-acid in the table. 1. this would suggest the division to 60 + 4 codons. the identification of additional 4 codons and corresponding amino-acids is not so straightforward as one might first think. 3 of the 4 additional codons could code for ”empty” amino-acid (ile) and 1 of them to ile (empty amino-acid). 2. what suggests itself strongly is a decomposition of codons in 3 different manners. 3 groups of 6 codons plus 2 groups of 1 codon (1 group of 2 codons), 5 groups of 4 codons, and 10 groups of 2 codons (9 groups of 2 codons plus plus 2 groups of 1 codon). this kind of decompositions are induced by the action on the triangles of icosahedron by thee subgroups of the isometry group a5×z2 of the icosahedron having 120 = 2×2×2×2×3×5 elements and subgroups for which number of elements can be any divisor of the order. the orbit associated with a subgroup with n elements has at most n triangles at its orbit. this allows immediately to deduce the values of n possibly explaining the genetic code in the proposed manner. 1. the 3 amino-acids coded by 6 codons must correspond to n = 6. this subgroup must have also two 1-element orbits (1 2-element orbit): in other words, 2 triangles must be its fixed points (form its orbit). (a) the non-abelian group s3 permuting the vertices of is the first candidate for the subgroup in question. the triangles at the opposite sides of the icosahedron remain invariant under these permutations. s3 however has two orbit consisting of 3 triangles which are ”wall neighbours” of the triangles which remains fixed. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2014 | volume 4 | issue 2 | pp. 141-160 151 pitkänen, m. pythagoras, music, sacred geometry and genetic code (b) second candidate is the abelian group z̃2 × z3. here z3 permutes the vertices of triangle and z̃2 is generated by a reflection of the triangle to opposite side of icosahedron followed by a rotation by π. this group has 3 orbits consisting of 6 triangles and 1 orbit consisting of 2 triangles (the triangles at opposite side of icosahedron). this group seems to be the only working candidate for the subgroup in question. 2. the 5 amino-acids coded by 4 codons must correspond to n = 4 and therefore to z̃2 × z2. this is indeed subgroup of icosahedral group which permutes triangles at the vertices of inscribed tetrahedron. now all orbits contain 4 triangles and one must have 5 orbits, which are obtained by acting on the 5 triangles emanating from a given vertex. note that also z5 is subgroup of icosahedral group: this would give a variant of code with 4 amino-acids coded by 5 codons if it were possible to satisfy additional consistency conditions. 3. consider next the group consisting of 9 amino-acids coded by 2 codons and ile (”empty” aminoacid) coded by 3 codons. since only the z̃2×z3 option works, this leaves 9 amino-acids coded by 2 codons and 2 amino-acids coded by 1 codon. the subgroup must correspond to n = 2 and thus z2 acting on fixed triangle and leaving it and its z̃2 image invariant. one has 9 2-triangle orbits and two single triangle orbits corresponding to the triangles at the opposite sides of the icosahedron. the 9 amino-acids coded by 2 codons are all real or 8 of them are real and 1 corresponds to ”empty amino-acid” coded by two codons. 3-element orbits are lacking and this forces to consider a fusion of of icosahedral code with tetrahedral code having common ”empty-acid” common triangle of icosahedron and tetrahedron) coded by 2 icosahedral codons and 1 tetrahedral codon. ile would be coded by 3 codons assignable to the orbit of z3 subgroup of tetrahedral symmetry group s3 and would be associated with the tetrahedron. this would predict 2 additional amino-acids which could be understood by taking into account 21st and 22nd amino-acid (sec and pyl [4]). the hamiltonian cycle is not explicitly involved with the proposed argument. some property of the cycle respected by the allowed isometries might bring in this dependence. in pythagorean spirit one might ask whether the allowed isometries could leave the hamiltonian cycle invariant but move the vertices along it and induce a mapping of faces to each other. the amino-acid triangle at given orbit cannot be chosen freely. the choices of amino-acid triangles associated with the three groups of 20 dnas must be different and this gives geometric conditions for the choices of the three subgroups and one can hope that the assignment of amino-acid toa given triangle is fixed about from rotational symmetries. 3.2.1 does the understanding of stopping codons and 21st and 22nd amino-acids require fusion of tetrahedral and icosahedral codes? several questions remain. could one also understand the additional 4 dna codons? could one understand also how one of them codes amino-acid (ile) instead of stopping codon? can one related additional codons to music? 3.2.2 attachment of tetrahedron to icosahedron as extension of isosahedral code the attachment of tetrahedron to icosahedron allows to understanding both stopping codons and ”empty” amino-acid as well as the 21th and 22nd amino-acids geometrically. 1. something is clearly added to the geometric structure, when 4 additional dna codons are brought in. they could represent orbits of faces of platonic solid with 4 faces. the four faces are most naturally triangles and actually must be so since tetrahedron is the only platonic solid having 4 faces and its faces are indeed triangles. tetrahedron has symmetry group s3 containing z3 and isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2014 | volume 4 | issue 2 | pp. 141-160 152 pitkänen, m. pythagoras, music, sacred geometry and genetic code z2 as subgroups. z3 leaves one of the tetrahedral triangles invariant so that one has two orbits consisting of 1 and 3 triangles respectively. 2. one amino-acid is coded by 3 rather than only 2 codons. one can indeed understand this symmetry breaking geometrically. if the tetrahedron is attached on icosahedron along one of its triangular faces and this icosahedral face corresponds to amino-acid (ile) belonging to a 2-triangle orbit under icosahedral z2 one obtains 3 codons coding for ile! i have actually proposed earlier a model involving attachment of tetrahedrons to icosahedron as a model for genetic code. 3. tetrahedron should bring in three additional amino-acids. ”empty” amino-acid could correspond to either one of them or to the common base triangle which is indeed geometrically in unique position. one could even demand that this triangle is ”empty” so that icosatetrahedron would be non-singular continuous manifold. this would mean exchange of the roles of ile and empty amino-acid both being coded by three codons. the 3-triangle orbit outside the icosahedron would correspond to ile and base triangle to empty amino-acid or vice versa. base triangle would be coded by 1 tetrahedral codon plus 2 icosahedral codons. one of the outsider triangles corresponds to ”empty” amino-acid or ile but two other triangles to two new exotic amino-acids. in some species there indeed are 21st and 22nd amino-acids (selenocysteine and pyrrolysine, http://en.wikipedia.org/wiki/amino_acid) with sulphur replaced with selene. this modification does not change the polarity properties of cys and lys: cys is non-polar and lys basic polar implying (n0, n1, n2)→ (4, 11, 7). 4. the naive assumption (n0, n1, n2) = (3, 10, 7) before the modification need not be correct and the numerous futile attempts to construct this cycle and the argument below for construction of icosahedral hamilton cycle suggests that (n0, n1, n2) = (4, 8, 8) is more feasible option. 5. the two outsider tetrahedral triangles could correspond to the orbits of z2 subgroup of s3 acting as reflection with respect to media of the bottom triangle. outside faces form orbits consisting of 1 triangle and 2-triangles. these orbits could correspond to 21st and 22nd amino-acids coded by 1 and 2 exotic variants of stopping codons respectively. the 2 exotic amino-acids are however coded by codons which are usually interpreted as stopping codons. something must however distinguish between standard and exotic codings. is it ”context” giving different meaning for codons and perhaps characterized by different magnetic bodies of codons? the base triangle is counted neither as amino-acid nor as a part of the ”icosatetrahedron”. the interpretation is natural since the resulting topological structure is non-singular and defines a continuous albeit not differentiable manifold topology (sphere). 3.2.3 how the icosahedral hamiltonian cycle is modified? the properties of exotic amino-acids give constraints on how the modification of the hamiltonian cycle should be carried out. the naive expectation that the outer triangles of added tetrahedron correspond to ”empty” amino-acid and 2 exotic amino-acids is not correct. a more appropriate interpretation is as a fusion of icosahedral and tetrahedral codes having common ”empty amino-acid” coded 2 icosahedral and 1 tetrahedral 1 stopping codons respectively and obtained by gluing these platonic solids together along the triangle representing the ”empty” amino-acid. that the common triangle corresponds to ”empty” aminoacid means geometrically that its interior is not included so that the resulting structure is continuous manifold having topology of sphere. consider now the detailed construction. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. http://en.wikipedia.org/wiki/amino_acid dna decipher journal | october 2014 | volume 4 | issue 2 | pp. 141-160 153 pitkänen, m. pythagoras, music, sacred geometry and genetic code figure 4: icosatetrahedron is obtained by attaching tetrahedron along one of its faces to icosahedron. the resulting structure is topological manifold if the common face is replaced with empty set and it is natural to identify it as ”empty” aminoacid. 1. one should be able to modify the icosahedral hamiltonian cycle so that the numbers (n0, n1, n2) charactering icosahedral cycle change so that they conform with the properties of the two exotic amino-acids. selenocystein (sec) is nonpolar like cys and pyrrolysine (pyl) basic polar like lys so that (4, 11, 7) seems to be the correct characterization for the extended system. one must have (n0, n1, n2)→ (4, 11, 7). 2. one must visit the additional vertex, which means the replacement of one edge from the base triangle with wedge visiting the additional vertex. there are several cases to be considered depending on whether the base triangle is 1-quint triangle or 2-quint triangle, and what is the type of the edge replaced with wedge. one can even consider the possibility that the modified cycle does not remain closed. if the icosahedral cycle has (n0, n1, n2) = (3, 10, 7), the value of n2 is not changed in the construction. for a closed cycle edge is replaced with wedge and the only manner to preserve the value of n2 is that the process producing 1 tetrahedral 2-quint triangle transforms 1 icosahedral 2-quint triangle identified as base triangle to 1-quint triangle. if the replaced edge of base triangle is of type 2-1, one has n1 → n1 + 1 since one icosahedral 1-quint triangle disappears and 2 tetrahedral ones appear. icosahedral n0 increases by 1 units. hence the condition (3, 10, 7) → (4, 11, 7) would be met. it however seems that (4, 8, 8) is more promising starting cycle as the argument below shows. 3. the number options is at most the number n2 of 2-quint triangles serving as candidates for ”empty” amino-acid. an additional condition comes from the requirement that replaced edge is of type 2-1. 3.2.4 direct construction of hamiltonian cycle corresponding to bioharmony consider bio-harmony as an example about hamiltonian cycle taking seriously the extension of the genetic code. i have made very many unsuccessful triangles starting from the assumption that icosahedral cycle isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2014 | volume 4 | issue 2 | pp. 141-160 154 pitkänen, m. pythagoras, music, sacred geometry and genetic code figure 5: the modification of (4, 4, 8) icosahedral hamiltonian cycle consistent with the constraints that icosatetrahedral cycle corresponds to (4, 11, 7) consistent the classification of amino-acids in three classes. satisfies (n0, n1, n2) = (3, 10, 7), and the following proposal starts from different icosahedral cycle. the following is just a trial, which should be checked by a direct calculation. 1. the most obvious guess for the cycle to be modified to cycle at icosatetrahedron having (n0, n1, n2) = (4, 11, 7) (the triangle corresponding to ”empty” amino-acid is not counted) is (n1, n2, n3) = (3, 10, 7). i have not found cycle with these characteristics. 2. it seems however possible to find cycle with (n1, n2, n3) = (4, 8, 8). from this can obtain the desired kind of extended cycle if the ”empty” triangle is 2-quint triangle and the edge replaced with the wedge is of type 2-2. the replacement of icosahedral edge eliminates two icosahedral 2-quint triangles and generates 1 tetrahedral 2-quint triangle giving n2 → n2 − 2 + 1 = n2 − 1 = 7. the disappearance of the icosahedral edge generates two icosahedral 1-quint triangles of which second one corresponds to empty amino-acid and is not counted and 2 tetrahedral 1-quint triangles giving n1 → n1 + 3 = 11. the figure below represents the construction of cycle (4, 8, 8, ). the icosahedron is constructed from regions p (i) glued to the triangle t along one edge each. the arrows indicate that the one pair of edges of type 1 and 2, 1 and 3 and 3 and 2 are identified. also the long edges i of t are identified with pairs of subsequent edges of p (i) as the arrows indicate. 3.2.5 stopping codons and music what could be the interpretation of the attached tetrahedron in terms of music harmony? the attachment of tetrahedron means addition of an additional note to the 12-note scale. the scale constructed in pythagorean spirit identifying quint as scaling by 3/2 contains the 12th note as scaling by (3/2)12 of the basic frequency modulo octave equivalence. this is slightly more than scaling by 27 so that exact octave is not obtained. the attempt to solve this problem has lead to scales in which one allows a pair of notes with a very small interval between them say g# and ab being regarded as different notes. this suggests that the outsider vertex of the attached tetrahedron corresponds to a note very near to some note of the 12-note scale. which note is in question depends on which of the 10 1-quint triangles is chosen as the base triangle. this is expected to imply additional refinements to the notion of bio-harmony. 2 or three additional 3-chords emerge depending on whether empty amino-acid is interpreted as a real chord. this could also allow to understand why it is natural to have non-closed hamiltonian path on tetraicosahedron. octave equivalence requiring closedness indeed fails in pythagorean scale. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2014 | volume 4 | issue 2 | pp. 141-160 155 pitkänen, m. pythagoras, music, sacred geometry and genetic code figure 6: a proposal for a hamilton cycle realizing bio-harmony (n1, n2, n3) = (4, 8, 8) allowing extension to cycle (3, 11, 7) on tetraicosahedron. circled ”0”, ”1” and ”2” indicates whether a given small triangle is 0-, 1-, or 2-quint triangle. it is relatively easy to verify that the condition (n1, n2, n3) = (4, 8, 8) for bio-harmony is satisfied. 3.2.6 geometric description of dna-amino-acid correspondence the mathematical structure which suggests itself is already familiar from some earlier attempts to understand genetic code [8]. for icosahedral part of code one would have a discrete bundle structure with 20 amino-acids defining the base space and codons coding the amino-acid forming the fiber. the number of points in the fiber above based point depends on base point and is the number of codons coding the corresponding amino-acid. a discrete variant of singular fiber bundle structure would be in question. forgetting for a moment the 4 troublesome codons, the bundle would be the union of the orbits associated with groups s3, z4 and z2 of icosahedral group, and the base would consist of 20 amino-acids, one for each orbit. the point of orbit must be selected so that the selections for orbits of two different groups are different. the addition of the additional codons, empty aminoacid and two exotic amino-acids would mean gluing of tetrahedron along one of its faces to icosahedron. this would induce extension of the singular bundle like structure. to each of the new faces one would attach the orbit of triangles representing the codons coding for the corresponding amino-acid. to sum up, in its strongest form the model makes several purely mathematical predictions, which could easily kill it. 1. the identification of the 3-chords assignable to the triangles of the icosahedron. 2. the existence of n2 = 7 hamiltonian cycle requiring however the lumping of acidic polar and polar isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2014 | volume 4 | issue 2 | pp. 141-160 156 pitkänen, m. pythagoras, music, sacred geometry and genetic code amino-acids in the same class. 3. the possibility to select one representative of amino-acid from each group orbit (s3, z4, z2) such that all amino-acids are different is non-trivial and one should prove that this is possible. one must decompose the set of amino-acids to orbits in 3 different manners (s3, z4, z2) into orbits and select for each decomposition 1 representative from each orbit such that the selection contains all 20 triangles. 3.3 how could one construct the hamiltonian cycles on icosahedron with a minimal computational work? although the construction of hamiltonian cycles is known to be an np hard problem for a general graph, one can hope that in case of platonic solids having high symmetries, a direct construction instead of straightforward numerical search might work. the following is a proposal for how one might proceed. it relies on paper model for icosahedron. 1. the basic observation about one can get convinced by using paper model is following. one can decompose the surface of icosahedron to three regions p (i), i = 1, 2, 3, with pentagonal boundary and containing 5 triangles emanating from center vertex plus one big triangle t containing 4 pentagonal triangles and one lonely small triangle t opposite to it. these 5 regions span the surface of icosahedron. there is clearly a symmetry breaking and there is great temptation to assume that t corresponds to the triangle along which the tetrahedron is glued to the icosahedron in the model of genetic code realizing the modification of icosahedral cycle for which the first guess is (3, 7, 10) but for which also (4, 8, 8) can be considered. 2. the hamiltonian cycle must visit at the centers of each p (i): one enters pentagonal region p (i), i = 1, 2, 3 along one of the five interior edges beginning at pentagonal vertex ai,i, i = 1, .., 5 and leaves it along second edge ending at vertex bi,j , j 6= 5. one can call these edges interior edges. the edges at boundaries of p (i) can be called boundary edges. interior edge can correspond to |i− j| = 0, 1 or i− j > 1. for |i− j| = 1 the interior edge gives rise to 2-quint triangle. for i− j = 0 there is no boundary edge after b(i, j). 3. pentagonal boundary edges come in three types. 2 of them are shared with t , 1 with t opposite to it, and 2 with another pentagonal region p (i). one can label p (i) in such a manner that the p (i) shares two boundary edges with p (i + 1). the boundary edges of small and big triangle are boundary edges of the 3 pentagonal regions so that they are not counted separately. 4. one can assume that the cycles begins from a vertex of t . since the cycle is closed it returns back to this vertex. the last edge is either at the boundary of t or goes through one or two edges of the small interior triangle of t so that this triangle is either 0-,1or 2-quint triangle. t can be 0-, 1-, or 2-quint triangle. 5. the total number of the interior edges inside the 3 pentagonal regions is 3 × 2 = 6 so that 6 remaining edges must be boundary edges associated with p (i) and interior edges of t : otherwise one would visit some pentagonal center twice and self-intersection would occur. the boundary edges associated with t and t are boundary edges of p (i), i = 1, 2, 3 6. at the vertex b(i, j) of pentagonal region one must turn right or left and move along the boundary edge. one can move at most ni = 4−j boundary edges along the pentagonal boundary in clockwise direction and ni = j− 2 edges in counterclockwise direction (clockwise is the direction in which the index labelling 5 vertices grows). the maximum number of boundary edges is 3 and obtained for j − i± 1. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2014 | volume 4 | issue 2 | pp. 141-160 157 pitkänen, m. pythagoras, music, sacred geometry and genetic code 7. the condition ∑ ni + n(t ) = 6, where n(t ) = 1, 2 is the number of interior edges of t , holds true so that one has ∑ n(i) ≡ ntot ∈ {4, 5}. the numbers and types (shared with pentagon, t , or t) of the boundary edges of p (i), the differences ∆(i) = ji − ii , the number of edges in t and the number of interior edges of t characterize the hamiltonian cycle besides the condition that it is closed. the closedness condition seems possible to satisfy. one must enter big triangle through one of the vertices of t and this vertex is uniqely determined once the third pentagon is fixed. one can therefore hope that the construction gives directly all the hamiltonian cycles with relatively small amount of failed attempts, certainly dramatically smaller than n = 224 ∼ 107 of blind and mostly un-succesful trials. 8. each p (i) containing boundary edges gives rise to least 2 2-quint triangles associated with bi(i) and ai+1. if all 3 p (i) have |i − j| > 1, one has n2 = 3 × 2 = 6. the contribution of regions p (i) is larger if some pentagon interiors have |∆(i)| = |j(i) − i(i)| = 1. |j(i) − i(i)| = 1 gives ∆n2(i) = 1 and ∆n1(i) = 0 since 2 1-quint triangles are replaced with single 2-quint triangle. the interior of the t can give 1 2-quint triangle. 9. the number n1 of 1-quint triangles can be estimated as follows. (a) each pentagonal interior edge pair leading from a(i, j) to b(i, j) contributes 2 1-quint triangles for ∆(i) 6= ±1, otherwise one obtains only 1 2-quint triangle. this would give maximum number of 6 1-quint triangles associated with the interior edges of 3 pentagons. (b) p (i) pentagonal boundary edges contribute 2× (p (i)− 1) additional 1-quint triangles. (c) t contributes at most 4 1-quint triangles. (d) t can correspond 1-quint triangle and would do so if the interpretation of extended code is correct. 10. the construction also breaks the rotational symmetry since the decomposition of icosahedron to regions is like gauge fixing so that one can hope of obtaining only single representative in each equivalence class of cycles and therefore less than 210. by the previous argument related to icosatetrahedral code, t and the triangle opposite to it cannot however correspond to amino-acids coded by 1 codon as one might guess first. rather, t corresponds to ”empty” aminoacid and to 1-quint triangle belonging to z2 orbit. the number of cycles should be 210. one can try to estimate this number from the construction. each bi,j can be chosen in 4 manners at the first step but at later steps some vertices of the neighboring pentagon might have been already visited and this reduces the available vertices by n+ 1 if n subsequent edges are visited. at each vertex bi,j one has 4 options for the choice of the boundary edges unless some boundary edges of pentagon (shared with other pentagons) have been already visited. it is also possible that the number of boundary edges vanishes. one can start from any vertex of triangle. this gives the upper bound of 24 choices giving n < 212 paths going through 4 pentagon-like regions. the condition that the path is closed, poses constraints on the edge path assignable to t but the number of choices is roughly 24. the condition that path goes through all vertices and that no edge is traversed twice must reduce this number to 210. the numerical construction of hamiltonian cycles should keep account about the number of vertices visited and this would reduce the number of candidates for b(i, j) and for the choices of p (i) for i > 1 as well as the number of edge paths associated with t . isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2014 | volume 4 | issue 2 | pp. 141-160 158 pitkänen, m. pythagoras, music, sacred geometry and genetic code 4 other ideas the book of merrick discusses also other ideas. the attempts to understand music in tgd framework relate to these ideas. 4.1 p-adic length scale hypothesis and music one of the key ideas is the reduction of the octave phenomenon to the p-adic length scale hypothesis predicting that octaves and half-octaves correspond to p-adic scalings allowed by the hypothesis p ' 2k for the preferred values of the p-adic primes, and yielding scaled variants of physical systems. this idea will not be discussed in the following: suffice it to say that pythagorean scale coming as powers of p = 3 strongly suggests approximate 3-adicity. 4.2 eeg and music first of the key ideas relates to the idea that genetic code relates to the music scale. 1. music metaphor is key element of tgd inspired view about biology and neuroscience. in particular, tgd based view about dark matter leads to the proposal that bio-photons are ordinary photons resulting as transformations of dark photons with large planck constant heff = nh to ordinary photons. the further hypothesis is that the energy spectrum of bio-photons is universal and contains visible photons and uv photons, which defined transition energies of biomolecules. this hypothesis follows if the value of heff assignable to a magnetic flux tube characterizes ion and is proportional to its mass number. the notion of gravitational planck constant identified as hgr = gmm/v0, where v0 is a velocity parameter assignable to the two-particle system can be identified in the case of elementary particles and ions with heff and predicts also the universality of bio-photon spectrum. 2. in this framework bio-photons would represent music as light inducing molecular transitions. notes that is different energies of bio-photons would correspond to different magnetic field strengths at magnetic flux tubes as was proposed much earlier in the quantum model of hearing [10]. could the biochemical and physiological aspects involved with the generation of music experience be realized in terms of bio-photon emission induced by the listening of music? 4.3 standing waves and music merrick consider the idea that standing waves are essential for music experience. preferred extremals of kähler action representing standing waves does not seem to be feasible. the known preferred extremals (with ”massless extremals” (mes) included) would represent superpositions of fourier components with four-wave-vectors which are proportional to each other. essentially pulse propagating in fixed direction. for more general extremals this direction can depend on position. although standing waves are not feasible, effects which would be explained in maxwell’s theory in terms of standing waves are possible in many-sheeted space-time. a particle in a region of minkowski space containing several space-time sheets touches all space-time sheets having non-vanishing minkowski space projection to this region and the forced experience by it is sum of the forces caused by them. this leads to an operational defines of gravitational and gauge fields of einstein-maxwell limit of tgd as sum of the deviations of the induced metric from minkowski metric and sum of the components of the induced spinor connection defining classical gauge potentials in tgd framework. test particles can clearly experience the presence of standing waves. it is enough to take two massless extremals with opposite directions of three momentum but same energy with non-empty projections to same m4 region. particle with experience standing wave oscillating with the frequency involved. the arrangements in which photons are taken to rest effectively could correspond to this kind of situations since if it is the motion of test particles which serves as a signature. note however that there are also isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2014 | volume 4 | issue 2 | pp. 141-160 159 pitkänen, m. pythagoras, music, sacred geometry and genetic code vacuum extremals for which the light velocity at the space-time surface corresponds to arbitrarily low velocity at the level of imbedding space. 4.4 emotions and 4-d character of music experience music experience involves in an essential manner time unlike visual experience which is essentially 3dimensional. music experience affects also emotions very directly. for instance, we somehow know the key of the piece and expect that it ends to the basic note and chord. we somehow know also the scale used (say major or minor) by the emotional response stimulated by it. all this requires information about entire time evolution of the music piece. the recent neuroscience based models of memory do not help much in attempts to understand how this is possible. the reason is that in the ordinary materialistic view in which the state of the brain at fixed time should determine the contents of consciousness. the general vision in zero energy ontology and quantum classical correspondence is that space-time surface provide classical physics correlates for quantum states and also quantum jumps: the failure of the strict determinism is essential for the latter. the space-time surfaces are restricted inside causal diamond (cd) and have space-like 3-surface as their ends: the interpretation is as counterparts for the initial and final states of physical events. the replacement of states with events makes it possible to understand mysterious looking facts about living matter such as standardized temporal patterns say those appearing during morphogenesis. the maxima of the vacuum function defined by the exponent of kähler function in term identified as kähler action for euclidian space-time regions representing analogs for the lines of feynman graph correspond to the most probably temporal patterns. the basic aspect of emotions is positive/negative dichotomy. an attractive identification for the physical correlated of this aspect is whether the quantum jump generating the emotion increases or decreases the negentropy of the subsystem involved. for instance, pain would correspond to a reduction of the negentropy for the body part involved. in music experience negentropy could flow between different parts of the system involved and create also sensation with local negative coloring but with overall positive coloring (by nmp [9]). the ability of temporal patterns of music to generate negentropy flows inside the system involved could explain its effectiveness in generating emotions. dissonances were used by composes like bach to generate melancholic emotions which suggests that the dissonance represent local reduction of negentropy. also vibrato has emotional content. physically dissonance and vibrato are assignable to the interference of frequencies which are near to each other (http://en.wikipedia.org/wiki/beat_(acoustics)). the basic formula is cos(x) + cos(y) = cos((x+ y)/2)× cos((x− y)/2) . acknowledgements: i want to thank tommi ullgren for directing my attention to the book of richard merrick as well as for fascinating discussions about music. i am also grateful for salla vasenius for drawing the illustrations. references mathematics [1] icosahedral graph. wolfram mathworld. http://mathworld.wolfram.com/icosahedralgraph. html. [2] why are there 1024 hamiltonian cycles on an icosahedron? http://mathoverflow.net/questions/ 37788/why-are-there-1024-hamiltonian-cycles-on-an-icosahedron. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. http://en.wikipedia.org/wiki/beat_(acoustics) http://mathworld.wolfram.com/icosahedralgraph.html http://mathworld.wolfram.com/icosahedralgraph.html http://mathoverflow.net/questions/37788/why-are-there-1024-hamiltonian-cycles-on-an-icosahedron http://mathoverflow.net/questions/37788/why-are-there-1024-hamiltonian-cycles-on-an-icosahedron dna decipher journal | october 2014 | volume 4 | issue 2 | pp. 141-160 160 pitkänen, m. pythagoras, music, sacred geometry and genetic code [3] b. hopkins. hamiltonian parths on platonic graphs. ijmms. http: // www. emis. de/ journals/ hoa/ ijmms/ 2004/ 29-321613. pdf , 30:1613–1616, 2004. biology, neuroscience, and consciousness [4] amino acid. http://en.wikipedia.org/wiki/amino_acid. [5] genetic code. http://en.wikipedia.org/wiki/genetic_code. [6] r. merrick. interference: a grand scientific musical theory. http: // interferencetheory. com/ files/ interference. pdf . 2009. material related to tgd [7] m. pitkänen. dna as topological quantum computer. in genes and memes. onlinebook. http: //tgdtheory.fi/public_html/genememe/genememe.html#dnatqc, 2006. [8] m. pitkänen. genes and memes. in genes and memes. onlinebook. http://tgdtheory.fi/public_ html/genememe/genememe.html#genememec, 2006. [9] m. pitkänen. negentropy maximization principle. in tgd inspired theory of consciousness. onlinebook. http://tgdtheory.fi/public_html/tgdconsc/tgdconsc.html#nmpc, 2006. [10] m. pitkänen. quantum model for hearing. in tgd and eeg. onlinebook. http://tgdtheory. fi/public_html//tgdeeg/tgdeeg/tgdeeg.html#hearing, 2006. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. http://www.emis.de/journals/hoa/ijmms/2004/29-321613.pdf http://www.emis.de/journals/hoa/ijmms/2004/29-321613.pdf http://en.wikipedia.org/wiki/amino_acid http://en.wikipedia.org/wiki/genetic_code http://interferencetheory.com/files/interference.pdf http://interferencetheory.com/files/interference.pdf http://tgdtheory.fi/public_html/genememe/genememe.html#dnatqc http://tgdtheory.fi/public_html/genememe/genememe.html#dnatqc http://tgdtheory.fi/public_html/genememe/genememe.html#genememec http://tgdtheory.fi/public_html/genememe/genememe.html#genememec http://tgdtheory.fi/public_html/tgdconsc/tgdconsc.html#nmpc http://tgdtheory.fi/public_html//tgdeeg/tgdeeg/tgdeeg.html#hearing http://tgdtheory.fi/public_html//tgdeeg/tgdeeg/tgdeeg.html#hearing introduction could pythagoras have something to give for the modern musicology? pythagoras and transition from rational numbers to algebraic numbers pythagoras and music music and platonic solids numbers of different triangles as characterizers of harmony additional topological invariants characterizing the notion of harmony distribution of different types of edges would you come to icosadisco with me? connection between music molecular biology? could amino-acids correspond to 3-chords of icosahedral harmony? can one understand genetic code? does the understanding of stopping codons and 21st and 22nd amino-acids require fusion of tetrahedral and icosahedral codes? attachment of tetrahedron to icosahedron as extension of isosahedral code how the icosahedral hamiltonian cycle is modified? direct construction of hamiltonian cycle corresponding to bioharmony stopping codons and music geometric description of dna-amino-acid correspondence how could one construct the hamiltonian cycles on icosahedron with a minimal computational work? other ideas p-adic length scale hypothesis and music eeg and music standing waves and music emotions and 4-d character of music experience microsoft word richardamoroso_v11n1 dna decipher journal | october 2021 | volume 11 | issue 1 | pp 01-10 amoroso, r. l. & rowlands, p., algebraic and geometric representations of the genetic code issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 1 article algebraic and geometric representations of the genetic code richard l amoroso ,1 , peter rowlands 2 1noetic advanced studies institute, usa 2university of liverpool, uk abstract algebraic and geometric representations of the genetic code are used to show their functions for coding amino acids. the algebra is a 64-part vector quaternion combination, and the related geometry is based on the structure of the regular icosidodecahedron. an almost perfect pattern suggesting that this is a biologically significant way of representing the genetic code that may lead to a deeper understanding of a relationship between geometry and teleological life principles of complex self-organization. keywords: genetic code, triplet codons, amino acids, vector-quaternion algebra, teleology, icosidodecahedron. 1. introduction we explore an interesting way to represent the genetic code using a correspondence between algebra and geometry. the algebraic component is based on an icosian calculus with a noncommutative algebraic structure discovered by william rowan hamilton in 1856, which he called quaternions. in modern terms, hamilton produced a group presentation of the icosahedral rotation group by generators and relations. hamilton’s discovery was derived from his attempts to find an algebra of ‘triplets’ that he believed would reflect the three cartesian axes in a manner extending the complex numbers, which took the form, 2 2 2 1i j k ijk     . the symbols of the icosian calculus can be equated to moves between vertices on a dodecahedron. 2. the algebraic representation in previous work [1-3] we have used various mathematical structures to represent the genetic code, including a 64-part vector quaternion algebra, which is isomorphic to the algebra of the quantum mechanical dirac equation, and a combination of the faces and vertices of a regular icosidodecahedron. here, we aim to show that it is possible to represent the codon structures both algebraically and geometrically in a way that relates to their function in coding for amino acids. correspondence: prof. richard l. amoroso, director of physics lab., noetic advanced studies institute, utah, usa. https://orcid.org/0000-0003-2405-9034; http://www.noeticadvancedstudies.us e-mail: amoroso@noeticadvancestudies.us dna decipher journal | october 2021 | volume 11 | issue 1 | pp 01-10 amoroso, r. l. & rowlands, p., algebraic and geometric representations of the genetic code issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 2 it is based on a vector-quaternion algebra whose units can be represented as follows [4-6]: i j k vector i pseudoscalar i j k quaternion 1 scalar they can be considered as the units of two spaces: (‘real’, constructed from i, j, k) and (‘vacuum’, constructed from i, i, j, k, 1). in principle, any self-organizing system, whether physical, chemical or biological, forms a space, which has a kind of distorted mirror image in another ‘space’ representing the rest of the universe. the double space creates the entire combination of system and ‘vacuum’ as a zero totality. in principle, any self-organizing system, whether physical, chemical or biological, forms a space, which has a kind of distorted mirror image in another ‘space’ representing the rest of the universe. the double space creates the entire combination of system and ‘vacuum’ as a zero totality. the algebraic structure has an exact parallel with a geometric one which can be represented using platonic or archimedean solids in which each structure has a dual which could be imagined as constructed in another space. the units of the vector-quaternion algebra constructing the double space can be represented as follows: i j k ii ij ik i 1 –i –j –k –ii –ij –ik –i –1 i j k ii ii ik –i –j –k –ii –ii –ik ii ij ik iii iii iik –ii –ij –ik –iii –iii –iik ji jj jk iji iji ijk –ji –jj –jk –iji –iji –ijk ki kj kk iki iki ikk –ki –kj –kk –iki –iki –ikk an alternative ordering would separate the four complex numbers from 12 nilpotent structures, each formed from 5 units. here, we create a subset of 60 units, which has significance in the dodecahedral and icosahedral representations and in hamilton’s icosian calculus: 1 –1 ii ij ik ik j –ii –ij –ik –ik –j ji jj jk ii k –ji –jj –jk –ii –k ki kj kk ij i –ki –kj –kk –ij –i i –i iii iij iik ik j –iii –iij –iik –ik –j iji ijj ijk ii k –iji –ijj –ijk –ii –k iki ikj ikk ij i –iki –ikj –ikk –ij –i one way of generating the 64 units is by taking the product of 4 options × 4 options × 4 options, as is done in the case of the genetic code, where each of three bases may be u (or t), g, a or c. to represent this algebraically, we may use the vector units i, j, k and 1 for the options u, g, a dna decipher journal | october 2021 | volume 11 | issue 1 | pp 01-xx amoroso, r. l. & rowlands, p., algebraic and geometric representations of the genetic code issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 3 and c for the first base. then, for the second base, we may represent u, g, a and c by the quaternion units i, j, k and 1. then u, g, a and c on the third base may be represented by the units of complex algebra 1, i, –1, –i. using three different algebras (vectors, quaternions and complex numbers) allows us to track the three bases individually according to their positions in the codon. we have previously grouped the amino acids produced by the genetic code mechanism according to the second base in the codon which produced it. the second base seems, in this respect, the most important, and the third base the least, becoming in some sense almost redundant. using this division, the 64 codons fall naturally into 4 groups of 16: amino codon first second third acid base base base the group ii cys ugu i j 1 ugc i j i trp ugg i j –i stop uga i j –1 gly ggu j j 1 ggc j j i gga j j –1 ggg j j –i ser agu k j 1 agc k j i arg cgu 1 j 1 cgc 1 j i cga 1 j –1 cgg 1 j –i aga k j –1 agg k j –i group i phe uuu i i 1 uuc i i i leu uua i i –1 uug* i i –i cuu 1 i 1 cuc 1 i i cua 1 i –1 cug* 1 i –i val guu j i 1 guc j i i gua j i –1 gug j i –i ile auu k i 1 auc k i i aua* k i –1 met aug* k i –i group iii stop uaa i k –1 uag i k –i tyr uau i k 1 uac i k i asp gau j k 1 gac j k i glu gaa j k –1 gag j k –i lys aaa k k –1 aag k k –i asn aau k k 1 aac k k –i his cau 1 k 1 cac 1 k i gln caa 1 k –1 cag 1 k –i group iv ser ucu i 1 1 ucc i 1 i uca i 1 –1 ucg i 1 –i ala gcu j 1 1 gcc j 1 i gca j 1 –1 gcg j 1 –i thr acu k 1 1 acc k 1 i aca k 1 –1 acg k 1 –i pro ccu 1 1 1 ccc 1 1 i cca 1 1 –1 ccg 1 1 –i dna decipher journal | october 2021 | volume 11 | issue 1 | pp 01-10 amoroso, r. l. & rowlands, p., algebraic and geometric representations of the genetic code issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 4 asterisks represent codons that can act as a start. notably they are all in the same group. conveniently also (though this is mainly an artefact of our representation) all the start and stop codons are represented by negative units. the way that the various structures are relevant to the formation of amino acids will become clearer in the following table: group i phenylalanine uuu uuc ii iii leucine uua uug* cuu cuc cua cug* –ii –iii i ii –i –ii valine guu guc gua gug ij iij –ij –iij isoleucine auu auc aua* ik iik –ik methionine aug* –iik group ii cysteine ugu ugc ji iji tryptophan ugg –iji stop uga –ji glycine ggu ggc gga ggg –jj –ijj jj ijj serine agu agc jk ijk arginine cgu cgc cga cgg aga agg j ij –j –ij –jk –ijk dna decipher journal | october 2021 | volume 11 | issue 1 | pp 01-xx amoroso, r. l. & rowlands, p., algebraic and geometric representations of the genetic code issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 5 group iii stop uaa uag –ki –iki tyrosine uau uac ki iki aspartate gau gac kj ikj glutamate gaa gau –kj –ikj lysine aaa aag –kk –ikk asparagine aau aac kk ikk histidine cau cac k ik glutamine caa cag –k –ik group iv serine ucu ucc uca ucg i ii –i ii alanine gcu gcc gca gcg j ij –j –ij threonine acu acc aca acg k ik –k –ik proline ccu ccc cca ccg 1 i –1 –i we can see the pattern is nearly perfect; illustrated, particularly by the complete regularity of groups ii and iv. only the two serine codons in group ii are anomalous (not in their biological group), and they will be in any arrangement. arginine and serine in this group seem to each have two codons that could, originally, have coded a different amino acid. almost certainly, the codons for arginine and serine have become mixed at some stage in biological evolution. (we may note also that arginine seems to be an exception to the general tendency for the more dna decipher journal | october 2021 | volume 11 | issue 1 | pp 01-10 amoroso, r. l. & rowlands, p., algebraic and geometric representations of the genetic code issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 6 complicated amino acid molecules to be coded using fewer codon pathways.) the table we have given is only for one species, and it may be that evolutionary drift may be determined to some extent by the variations in the patterns from the assumed perfect norm. the codon for tryptophan, notably, can become the stop codon in some species, and vice versa. 3. the geometrical representation algebraic and geometrical structures are fundamentally dual. where there is an algebra, there is also a geometry, and vice versa. it is easy to show that this is the case here. the four groups of codons can now be represented on the faces of a regular icosidodecahedron, divided into four equal sections. (we could use the combined faces plus vertices of a dodecahedron or icosahedron.) the negative units are not shown in the figures, but can be assumed either to be represented on the corresponding vertices of the dual rhombic triacontahedron, or on the inner, rather than outer, surface of the icosidodecahedron. figure 1. algebraic geometry for representing codons on the icosidodecahedron. dna decipher journal | october 2021 | volume 11 | issue 1 | pp 01-xx amoroso, r. l. & rowlands, p., algebraic and geometric representations of the genetic code issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 7 the codons can be represented on these diagrams in the form: figure 2. codons representations the amino acids coded can be represented as follows: dna decipher journal | october 2021 | volume 11 | issue 1 | pp 01-10 amoroso, r. l. & rowlands, p., algebraic and geometric representations of the genetic code issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 8 figure 3. amino acids on the icosidodecahedron. here, the position of serine in two separate groups gives an idea of how the four sections might be connected. one of the significant aspects of the first three sections in alternative arrangement (below) is that the algebraic units of the three pentagons in each, combined with those of the two outer triangles on the lowest pentagon form the basis of a nilpotent structure, such as we find in the amplitude term in the nilpotent dirac equation (ike + iipx + ijpy + ikpz + jm). at the same time, the five triangles taken together form the basis of another nilpotent structure. so, the three inner triangles and the three pentagons display a duality in that either group can be used with the two outer triangles to generate a set of nilpotent units (though with their roles switched in the two cases). this provides another way of generating 12 nilpotent structures from the algebra. even using the first version of the icosidodecahedral sections, we can connect these triangles making up the nilpotent units with the upper pentagons, and so maintain the nilpotent structure. nilpotency is one of the assumed bases of the overall pattern that we have described as nature’s code, and it appears to be the means by which a self-organizing system connects with its external dna decipher journal | october 2021 | volume 11 | issue 1 | pp 01-xx amoroso, r. l. & rowlands, p., algebraic and geometric representations of the genetic code issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 9 environment. its presence in these geometric structures indicates the real importance of geometry in the genetic code as a route towards self-organization. figure 4. quaternion algebraic representation. appendix: note on the regular icosidodecahedron geometrically, an icosidodecahedron is a polyhedron with twenty (icosi) triangular faces and twelve (dodeca) pentagonal faces. an icosidodecahedron has 30 identical vertices, with two triangles and two pentagons meeting at each vertex. it also has 60 identical edges, each separating a triangle from a pentagon. because of this, it is one of the archimedean solids dna decipher journal | october 2021 | volume 11 | issue 1 | pp 01-10 amoroso, r. l. & rowlands, p., algebraic and geometric representations of the genetic code issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 10 figure 5. two views of the icosidodecahedron. all archimedean solids can be produced from platonic solids, by ‘cutting the edges’ of the platonic solid. likewise, platonic solids can be turned into archimedean solids by following a series of rules for their construction. interestingly, in cartesian coordinates, the vertices of an icosidodecahedron with unit edges are given by the even permutations of   2 0,0 1 , , 2 2 2            , where  is the golden ratio, 1 5 2  [7]. received june 8, 2021; accepted june 26, 2021 references [1] hill, v.j. and rowlands, p. (2008) nature’s code, aip conference proceedings, 1051, 117-126. [2] hill, v.j. and rowlands, p. (2010) nature’s fundamental symmetry breaking, international journal of computing anticipatory systems, 25, 144-159. [3] hill, v.j. and rowlands, p. (2010) the numbers of nature’s code, international journal of computing anticipatory systems, 25, 160-175. [4] rowlands, p. (2007) zero to infinity: the foundations of physics, singapore and hackensack, n.j., world scientific. [5] rowlands, p. (2010) dual vector spaces and physical singularities, aip conference proceedings, 1316, 102-111. [6] amoroso, r.l., rowlands p., kauffman, l.h. (2013) exploring novel cyclic extensions of hamilton’s dual-quaternion algebra, in r.l. amoroso, l.h. kauffman, p. rowlands (eds.) the physics of reality space, time, matter, cosmos, proceedings of the 8th symposium honoring mathematical physicist jean-pierre vigier, pp. 81-92, singapore: world scientific; https://vixra.org/pdf/1711.0468v1.pdf. [7] weisstein, e. w. (2010) icosahedral group, mathworld, a wolfram web resource; https://mathworld.wolfram.com/icosahedralgroup.html. dna decipher journal | october 2019 | volume 9 | issue 2 | pp. 44-64 44 pitkänen, m., an overall view about models of genetic code & bio-harmony article an overall view about models of genetic code & bio-harmony matti pitkänen 1 abstract during last years kind of brain storming period has occurred in the tgd inspired models of bioharmony and genetic code. a lot of ideas, some of them doomed to be short lived, have emerged, and it seems that now it its time for a thorough cleanup and integration with the general ideas of tgd inspired quantum biology. tgd leads to 3 basic realizations of the genetic code. one can also consider 3 realization also for bio-harmony. the question is which of them is the realistic one or whether several options can be considered. in this article these ideas are discussed critically and open problems are summarized. the three genetic codes correspond to a fundamental realization in terms of dark proton sequences (dark nuclei) with 3-proton representing codon. second realization is the chemical realization and the third realization is in terms of dark photon 3-chords mediating the interaction between various realizations. frequency resonance is very natural interaction between dark levels and energy resonance between dark level and chemical level. the possibility to modify the value of heff for flux tube makes possible to have for given codon single resonance energy. the homonymy of the genetic codes at various levels is discussed. at the dark level the fact that icosahedral harmonies can have common 3-chords implies the first homonymy. the basic difficulty of pythagorean scale realized in terms of quint cycle realized already by pythagoras becomes the solution of this problem. the well-known homonymies in rna-trna correspondence and even in rna-aa correspondence can be understood in the model in which dark photon 3-chords mediate the interactions. also questions related to the relationship of bio-harmony with ordinary genetic code are considered. why 3 copies of icosahedral harmony and only one copy of tetrahedral harmony? a special triangle assignable to the 3 copies of icosahedron and tetrahdron is analogous to a singular point of covering: do these 4 triangles correspond to exceptional codons breaking symmetries? how do the dissonant 3-chords present in some icosahedral harmonies relate to stop codons? how do the codons of bio-harmony and ordinary codons relate and is this relation consistent with what is known about transcription and translation? 1 introduction during last years kind of brain storming period has occurred in the model of bio-harmony [13]. a lot of ideas, some of them doomed to be short lived, have emerged, and it seems that now it its time for a thorough cleanup and integration with the general ideas of tgd inspired quantum biology. tgd leads to 3 basic realizations of genetic code: this is now relatively well established part of tgd inspired quantum biology. one can also consider 3 realization also for bio-harmony. the question is which of them is the realistic one or whether several options can be considered. 1.1 3 basic realizations of the genetic code in tgd universe there are at least 3 realizations of the genetic code. besides biochemical realization one has a realization in terms of dark nuclei realized as dark proton sequences and possibly in terms of more general sequences involving effective dark neutrons. the states of 3 dark protons defining the dark codon have multiplet decomposition 64 + 64+ 40 + 20 corresponding to dark variants of dna, rna, trna, and amino-acids (aa). i will denote these dark variants by ddna, drna, dtrna, and daa. 1correspondence: matti pitkänen http://tgdtheory.com/. address: rinnekatu 2-4 a8, 03620, karkkila, finland. email: matpitka6@gamail.com. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.com/ mailto:matpitka6@gmail.com dna decipher journal | october 2019 | volume 9 | issue 2 | pp. 44-64 45 pitkänen, m., an overall view about models of genetic code & bio-harmony if one allows also dark analogs of neutrons by allowing negatively charged color bonds between protons, the number of code letters doubles: this could relate to the recently constructed hachimoji dna [3] (see http://tinyurl.com/y2mcjb4r) discussed from tgd viewpoint in [21]. dark photon 3-chords assignable to the realization of bio-harmony with the note scale identified as hamilton cycle on a polytope with triangular faces gives a third realization coupling dark and ordinary representations together. i have proposed 3 realizations in terms of icosahedral and tetrahedral [13], icosahedral and toric [16], and icosahedral and dodecahedral [21] geometries (for the latter 5-chords would effectively reduce to 3-chords). if there is ddna-dna, drna-rna, daa-aa pairing, the negative charges of dna, rna, and trna nucleotides finds explanation in terms of positive charge of dark proton sequence. for aas the situation is not clear since the charge per unit length for amino-acids varies and depends on ph. daa-aa pairing would require that dark analogs of neutrons are present in the dark proton sequence. 1.2 3 models of bioharmony there are now 3 models of bioharmony [13, 16, 21] making very similar pedictions. harmony for given graph is defined as a hamiltonian cycle connecting neighboring points and going through all points of the graph without self-intersections. scale is identified by assigning notes to the vertices and faces correspond to the chords of the harmony obtained in this manner. bio-harmonies are fusions of 3 or 4 sub-harmonies. 1. the original proposal icosa-tetrahedral bio-harmony is based on the fusion of 3 icosahedral harmonies with symmetry groups z6, z4 and z2 permuting the triangles of given orbit of zn. given icosahedral harmony corresponds to an imbedding of 12-note scale as a hamilton cycle at icosahedron. the 12 vertices of icosahedron are identified as the notes of 12-note scale and 20 triangular faces define the 3-chords of the harmony. the distance between nearest vertices is assumed to correspond to quint that is scaling of the frequency by 3/2. each cycle defines a collection of 20 3-chords defining an icosahedral harmony. octave equivalence is used to map the 12 frequencies obtained to single octave. there is however a slight inconsistency since 12 quints corresponds to slightly more than 7 octaves as already pythagoras realized. the addition of tetrahedron to icosahedral harmony is interpreted as an addition of one vertex adding one note which should be very near to one of the 12 notes. icosahedral harmonies are characterized by a symmetry group zn, n = 6, 4, 2, 1, n = 1 corresponds to chaotic cycles, which might serve as correlate for dis-harmony and might relate to the correlates of emotions: at the level of genetic code is aa would be coded by single dna codon. icosahedron decomposes to orbits of zn consisting of triangles or equivalently chords. the chords can be classified further by the frequency ratios correlating with the emotional effect. one has the orbits 3 × 6 + 2 = 20 for z6, 5 × 4 = 20 for z4 and 10 × 2 for z2. z6 harmony is unique but there are 3 z4 and even more z2 harmonies for which z2 can correspond to rotation by π or reflection. this can be understood as breaking of symmetry splitting the z6 orbits to pieces. this gives 60 = 2 + 20 + 20 3-chords. the numbers of chords at give orbit rather neatly correspond the numbers of dna codons coding for given aa. 4 chords and dnas and aas are however missing. tetrahedral harmony would add 3 + 1 = 4 chords: z3 would the symmetry group instead of z4. this would be due to the symmetry breaking due to gluing of one-tetrahedral face with icosahedral face, which is however counted as separate face and corresponds to 1-triangle orbit under z3 permuting its vertices. this gives 64 3-chords corresponding to codons of genetic code. 3 + 1 decomposition would naturally correspond to (ile, ile, ile,met) 4-plet coded by codons aux. the numbers of codons coding given aa identified as orbit of zn come out almost correctly. the only exception is trp-stop doublet for which doublet decomposes to stop and singlet. one must issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/y2mcjb4r dna decipher journal | october 2019 | volume 9 | issue 2 | pp. 44-64 46 pitkänen, m., an overall view about models of genetic code & bio-harmony understand the reason for this symmetry breaking it might just the need to have stop codon and this could be arranged if there is no trna coupling to this codon. note that for some code variants stop codon uag corresponds to pyl and uga to sec. since music generates and expresses emotions, the interpretation would be in terms of moods. even molecules would have moods. 2. also icosa-dodecahedral and icosahedral-toric harmonies contain the z6 and z4 icosahedral harmonies (201 and 202) so that one must only add the missing 10 doublets and 3+1 codons assigned to tetrahedron in icosa-tetrahedral case. the dodecahedral harmony with 6 chords arranged in doublets is unique from the uniqueness of the hamiltonian cycle [21]. the icosa-dodecahedral harmony would give 201 + 202 + 121 + 122 = 64. 12 decomposes into 6 z2 doublets so that one has 12 doublets. the realization of scale for dodecahedral harmony would in 20 powers of rational scaling x such that x20 is as near to a power of two as possible [21]. x = 21/20 would correspond to the eastern variant of well-tempered scale. there are objections against icosa-dodecahedral harmony. chords are 5-chords rather than 3chords. the 5-chords of dodecahedral harmony however turn out to be equivalent to 3-chords as far as information content is considered [21]. the number of vertices for dodecahedron is 20, not 12, but one could argue that dodecahedron corresponds to eastern harmony having micro-intervals. two copies of the dodecahedral harmony are needed. what could distinguish between these copies will be discussed later. also 3+1 is missing. 3. the icosahedral-toric harmony [16] decomposes as 201 + 202 + 24 = 64 involving torus with 24 triangles and 12 vertices. toric harmony has z24 as isometries and gives 12 doublets. one could argue that the fusion of icosahedral and toric harmonies is geometrically un-natural. one must be however cautious if the geometric realization is in extension of rationals. also now 3+1 is missing. the considerations in the sequel suggests that the icosa-tetrahedral option is the most realistic if not unique. 1.3 about the geometric interpretation of icosahedral and other symmetries the geometric interpretation of icosahedral and possible other geometries is a challenge. the 60-element group a5 of rotations alternating group of 5-letters acts as orientation preserving isometries of icosahedron. 1. since galois group is central in adelic physics, and all finite groups can appear as galois groups, one can ask whether icosahedral group and tetrahedral groups could act as galois group for some extension of rationals relevant for biology. going to web gives an affirmative answer [1] (see http: //tinyurl.com/y4qsea6h)! icosahedral symmetry appears as galois group of the general quintic equation! the lowest order polynomial equation not allowing closed expressions for the roots. galois theory (see http://tinyurl.com/y6e955ke) allows to understand the situation in terms of the discriminant defined as product d = ∏ i<j(ri − rj)2, where ri are the roots of the irreducible polynomial considered. sn is the symmetry group in the generic case and odd permutations of sn change the sign of d. if d is square of rational number in the field k considered (which can be also extension of rationals now), galois group reduces to alternating group a5. remark: for octahedron and its dual cube the group is s4 and can be realized as galois group of 4th order polynomials. for tetrahedron the group is a4 and can be also realized as galois group of 4th order polynomials for which discriminant is square in k. 2. icosahedral and dodecahedral geometries having the same isometry group are common in biology, and one can wonder whether there could be a gometric realization perhaps at the level of magnetic issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/y4qsea6h http://tinyurl.com/y4qsea6h http://tinyurl.com/y6e955ke dna decipher journal | october 2019 | volume 9 | issue 2 | pp. 44-64 47 pitkänen, m., an overall view about models of genetic code & bio-harmony body. this might somehow relate also to the frequent appearance of golden mean involving √ 5 in biology and golden angle rated to the fifth root of unity. 3. m8 −h duality provides besides the usual formulation of tgd also a formulation in complexified m8 identified as complexified octonions [15]. the associativity of the tangent or normal space of space-time surface is assumed as a dynamical principle and implies quaternionicity. quaternions have so(3) as automorphism group analogous to galois group and have the finite isometry groups of platonic solids as finite subgroups. could quaternionicity give a connection with the geometric picture? in adelic physics discretizations of space-time points as points with coordinates in the extension of rationals are in central role. could discretizations contain orbits of the platonic isometries as quaternionic galois groups? this could also give to the geometric picture although icosahedral symmetries are not obvious in the geometry of say dna. 4. is the genetic code really unique as its dark nucleus realization and the fact that the isometry groups of platonic solids are finite subgroups of quaternionic isomorphisms suggests? could any galois group give rise to an analog of bioharmony and of genetic code? could the recent genetic code correspond to a first step in the process going beyond the solvable polynomial equations? what about toric code? the group of toric isometries is z24 and 24 is one of the magic number of mathematics, and dimension 24 is crucial in bosonic string model. could z24 correspond to the galois group for 24:th roots of unity defining 24-d algebraic extension of rationals. we cannot sensorily imagine higher dimensions but can do this cognitively. i have proposed that the ability to imagine higher dimensions could be due to the possibility of higher-dimensional extensions of rationals and p-adics. could one realize the icosahedron and 24-torus as imagined object in the algebraic extension of rationals? could the n-dimensional discrete geometric objects assignable to n-dimensional extensions of rationals have quite generally this kind of representations as a generalized platonic solid in algebraic extension. could they define cognitive harmonies as hamiltonian cycles? could one imagine also cognitive variant of genetic code whereas as sensory/biological variant of genetic code would be forced by dark proton physics? 1.4 mistracks in the attempts to understand the connection with standard realization of the genetic code i have also considered the possibility that the frequencies of 3-chord might be mapped to their sum in the interactions. this possibility was considered in the model of homonymy [18]. in the light of afterwisdom this proposal looks ad hoc. also a proposal for how 12-note scale could quite concretely correspond dna codons was discussed [19]. the idea was to assign notes with individual letters of the codon such that the note depends on the position of the letter whereas the model of harmony assignment the chord to the entire codon represented as entangled state of 3 dark protons. it is now clear this proposal very probably cannot realize all possible harmonies and is in conflict with the general model which as such fixes the correspondence between chords and codons without any additional assumptions. 2 interactions between various levels one challenge is to understand how the various realizations of the genetic code interact with each other. there are dx-dy interactions, dx-y interactions and x-y interactions and in living matter they should occur in long length scales so that they should be mediated by dark photons. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2019 | volume 9 | issue 2 | pp. 44-64 48 pitkänen, m., an overall view about models of genetic code & bio-harmony 1. how dark photon triplets assumed to be generated by dark nucleon sequences interact with ordinary dna? here one can bring in rather stable ideas of tgd inspired view about quantum biology. dark matter in tgd sense represents long length scale quantum coherence and bio-chemistry short scale coherence. the interaction is therefore between long and short scales. 2. there are two manners to interact: frequency resonance and energy resonance. frequency resonance mediates long length scale interactions and if dx-x pairing exists, the exchange of dark photon triplets 3-chords allows long range dx-dy interactions. dx-x interaction by energy resonance is short range interaction so that x-(dx-dy)-y interaction would give rise to long range interaction between x-y as interaction induced by dark level (mb). 3. dx-x interaction involves energy resonance and transformation of dark photons to ordinary photons with the same energy. bio-photons would be an outcome of the transition heff → h. also the reversal of this transition and more general transitions heff,1 → heff,2 are of course possible. bio-photons have a universal energy spectrum corresponding to molecular and atomic transition energies. this is possible if they result from dark cyclotron photons if the condition heff = hgr = gmm/v0 introduced originally by nottale and implying that the cyclotron energy does not depend on the mass of the charged particle producing the dark cyclotron photons. 2.1 the independence of the interaction energy on frequency dark matter as a hierarchy phases labelled by heff/h0 = n identifiable as a dimension of extension of rationals implies evolutionary hierarchy: n serves as a kind of iq. this strongly suggests that ordinary matter is controlled by dark matter at mb and mimics its behavior. evolution would not proceed by change and necessity but would be a process controlled and guided by mb. mb would be an active intentional agent guiding the evolution. situation in biology would be much like that in modern technological society where intentional technical progress leads to more and more refined products. how could this be realized at the level of basic bio-molecules? one should also understand how genetic code evolves gradually to a more refined form. 1. the selection of basic bio-molecules having energy resonance with their dark variants mediated by dark photon 3-chords by change would be extremely in-effective process. mb should have mechanisms of tuning the energies of dark photons to achieve energy resonance. this is achieved if the value of heff at the flux tubes mediating the interaction can be controlled. since the length of flux tube is proportional to the heff by uncertainty principle, the variation of heff would mean variation of the length l of the flux tube: a kind of motor action of mb. cyclotron frequencies are proportional to the value of monopole magnetic field b at flux tube and by flux quantization one has b ∝ 1/s, s the area of flux tube cross section (which for monopole flux tubes is closed 2-surface). the variation of the thickness/area of the flux tube, second motor action of mb, would allow to vary cyclotron frequencies. 2. the ideal situation concerning the coupling to ordinary matter would be that same chemical transition with fixed energy for given molecule could couple to several frequencies. this would be achieved if the cyclotron energy is constant. the condition that the cyclotron energies in a coupling to a given molecule do not depend on the frequency requires that heff,i at flux tube i compensates this dependence. mb can vary the value of b to vary frequencies and the value of heff,i to keep energy unaffected. the areas s and length l of flux tubes are varied so that the volume remains unaffected. b ∝ 1/s and l ∝ heff by uncertainty principle. ec ∝ ~effb = constant implies that l/s is constant. s increases like s → x2s and l → x2l in the scaling changing fc → fc/x 2. the magnetic energy emagn = b2sl ∝ l/s of the flux tube is not changed. kind of energy criticality would be in question one would have a large issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2019 | volume 9 | issue 2 | pp. 44-64 49 pitkänen, m., an overall view about models of genetic code & bio-harmony number of flux tube configurations with the same energy and volume ideal for control purposes. quantum criticality is actually basic dynamical principle of quantum tgd allowing to predict the spectrum of various coupling parameters. 3. besides cyclotron frequences josephson energies are central in tgd based model of nerve pulse and eeg. josephson energy ej = zev and cyclotron frequency fc = zeb/m do not depend on heff . an attractive possibility is that cyclotron photons couple to josephson junctions meaning that they become josephson photons and then transform to ordinary photons inducing molecular transitions. 4. in the case of bio-harmony the frequencies would be rational multiples of basic frequency and by separating common numerator they are certain integer multiples fi = nif0 of a basic frequency f0. the integers ni have decomposition to products of powers of certain primes: ni = ∏ pki i and each of pi appears as some maximal power ki,max. if one has n = ∏ i p ki,maxn0 one can obtain heff,i = heff/ni. in this manner one would obtain the desired independence of ec,i on fi. for pythagorean scale only primes p = 2 and p = 3 would be involved. all codons coding for given aa could have same coupling energy. unless the values of planck constants and frequencies associated with flux tubes coupling to given codon are fixed, one could have same transition energy for all letters but this is an unrealistic condition. transition energies are naturally different and can code for letters if not even codons. for this option only the correct combination of frequencies and values of heff,i allows resonant coupling. the 3-chords associated with different harmonies would naturally correspond to the same energy. the physics of emotions would not be directly visible at the level of chemistry: chemist would certainly agree with this. the values of planck constants would characterize the frequencies: i have indeed speculated that nucleotides could be labelled by values of heff . number theory would be essential for the understanding life at the level of genes: galois groups would characterize the nucleotides. galois groups code for complexity at the level of dark matter so that the behavior guided by the mb of molecule would depend on the iq = n = heff/h0 of mb. 2.2 the independence of cyclotron energy on frequency and nottale hypothesis is the independence of interaction energy on frequencies consistent with hgr = gmm/v0 hypothesis [2] [9, 10, 11]? here one might encounter difficulties. the division by ni should change one of the parameters appearing in the formula. the interpretation has been m corresponds to the dark proton mass at the end of the flux tube connecting it to large mass m . if so m cannot be varied. could m be varied? 1. the parameter v0 ' 2−11 can be varied by powers of two, which do not affect the notes identified by octave equivalence. 2. could m correspond to atomic or molecular mass in good approximation equal to sum of atomic numbers a of atoms involved? the divisors of the total atomic number atot would define the allowed integers ni characterizing the frequencies of pythagorean scale in the model of bio-harmony. one must have hgr/h > 1 with requires m > ~/gm = 1.3× 1019mpv0. for v0 = 2−11 this corresponds to m > ~/gm = 6 × 1015mp. the scale of a water blob with a = 20 containing this number of protons is about 70 µ, which is of order cell size. one can wonder how atot could be kept as divisible by ni characterizing the frequencies of the pythagorean scale. the problem is that an addition of one proton spoils the divisibility conditions completely. 3. the solution of the problem could be based on a more precise view about heff [20]. the understanding of the variation of newton’s constant too large to be due to experimental errors led to the realization of the meaning of the fact that space-time surfaces can be regarded simultaneously issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2019 | volume 9 | issue 2 | pp. 44-64 50 pitkänen, m., an overall view about models of genetic code & bio-harmony coverings of n2-fold m4 and n1 fold cp2 and that one has n = n1n2 in heff/h0 = n and n1 would have interpretation as the number of flux tubes which are parallel in m4 and can be even disjoint. this would give hgr ∝ n1 and the factors of n1 should correspond to the integers characterizing the notes of the 12-note scale. one could perhaps say that effectively single proton is replaced with n1 protons located at different flux tubes so that also proton mass becomes n1m. one would have effectively a bose-einstein condensate like state of n1 protons (at different flux tubes). 4. in the pythagorean representation of octave the notes correspond to powers (3/2)k, k = 0, 1, ..., 11, if 3/2)12 ' 27 is not included. the corresponding integers are 3k211−k. only powers of primes p = 2 and p = 3 are involved and one just have n1 ∝ 311211. if one increases the number of octaves involved to 14 to get a representation for chords needed to avoid the mapping of two dark codons to same 3-chords, one must have n ∝ 323223 = 623. one can consider also simpler representations using integers expressible in terms of powers of primes p = 2, 3, 5 but one must give up exact quint cycle in this case. interestingly, a good guess for the standard value h of heff is as h = 6h0 [14, 17]. 5. small p-adic primes p = 2, p = 3 and perhaps also p = 5 (golden mean) are expected to be of special importance in tgd inspired biology [8]. p = 2 seems to appear everywhere and there is also support for p = 3 in biology [5, 6] (see http://tinyurl.com/ycesc5mq): great evolutionary leaps seem to correspond to time scales coming in powers of 3. 6. the branching of the flux tube bundle to ni sub-bundles ni = n/ni could correspond to the reduction heff → heff/ni. this could be seen as reduction of heff . one can also consider phase transitions reducing n to n/ni. 3 homonymy of the genetic code in the following i will discuss briefly the basic facts about genetic code at wikipedia level with emphasis on the poorly understood aspects of the code. there are two interesting phenomena: synonymy and homonymy. synonymy means several names for aa or trna codon so that that several rnas are mapped to the sama aa or trna codon: the understanding of the genetic code is the understanding of synonymy. homonymy means that the same rna codon can correspond to several trnas or even aas. a general tgd based view about homonymy differing from that discussed in [18] based on the recent understanding of the interaction between various representations of the genetic code is described below. 3.1 variations of the genetic code there exists also as many as 31 genetic codes (see http://tinyurl.com/ydeeyhjl) and an interesting question is whether this relates to the context dependence. mitochondrial codes differs from the nuclear code and there are several of them. the codes for viruses, prokaryotes, mitochondria and chloroplasts deviate from the standard code. as a rule, the non-standard codes break u-c or a-g symmetries for the third code letter. some examples are in order (see http://tinyurl.com/puw82x8). 1. uuu can code leu instead of phe and cug can code ser rather than leu. in bacteria the gug and uug coding for val and leu normally can serve as start codons. 2. uga can code to trp rather than stop: in this case the broken symmetry is restored since also ugg codes for trp. 3. there is variation even in human mitochondrial code (see http://tinyurl.com/puw82x8). in 2016, researchers studying the translation of malate dehydrogenase found that in about 4 per cent of the mrnas encoding this enzyme the uag stop codon is naturally used to encode the aas trp and issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/ycesc5mq http://tinyurl.com/ydeeyhjl http://tinyurl.com/puw82x8 http://tinyurl.com/puw82x8 dna decipher journal | october 2019 | volume 9 | issue 2 | pp. 44-64 51 pitkänen, m., an overall view about models of genetic code & bio-harmony arg. this phenomenon is known as stop codon readthrough (see https://www.ncbi.nlm.nih. gov/pmc/articles/pmc5133446/). 4. there is also a variant of genetic code in which there are 21st and 22nd aas sec and pyl coded by stop codons. uga can code for sec and stop in the same organism. uag can code for pyl instead of stop and introduces additional breaking of a-g symmetry for the third letter (uaa to stop and uag to pyl). 3.2 wobble base pairing wobble base pairing (see http://tinyurl.com/y73se8vs) emerges from the observation that the number of trnas pairing with mrnas is smaller than 45 and considerably smaller than that of mrnas. the needed minimum number of trnas is 32. therefore the rna-trna pairing cannot be 1-1 and some mrna codons must correspond to several trna codons. remark: one could ask whether mrnas code for trnas just like dnas code for aas. homonymy for mrna-trna pairing implies that the pairing can be many-to-1 only in given context. 1. according to the standard code, the first two bases of mrna codon corresponds to two last bases of trna anti-codon and obey standard code. wobble base pairing hypothesis applies to the pairing of the 3rd mrna base to the 1st base in trna anticodon. at the level of chemistry the hypothesis is that the position of the first trna anticodon base pairing with the third mrna base is variable and allows it to pair with several bases appearing as 3rd base in mrna. this homonymy would be due to ”wobbling” of the position of the first trna anticodon. 2. in the original model for wobble base pairing trna bases contain besides standard a, c, g, u also inosine i as a modification of g obtained by dropping nh2 from the 6-cycle of g. it has turned out that there are actually variants of c and 5 variants of u (see http://tinyurl.com/y73se8vs). the large amount of homonymy for trnas forces to ask whether chemistry alone really dictates the genetic code. 3. the first trna letter is assumed to be spatially wobbling so that the association of trna with rna is not unique and mrna-trna pairing involves both synonymy and homonymy as the two tables for the pairing of the 1st 5’ anticodon base of trna and 3rd 3’ codon base of mrna show. in the second column bold letters for mrn bases allow to read the standard pairing with trna codons in the first column and non-bold letters allow to deduce the non-standard behavior. 4. the first table (see http://tinyurl.com/y73se8vs) represents the original watson-crick proposal. (a) the pairings of the 3rd letter of mrna codon to the 1st letter of trna anti-codon are following. • u → g. • g → u • {a, c or u} → i. the 2nd and 3rd trna letters a and c are paired with the 1st and 2nd mrna letters in the canonical manner. there are only 3 trna letters, which implies that the number of trnas is smaller than maximal. (b) there is single 1-to-many pairing: u→ {g, i} giving rise to 2-fold homonymy. 5. revised pairing rules (see http://tinyurl.com/y73se8vs) are more complex since the number of trna bases is larger (u has 5 variants and c has 2 variants). all mrna letters have 1-to-many pairing. even if one counts the variants of u as single u there is 4-fold homonymy for u and homonymies for other codons. for a one has 9-fold homonymy. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://www.ncbi.nlm.nih.gov/pmc/articles/pmc5133446/ https://www.ncbi.nlm.nih.gov/pmc/articles/pmc5133446/ http://tinyurl.com/y73se8vs http://tinyurl.com/y73se8vs http://tinyurl.com/y73se8vs http://tinyurl.com/y73se8vs dna decipher journal | october 2019 | volume 9 | issue 2 | pp. 44-64 52 pitkänen, m., an overall view about models of genetic code & bio-harmony these variations do not induce variation in dna → aa pairing if the aa associated with the homonyms of trna are identical. this seems to be the case almost always since the variation of the genetic code is surprisingly small. this raises the question whether there is some mechanism eliminating to high degree the expected effects of homonymy in mrna→ trna pairing. 4 tgd view about homonymies one should understand the homonymies of the genetic code [18]. one can imagine homonymies at the level of ddna-3-chord and drna-3-chord correspondences and between rna-aa and rna-trna correspondences. 4.1 homonymies for drna-3-chord correspondence it is possible that homonymies are present already at the dark photon level in the sense that the subharmonies have common chords. 1. are the icosahedral orbits for different symmetry groups z6, z4, z2 disjoint? if they contain common triangles, the outcome is homonymy for dark codons unless one can scale the 12-note scales with respect to each other (different keys) to avoid common chords. this question finds an answer from the tables of [13] representing the chords. if the two scales considered contain 3-chords with the same frequency ratios this can happen. z6 harmony contains chords of same type with whole note intervals: cx, dx, ex, ..., x = m, 6, 9 coding the frequency ratios as is done in popular music. if second harmony contains several types such that they are not separated by a multiple of whole note interval, at least one common chord is unavoidable also for shifted harmonies. 2. from the tables 1 and 2 of appendix one finds that for z6 and 2 z4 harmonies this is indeed the case and they have 2-chords involving 2 quints in common: 6-orbit and 4-orbit containing x = 9 3-chords have 2 common chords. one has homonymy at dark level. if entire orbits are mapped to the same aa there would be 8 aas in the same multiplet. some ddna and drna codons are mapped to the same 3-chord of dark photons. this problem is shared by all 3 models of bio-harmony. 3. for the unique z6 harmony and 3 z2,rot (table 3 of appendix) of harmonies common chords can be avoided by shifting the latter harmonies by a half-note. the reason is that the chords of same type are now separated by a multiple of whole note interval. for z2,refl harmonics (table 4 of appendix) the chords of same type are separated by odd number of half-notes so that common chords are unavoidable since 3-chords of the same type appear. there are also common chords with z4 harmony. 4. z6 and z2,rot harmonies possess no common chords by a shift by odd number of half notes. z4 and z2,rot and z4 and z6 possess at least 2 common chords. z2,refl possesses more common chords with z4 and z6. the fusion of z6, z4, and z2,rot harmonies with 2 common chords between in z6 ∩ z4 z4 ∩ zr,rot seems seems to be best that one can achieve. this would give 1 × 2 × 3 = 6 harmonies altogether unless one obtains new harmonies by by relative shifts of the key. how to solve the problem? 1. the above described homonymies involving 6-plets involve either 6-plet or 2-plet as second multiplet so that these deviations cannot be due to homonymy at the level of drna-3-chord correspondence. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2019 | volume 9 | issue 2 | pp. 44-64 53 pitkänen, m., an overall view about models of genetic code & bio-harmony 2. should one take seriously the puzzle that teased pythagoras and led him to seriously consider that the structure of the universe based on rationals has serious flaw in it. 12 quints give slightly more than 7 octaves: one has (3/2)12 = 129.746337890625 rather than (3/2)12 = 128 so that one obtains slightly more than octave under octave equivalence. why not represent notes as powers of algebraic number 21/12 and this is indeed done in practice (in rational approximation of course) but very musical people notice the difference and dislike this representation. there should be something deep in the representation of the scsale in terms of rationals as tgd indeed predicts. note that a strict resonance is not required, it represents only the optimal situation. 3. repeating the quint cycle gives slightly displaced chords: one can of course do this several times [21]. could these slightly displaced chords represent ddna and rna codons as 3-chords otherwise mapped to the same chords? this would also mean that the corresponding dnas and rnas correspond to 3-chords with at least one note differing only slightly. this kind of notes is shared by 5 chords in icosa-tetrahedral harmony. the addition of second quite cycle means that the integers ni = 2k323−k characterize the notes of the 3-chords and 2k323−k and 2k+12311−k represent the nearby notes. 4. the minimal modification would replace only minimum number of notes in the problematic chords with new ones. a stronger modification would replace the problematic chords with displaced variants with notes in the second quint cycle. one could also do the same for all chords and say that the number of codons for non-problematic dark codons is doubled. one could also consider the doubling of each letter of the codon so that each chord would be replaced with 8 almost copies except in the case of homonymic aas. a non-homonymic aa coded by n rnas would be coded by 8n 3-chords. if the frequency differences are small enough this is not seen at the level of transition energies of aas: this must be the case for non-homomymous aas. for homonymous rnas the energy differences must be seen and remove the homonymy. this drna-3-chord homonymy would be analogous to the rna-trna homonymy. 5. one can consider the problem from a different perspective. for hachimoji dna [3] (see http: //tinyurl.com/y2mcjb4r) the number of dna letters seem to double so that codon is replaced with 8 codons. an explanation based on the pythagorean dilemma was discussed in [21]. in the model it was however assumed that the doubling of dark dna and dna is real being due to the possibility of having also negatively charged color bonds between dark protons so that dark proton is effectively dark neutron (this might happen even in ordinary nuclear physics in nuclear string model [7]). the pythagorean double covering of 3-chords could describe the doubling of codons. the doubling would not occur for the codons for which one has the homonymy a prediction, which could be perhaps tested. 4.2 the map drna-dtrna by 3-chords the map 64 → 40 for drna-dtrna inducing the corresponding map for rna − trna is not unique since there are many manners to reduces 64 to 40. could this relate to trna-rna homonomy? consider icosa-tetrahedral code 20 + 20 + 20 + 4 = (3× 6 + 2) + (5× 4) + (10× 2) + (3 + 1) as example. 1. suppose z2 is the divisor group (also z4 and z3 ⊂ z6 can be considered) so that the orbit can split to two and two trnas are associated with given amino-acid coded by n codons. at the first step one can take 201 + 202 + 203 + 4 → 201 + 102 + 103 + 4 = 44. also 101 + 202 + 103 + 4 and 101 +102 + 202 +4 can be considered. since zn has z2 as subgroup, the simplest manner to achieve 20k = 10k is to divide all orbits to 2 z2 cosets. this can be carried out in 3 manners. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/y2mcjb4r http://tinyurl.com/y2mcjb4r dna decipher journal | october 2019 | volume 9 | issue 2 | pp. 44-64 54 pitkänen, m., an overall view about models of genetic code & bio-harmony 2. one must get rid of 4 trnas. this can be achieved in several manners. in 201 = 3×6+2 one could have 6 + 2→ 3 + 1: there are 3 alternatives. in 202 = 5× 4 one could have 5× 4→ 3× 4 + 2 + 2 (10 manners). in 203 = 10× 2 one can take two 2:s to 1 (45) manners. 3. could all these maps be realized and could they correspond to different maps at the level of dark codons? if the independence of resonances energies on frequencies is true with an appropriate choice of heff,i, it would seem that in all these cases same chemical trna is possible. 4.3 homonymies for rna-aa correspondence there are two basic types of homonymies involving bio-molecules. 1. rna-aa correspondence can vary somewhat and there are 31 variants of genetic code. rna-trna homonymies are common and wobble phenomenon could be regarded as as such homonomy. this homony is poorly understood. i made the first attempt to understand homonymies in [18] but failed to realize one absolutely essential feature. despite rna-trna homononmies there are practically no rna-aa homonymies. they might be completely absent for given genetic code. there must be a simple explanation for this. 2. in tgd framework the genetic code is replaced with 3 codes. there is drana-dtrna code mapping 64 drna codons to 40 dtrna codons and dtrna − daa code mapping 40 dtrna codons to 20 daas. the composition of these codes gives drna-daa code inducing the rna-aa code. the highly non-trivial fact is that one has what mathematician would call commuting triangle: rna-trna-aa = rna-aa for given code. all the homonymies of rna-trna code are possibly completely compensated for given rna − aa code. this must have simple explanation and once one has made this question, one also knows its answer in tgd framework. 3. for hamiltonian cycles the n(a) codons coding for given aa corresponds to orbit of a fixed codon at the orbit having symmetry group zn(a). genetic code maps the codons at the orbit to the aa corresponding to the orbit and replaces the symmetry group zn with trivial group zn/zn = z1. remark: there are 6 chaotic icosahedral hamiltonian cycles with symmetry group z1 so that therefore 20 amino-acids each coded by single codon. could one interpret the 20 amino-acids with the chaotic representation of chaotic icosahedral hamiltonian cycle? for rna-trna correspondence similar process is possible. now one replaces zn/zk where k is factor of n. consider icosa-tetrahedral code as an example. k = 2 is simplest choice since it divides n = 6, 4, 2 for icosahedral codes but not for tetrahedral code for which one has n = 3: (ile, ile, ile,met) would naturally correspond to the 2 orbits under tetrahedral z3. this symmetry appears only for icosatetrahedral option. for other options one can explain it as an outcome of symmetry breaking for doublets and (ile,ile) and symmetry broken (ile,met) would have ile in common. this looks un-natural. one can indeed construct 64→ 40 map for drna and dtrna codons by replacing some orbits with their z2 cosets but this map is not completely unique. this is possible for all code candidates, which all contain z6 and z4 symmetric icosahedral harmonies giving rise to amino-acids corresponding to 3 6-orbits and one 2-orbit for z6 symmetry and 5 4-orbits with z4 symmetry. the remaining orbits are 3-orbit and 1-orbit for tetrahedral symmetry broken to z3 and 2-plets for z2 orbits. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2019 | volume 9 | issue 2 | pp. 44-64 55 pitkänen, m., an overall view about models of genetic code & bio-harmony there are are however codes for which rna-aa correspondence is non-standard. as explained above, the simultaneous replacement uuc-leu → uuc-phe and uug-leu → uug-ser can take place. also aug-met → cug-met and gug-met → gug-met can occur. a general explanation could be as follows. if the two homonymous amino-acids phe and leu and leu and ser in the first example and met and leu and val in the second examplehave very nearly same transition energy, and if the 3-chords correspond transition energies of aa irrespective of frequencies, homonymy becomes possible. this problem can be avoided if the trna pairing second aa with the rna codon is not present. both options might be realized in the same organism. it could also happen that second aa is so far from energy resonance that it is only rarely translated. 4.4 homonymies for rna-trna correspondence could the possibility of several harmonies/moods with different chords increase the number of trna codons from the minimal value 40? are these homonymies forced by necessity or do their reflect freedom of mb to choose? do dialects emerge already at the molecular level and do they have some practical advantage? 1. could the possibility of several moods demand more than the minimal number of trnas. harmonies correspond to different collections of triplets (n1, n2, n3) characterizing the chord. it was however already noticed that the variation of the planck constants heff → heff/ni associated with the flux tubes can modify the cyclotron energies. this would mean that the emotions are not directly seen at the level of molecular transitions as bio-chemist would certainly argue. if energy resonance couples dark photons to ordinary matter it could be possible to guarantee the coupling energy does not depend on the values of frequencies of the 3-chord at flux tubes. this would suggest that there is no motivation to increase the number of trnas for the lack of required resonance energies. 2. could a large number of trnas as mediators of rna-aa pairing be something chosen intentionally by mb rather than being forced by chemical limitations. could surplus of different trnas be a safer option when some trnas are not produced. in natural languages there is large number of dialects and new are born all the time. no hard-wired correspondence would exist at chemical level. mb would be to some degree creative and able to build trnas from the stuff that it happens to find from the lab! biology could be creative already at rna-trna level and this flexibility could emerge from the intelligence coded by heff = n: the larger the number of factors of n the higher the intelligence of the system would be. this flexibility might also explain the homonymy at rna-aa level and different genetic codes as a formation of dialects. 5 about the details of the genetic code based on bio-harmony tgd suggests several realizations of music harmonies in terms of hamiltonian cycles representing the notes of music scale, most naturally 12-note scale represented as vertices of the graph used. the most plausible realization of the harmony is as icosahedral harmony [13] (see http://tinyurl.com/yad4tqwl and http://tinyurl.com/yyjpm25r). 1. icosahedron (see http://tinyurl.com/l5sphzz) has 12 vertices and hamiltonian cycle as a representation of 12-note scale would go through all vertices such that two nearest vertices along the cycle would differ by quint (frequency scaling by factor 3/2 modulo octave equivalene). icosahedron issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/yad4tqwl http://tinyurl.com/yyjpm25r http://tinyurl.com/l5sphzz dna decipher journal | october 2019 | volume 9 | issue 2 | pp. 44-64 56 pitkänen, m., an overall view about models of genetic code & bio-harmony allows a large number of inequivalent hamiltonian cycles and thus harmonies characterized by the subgroup of icosahedral group leaving the cycle invariant. this group can be z6, z4, or z2 which acts either as reflection group or corresponds to a rotation by π. 2. the fusion of 3 icosahedral harmonies with symmetry groups z6, z4 and z2 gives 20+20+20=60 3-chords and 3+1 + 5 + 10 =19 orbits of these under symmetry group and almost vertebrate genetic code when 3-chords are identified as analogs of dna codons and their orbits as amino-acids. one obtains counterparts of 60 dna codons and 3+1 + 5 + 10 =19 amino-acids so that 4 dna codons and 1 amino-acid are missing. 3. the problem disappears if one adds tetrahedral harmony with 4 codons as faces of tetrahedron and 1 amino-acid as the orbit of the face of tetrahedron. one obtains 64 analogs of dna codons and 20 analogs of amino-acids. i call this harmony bio-harmony. the predicted number of dna codons coding for given amino-acid is the number of triangles at the orbit of given triangle and the numbers are those for genetic code. 4. how to concretely realize the fusion of harmonies? perhaps the simplest realization that i have found hitherto is based on union of tetrahedron of 3 icosahedrons obtained by gluing tetrahedron to icosahedron along its face which is triangle. the precise geometric interpretation of this realization has been however missing and i have considered several variants. i have proposed that the model could explain the two additional amino-acids pyl and sec appearing in nature. there is also a slight breaking of symmetries: ile 4-plet breaks into ile triplet and met singlet and trp double breaks into stop and trp also leu 4-plet can break in leu triplet and ser singlet (see http://tinyurl.com/puw82x8). this symmetry breaking should be understood. 5.1 why 3 icosahedral harmonies and 1 tetrahedral harmony? the following argument suggests a more detailed solution of these problems than proposed earlier. 1. the copies of icosahedron would differ by a rotation by multiples of 2π/3 (z3) around axis through the common triangular face. this face unlike the other faces remains un-affected. also tetrahedron remains un-affected so that it is counted only once. if the 3 copies of the icosahedral common face are counted as separate (this is important!), one obtains 20+20+20 faces from icosahedron. if also tetrahedral shared faces is counted as separate, tetrahedron gives 4 faces: 64 codons altogether as required. one obtains 19 orbits from the 3 icosahedra and 1 orbit from tetrahedron: 20 orbits as counterparts of amino-acids altogether. 2. but can one really counter the 4 common faces as separate? one must do so. could these faces be interpreted as somehow special codons? maybe as stop codons or start codons for the vertebrate genetic code which also corresponds to the realization of dna, rna ,trna, and amino-acids as dark proton triplets so that dna sequences would correspond to dark proton sequences. could the shared codons be assigned with various modifications of the vertebrate code involving also exotic amino-acids pyl and sec. 3. consider first the tetrahedral face. if the common face is removed from the 4-face orbit of tetrahedron, the orbit has only 3 faces and correspond to an amino-acid coded by 3 dna codons. ile is the only such amino-acid and the interpretation could be that one ile corresponds to the 3 tetrahedral faces and met acting as start codon to the fourth shared face. 4. also 3 icosahedral amino-acids corresponding to orbits containing the shared face can lose 1 codon each. to nake this more concrete, one can look for the deviations from the vertebrate code. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/puw82x8 dna decipher journal | october 2019 | volume 9 | issue 2 | pp. 44-64 57 pitkänen, m., an overall view about models of genetic code & bio-harmony (a) there are 10 doublets if the doublet uaa, uag acting as stop codons is counted as doublet coding for stop regarded formally as amino-acid. (b) the second member in the doublet uga, ugg coding for tyr in code table could correspond to a common face and act as a stop codon. (c) for the modifications of genetic code uag coding for stop can code for pyl and uga coding for stop can also code for sec. uga can also code for trp so that there would not be any symmetry breaking in this case. could uag and uga correspond to common faces for two icosahedra? (d) there is also third icosahedral shared face. cug coding for leu can also code for ser. could this correspond to the third exceptional codon associated with the icosahedral part of the code? 5. if the answers to the questions are affirmative, all basic deviations from the vertebrate code can be understood. the translation of the codons associated with shared face would be unstable for some reason. (a) 3-chord representation is more fundamental than the chemical one. this could mean that the chords associated with the shared faces are very near to each other so that the correspondence between 3-chord representation and chemical representation of codons becomes unstable if based on triple resonance. (b) the proposal has indeed been that the 13th vertex implied by tetrahedron corresponds to a note very near to one of the notes of 12-note scale this note is necessary since the 12-note scale defined by quints gives 12th note slightly more than octave under octave equivalence as discovered already by pythagoras. if this picture is correct, the symmetry breaking of the genetic code would be due to the presence of the face common to icosahedron and tetrahedron and reflect the problem discovered already by pythagoras. the rational number based pythagorean scale defined by quints is special: people with absolute pitch prefer it over the well-tempered scale involving powers of irrational number 21/12 requiring extension of rationals. 5.2 could stop codons correspond to dissonant 3-chords? one can approach the situation also from the point of view of harmony or rather, dis-harmony: could dissonance 3-chords act as stop codons. the 3-chords of icosahedral harmonies can be classified to three groups depending on whether the triangle representing the chord contains 0, 1, or 2 sides [13]: in in other words, whether the chord contains 0 , 1, or 2 quints. the harmonies can be labelled by the triplet (n0, n1, n2) telling the numbers of chords with 0, 1, and 2 quints. 1. the unique z6 harmony necessarily present in the bio-harmony has (2, 12, 6). it has two augmented chords (transposes of caug = cdg]) containing two major thirds and defining the 3-chord of a harmony assignable to triangle). this beautiful chord to which finnish tangos so often end, cannot be regarded as dissonance. 2. the 2 z4 harmonies have (n0, n1, n2) = (0, 16, 4) and (4, 8, 8). for the latter harmony one has genuine dissonances since the the highest and lowest note of 3-chord are separated by major or minor third. the chords with 0 quints labelled by script ”ex1”,”ex2”,...,”ex6” (for the notation see [13]) are dissonances in this sense. ”ex7” and ”ex8” (cdf] and cdg]) cannot be regarded as dissonances in this sense. 3. the 3 z2,rot harmonies have (0, 16, 4), (2, 12, 6), and (4, 8, 8). both 2-plets and 4-plets contain 2 dissonances. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2019 | volume 9 | issue 2 | pp. 44-64 58 pitkänen, m., an overall view about models of genetic code & bio-harmony 4. there are 3 z2,refl harmonies with (2, 12, 6) and 1 with (4, 8, 8). these harmonies have genuine dissonances. interestingly, (2, 12, 6) corresponds to a doublet for which only the second member corresponds to dissonance. 5. for tetrahedral harmony single step should correspond to 1/4:th of octave (using suitable power of 3/2 as a rational approximation) so that the notes at the vertices of tetrahedron should correspond to ce[f] defining cdim. this does not appear in the icosahedral code table as 0-quint chord. although the triangles of tetrahedron and icosahedron would be shared in some sense, the chords cannot be same. this support the idea that ile triplet and met are coded by tetrahedral faces. the chords containing 0 quints appearing in z4 and z2 harmonics can be regarded as dissonant. the minimization of dissonance would give a fusion of the unique z6 harmony (2, 12, 6), unique z4 harmony (0, 16, 4) and unique z2,rot harmony (0, 16, 4). bio-harmony would be unique and contain no dissonances. recall however that the proposal is that bio-harmonies serve as correlates for moods realized even at the level of basic bio-molecules. for other options one would have dissonant chords. z2,refl harmony (2, 12, 6) has only single dissonant chord. since stop codons would naturally correspond to dissonances, this observation raises some questions. 1. could the dissonant chord of z2,refl harmony (2, 12, 6) correspond to the triangle shared by tetrahedron and icosahedron? could this correspond to (stop,trp) pair with stop coded by dissonant chord ”ex”7 (cdf] defining part of d7 chord). this would fix the code to contain z6 harmony (2, 12, 6), unique z4 harmony (0, 16, 4) and unique z2,refl harmony (2, 12, 6). there would be single dissonance coding for stop in stop,trp doublet. 2. the doublet coding for stop should formally code for amino-acid. one cannot realize this doublet as a doublet of dissonances with ”ex”n, with n ∈ {1, .., 6} for single bio-harmony. the second member of this doublet could however correspond to the shared triangle. this tentative picture should be of course checked. there are also cycles without any symmetries. could these chaotic cycles be interpreted as disharmonies. 5.3 how could the representations of genetic code as dark 3-chords and nucleotide triplets relate? one of the poorly understood aspects of the model is how the various representations of the code relate. 5.3.1 frequency coding of nucleotides is not possible frequency coding of nucleotides would look natural but it is easy to see that it is in conflict with bioharmony. 1. the representations as dark proton triplets and dark photon triplets do not involve decomposition to ordered triplet of letters as the ordinary chemical representation does. dark protons are entangled and one cannot order them and there is no obvious ordering of the frequencies of dark photons. this is not a problem for the correspondence between dark proton triplets and dark photon triplets and one can even imagine assignment of dark cyclotron photons with 3 parallel flux tubes acting as wave guides. this could mediate the interaction between dark variants of basic biomolecules with same value of heff as frequency resonance. 2. the interaction between ordinary dna/rna/trna and its dark variant should involve the transformation of dark photon triplet associated with flux tube triplet emanating from dark bio-molecule to ordinary photons (possibly bio-photons) and energy resonance would be involved. is the energy issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2019 | volume 9 | issue 2 | pp. 44-64 59 pitkänen, m., an overall view about models of genetic code & bio-harmony resonance involved with the formation of the dark-ordinary pairs or with the sustainment of these pairings? the example of benzene suggests sustainment. 3. the assumption that energy resonance is involved with dark-ordinary pairing indeed leads to problems. the first guess would be that ordinary photon triplet somehow carries information about the position of nucleotide in the codon. the 4 nucleotides would correspond to 4 frequencies with frequency scale depending on the position inside the codon. there are indeed 12 frequencies in the 12-note scale so that 3 frequency scales with 4 frequencies associated with each of them would give 64 combinations of frequencies. frequency coding of nucleotides however leads to a problem. the first two letters of the codon are known to determine the amino-acid coded by it to a high degree since the third letter typically distinguishes between 1 or 2 amino-acids only, and labels codons at the orbit of dna codon defining amino-acid. therefore for dna codons coding same amino-acid the first two frequencies should be same. this is not the case for bio-harmony for the simple reason that the frequencies of 3-chords along the orbit defining amino-acids are different. only the frequency ratios defining the type of the chord are same along the orbit. the frequency ratios determine the correspondence so that the correspondence can be only between entire dark and ordinary codons, and cannot be reduced to correspondence between frequencies and letters. holism does not reduce to reductionism. 5.3.2 does the impossibility of frequency coding of nucleotides lead to problems with the models of replication and transription? this becomes a potential problem in the model for dna replication and transcription to rna. 1. the basic picture about bio-catalysis in tgd framework is following. u-shaped magnetic flux tubes emanate from the reactants and can reconnect to form a pair of flux tubes connecting the reactants. the shortening of the flux tube pair by a reduction of heff brings the reactants together and liberates the energy needed to kick the reactants over the potential wall making the reaction rate extremely low otherwise. the u-shaped flux tubes or flux tube triplets would be associated with dark codons of dark dna accompanying dna strand, and would be formed as the flux tube pair(s) connecting the strands split by the reversal of reconnection. the heff associated with resulting u-shaped flux tubes associated with replicating strands would increase requiring metabolic energy. they would get longer and could act as tentacles scanning the environment to spot similar flux tubes assignable to nucleotides or codons by resonance. 2. in the standard picture one assumes that nucleotides defining the letters of the codons appear as non-correlated molecules in the environment, and that each codon is built by a stepwise process in which letters attach to it. the letters can respond only to single frequency and cannot ”know” which position to attach to. thefrequency coding is not consistent with the idea that dark photon triplet assigned with the dark codon gives rise to energy resonance with the letters one by one. could the triple resonance occur as single step and attach all 3 nucleotides in single step? or could the triple resonance be a collective frequency resonance with dark codon already attached to the ordinary codon in the environment. ordinary-dark pairing by energy resonance would sustain rather than generate dna strand since otherwise the coulomb repulsion due to the large negative charge of dna does not allow stability. 3. the problem is that it is nucleotides seem to appear in the environment rather than codons. could the nucleotides of the environment actually form loose codons connected to dark codons by long flux tubes with large value of heff? could the reduction of heff bringing nucleotides together induce issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2019 | volume 9 | issue 2 | pp. 44-64 60 pitkänen, m., an overall view about models of genetic code & bio-harmony the reduction of flux tube lengths giving rise to ordinary codon? if the reduction of heff for flux tubes occurs nucleotide-by nucleotide, one would have consistency with the standard picture. the simplest picture is following. dark codons are paired with the loose variants ordinary codons. the opening of dna double strand leads to the splitting of the flux tube pairs connecting the ordinary codons of strands to u-shaped flux tubes, which reconnect with u-shaped flux tubes coming dark codons paired with loose ordinary codons. the reduction of heff d pairs nucleotides of loose codons with those of ordinary codons. 4. the pairs of dark codons and loose codons would be analogous to trna molecules. one can imagine even pre-trna molecules with loose coupling of rna and amino-acid so that replication and transcription would be very similar topological processes. also rna transcription and translation of rna to amino-acids would rely on similar mechanism. the only difference would be that only the second active strand would form u-shaped flux tubes connecting with dark rna codons. 5.3.3 what about remote dna replication this model could also explain remote replication of dna for which montagnier et al have reported evidence [4]. also remote transcription is predicted to be possible. i have already earlier considered a model of remote replication [12] in an article written together with peter gariaev who has reported this kind phenomenon already earlier. i have discussed the findings of montagnier et al in [22]. 1. the experiment involves two vessels, call them a and b. a contains genes and b only nucleotides at least according to the standard picture. there is irradiation using 7 hz frequency not far from the lowest schumann frequency having a nominal value of 7.8 hz. what happens is that the replicas of genes appear in b. it is also reported that the dna generates em radiation possibly responsible for the information transfer. 2. the proposed model for the ordinary dna replication generalizes easily to describe also remote replication. the new element would be that the u-shaped flux tubes from a would extend to b here 7 hz radiation could be essential , would be parallel to each other, and have same average length, which is natural if they have same value of heff . also the experimental arrangement could favor parallel flux tubes. in b the dark codons paired with loose codons formed from ordinary nucleotides would be present, and their u-shaped flux tubes would reconnect with those coming from a. remote replication could take place: here it is essential that the u-shaped flux tubes are parallel and have very nearly the same length. the tgd interpretation would be that the earth’s magnetic body is involved and generates quantum coherence in the length scale at least the size of the system studied. the reported em radiation would naturally relate to the dark photon triplets representing the codons. 5.3.4 is zeo needed to understand the replication? in tgd one must give up thinking in terms of standard ontology of bio-chemistry in which the process is a kinetic process governed by differential equations for the populations of molecules and proceeding in step-wise manner nucleotide by nucleotide. zeo suggests temporal holism at least at the level of single dark codon, which cannot be built building brick by building brick. 1. an open question is in which time scale this temporal quantum holism holds true: in the time scale of addition of single codon or in the time scale of replication of gene or something else? in the following the possibility that temporal holism holds in the time scale for the pairing of dark codons. 2. in zeo one could have state function reduction in which initial state corresponds to dark codon plus population of nucleotides and final state to dark codon paired with the ordinary codon formed issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2019 | volume 9 | issue 2 | pp. 44-64 61 pitkänen, m., an overall view about models of genetic code & bio-harmony from 3 nucleotides in energy resonance with the codon formed from nucleotides. what matters are only the initial and final states. 3. if ”big” state function reduction (bsfr) is in question, the final state would correspond to a superposition of deterministic time evolutions leading from the outcome of the reduction to geometric past, possibly but not necessary to a state in which nucleotides do not form codon paired with the dark codon. 4. the process would create strong correlations between the position of nucleotides of the codon and between the positions of codon and its dark variant and therefore a generation of entanglement. unitary evolutions followed by ”small” state function reductions (ssfrs) would generate a state as a superposition of the states satisfying the criteria of the desired final state and other states and bsfr would select the desired final state. it could be followed by bsfr returning the original arrow of time but doing nothing for the state. 6 appendix: tables of basic 3-chords for the icosahedral harmonies with symmetries the tables below give list for the three types of 3-chords for the 11 harmonies possessing symmetries. one must remember that the reversal of the orientation for the cycle induces the transformation c ↔ c, f]↔ f], h ↔ c], f ↔ g, d ↔ b[, e ↔ g], a↔ d] and produces a new scale with minor type chords mapped to major type chords and vice versa. also one must remember that all 3-chords except those which are simple majors or minors lack the third so that their emotional tone remains uncharacterized. for instance, c6 does could be replaced with cm6 and g7 with gm7. the reader can check the chords by direct inspection of the figures. the convention used is that vertex number one corresponds to c note. (n0,n1,n2) 0-chords 1-chords 2-chords (2, 12, 6) (faug,gaug) (cm,dm,em,f]m,g]m,b[m), (c9, d9, e9, f ]9, g]9, b[9). (f6, g6, a6, b6, c]6, d]6). table 1: table gives various types of 3-chords for harmonies with z6 rotational symmetry. note that half-octave shift is an exat symmetry. note that gaug = ceg], f aug act as bridges between the groups related by half octave shift. the chords have been arranged so that they form orbits of z6. ”amino-acid chords” correspond to preferred chords at the orbits. (n0,n1,n2) 0-chords 1-chords 2-chords (0, 16, 4) (d7, d6, g]7, g]6), (b[9, b9, e9, f9). (g4+, a9−, c]4+, d]9−), (emaj7, gmaj7, b[maj7, c]maj7), (c9−, a9−, f ]9−, d]9−). (4, 8, 8) (cex3, eex2, f ]ex3, b[ex2). (dmaj7, e9−, a7, a6), (b[9, f9, c9, g9). (g]maj7, b[9−, d]7, d]6). (e9, b9, f ]9, c]9). table 2: table gives various types of 3-chords for the two harmonies with z4 = zrot 2 × zrefl 2 symmetry. 4-plets represent the orbits. first cycle has no harmonic loners. second cycle gives rise to bio-harmony (4, 8, 8) for which 0-quint chords are dissonant. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2019 | volume 9 | issue 2 | pp. 44-64 62 pitkänen, m., an overall view about models of genetic code & bio-harmony (n0,n1,n2) 0-chords 1-chords 2-chords (0, 16, 4) (em,b[m), (cm,f]m), (d9, g]9), (g6, c]6), (a6, d]6), (e9, b[9). (d4+, g]4+), (b4+, f4+), (cmaj7, f ]maj7), (g6−, c]6−). (2, 12, 6) (aex4, d]ex2). (am,d]m), (g9−, c]9−), (c9, f ]9), (c4, f ]4), (e4+, b[4+), (a9, d]9), (dmaj7, g]maj7), (d9, g]9). (bmaj7, fmaj7). (4, 8, 8) (aex2, hex8, d]ex2, f ex8). (d7, g]7), (amaj7, d]maj7), (g9, c]9), (a9, d]9), (a4+, d]4+), (e7, b[7). (b9, f9), (e9, b[9). table 3: table gives various types of 3-chords for harmonies with z2 rotation symmetry acting as halfoctave shift. the doublets represent 2-chord orbits. (n0,n1,n2) 0-chords 1-chords 2-chords (2, 12, 6) (f]ex3, hex4), (am,d]), (a6, d]7), (c9, f9), (b9, f ]9), (d7, b[6), (g6−, fmaj7), (e9−, c]9). (d4+, b[9−), (e9, g]4+), (2, 12, 6) (dex4, hex4). (f, fm), (c6−, b[maj7), (c9, d]9), (d7, g]6), (gmaj7, d]6−). (d]9, c]9), (c]4−, a4+), (e4+, f ]6). (e9, b9). (4, 8, 8) (fex1, d]ex3, g]ex1, aex2). (e7, e6), (amaj7, b9−), (d9, b9), (c9, c]9), (g,c]m), (d7, f ]6). (f9, g]9), (d]9, b[9). (2, 12, 6) (hex3, eex7). (d7, g]6), (g,d]m), (c9, d]9), (f, fm), (c6−, b[maj7), (d9, c]9), (a9−, c]4+), (e7, f ]6). (e9, b9). (2, 12, 6) (f]ex2, f ex3). (f,b[m), (c7, g]6), (b[9, d]9), (amaj7, b9−), (e6, e7), (c9, c]9), (g,c]m), (d7, b6). (d9, h9). table 4: table gives various types of 3-chords for harmonies with single reflection symmetry. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2019 | volume 9 | issue 2 | pp. 44-64 63 pitkänen, m., an overall view about models of genetic code & bio-harmony references [1] canfield er king rb. icosahedral symmetry and the quintic equation. computers & mathematics with applications.available at: https://www.sciencedirect.com/science/article/pii/ 0898122192902109, 24(3):13–28, 1992. [2] nottale l da rocha d. gravitational structure formation in scale relativity. available at: http: //arxiv.org/abs/astro-ph/0310036, 2003. [3] hachimoji dna and rna: a genetic system with eight building blocks. science. available at: http://tinyurl.com/y2mcjb4r, 363(6429):884–887, 2019. [4] montagnier l et al. dna waves and water. available at: http://arxiv.org/abs/1012.5166, 2010. 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[22] pitkänen m. dna waves and water . available at: http://tgdtheory.fi/public_html/ articles/mont.pdf, 2011. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.fi/public_html/articles/harmonynew.pdf http://tgdtheory.fi/public_html/articles/harmonynew.pdf http://tgdtheory.fi/public_html/articles/gfluct.pdf http://tgdtheory.fi/public_html/articles/freakydna.pdf http://tgdtheory.fi/public_html/articles/freakydna.pdf http://tgdtheory.fi/public_html/articles/mont.pdf http://tgdtheory.fi/public_html/articles/mont.pdf introduction 3 basic realizations of the genetic code 3 models of bioharmony about the geometric interpretation of icosahedral and other symmetries mistracks interactions between various levels the independence of the interaction energy on frequency the independence of cyclotron energy on frequency and nottale hypothesis homonymy of the genetic code variations of the genetic code wobble base pairing tgd view about homonymies homonymies for drna-3-chord correspondence the map drna-dtrna by 3-chords homonymies for rna-aa correspondence homonymies for rna-trna correspondence about the details of the genetic code based on bio-harmony why 3 icosahedral harmonies and 1 tetrahedral harmony? could stop codons correspond to dissonant 3-chords? how could the representations of genetic code as dark 3-chords and nucleotide triplets relate? frequency coding of nucleotides is not possible does the impossibility of frequency coding of nucleotides lead to problems with the models of replication and transription? what about remote dna replication is zeo needed to understand the replication? appendix: tables of basic 3-chords for the icosahedral harmonies with symmetries login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x mattipitkanen1_v5n2.pdf dna decipher journal | october 2015 | volume 5 | issue 2 | pp. 111-143 111 pitkänen, m. more precise tgd based view about quantum biology and prebiotic evolution article more precise tgd based view about quantum biology and prebiotic evolution matti pitkänen 1 abstract in this work i try to clarify the relation of the basic notions of tgd and of tgd inspired biology to the ordinary bio-chemistry. i also try to improve my understanding about work of fröhlich, del giudice, and pollack using the notions of tgd. the key idea is the notion of coherence induced by weak em fields with preferred frequencies, which in ordinary quantum theory correspond to energies much below the thermal energy in quantum theory this creates what is called kt paradox. in tgd framework one can do without coherence regions, which can be much larger. the basic observation is that for a pair of hydrogen bonded water molecules the reaction 2h2o→ h3o − 2 + dark proton require uv photon with energy of o-h bond of about 5.15 ev. quantum criticality suggests that this process should occur spontaneously as a chain reaction. this is achieved in the same manner as in nuclear fusion if the dark protons at the flux tube fused to nuclear strings giving rise to dark nuclei. if dark nuclear binding energy transforms as coulomb energy, the nuclear energy scale of mev scales down to 1-10 ev depending on the value of heff . an attractive guess is that the energy range of bio-photons corresponds to that for dark nuclear binding and excitation energies. their spontaneous transformation back to ordinary nuclei would liberate energy could at least partially explain the evidence for bio-transmutations [3, 4]. also the relation to cold fusion is interesting[32]. tgd inspired proposal for prebiotic evolution was inspired by the tgd based realization of expanding earth hypothesis and assumes that life evolved in underground oceans and burst on the surface of earth in cambrian explosion. this view leads to a more precise view about prebiotic evolution. possible technological implications of this picture if true are quite impressive. cold biofusion could make possible artificial generation of technologically important elements and the mechanism generating ezs could make possible creation of artificial intelligent life forms involving silicates and water. 1 introduction this work is an attempt to clarify the relation of the basic notions of tgd and tgd inspired biology in particular the vision about prebiotic evolution to chemistry and to the standard views about prebiotic evolution. there are frustratingly many different approaches and i have been working hardly to see whether tgd could allow to identify the common denominator of these approaches. in tgd framework one can do without coherence regions (one could perhaps identify them as special cases of pollacks ezs), which can be much larger. the basic observation is that for a pair of hydrogen bonded water molecules the reaction 2h2o→ h3o − 2 + dark proton require uv photon with energy of o-h bond of about 5.15 ev. water clathrates are good candidates for the precursors of ezs since they have size scale in the same range as ezs and contain hydrogen bonded water. quantum criticality suggests that this process should occur spontaneously as a chain reaction. this is achieved in the same manner as in nuclear fusion if the dark protons at the flux tube fused to nuclear strings giving rise to dark nuclei. if dark nuclear binding energy transforms as coulomb energy, the nuclear energy scale of mev scales down to 1-10 ev depending on the value of heff . an attractive guess is that the energy range of bio-photons corresponds to that for dark nuclear binding and excitation energies. their spontaneous transformation back to ordinary nuclei would liberate energy could at least partially explain the evidence for bio-transmutations [3, 4]. also the relation to cold fusion is interesting [32]. 1correspondence: matti pitkänen http://tgdtheory.com/. address: köydenpunojankatu 2 d 11 10940, hanko, finland. email: matpitka@luukku.com. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2015 | volume 5 | issue 2 | pp. 111-143 112 pitkänen, m. more precise tgd based view about quantum biology and prebiotic evolution dark nuclear binding energy is liberated as dark photons decaying into bunches of ordinary photons inducing further reactions 2h2o→ h3o − 2 + dark proton also other kind of dark ionizations. the size of ezs varies from about 1 micron to 100 microns. suppose that the size scale of ez corresponds to the wavelength of dark photon with energy of order dark nuclear binding, and that heff is such that the nuclear binding energy corresponds to the lower end about 1 ev in the range of bio-photon energies. if so then heff/h varies in the range 1− 100. this would be the total number of dark photons resulting in the decay to ordinary photons. in this process ordinary protons transform dark protons at magnetic flux tubes outside ez. dark ionization differs from ordinary ionization only in that the proton is dark. the difference between dark and ordinary ionization would define the borderline between ordinary and bio-chemistry (or dark chemistry). chemical quantum criticality is possible also for other cations and also anions and all biologically important ions can appear as dark ions. the urey-miller experiment was very successful: it produced a large variety of amino-acids crucial for life from simple basic constituents. the variant of this experiment has even produced adenosine, dna nucleotide fundamental for atp. there is however a severe problem. the prebiotic atmosphere was not reducing as in the urey-miller experiment simulating it. clays are good candidates for the key structures in prebiotic evolution since they can replicate. one can even speculate with an analog of genetic code. phyllosilicates containing -o-h groups are especially interesting: they can adsorb basic biomolecules and induce their polymerization to oligomers. they also induce a formation of vesicles formed from lipid bilayer and serving as a candidate for a predecessor of cell. dna is the problem and has led to a scenario known as rna world. phyllosilicates are also known to generate radiation with positive health effects. the natural and testable hypothesis is that the presence of ezs allows to circumvent the difficulties of the standard rna world scenario and also generate dna and biologically active phosphates containing the mysterious phosphate bond as ionized dark proton. the dark magnetic flux tubes and uv photon energy needed to generate ezs could be provided by gel in pollacks’s experiments and by electric discharges in urey-miller experiment. also dark photons from the formation of dark nuclei decaying to bunches of bio-photons can be considered. water clathrates can contain atoms and even micrometer sized phyllosilicate crystals, which could catalyze the formation of biomolecules at their surfaces as dark nuclear fusion chain reaction. clathrate could also develop phospholipid bilayer around it kind of primitive cell membrane. tgd inspired proposal for prebiotic evolution was inspired by the tgd based realization of expanding earth hypothesis and assumes that life evolved in underground oceans and burst on the surface of earth in cambrian explosion. this view leads to a more precise view about prebiotic evolution. possible technological implications of this picture if true are quite impressive. cold biofusion could make possible artificial generation of technologically important elements and the mechanism generating ezs could make possible creation of artificial intelligent life forms involving silicates and water. 1. the works of fröhlich [17] and del giudice [13, 6] have served as a theoretical background in many attempts to develop quantum view about biology and consciousness. the first key idea is that weak em fields with frequencies, which correspond to energies much below the thermal energy in ordinary quantum theory, induce coherence/synchrony maybe even quantum coherence and that metabolic energy can be stored into bose-einstein condensate type states (https://www.youtube. com/watch?v=rjf1_edesqc). for instance, the work of blackman [23] and others in turn suggests that cyclotron frequencies in magnetic field of .2 gauss have effects on vertebrate brain. living systems are full of electrets and dipoles and charge separation in water environment is key aspect of living matter. fröhlich sees electric dipoles and dipole oscillations as something fundamental. also microtubule based view about consciousness relies on the ideas of fröhlich. del giudice introduces the notion of coherence regions with size of about 1 micron as regions of water. pollack [11] has discovered exclusion zones (ezs) as a characteristic of what he calls fourth phase of water. charge separation occurs in ezs created in presence of gel: ez is negatively charged and obeys h3/2 stoichiometry instead of the usual. part of protons goes outside ez. water clathrates isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2015 | volume 5 | issue 2 | pp. 111-143 113 pitkänen, m. more precise tgd based view about quantum biology and prebiotic evolution (https://en.wikipedia.org/wiki/clathrate_hydrate) have size scales in the same range as ezs and could be precursors of ezs. questions: what does the coherence/synchrony forced by oscillating external emf really mean? does it really create bose-einstein condensates for oscillatory modes coupled with it? how coherence regions and ezs emerge? frequency clearly matters as in quantum theory but the photon energies are typically far below thermal energy: how can external emfs with extremely low frequencies have quantal effects? 2. the experimental work carried out to understand prebiotic evolution has led to various insights but no unified view exists. urey and miller [10] found that amino-acids emerge from simpler building blocks in an environment believed to mimic the boundary region between water, dry land, and atmosphere. the recipe for the prebiotic soup was simple: take simplest biomolecules such as nh3, ch4, water, lightnings to feed energy (they might have also some other functions), and assume reducing atmosphere. by adding some further simple ingredients also adenine essential for metabolism, was generated in this kind of environment. it has however become clear that the atmosphere very probably was not reducing. question: is it possible to imagine any counterpart for the reducing atmosphere? 3. there is also a vision that clays represented prebiotic life. clays form complex chemical and geometric structures consisting of layers microscopically, and also replicate by simply splitting to two. one can even speculate about a simple predecessor of genetic code. perhaps chemical life evolved in symbiosis with clays. phyllosilicates (https://en.wikipedia.org/wiki/category:phyllosilicates) in particular kaolinite and montmorillonite are most studied clays. there is large variant of them containing basic biologically important ions in their lattice structure. montmorillonites adsorb amino-acids and rna nucleotides and promote polymerization of oligomers of rna although the lengths of the resulting oligomers are considerably shorter than required by rna world. dna is not obtained since it is highly unstable in ordinary water. even vesicles formed by double lipid layers are formed and could serve as predecessors of cells. but something is clearly missing. questions: what is needed to get longer rna strands and perhaps even dna? how could one obtain prebiotic genetic code? what kind of environment could contain the biologically important atoms/ions in particular phosphate ion? 4. one can try to combine the experimental vision with the theoretical visions of fröhlich and del giudice and with the experimental discoveries of blackman and pollack. this leads to ask whether the layers phyllosilicate structures could generated frequencies which promote coherence (maybe even quantum coherence) in living matter. it is now known (as i learned from hans geesink) that phyllosilicates have positive effects on health. maps are constructed for their frequency spectrum and it is even found that they can serve as kind of frequency storage this is analogous to water memory [30]. even cyclotron frequencies assignable to .2 gauss magnetic field have been identified, and there is evidence that the powers of 3 and 2 about these frequencies are also biologically important. quite generally, the thz/microwave region for which energies are below thermal energy (kt paradox) seems to be of special importance. questions: could basic biomolecules and surfaces of phyllosilicate layers in interaction with water have been predecessors of the recent chemical life? water clathrates can contain various elements and probably also phyllosilicate crystals: could their transformation to ezs be an essential step in prebiotic evolution? tgd suggests an answer to the questions posed above. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2015 | volume 5 | issue 2 | pp. 111-143 114 pitkänen, m. more precise tgd based view about quantum biology and prebiotic evolution 1. in tgd universe dark matter corresponds to ordinary matter with large value heff = n × h of effective planck constant. the oscillating classical em fields are classical correlates for dark photons. this solves the kt paradox. the forced oscillations are induced by absorption of these quanta: macroscopic quantum coherence forces the coherence of ordinary biomatter. the additional assumption heff = hgr = gmm/v0 [45, 38] (to be explained in more detail later) implies universal energy spectrum for dark cyclotron photons and their transforms to ordinary photons can be identified as bio-photons [41] in energy range containing visible and uv frequencies. generalized josephson radiation from membrane proteins acting as generalized josephson junctions has also a branch for which energy spectrum is universal but frequencies depend on heff . these two dark photon species are used by magnetic body to control, coordinate, and communicate with ordinary matter in living systems. 2. in tgd framework one can do without coherence regions (one could perhaps identify them as special cases of pollacks ezs), which can be much larger. the basic observation is that for a pair of hydrogen bonded water molecules the reaction 2h2o→ h3o − 2 + dark proton require uv photon with energy of o-h bond of about 5.15 ev. water clathrates (https://en.wikipedia.org/wiki/ clathrate_hydrate), whose importance hans geesink emphasizes [18], are good candidates for the precursors of ezs since they have size scale in the same range as ezs and contain hydrogen bonded water. quantum criticality suggests that this process should occur spontaneously as a chain reaction. this is achieved in the same manner as in nuclear fusion if the dark protons at the flux tube fuse to nuclear strings giving rise to dark nuclei. if dark nuclear binding energy transforms as coulomb energy under scalings of heff inducing similar scaling of the size of the system, the nuclear energy scale of mev scales down to 1-10 ev depending on the value of heff . an attractive guess is that the energy range of bio-photons corresponds to that for dark nuclear binding and excitation energies. their spontaneous transformation to ordinary nuclei would liberate energy could at least partially explain the evidence for bio-transmutations. also the relation to cold fusion is interesting. dark nuclear binding energy is liberated as dark photons decaying into bunches of ordinary photons inducing further reactions 2h2o→ h3o − 2 + dark proton also other kind of dark ionizations. the size of ezs varies from about 1 micron to 100 microns. suppose that the size scale of ez corresponds to the wavelength of dark photon with energy of order dark nuclear binding, and that heff is such that the nuclear binding energy corresponds to the lower end about 1 ev in the range of bio-photon energies. if so then heff/h varies in the range 1 − 100. this would be the total number of dark photons resulting in the decay to ordinary photons. in this process ordinary protons transform dark protons at magnetic flux tubes outside ez. dark ionization differs from ordinary ionization only in that the proton is dark. the difference between dark and ordinary ionization would define the borderline between ordinary and bio-chemistry (or dark chemistry). chemical quantum criticality is possible also for other cations and also anions and all biologically important ions can appear as dark ions. 3. dark proton states correspond to states of dna, rna, amino-acids and trna and therefore provide a fundamental representation of genetic code. the dark ionization of -o-h:s of any linear molecular structure generates dark proton sequence. in particular, the -o-h in phosphate of dna nucleotide can become o− plus dark proton, so that one has pairing or dna with dark proton sequence carrying the genetic information. this splitting can occur also for amino-acids containing -o-h as standard part and also for atp. dark ionization can also occur for -o-h:s at of phyllosilicates layers and at their 1-d boundaries. depending on the correlation between dark proton states and phyllosilicate units one could have an analog of genetic code. one can also imagine formation of dna, rna, etc... as their inorganic forms ”steal” dark proton sequence from phyllosilicate: dark proton sequence would serve as a template. this would make possible very effective generation of complex biopolymers. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2015 | volume 5 | issue 2 | pp. 111-143 115 pitkänen, m. more precise tgd based view about quantum biology and prebiotic evolution 4. as geesink emphasizes [18], clays are good candidates for the key structures in prebiotic evolution since they can replicate. one can even speculate with an analog of genetic code. phyllosilicates containing -o-h groups are especially interesting: they can adsorb basic biomolecules and induce their polymerization to oligomers. they also induce a formation of vesicles formed from lipid bilayer and serving as a candidate for a predecessor of cell. dna is the problem and has led to a scenario known as rna world. phyllosilicates are also known to generate radiation with positive health effects. the natural and testable hypothesis is that the presence of ezs allows to circumvent the difficulties of the standard rna world scenario and also generate dna and biologically active phosphates containing the mysterious phosphate bond as ionized dark proton. the dark magnetic flux tubes and uv photon energy needed to generate ezs could be provided by gel in pollacks’s experiments and by electric discharges in urey-miller experiment. also dark photons from the formation of dark nuclei decaying to bunches of bio-photons provide this energy. water clathrates serving as precursors of ezs can contain atoms and perhaps even micrometer sized phyllosilicate crystals, which could catalyze the formation of biomolecules at their surfaces as a dark nuclear fusion chain reaction. clathrate could also develop phospholipid bilayer around it kind of primitive cell membrane. a possible objection is that pollack observed that ezs repel impurities from their interior. what ”inpurity” exactly means is of course a crucial question. 5. prebiotic life could have evolved in underground oceans even below the earth’s crust. the metabolic energy feed could have come as dark photons from the core, whose temperature is rather near to that of solar radiation. also dark photons from solar radiation could have contributed. ezs could have been generated by dark uv quanta accompanying lightnings. dark photons would propagate along dark magnetic flux tubes through the crust and transform to bio-photons in underground oceans (this is not the only possibility). geesink [18] mentions that fir and thz/microwave radiation is accompanied by the clathrate aerosols in atmosphere, which suggests the importance of atmosphere. if ezs generated by solar radiation from clathrates are present, this radiation could be dark and have energies above thermal energy and propagate along dark magnetic flux tubes. ezs could also transform ordinary solar radiation to dark radiation so that the radiation from atmosphere could enter underground oceans as dark radiation. in cambrian explosion the radius of earth was doubled (in tgd universe cosmic expansion occurs in rapid jerks at the level of astrophysical objects in given scale) the underground life was burst to the surface of earth [29]. possible technological implications of this picture if true are quite impressive. cold biofusion could make possible artificial generation of technologically important elements and the mechanism generating ezs could make possible creation of artificial intelligent life forms involving silicates and water. 2 background recently i have had very interesting discussions with hans geesink (http://www.biotech-silicates. com/en/team-3/) and have also received a lot of highly interesting material from hans, in particular his book ”proposal for a quantum field theory about coherence concerning non ionizing radiation” [18], which can be found from his blog (https://geesinkresearch.wordpress.com). his views have much in common with my own vision and differences are especially useful since they force to direct attention to ideas that i have not directed enough attention. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2015 | volume 5 | issue 2 | pp. 111-143 116 pitkänen, m. more precise tgd based view about quantum biology and prebiotic evolution 2.1 about experimental work of hans geesink i was contacted by hans geesink, who works in biotech silicates, which tries to develop technology intended to reduce negative health effects caused by man-made non-thermal non-ionizing radiation involving typically frequencies from elf (eeg region) to far infrared region. these effects are caused by emfs from antennae, mobile phones, and power cables. perception tests are carried out to see the possible effects on well-being. using the words of geesink: we have measured more precisely the resonances of the phyllosilicate minerals (used to compensate negative biological effects caused by non thermal non ionizing radiation; having multiple stacked sheets; each platelet 1 nanometer thick, and in stacks of micrometers, and total lengths of more than earth diameter, able to be organized as a metamaterial, nearly all types of ions incorporated in and between the platelets and we measured: quantized light, ir and fir spectra properly ordered in powers of 2, and ratios of 1:2, 2:3, and adding multiple frequencies of 2 and 3. the general vision is that weak external em fields oscillating at frequencies utilized by biosystems to coordinate their behavior by inducing coherent oscillations make possible coherence and perhaps even quantum coherence. the man-made emfs tend to destroy this coherence and weak emfs would restore the coherence if the frequencies are correct. phyllosilicates seem to provide the materials producing the correct frequencies. 2.2 some theoretical ideas in his articles geesink has done hard work in building a unified view about the enormous literature related to the biosystems and quantum coherence. geesink sees the role of classical oscillating em fields central in biology. these fields somehow give rise to the coherent behavior of biomatter and perhaps even quantum coherence. fröhlich is one of the pioneers, who thought that electric dipoles and dipole oscillations could be central in living matter and give rise to analogs of bose-einstein condensates. a further important notion would be that of coherence region developed by del giudice as a quantum field theoretical (qft) concept important for understanding of quantum biology. unfortunately, this notion is not established experimentally unlike the exclusion zones (ezs) discovered by pollack. in the following i try to relate these ideas to tgd framework. 2.2.1 fröhlich’s ideas fröhlich [17] (see http://onlinelibrary.wiley.com/doi/10.1002/qua.560020505/abstract) proposes the importance of liquid crystals (https://en.wikipedia.org/wiki/liquid_crystal) and electric dipoles in biology. cell membrane is only one example of liquid crystal and electret important in biology. already becker [22] demonstrated that electric potentials serve as correlates of consciousness. fröhlich suggests the importance of the longitudinal em modes assignable to dipole oscillations and metabolic energy storage as analogs bose einstein condensates (http://www.springer.com/us/book/9783642733116). for instance, the tubulins inside microtubules are electric dipoles and hameroff was the first researcher to propose that they might be important for consciousness. i have myself developed this idea from tgd perspective in a model of anesthetes based on electric fields associated with microtubules and give rise also to becker’s dc currents as supra-currents inside microtubules [36]. one can imagine that dipole oscillations are quantized just like sound waves. mathematically this is not a problem. the simplest situation corresponds to electrons oscillating in unisono with respect to the ionic lattice and accompanied by an electric field varying in a periodic manner. these oscillations can propagate and define longitudinal electric waves analogous to longitudinal sound waves. personally i am a little bit skeptic about quantizing the plasma oscillations but i might be wrong also acoustic oscillations are quantized. the point is that the density of electrons appears in the formulas for frequencies, which suggests that a phenomenological description is in question. but the density of particles appears also in the frequency for sound waves and we talk fluently about phonons! isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2015 | volume 5 | issue 2 | pp. 111-143 117 pitkänen, m. more precise tgd based view about quantum biology and prebiotic evolution i would propose that both phonons and plasma waves have a genuine quantum description at deeper level. in tgd this deeper level would correspond to strings connecting points of partonic 2-surfaces serving as carriers of fermion number. the oscillations of strings would be fundamental besides the oscillations of their ends. even elementary particles would consist of pairs of wormhole contacts in turn consisting of two partonic 2-surfaces at parallel space-time sheets and connected by strings and string oscillations would represent the fundamental phonons. phonons would be 2-particle phenomenon and photons single particle phenomenon. this two-particle aspect is missing from qft description. in string model description only the string aspect is present. in tgd both are involved and this is crucial for obtaining macroscopic gravitationally bound states: in tgd framework string model is doomed to be only a model of gravitation in planck length scale. fröhlich uses the phrase ”governed by negentropy”. the notion of negentropy has somewhat fuzzy content in standard physics framework. 1. fantappie [24] introduced the notion of syntropy, which in zero energy ontology (zeo) can be regarded as entropy but with different arrow of time. spontaneous self assembly would be a process, which would be decay in the reversed direction of time and obey time reversed second law. 2. i have talked about negentropy maximization principle and number theoretic negentropy [31, 46]. nmp defines the basic variational principle behind state function reduction central for both tgd and tgd inspired theory of consciousness. number theoretical entropy is a variant of shannon entropy for which the probabilities appearing as arguments of logarithms are replaced with their p-adic norms: this requires that probabilities are rational or at least algebraic numbers. if the entanglement probabilities do not belong to the algebraic extension of rationals used, the entanglement is rather stable since it requires a phase transition to large algebraic extension. he final states of state function reduction can have non-vanishing rational entanglement probabilities with projector as a density matrix: this corresponds to unitary entanglement matrix. the number theoretic entanglement entropy is negative for these states and one can say that entanglement carries information. nmp is not in conflict with second law: the thermodynamical ensemble entropy characterizes the average particle of ensemble and entanglement entropy characterizes pair of systems. second law would however hold true only when restricted to the visible sector with standard value of planck constant. 3. the most powerful implications of nmp in zero energy ontology (zeo) are precise identification of self as the sequence of state function reductions at a fixed boundary of causal diamond (cd). this leads to the understanding of metabolism and homeostasis as the attempt of conscious entities (selves) to survive: the ”death” of self occurs in the first state function reduction to the opposite boundary of cd and actually means re-incarnation in geometric past as far as sensory input is considered. selves do not however know about this(!) and fight for survival trying to gather negentropy associated with sub-selves to satisfy the needs of nmp. metabolism is at deeper level gathering of negentropy resources as negentropic entanglement and nutrients are carriers of the negentropic entanglement. this picture is a powerful guideline in attempts to understand how the prebiotic life was initiated. 2.2.2 forced coherence, coherence regions, and exclusion zones (ezs) the notion of forced coherence is crucial idea behind the development of devices allowing to reduce the negative health effects caused by man-made non-thermal non-ionizing radiation. coherent em fields at various frequencies are assumed to play a key role in bio-coordination and artificially generated emfs interfere with this coordination causing negative health effects. the use of phyllosilicate based devices is argued to help to re-establish the coordination if thee generate radiation at frequencies important for maintaining biological coherence via external weak synchronizing isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2015 | volume 5 | issue 2 | pp. 111-143 118 pitkänen, m. more precise tgd based view about quantum biology and prebiotic evolution signal (for illustration of synchrony see https://www.youtube.com/watch?v=rjf1_edesqc). if phyllosilicates indeed achieve they might have played important role in prebiotic evolution. del giudice [6] [13] has introduced the notion of coherence region. these regions would have size of order 1 micrometer and would be characterized by both acoustic and plasma oscillations induced by the synchronizing external fields. velocity of propagation is dramatically reduced. i have considered a model of coherence regions as a phase of water in which certain fraction of -o-h bonds of water molecules are excited to high energy state with energy abound 4.8 ev and near the bond breaking energy about 5.15-5.3 ev so that only metabolic energy quantum of about in the range .05-.3 ev is needed to break these bonds. note that .05× z ev corresponds to the minimal energy assignable to protein josephhson junctions of neural membrane and that .3 ev is slightly below the nominal value of metabolic energy quantum with nominal value of .5 ev. this would give rise to the formation of fourth phase of water discovered by pollack [11]. it however turns out that one can do without coherences regions in tgd framework. the exclusion zones (ezs) of pollack are generated in water bounded by gel in presence of irradiation by visible light. they have sizes up to 100 micrometers the size of large neuron are a fundamental concept in tgd inspired attempts to understand living matter. ezs have high electron density and obey the stoichiometry h3/2o. part of protons must go outside the ez and tgd inspired proposal is that they go to dark protons at magnetic flux tubes. electrons inside ez have large fermi energy above thermal energy maybe even of order 1 ev as in condensed matter and could be key players in tgd based mechanism of bio-super-conductivity. the electrons would be transferred to magnetic flux tubes as dark electrons at quantum criticality. ezs would accompany all bio-active molecules in particular dna, which has charge -e per nucleotide associated with the phosphate. also microtubules possess gtp molecules with same charge. the basic problem is to understand how the ezs and coherence regions or clathrates as their possible precursors can be created. quantum criticality is a key notion of quantum tgd and tgd inspired biology but has been discussed also by other scientists. for instance, stuart kauffman has developed this notion [19] (http: //arxiv.org/pdf/1502.06880v2.pdf). there are of course many views about quantum criticality: the characteristic difference between tgd inspired proposal [44] and other proposals is that quantum theory is generalized by introducing the hierarchy of planck constants heff = n×h labeling a fractal hierarchy of isomorphic sub-algebras of so called super-symplectic algebra having the structure of conformal algebra. 2.2.3 water clathrates geesink emphasizes [18] the importance of water clathrates or clathrate hydrates (https://en.wikipedia. org/wiki/clathrate_hydrate) crystalline water based solids resembling ices and consist of hydrogen bonded water. clathrates contain also guest molecules such as small non-polar molecules (typically gas molecules) and polar molecules with large hydrophobic moieties (parts) trapped inside ”cages” of hydrogen bonded frozen water molecules. methane is one gas trapped in deposits of methane clathrate. clathrates appear also at outer planets, moons, and trans-neptunian objects. the size scale range for clathrates varies from 1-100 micros and is same as for ezs of pollack and the natural identification would be as precursors of ezs. this makes clathrates ideal prebiotic structures inside which molecular life could have evolved. geesink notices also the significance of atmospheric aerosol of water clathrates as emitters of radiation in fir and thz/microwave region inducing coherence and transition betweens protein conformations and rydberg states (https://en.wikipedia.org/wiki/rydberg_state). rydberg states themselves could be excited by uv radiation. the absorption of solar light could transform also atmospheric clathrates to ezs. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2015 | volume 5 | issue 2 | pp. 111-143 119 pitkänen, m. more precise tgd based view about quantum biology and prebiotic evolution 3 basic tgd based vision about quantum biology from tgd point of view the findings discussed by geesink in his article [18] are highly interesting for several reasons. geesink underlines the importance of external classical fields as inducers of coherence which differs from ordinary coherence in that there is external energy feed as in self-organizing systems, and also the importance of coherence regions of size about 1 micrometer. this raises questions. 1. is the coherence really quantal or is it the external classical fields classical correlates for quantum coherence? can one really speak about bose-einstein condensates of longitudinal oscillations of electric or is a more fundamental quantum description needed? 2. do the coherence regions of del giudice exist except as theoretical entities? what is their origin in tgd universe if they exist? could the ezs of pollack, which certainly exist involve the fusion of coherence regions accompanied by a phase transition to h1.5o stoichiometry generating charge separation. or could one do without coherence regions as separate entities and perhaps identify them with ezs? or could water clathrates replace them as precursors of ezs? note that theoretically the size of coherence regions would be about 1 micrometers whereas the sizes of ezs vary up to 200 micrometers. the clathrate option looks to me highly attractive. 3. geesink reports that the phyllosilicate minerals created in the interaction of water with silicate minerals and possessing characteristic -o-h groups have positive health effects and can be used to reduce the negative effects caused by man-made non-ionizing radiation. when doped with biologically important ions they produce specific biological effects characterizing the ion and also the cyclotron frequencies assigned to .2 gauss magnetic field by blackman are detected. this leads to a series of questions. (a) could the physics of phyllosilicate-water system involve ezs and possibly also coherence regions in a key role? -o-h groups and their ionized variants -o− are a common denominator of both water, biologically active phosphate and there of dna and rna nucleotides as well as phospholipids containing phosphate, of amino-acids, etc... could the transformation of -o-h to -o− plus dark proton be the fundamental reaction generating dark protons. note that this transformation would be dark counterpart for what what happens as acid gives up proton. for instance, a fraction of water molecules characterized by ph decomposes to oh− and h3o + ions. in presence of ez this process would produce dark h+ rather than h3o + ions. this generalizes to other cations and also to anions. the distinction between dark anion/cation (usually proton/electron) is the boundary between non-organic chemistry and bio-chemistry. (b) phyllosilicates involve all biologically important ions: did their dark variants emerge already in the prebiotic phase in the interaction of water with phyllosilicate? what is this interaction? could the process -o-h to -o− also phyllosilicates in interaction with fourth phase of water and transform also the biologically important ions to their dark counterparts and at the same time ionize the mineral surface? 4. what makes possible coherent generation and liberation of metabolic energy? is this a quantum coherent process or chain reaction as the model for the generation of ez suggests or are both options realized? 5. quantum criticality and dark variants of biologically important ions. what is the mechanism giving rise to the pairing of the biopolymers with their dark analogs at magnetic flux tubes? how dark ions such as k+,na+, ca++, cl− are generated? could the interaction of water with ezs provide a prebiotic mechanism for the generation of these dark ions? isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2015 | volume 5 | issue 2 | pp. 111-143 120 pitkänen, m. more precise tgd based view about quantum biology and prebiotic evolution 6. cell membranes consisting of double lipid layers are in tgd universe josephson junctions and josephson currents between them generate josephson radiation with energy, which is just above the thermal energy and have frequency proportional to 1/heff and thus give rise to classical counterpart of thz radiation known to be important in the interaction of phyllosilicates with living matter. it is known that vesicles consisting of lipid bilayers are formed in water-montmorillonite system. could the predecessor of cell emerge in water-phyllosilicate interaction? phyllosilicates appear in biand triple-layered structures and are semiconductors. could they act perhaps in presence of ezs as high temperature superconductors in the sense that their resistance would be associated only with the ends of the ”wires” (the resistance would be thus independent of length)? could a charge separation develop in the presence of ezs so that there would be potential difference through the layered structure? could the layers form josephson junctions generating radiation with energy above thermal energy and frequency determined by the value of heff? the lattice spacing for layered structures is of order 1 angstrom so that one expects josephson energy zev to have order of magnitude of 102 ev. 7. doped phyllosilicates are also catalysts and could have served as prebiotic bio-catalysts. a highly attractive idea is that both prebiotic molecules, atoms of various elements, and phyllosilicate crystals were trapped inside water clathrates so that all important building bricks of bio-molecules would have been automatically inside ezs after their birth. 3.1 how could external fields induce coherence? by general arguments (planck constant istoo small) the coherence induced by classical fields in visible matter is like forcing soldiers to march in the same pace and should not be regarded as a genuine quantum coherence. quantum coherence would be at deeper level and allows to understand why the external classical field is coherent in long scales. in tgd universe resonance frequencies of eeg etc... perform this task in brain functioning and dark eeg photons are behind eeg mediating sensory information to magnetic body and control commands back to biological body [27]. (quantum) criticality is the key notion: at (quantum) criticality large heff dark matter phases can appear. in applications one should try to identify quantum critical aspects of systems considered. in tgd framework dark cyclotron photons having oscillating fields as classical correlates and with energy e = heff × f above thermal threshold would be inducers of coherence. this picture solves the kt paradox, which originally led to heff = n × h hypothesis, which can be now deduced from the number theoretic vision about tgd [46]. dark cyclotron photons could transform to ordinary photons in energy conserving manner and have biophotons as their decay products with energies in visible and uv range. heff = hgr hypothesis [45] implies that dark cyclotron photons and therefore also bio-photons have universal spectrum reflecting the spectrum of magnetic field strengths. the model for cell membrane as generalized josephson junction can act also as an ordinary josephson junction and thus allows also a piece of spectrum with josephson photon energy coming as multiples of e = zev , v resting potential, where z is the charge of the superconducting charge carrier. just in the vicinity of thermal threshold for z = 2 (cooper pairs or ca+2, mg+2). dark josephson radiation with energies near thermal energy and with frequency inversely proportional to 1/heff so that arbitrary low frequencies would be obtained. these dark photons have always same energy irrespective of the value of heff . thz/microwave frequency range is considerably below the thermal threshold for the ordinary value of planck constant and dark josephson photons with appropriate value of planck constant could be transformed to these photons. the simplest transformation is the decay of the n = heff/h sheeted spacetime surface to n sheets each carrying ordinary thz photon. also energy conserving decay to single photon can occur. the values of planck constant would not be very large for thz range if josephson photons are in question. the dark thz/microwave photons emitted by say ezs generated from atmospheric isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2015 | volume 5 | issue 2 | pp. 111-143 121 pitkänen, m. more precise tgd based view about quantum biology and prebiotic evolution water clathrates by solar radiation could propagate through the crust along magnetic flux tubes to the underground oceans. the basic mechanism in the interaction of dark matter with visible matter would be phase transition transforming dark photon to ordinary photon(s) in energy conserving manner. all particles can be in dark phase and this makes possible super-conductivity and superfluidity. 3.2 coherence regions and ezs the proposal of del giudice is that what he calls coherence regions/domains play a central role in biology and are induced by oscillating external fields by forcing units of visible matter to march in the same rhythm. in tgd framework one must take a skeptic attitude towards the existence of coherence regions postulated by del giudice. to my best knowledge there is no direct experimental support for coherence regions and they might be identifiable as special cases of ezs. 1. ezs of pollack are an experimental fact and are generated in presence of gel phase and incoming radiation. the open question is whether gel phase also serves as an energy source or does it have some kind of control function feeding in information. it might well be that coherence regions of del giudice are not needed and the water clathrates serve as natural precursors of ezs. the transition hydrogen bonded 2h2o→h3o − 2 + dark proton could be induced by uv light as breaking of -o-h bond. ezs carry negative electronic charge and part of protons would become dark and would be transferred to the dark magnetic flux tubes. dark protons form sequences, which could be seen as scaled up variants of atomic nuclei in the first approximation. the states of dark proton in the model that i have proposed are in one-one correspondence with dna, rna, amino-acids, and 40 trna states [30]. the coherence regions could be created by uv light splitting -o-h bonds and possibly also other kinds of bonds to the verge of phase transition. later various options for the energetics of coherence regions are discussed. the simplest assumption is that nuclear binding energy transforms as coulomb potential in the scaling of h → heff scaling also the system size. if so, the dark nuclear energy spectrum could be that for bio-photons and basic bio-molecules. the transformations of dark nuclei to ordinary nuclei could take place and would provide new source of nuclear power and ability to artificially generate elements: there is indeed evidence for biofusion [3, 4]. 2. if the coherence regions of del giudice exists they must relate closely with ezs. the simplest tgd inspired analog would be as micron sized regions as regions near criticality of a phase transition of water to fourth phase of pollack. the simplest guess is that josephson energy quantum for cell membrane (above .05×z ev) or energy quantum somewhat below metabolic energy quantum ∼ .5 ev is needed to transform h2o stoichiometry to h1.5o so that ez would be obtained. hence the josephson radiation from membrane protein josephson junctions could have a role in the control of ezs. on the other hand, the hydrogen bonds ezs with high enough bond energy would be stable against absorption of josephson radiation and metabolic energy quanta. the proposal is that fourth phase of water realizes genetic code at the level of dark nuclear physics and ordinary biomatter has condensed around the dark matter. dna, etc. are paired to the dark proton sequences representing their dark variants and transcription and translation occurs at the dark level primarily and ordinary biomatter makes this visible. the recent finding that so called knocked out genes are transcribed correctly [14] (http://www.nature.com/nature/journal/vaop/ncurrent/full/ nature14580.html) supports this view [45]. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2015 | volume 5 | issue 2 | pp. 111-143 122 pitkänen, m. more precise tgd based view about quantum biology and prebiotic evolution 3.3 quantum criticality bio-chemically quantum criticality [44] has become key concept of quantum tgd and tgd inspired biology. quantum criticality allows to understandard the hierarchy of planck constants and also its relationship to p-adic length scale hypothesis, whose origin reduces to number theoretic vision about tgd [46]. dark matter phases characterized by heff = n × h accompany any quantum critical system, maybe even thermodynamimcally critical systems. the challenge is to find concrete realizations of quantum criticality in various scales. in biology biochemical realization is of special interest. the basic aspect of quantum criticality is that the increase of heff occurs spontaneously since the process corresponds to increase of negentropy and nmp states that negentropic entanglement resources of the universe are increasing as kind of akashic records or cosmic library. at the level of selves this means that self ”dies” and re-incarnates as its time reversal. selves fight for survival and try to grow their negentropic resources to satisfy the requirements of nmp. this leads to metabolism and homeostasis characterizing living systems. the emergence of life would not be extremely rare accident but doomed to occur spontaneously sooner or later by basic law telling what happens in state function reduction in tgd universe obeying zero energy ontology (zeo). hence the process should occur spontaneously and increase heff . 1. the basic question is how quantum criticality is realized biochemically. are the molecules excited near to a critical energy at which a dark ion at magnetic flux tube is generated and a phase transition analogous to that leading from ordinary to fourth phase of water occurs? or are large systems near criticality to a generation of dark phase as the general vision about quantum criticality of tgd universe suggests. 2. a natural assumption is that metabolic energy quantum should be able to induce the phase transition producing dark particles at criticality. could dark photons in visible and uv range accompany criticality at the level of single molecule? are cell membrane and neuronal membrane quantum critical systems and how they differ? 3. dark variants of biologically important ions residing at magnetic flux tubes are in fundamental role in tgd inspired quantum biology. in particular, dark proton states are proposed to give rise to the dark analogs of dna, rna, amino-acids, and trna. the pairing of ordinary dna/rna/aminoacids with their dark analogs is expected to be fundamental in biology and transcription and translation are proposed to take place at dark level as the recent experimental findings indicate. how is this pairing realized? how ordinary dna becomes paired with dark dna or is it already paired with it? 4. what could be the fundamental mechanism liberating metabolic energy coherently? this question will be discussed later. 3.3.1 the role of fourth phase of water pollack’s ezs [11] and fourth phase of water should be in key role. 1. ezs are generated under conditions equivalent with those prevailing in pollack’s experiments (water bounded by gel plus irradiation). charge separation occurs: ez is negatively charged and dark protons reside at magnetic flux tubes. this process could occur also for systems in contact with water such as phyllosilicates. cations (in particular protons) or anions at these surfaces could be transferred to magnetic flux tubes. dark proton sequences could realize the genetic code. 2. -o-h bond near quantum criticality would become -o− in the formation of ezs most naturally from water clathrates since also ezs have crystal structure. actually much more general process can be considered: also the -o-h bonds associated with say phyllosilicates in contact with ez could isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2015 | volume 5 | issue 2 | pp. 111-143 123 pitkänen, m. more precise tgd based view about quantum biology and prebiotic evolution suffer the same fate. o− appears in the phosphates associated with xtps of dna n and rna nucleotides, phospholipids, and with gtps of microtubules. are all these o−:s accompanied by dark proton in some spin state at parallel magnetic flux tube. in the case of dna there should be a correlation between the code letter a, t, c, g and dark proton state. could the 3-electron state possibly assignable to the codon be same as 3-quark state of corresponding dark proton? in particular dna as topological quantum computer could involve pairing of dark protons associated with dna and with phospholipids by flux tubes which can become braided. 3. -o-h bonds associated with o=c-o-h is the basic building brick of amino-acid and could make it acid that is able to donate h+ received by water molecule becoming h3o +. could amino-acid become biologically active as -o-h becomes -o− plus dark proton at flux tube possibly defining dark proton sequences dark variant of amino-acid as dark proton sequences? another possibility is that he phosphorylation of amino-acids brings associates dark protons with amino-acids and can even generate dark nuclei. there should be a correlation with spin state of dark proton and amino-acid side-chain if genetic code is realized. 4. there is no need to restrict this mechanism to -o-h→ o−. any chemical bond could be kicked near to criticality either by the combination of dark and p-adic phase transitions liberating zero point kinetic energy or by dark photons absorbed in the time reversal of bose-einstein condensation. this would allow generation of dark variants of biologically important ions by ezs associated with phyllosilicates. one could test this vision empirically by looking whether ezs induce generation of dna sequences or at least dehydration of dna and checking whether ezs could stabilize dna against hydrolysis. also the interaction between ezs and phyllosilicates could be studied. 3.3.2 simplest model for the formation of fourth phase of water the basic ideas about quantum criticality apply to the formation of ezs and possibly existing coherence regions serving as their predecessors. the simplest model for the formation of ezs discussed in the following does not require coherence regions at all and could occur spontaneously as a chain reaction. this is what occam’s razor suggests. the simplest option does not require pre-existing coherence regions. the basic idea is simple: radiation at visible light induces the transition 2h2o → h3o − 2 + dark proton where water molecules are hydrogen bonded. if dark protons at magnetic flux tubes fuse to form dark nuclei, they liberate dark gamma rays. if they decay to ordinary photons with correct energy they induces further transitions which ca decay to ordinary photons. if their energies are correct they induce further transitions 2h2o → h3o − 2 + dark proton and ez is generated as a nuclear chain reaction. 1. h3/2o is stoichiometric shorthand for hydrogen bonded h3o − 2 molecule forming a loosely bound lattice structure with lattice binding energy small compared to the molecular bond energies. a pair of hydrogen bonded water molecules forming h2o–h-o-h structure (”–” denotes for hydrogen bond) could suffer dark ionization by giving up dark proton so that h3o − 2 molecule is formed. the dark proton would be transferred to the dark magnetic flux tube. the bond energy of o-h bond is 5.15 ev (https://en.wikipedia.org/wiki/bond-dissociation_energy) is in the first approximation the net energy needed to transform 2h2o to h3o − 2 + dark proton directly. this corresponds to uv energy. this is of course extremely rough estimate. 2. the objection is that the large negative electronic charge gives the system very large coulomb energy so that it explodes. a possible manner to circumvent the problem is that dark protons fuse to dark nuclear strings and liberate nuclear binding energy, which compensates the coulombic energy and stabilizes the system. dark nuclear fusion would liberate dark gamma rays decaying into ordinary photons. if the photons have energies in the range of visible and uv photons they isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2015 | volume 5 | issue 2 | pp. 111-143 124 pitkänen, m. more precise tgd based view about quantum biology and prebiotic evolution could generate more h3o − 2 molecules and the generation of ez could proceed as a chain reaction. hence dark phase of protons would be generated spontaneously in accordance with nmp and the resulting phase would be stable. these photons can also induce dark ionization of other biologically important ions appearing as anions or cations. dark proton sequences could also transform more complex nuclei containing dark neutrons and in tgd framework also exotic nuclei with charged bonds between nucleons are possible. the transformation of dark nuclei to ordinary ones would provide a new mechanism of nuclear fusion producing various elements outside solar core. there is indeed evidence for bio-transmutations [3, 4]. i have discussed this possibility as a possible explanation of lithium anomaly [32]. one can even ask whether the prebiotic life could have generated some of the needed atomic nuclei artificially! 3. gel phase in pollack’s experiments could provide the dark magnetic flux tubes for protons. in experiments of urey and miller electric discharges accompanied by magnetic flux tubes would do the same rather than providing metabolic energy as one might also imagine. this could be tested by replacing electric discharges with gel in the analogs of urey-miller experiments. lightnings would have the same role in the evolution of prebiotic life. dark flux tubes might have been associated with the magnetic fields of earth. the endogenous magnetic field from the experiments of blackman [23] has value 2be/5, be = .5 gauss is the magnetic field of earth. second option is that coherence regions of del giudice are created first. a subset of -o-h bonds is first transformed near criticality by uv light with energies around 4.8 ev as coherence regions are formed. after that metabolic energy quantum kicks the molecules over the threshold for the formation of h3o2 and liberates about 2 ev per bond. the burst of these ∼ 2 ev photons should have been detected so that this option is not plausible. there is also the problem due to the fact that two many o-hs could be taken to the criticality and and both -o-h bonds of given water molecule could be taken to criticality. 3.3.3 could dark proton sequences at flux tubes form dark nuclei? in tgd framework nuclei correspond to nuclear strings [32] consisting of strings formed from dark protons and neutrons. neutrons and protons could even form their own dark strings. therefore dark proton sequences could but need not to fuse to dark nuclear strings with some nuclear binding energy and liberate the nuclear binding energy in the process. suppose that the fusion can occur so that a dark proton created in dark ionization is bound to an already existing dark proton sequence representing dark nuclear string at magnetic flux tube. by a naive extrapolation the binding energy would be same as in ordinary nuclear physics and would be measured in mev range assignable to gamma rays. this estimate is probably wrong. as already explained, the nuclear binding energy could more naturally behave as 1/heff like coulomb energyand nuclear excitation energy spectrum would be naturally in bio-photon energy range. the situation could become analogous to nuclear fusion liberating large amounts of energy. this would conform with nmp and with the idea that formation of large heff phases occurs spontaneously. in the case of linear structures containing -o-h sequences with small enough distance dark nuclear fusion can be imagined. could the fusion occur at phyllosilicate surfaces and generate dark analogs of dna codons as highly stable structures? could the fusion occur as a chain reaction liberating large amounts of energy at biophoton energies and lead to a formation of dark proton sequences with some maximum length dictated by coulomb repulsion? could dna nucleotides associate with these dark codons? if o− associated with phosphates inside cell nucleus can can combine with ordinary protons the hydrolysis of dna can occur inside nucleus. the pairing of dna and dark proton sequence by connecting magnetic flux tubes could prevent hydrolysis. one prediction would be that the negative charge of dna (one units per single nucleotide) is screened by dark proton sequences in vivo in the scale of the system formed by dna and dark proton sequence. usually it is believed to be screened by na+ counter ions. if the distance between dna and dark proton isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2015 | volume 5 | issue 2 | pp. 111-143 125 pitkänen, m. more precise tgd based view about quantum biology and prebiotic evolution sequences is large enough, a local screening by na+ counter ions can indeed occur. what happens inside cell nucleus is far from clear to me. 3.3.4 could dark nuclei collapse to ordinary nuclei? one can also wonder whether the phase transition heff → h could produce ordinary nuclei and liberate energy in nuclear energy range. could living matter be at criticality against nuclear explosion? the occurrence of bio-transmutations has been indeed claimed [3, 4]. this possibility would mean a manner to generate both nuclear energy and generate artificially those elements, which are depleted. the observation that the isotope ratios reported to appear in the cold fusion experiment of andrea rossi are the natural ones (http://en.wikipedia.org/wiki/rossi_reactor) has been used to claim that the e cat reactor developed by rossi [2] is fraud. lithium anomaly however forces to ask how large fraction of ordinary matter emerged via dark fusion in interstellar space, and how large fraction was generated in the stellar cores. could even the fusion in stellar cores have occurred as dark fusion at magnetic flux tubes followed by a phase transition to ordinary matter? one can argue that since the increase of heff and generation of negentropic entanglement (ne) occurs spontaneously, the fusion to ordinary nuclei must be a rare process. nmp suggests strongly that the existing ne must be transferred from the dark nucleus magnetic flux tube shortening to ordinary nuclear string in heff → h. if this ne is associated with the transversal flux tubes connecting dark protons of the nuclear string with other similar system, the transfer could take place by reconnection of flux tubes with those of second analogous system (the model for dna as tqc assumes that flux tubes connect dark protons assignable to dna codons and lipids of nuclear/cell membrane [28]). the transfer of single transversal flux tube connecting a and b to that connecting c and d would require two reconnections: ab+ cd→ ac+ bd → ab+cd. cd would have no ne in the initial situation and would have that of ab in the final situation whereas ab would have no ne. the probability that all flux tubes are doubly reconnected within a reasonable time span is expected to be small and only light nuclei might be generated. the occurrence of biofusion however suggest that this objection might be circumvented in some quantum critical situations. 3.3.5 decay of very energetic dark photons to low energy photons it is known that x and gamma rays accompany lightnings (http://physicsworld.com/cws/article/ news/2013/apr/17/dark-lightning-sheds-light-on-gamma-ray-mystery). this is impossible in standard physics since x and gamma rays should be absorbed in atmosphere. i have proposed that that this radiation as also the radiation at lower energies propagates along magnetic flux tubes as dark photons. suppose that dark proton sequences indeed fuse to dark nuclei and liberate large amount of energy in the process as dark analogs of gamma rays but possibly much lower energy in the energy range of dark bio-photons and possessing much longer wave-length than usually. these dark photons can decay to ordinary photons and an interesting possibility is that this range includes visible photons (bio-photon energy range is a good in lack-of-anything-better-guess). could this decay promote the visible light promoting the generation of ez? if this were the case the formation of living matter could take place as a chain reaction as nmp encourages to think. similar chain reaction could have taken place also in prebiotic circumstances, where lightnings could have provided the initiating photons and perhaps also dark photons in dark nuclear binding energy range decaying to visible photons initiating the process. same could have happened in urey-miller experiments. 3.3.6 anomalies possibly related to ezs there are several anomalies which might allow explanation in terms of ezs. 1. tesla studied what happens in di-electric breakdown and was perhaps the first experimentalist to discover dark matter. critical phenomenon is in question and could in tgd universe be accompaisbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2015 | volume 5 | issue 2 | pp. 111-143 126 pitkänen, m. more precise tgd based view about quantum biology and prebiotic evolution nied by the formation of dark matter perhaps even dark nuclear matter accompanied by liberation of energy. also dark radiation with wavelengths proportional to heff making possible long range communications and energy transfer could be involved [40]. the most fascinating phenomenon reported by tesla was charge separation in length scales much longer than one might have expected and could directly reflect the generation of dark charged particles. 2. the article of kanarev and mizuno [7] reports findings supporting the occurrence of cold fusion in naoh and koh hydrolysis. the situation is different from standard cold fusion, where heavy water d2o is used instead of h2o. i have considered this finding in [32]. obviously the mechanism generating dark proton sequences as dark nuclear fusion could explain the findings of kanarev and mizuno. 3. the irradiation of salt water with microwaves induces the ”burning” of water with a visible flame [5]. the phenomenon is believed to involve the breaking of salt water into oxygen, hydrogen and salt. if ez is formed this could mean formation of h-o-h–oh2 → h3o − 2 + dark proton. nuclear fusion need not be initiated since polymer structures are absent. the burning process could be induced by microwaves accompanied by dark photons having energy in the energy range of uv photons and transforming to uv photons. 4. free energy anomalies are not taken seriously by the main stream since they are not consistent with energy conservation in standard physics framework. i have proposed they they could be understood in terms of generation of dark proton sequences and cold fusion liberating energy [43]. the so called brown gas [8] (might be same as fourth phase of water) produced from water by electrolysis is reported to be able to melt metals at much below the melting temperature. the explanation would be that the presence of metal initiates transition to ordinary nuclei liberating nuclear energy. the original explanation was quite not like this [43] although the energy was assigned with dark proton sequences. another interpretation is that the process generating dark proton sequences continues. 5. there is also analogy of charged water clusters (ezs) with two poorly understood phenomena: steam electricity [9] (http://www.esdjournal.com/techpapr/prevens/previndx.htm) and waterfall ionization. also thunder cloud charge separation and sonoluminescence might involve the formation of charged water clusters. 3.3.7 how biosystems could control protein dynamics? hans frauenfelder et al propose a unified model of protein dynamics based on experimental findings [15]. the key proposal is that protein dynamics is slaved by the hydration shell and by the bulk solvent. the dynamics of master should be slower than that of slave. the conformational motions of proteins have time scale in the range 1 ns-1 s. the frequencies corresponding to the splitting of hydrogen bonds are above 10 thz and hence splitting dynamics is faster than protein dynamics. therefore the claimed master-slave relation looks strange at the first glance. one can however think that the cleaving of hydrogen bonds defines the control dynamics as dynamics of switching and is much faster process than processes occurring between switchings. changing the position of switch would correspond to a catastrophe in catastrophe theoretic formulation. the dynamics at a given sheet of catastrophe is indeed slow except at the critical lines defining its boundaries [1]. this suggests that various phases of water define environments for water controlling the behavior of proteins. quantum phase transitions would put switches on and off. if the phase is hydrogen bonded water clathrate, the protein finds itself inside ”ice” layer and cannot move. protein unfolding proceeding as quantum phase transition would represent a basic example of this situation. when the hydrogen bonds disappear due to the melting of the ez around protein by the splitting of protein-water and water-water hydrogen bonds, protein becomes able to change its conformation and protein un-folding can occur. the isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2015 | volume 5 | issue 2 | pp. 111-143 127 pitkänen, m. more precise tgd based view about quantum biology and prebiotic evolution ”ice” layer around protein can melt by the feed of external energy at energies below metabolic energy quantum. this radiation could arrive as dark photons from dark magnetic body decaying into bunches of ordinary photons with same frequency and inducing fast melting of the entire layer. the bulk solvent could control large scale protein motions by changing the viscosity achieved by modifying the density of hydrogen bonds. protein would move in the direction where the resistance is smallest. in zeo the reverse process would correspond to melting but in non-standard time direction. one can interpret the situation also in terms of consciousness theory. the period between folding and unfolding would define self and the control action would generate the time reversal of self. but ”who” is the master? in tgd framework it would be naturally the dark magnetic body containing at its flux tubes dark proton sequences associated with proteins. the motor actions of the magnetic body would induce those of proteins. the only condition is that the inherent protein dynamics is fast enough to follow the dynamics of the magnetic body. the fingerprints of biomolecules are in energy region .05-.25 ev (this is also the energy range for hydrogen bond energies) and the frequencies are above 10 thz. therefore the time scales of protein dynamics would actually reflect those of dark magnetic body. the modelling of protein folding as a random process in which system tries all options and ends up to the bottom of potential well representing the final configuration has problems: the basic paradox is that the folding should take extremely long time. if protein folding is macroscopic quantal self-organization process governed by nmp in present of large heff phases, these problems might be circumvented. folding could to high extent reduce to the folding of the underlying magnetic flux tube structure: proteins would follow automatically if they are surrounded by the ”ice” layer of ordered water. 3.3.8 relationship to dna as topological quantum computer hypothesis dna as topological quantum computer (tqc) hypothesis [28, 37] emerged roughly decade ago. the basic idea is that dna and lipid layer of nuclear membrane are connected by magnetic flux tubes. also connections to cell membrane and membranes of the other cells are in principle possible. the braiding of the flux tubes induced by the flow of lipid layer in liquid crystal (lc) state makes possible topological quantum computations. similar topological quantum computations could be associated with the system formed by microtubules and axonal membranes. a more general idea is that flux tubes are analogous to coordinate lines of 3-d coordinate grid forming a backbone of the organism [39] implying that the morphogenesis of magnetic body would induce that of visible part of organism. for instance, each dna codon could be accompanied by flux tubes parallel to dna plus flux tubes in two orthogonal directions perhaps connecting dna to the lipid layers of nuclear membrane. the orthogonal flux tubes could emanate from the dark protons associated with the phosphates of the strands. one can imagine several identifications for the particles involved with the topological quantum computation. the basic condition is that dna codons or codewords are represented in terms of dark variants of some particles. 1. if one assumes that individual nucleotides (a,t,c,g) are involved, it is natural to assume that the particles involves correspond to these in 1-1 manner. the realization discussed in [28] assume that the codons correspond to the 2+2=4 spin states of u and d quarks and anticodons to corresponding states for antiquarks. the quarks would be of course dark to avoid annihilation. one can also imagine realizations in terms of 3+1 = 4 spin states of pairs electrons associated with a pair of flux tubes connecting dna nucleotide and lipid layer. 2. if the codewords of the genetic code formed by three codons are taken as basic units then the states of the particles used must correspond to 64 dna codons. rna nucleotides and amino-acids could also involve analogous flux tubes beginning from the paired dark protons. the obvious choice at dna end are those dark proton states, which correspond to 64 dnas. at the lipid end the dark proton state would be fixed by base pairing condition. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2015 | volume 5 | issue 2 | pp. 111-143 128 pitkänen, m. more precise tgd based view about quantum biology and prebiotic evolution an interesting question is whether phospholipid states can be said to be coded by dna codons (surjective many-to-1 map of dnas to lipid states). this question is quite general: is the possible dna dark proton-biomolecule correspondence surjective so that genetic code would be much more general than thought. hu and wu [26] have observed that proton pairs with members at opposite sides of cell membrane have spin-spin interaction frequencies in elf scale. the tgd inspired the proposal [42] was that the protons are dark and form sequence at both sides of the lipid layer. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 202-225 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part iii) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 202 article the resplendence codex: reflowering apocalypse in the tree of life (part iii) chris king * abstract this article was written in response to a life-and death wake-up call, in which i realized i needed urgently to write down before it was too late and the threads became scattered and lost. resplendence is an innovative concept and nascent social movement, complementing science and transcending religion, with the wisdom of conscious insight and motivation, to reflower the planet as a living paradise, abundantly resilient over evolutionary time, and ultimately, to reach to the stars. part iii of this four-part article includes: 9. resplendence: a paradigm beyond religion to reparadise the earth; 10. transcendence and the physical universe; 11. ten clarifications on the nature of existence; and 12. accounting religious apocalypse and its greening in the traditions. keywords: resplendence, apocalypse, evolution, science, religion, reflowering, tree of life. 9. resplendence: a paradigm beyond religion to reparadise the earth this article is the resplendence codex. resplendence evokes the paradigm shift from religion to paradise in a single word. codex caudex means the "trunk of a tree" in this case the tree of life. resplendence means many things. we usually think of it as a glorious state of natural splendour, but its root meaning re-splendere is to "shine brightly" or "shine again". it is thus both the full overflowing abundance of paradise, and as a global consciousness, it is the light of the world. but it has a deeper meaning, as the true immortal condition of humanity and is hence the natural paradigm successor to religion. resplendence is both an attitude of mind and a social dynamic attuned to bringing earth back to a state of resplendent paradise, sustainable and resilient over evolutionary time scales, to ensure our own survival and the survival of the diversity of life. revealing resplendence text of the talk instead of leading to the physically unrealizable imaginary scenarios of religions, such as heaven and hell in the day of judgment, resplendence leads to a single real and positively resplendent * correspondence: chris king http://resplendence.org e-mail: dhushara@gmail.com https://www.youtube.com/watch?v=rx1aflxd8us http://dhushara.com/resplendence/index.htm#anchor-here-47857 dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 202-225 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part iii) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 203 outcome the reparadising of earth in natural abundance, through a democratic culture empowered by climax technology, medicine and science and based on the principles of ecosystemic diversity. resplendence complements the knowledge provided by science with the wisdom of what to do about it, in the same way religion has sought to complement practical knowledge in human history. science deals with the pursuit of the knowledge of how nature and the universe work, while the wisdom of resplendence deals with what we creatively do with this knowledge, in reflowering paradise the ultimate manifestation of wisdom in action. we all want to find meaning in life and want it to have a meaning which extends beyond our own lifetime. we also want the security that we are living in a world that has a viable future for our offspring and the future generations. the critical source of our angst that many of us turn to religion to alleviate, is that we are living in a world which is not only teeming with injustice, violent conflicts and weapons of mass destruction, but is lurching towards an uncertain future as a result of human impacts on the world's living habitats, climate and resources which could take us to an irreversible tipping point, undermining the future of unborn generations. okavango delta. one of africa's richest biodiversity hotspots. these are problems we need to deal with and heal in this life to have a sense of fulfillment, not just pass them on to future generations to worry about, or to an imagined afterlife full of even more graphic tortures and punishments. the only meaningful contribution we can make to the future is through our offspring, our contributions to understanding in culture and society, in the humanities, science, art and music, through innovations we bring to society which produce lasting benefit and through actually protecting the living planet through our actions to guard the diversity of life. no selfish, expedient, greedy or jealous motive, or action can serve to give anything more than a futile and temporary distraction from the central goal of creative integration with the immortal http://dhushara.com/apoc/apocalypse_files/image058.jpg dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 202-225 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part iii) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 204 flow of life around us. redemption comes through coherence and integration with paradise pure and simple. and paradise is a realizable condition, if we only put our collective resources and inspiration to work to achieve it. science, resplendence and religion in a nutshell science science is the foundation of our description of nature and the physical universe: 1. cosmic evolution: symmetry-breaking of the forces of nature leads to the physical and biological structures in the universe. gravitation causes collapse to form galaxies full of stars radiating through the nuclear forces in turn forming planetary systems, with gravitation causing collapse to black holes, also modulated by the effects of dark matter and dark energy. 2. biogenesis: there is strong evidence that life is an emergent property of the laws of nature, ubiquitous throughout the universe. biomolecules, including amino acids have been found in gaseous nebulae, on meteorites and in primitive lab syntheses. the process has a cosmological basis. stellar radiation leads to the formation of complex molecules, including the organic precursors of life. in interaction, these from fractal structures constituting the most complex interaction of the forces of nature. under favorable conditions, these can lead to cellular life,, which evolves at the edge of chaos to form ever more complex life-forms. 3. complex organisms: symbiosis between the two main branches of life then existent on earth, bacteria and archaea, has then led to the complex nucleated eucaryote cell that forms the basis of complex animals, algae and fungi, with further symbiotic events involving photosynthesis leading to the land plants. 4. sexuality is essential to the evolution of complex organisms because recombination creates an almost endless variety of viable individuals, which can manifest new evolutionary features, fend off mutational decline and resist catastrophic epidemics from diseases and parasites. humans are¬†one of the most sexually polarized mammalian species. the reproductive strategies of men and women are thus in a state of strategic conflict. 5. sentient consciousness arises as an emergent property of complex organisms through sexual evolution, as their interactive behavior creates new survival crises requiring a field-of-view anticipation of the world in real time. while science has made great progress in identifying brain regions giving rise to certain kinds of conscious experience, how objective physical processes could in principle give rise to subjective experience, remains one of the deepest unresolved enigmas of science. http://dhushara.com/book/bchtm/biocos.htm http://dhushara.com/book/bchtm/biocos.htm http://dhushara.com/book/unraveltree/unravel.htm#anchor-the-49575 http://dhushara.com/book/unraveltree/unravel.htm#anchor-leca-49575 http://dhushara.com/paradoxhtm/contents.htm http://dhushara.com/paradoxhtm/contents.htm http://dhushara.com/stc/ct.htm dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 202-225 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part iii) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 205 6. cognizant culture: the evolution of intelligence ultimately leads to a species developing culture and with it a capacity to describe and understand the nature of the universe around it. this runs a significant risk of planetary crisis and a mass extinction of life, as this species multiplies, and appropriates a disproportionate share of the planet's resources. critical is the active symbiotic relationship between such a species and life as a whole, so that the biosphere retains fecundity and robustness to external crises. resplendence resplendence complements scientific cosmology providing three existential raisons d'etre for humanity as a climax cultural species: (a) to cherish and replenish the diversity of life on the planet so that the immortal passage of the generations will continue (b) to facilitate the unfolding illumination of all conscious beings. (c) to support a caring community to realize resplendence as a creative process. 1. replenishing planetary paradise: our primary goal in life is to sustain earth as a living paradise so that the generations both of humanity and the other diverse lifeforms including those on which we co-depend shall continue to flourish. 2. mortality and sexuality: we experience mortality as individuals because fertilization contributes only half our genes to make up each new individual, with half coming from our sexual partner, our most altruistic act, resulting in the almost endless variety of sexual individuals. since we arise from the fertility process, we redeem our individual mortality by giving our energy and creativity back to the flow of life in our creative life expression. 3. female reproductive choice: in the fertility between the sexes, due to a high degree of sexual polarization, women have a primary place as the live bearers of the next generation, enduring a massive sometimes risky pregnancy, lactation and long periods of early child-rearing. it is thus essential, both genetically and socially, that women retain the right to reproductive choice. 4. conscious transcendence: as a climax species, we experience subjective consciousness, in several forms waking life, dreams, contemplation and visionary and entheogenic states, which may in turn be a manifestation of cosmological principles and may thus have transcendent properties. we need to keep this quest completely free of religious doctrines, so that we can explore it in an unfettered discovery process. 5. autonomy and personal responsibility: replenishing life is an existential necessity providing our central meaning in existence, not a moral imperative. it is however a fulfilling ethic. we are autonomous beings and so we need to take responsibility as intentional agents. what each of us do as individuals of a climax cultural species will affect the future viability of the planet. this is the one and only meaningful response to the existential condition. http://dhushara.com/paradoxhtm/contents.htm http://dhushara.com/paradoxhtm/contents.htm http://dhushara.com/psyconcs/psychconsc8.htm dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 202-225 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part iii) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 206 religion traditional religions are in fundamental conflict with both scientific cosmology and human survival. monotheism is particularly dangerous, because it invokes a violent end of days, leading to conflagration, triage of all life and destruction of the earth in favor of a heavenly kingdom: 1. creation by command: monotheism conflicts with the generative nature of the physical universe by claiming that the earth and heavens were ordered by a creator deity out of formless chaos in six days by verbal command. the heavens are a firmament, or great dome over the flat earth in with the stars are placed. the plants are made before the sun and moon. and the animals of the sea air and land created complete and fixed for all time, designed much as we shape our artifacts. finally man and woman are made male and female in the likeness of the 'elohim, to be fruitful, and multiply, to replenish the earth and subdue it: and have dominion over over every living thing that moveth. 2. mortality and god's curse on women: but then in the paradisiacal garden of eden a falling out occurs which has corrupted history ever since. woman seduced by the serpent for seeking wisdom, eats of the tree of knowledge of good and evil and persuades man to do likewise, making them both sexually aware. yhvh then withdraws the tree of life which could have made them immortal and throws them out into the wilderness to struggle by vanquishing the thorns and thistles, with woman cursed with the pain of childbirth, to be ruled over by her husband and both doomed to mortal existence. 3. jealous conflict and apocalypse: the entire biblical paradigm becomes a moral cosmology reinforced with fire and brimstone against the whoring of the unfaithful wife israel by the jealous god jehovah. jesus referred to the loving father god, but this deity is claimed to have sacrificed him as his only begotten son in the crucifixion leading to centuries of martyrdom, crusade and inquisition. rolled into this toxic mix is apocalypse in the end of days a time of tumult and triage of all life, annihilating all in a day of judgment leading to a heavenly jerusalem. 4. dominion over nature: christians throughout history, have thus regarded it as our sacred duty to have dominion over nature, while women became the 'devil's gateway', to be seen but not heard, or burned at the stake as witches. although some denominations, now advocate responsible stewardship to address climate change and species loss, the basic influences remain those of a desert religion regarding nature as an inferior realm to be conquered. 5. jihad, repression of women and genocide: islam adapted the same end of days desert tradition to the patriarchal tribal law of muhammad's day, turning the violence outward in jihad, partitioning the world between the domain of submission to allah and the domain of war, in conversion by the sword. in addition to beheading 700 jewish men in the souk of medina, taking their wives and children into sexual slavery, muhammad adopted the invocation to stone women for adultery, discarded for centuries by the jews, so that it continues to this day in sharia as a cruel homicidal punishment for female http://dhushara.com/fallacies/fallacies.htm http://dhushara.com/fallacies/fallacies.htm http://dhushara.com/fallacies/fallacies.htm dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 202-225 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part iii) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 207 reproductive choice. women are only half the value of men, forcibly veiled, chaperoned and sequestered as instruments of male control of female fertility. religion is compulsory, with death for apostasy and blasphemy, in contradiction to the claim that allah is compassionate and merciful. 6. reproductive domination: both christianity and islam attempt to out-populate their competitors at a time when overpopulation is stressing the planet's resilience. 7. nirvana and samsara vs nature: buddhism is an atheistic meditative religion based on the renunciation of egotistical desires and the ensuing fear of mortality, through escaping the round of birth and death in the emptiness of nirvana. however samsara and its karma of rebirth remains a morally causal mind-over-nature cosmology in which the animals are assigned to the inferior status of ignorant or corrupted sentient beings. it thus tries to solve the existential dilemma by negation without the key redeeming life purpose of replenishing living diversity, although both buddhism and upanishadic hinduism invoke an autonomous path of contemplation in which individual consciousness can ultimately gain transcendence. religion, according to augustine comes from re-ligare to "bind again" or "bind fast". religions bind together spiritually-minded people into mass movements, but religions are also contaminated with the notion of bondage to a potentially oppressive utopian moral order. this is a fascist totalitarian notion that makes traditional religions dangerous and harmful to world futures. the fasces is a bundle of sticks, sometimes with a protruding axe, or labrys, whose strength bound together is greater than the sum of its parts. cosmological paradigm shift: ancient religious notions of a universe created by god are in fundamental conflict with the scientific description of reality confirmed by experimental investigation. the six day sabbatical creation of genesis (a) has the 'elohim or god as a manufacturing designer creating the life forms and the firmament of stars as a dome over the flat earth. the sun and moon are created before the plants. this view continued into the middle ages http://dhushara.com/repcult/reproduction-and-culture.htm http://dhushara.com/repcult/reproduction-and-culture.htm http://dhushara.com/resplendence/origins.jpg dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 202-225 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part iii) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 208 (b), but with the scientific revolution a conflicting paradigm has emerged (c), in which the earth is a planet in a vastly bigger more complex universe, which has emerged from an explosive origin over 13 billion years ago, with processes such as cosmic inflation providing the dynamics to induce the formation of galaxy clusters, stars and planets in the form we see today amid accelerating expansion caused by dark energy. this is a cosmogenic process with no evidence for an external creator god. life was not generated de-novo in a fixed machine-like act of manufacture at a single point in time, but shows exhaustive genetic, fossil and developmental evidence of evolution (d) to form complex organisms and ultimately conscious sentient beings. resplendence, as a democratic social process, seeks to reparadise the earth by applying the scientific paradigm correctly to the human existential condition. this provides a more effective view of our life-giving role in the universe, in terms of protecting the generations of living diversity and of conscious beings on the planet over evolutionary time scales, thereby enabling a deepening of conscious awareness as a whole in the universe, as a cumulative emergent manifestation of cosmology. in scientific revolutions, the sceptical principle of inquiry, seeks verification from nature, confirming a theory to be true only when all attempts to negate it result in contradiction, rather than imposing preconceived beliefs. this means that descriptions of reality only remain stable over limited epochs, called paradigms, punctuated by evolutionary leaps. when a new theory, or description of reality, is discovered, which generalizes, or replaces a previous one, a new scientific paradigm is born. the term paradigm itself has an ancient origin in greek paradeigma, "pattern, example" from para, "beside, beyond" and deiknumi "to show, to point out" meaning "exhibit, represent, expose". the term was used in plato's timaeus as the model or pattern that the demiurge (god) used to create the cosmos. resplendence in making a paradigm transition from religion does precisely this, transforming the naive view of religious creation of the cosmos by god into a wisdom tradition to guide human action based on the extraordinarily confounding and detailed scientific knowledge of the universe we have more recently accumulated. human societies and individual consciousness have been driven by two complementary sensibilities. on the one hand, the practical understanding of nature is essential for survival, manifest in gatherer-hunter society, for example in knowledge of diverse food and medicinal plant species and in the practicalities of hunting and developing arrow poisons and this has eventually become science. complementing this are feelings of belonging and meaning in a precocious natural world, associated with beliefs in spirits and deities that guide behavior towards societal strength through morality, and explain the mortal condition and the vagaries of fate. these have over time become what we call science and religion. however, religions have resisted natural paradigm evolution because they seek permanent ascendancy. thus jesus, buddha and muhammad remain fixed male entities impeding the natural evolution of human insight and world guardianship of nature. buddha has become a symbol of perfection unattainable in the round of birth and death. muhammad is claimed to be the last prophet under pain of execution. jesus is claimed to be going to return in the 'second coming' as the avenging lord. this prevents natural evolution, even though our understanding of the world, and the closing circle of the biosphere have been transformed, both by science, and human impacts of our burgeoning planetary technological society, leading to climate change, ecocrisis and potentially irreversible risks to human and natural survival. dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 202-225 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part iii) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 209 resplendence accepts the paradigm shift to the scientific description of reality in all its manifestations, while at the same time resolving the dilemma of existence in a way religions are failing to do, by coupling our sense of purpose and collective action to the one thing that immortalizes us protecting the life flow of the living planet and its generations. morality and redemption: christianity asserts a corrupt moral imperative that human beings are flawed by original sin, stemming from eve's transgression, and that human free will is set in a moral cosmology, in which those who do not believe in god, and/or commit any of the seven deadly sins, will suffer eternal damnation in the day of judgment. resplendence asserts that humans possess original virtue in their emotional makeup, which allows for love and empathic relationship as well as expedience and betrayal, and that moral behavior is a natural feature of sociobiology in which individuals in a species, or human society, or religion, forgo immediate advantages over their peers to enable the society as a whole to gain dominance over competing societies and better survive in the wider environment. below: three features of morality in dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 202-225 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part iii) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 210 mammals (a) protective behavior at risk to the individual. lion attacking a wildebeast. a pride of lionesses cooperating to try to capture a young, or weaker, straggler are rounded on by a herd of buffalo also cooperating with one another, making a classically moral decision to act together for the benefit of the group at some risk to their individual lives, forcing the predators to flee. (b) clear evidence of emotional bonding in elephants and chimps showing they can make emotional decisions. (c) collective altruistic action. a group of hippos act together to save a zebra at a waterhole from a crocodile. altruistic punishment is neither necessary, nor sufficient for morality, although it is very effective in human societies. compassion and empathy are natural mammalian emotions which have also been observed, even across species in animal societies. notice also that the carnivores have an essential role in the ecosystem of avoiding boom and bust in the herbivores, which could lead to a famine resulting in them becoming extinct, so their role in tooth and claw is also beneficent. the lion lying down with the lamb of isaiah is thus a misguided fantasy. the religious moral imperative in urban societies arises from the imposition of cultural values which rob the human individuals of their deeper relationship with the passage of the generations in nature. as a climax species having major impacts on the planet, we are only now becoming aware of our cognizant role in planetary life. resplendence, by restoring the natural relationship between humanity and life as a whole, applies the redemptive principle, which heals cultural tendencies towards selfish exploitation, because they are futile mortal strategies with no long-term fulfillment and no lasting outcome, except for diminishing the regenerative process by short-term exploitation and tragedy of the commons.. gods are projections of conscious personalities onto the cosmos that come from an earlier phase in human emergence, where gatherer-hunters devised parent-like entities to guard over their vulnerable lives in a tumultuous world, and later in our cultural adolescence, agricultural civilizations used increasingly powerful deities as punishing moral entities holding sway over life and death, and the implied after-life as the final moral end-of-days scenario. with the coming to maturity of human culture in reaching a state today where human actions themselves can irreversibly harm the planet's future, we have to accept we have entered a state of de-facto maturity and accept that it is we ourselves, neither god, nor jesus as lord in the day of judgment, who must assume responsibility for beneficent guardianship of the planetary future, and achieve the enlightenment to be able to do this successfully. this is a complete fulfillment of our life meaning and purpose and enables the mystery of conscious existence to be more and more deeply explored over the lifetimes of all the sentient participants as an open-ended process. resplendence seeks a condition of unfolding visionary transcendence in sentient consciousness and in human society at large. this is a quest that spans both the foundations of cosmology and neuroscience and the deepest insights of the religious traditions. it is a greater perspective than the lofty pretensions of religions because it encompasses all conscious experience in an openended discovery process, neither limited by materialistic assumptions that the consious mind is no more than the workings of the chemical brain, nor pre-empted by doctrines and dogmas of prescribed religious assumptions.. spiritually, resplendence seeks a condition where every individual is able to explore the mystical and visionary undercurrents of the conscious condition first hand, without becoming subject to oppressive forces seeking to assert any religious belief or creed, or to deny people the dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 202-225 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part iii) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 211 opportunity to experience such states themselves through legislation to prevent the use of visionary sacraments or drugs which induce visionary states. attempting to ban access to mind altering substances is a benighted policy aimed more at shoring up mindless consumer materialism and existing traditional religious beliefs than any protection of society from misadventure. any forms of societal abuse of substances need to be treated as a heath matter to avoid the growth of violent criminal organizations seeking to profit from banned substances in an age where technology is making synthesis on demand ever more available. women and sexuality: left: enforced veiling and homicidal stoning. islam, imposes stringent and violent restrictions on female reproductive choice, social, educational and career opportunities, enforced by torture and homicide for adultery, as part of an archaic patriarchal tribal code. such reproductive control of the female to ensure patriarchal reproductive imperatives has been an almost universal feature of world religions for millennia. centre to right: in contrast with religion, resplendence seeks a high degree of sovereignty for female reproductive choice in an overall climate of mutual partner choice consistent with the needs of the human family. this is because humans are at an extreme among mammals in the dissonance between the male reproductive strategy which is primarily focused on fertilization and the female strategy focused on parenting. because mammals bear live young and the females engage lactation and a pivotal role in infant care, females need to be able to choose the best combination of resourcing partner and good genes for what is a massive commitment, with a long pregnancy leaving the woman vulnerable and travail, a risky delivery bearing a large head, months to years of breast feeding and years of young child care. in addition mammalian xy chromosome sexual selection favours males displaying single x-linked characteristics, while females are able to apply sexual selection to these, again emphasizing the importance of female reproductive choice. in an overpopulated world, universal access to contraception is essential, but in addition, there need to be social http://dhushara.com/paradoxhtm/vale.htm http://dhushara.com/paradoxhtm/vale.htm http://dhushara.com/paradoxhtm/fall.htm http://dhushara.com/paradoxhtm/fall.htm http://dhushara.com/paradoxhtm/biology.htm#anchor-in-57 dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 202-225 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part iii) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 212 incentives to enable capable achieving women to both pursue and maintain their professional careers and have security of parental leave, to avoid the conflict between parenting and women's careers that has blighted democratic countries from italy to japan. at the same time, this predicates a pro-choice position concerning terminating pregnancy, not least to avoid the risks women suffer when these rights are withheld in the name of religious conviction. finally resplendence implies ensuring natural childbirth remains a viable process, and advising against routine cosmetic caesarians based on a false image of womanhood, and giving responsible advice about the implications for future generations of technologies such as in-vitro fertilization and intra-cytoplasmic sperm implantation, as well as more advanced techniques such as generating gametes from stem cells, to avoid the human species becoming perpetually dependent on medical procedures to survive. right: sexuality commands respect as sacred to the natural order, as we each become conscious beings through sexual fertilization and sexual recombination to create the diversity of all sexual beings, without which higher life forms would never have come into existence. politically, resplendence aims at an ecosystemically diverse informed non-violent democratic society of mutually enlightened beings, possessing maximal autonomy of choice, avoiding the tyranny of the majority democracies are prone to , while recognizing the need to actively oppose all forms of totalitarianism that could lead to a loss of democratic autonomy, both from political movements such as totalitarian fascism and communism and from world religions with totalitarian doctrines that form an even more all-encompassing utopian threat to freedom of choice and world futures. technologically, resplendence seeks a society utilizing the most advanced techniques in a sensitive way, which works closely with evolutionary principles to achieve a high standard of living and fully informed intelligence, while having minimal impact on and actively restoring the biospheric resilience of the planet over evolutionary time scales. the energy economy needs urgently to move to renewable forms of energy not having deleterious impacts on the climate and biosphere as a whole. the information economy needs to remain as free as possible from governmental surveillance and accessible to all people. consciousness and enlightenment: resplendence rejects the notions of heaven and hell (top left) because they have no place in the physical universe and they are a product of a fantastic moral punishment causality that is in fundamental conflict with nature, where moral systems are simply a natural evolutionary manifestation of sociobiology, implying that heaven and hell are imaginary realms generated by conscious experience, as religions endeavour to come to terms with the mysteries and paradoxes of conscious existence. it likewise rejects the contrivances of cults, such as the galactic dictator xenu of scientology. top right: the buddhist realms of the hungry ghosts and titans are likewise representations of mental states with a false anthropocentric emphasis on a universal morality which falsely demotes the animals to a realm of inferior incarnations due to previous moral dereliction. biological incarnation is a sexual process inconsistent with the reincarnation of individual souls. resplendence wisdom thus remains clear of false misleading assumptions based on preconceived religious notions. however resplendence accepts the discoveries of neuroscience concerning the brain-mind relationship and the full diversity of experiences and personal accounts spanning the spectrum of mental states (lower right), from waking, through dreaming, meditative, contemplative, visionary and http://dhushara.com/paradoxhtm/reprod.htm#anchor-surviving-47857 http://dhushara.com/mental/cosmentst2.htm http://dhushara.com/mental/cosmentst2.htm dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 202-225 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part iii) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 213 sacrament induced, because these are a central part of the discovery of the inner nature of conscious experience. cosmology would suggest that, since the brain is the most complex interactive process manifest by the forces of nature in interaction, consciousness may be the most inscrutable mystery in cosmology and one that may take evolutionary time scales to fully elucidate. this in no way rules in or out forms of consciousness extending beyond our biological life spans, consciousness being shared directly between beings, or prophetic forms of conscious anticipation, all of which remain to be explored over time, without prejudging the nature and scope of consciousness in fixed religious doctrines, or preconceived beliefs a fatal error, given the sensitive nature of consciousness. right: the huichol nierika or portal to the visionary world induced by peyote is a valid part of subjective sacramental exploration of the conscious condition because it can be experienced first-hand. above all resplendence seeks to prevent the destabilization of the entire planet's resilience and robustness to survive, through rampant habitat destruction, burning the fossil fuels accumulated over three hundred million uears and climate change running to tipping points which could compromise both human survival and the survival of the diverse species upon which we codepend. http://dhushara.com/book/twelve/tw2.htm#anchor-11481 dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 202-225 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part iii) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 214 weapons of mass destruction need to be replaced by programs to provide defences against events on an astronomical scale threatening to the continuity of life, such as asteroid impacts and nearby supernovae. questions of interstellar migration, or communication, need to be considered cautiously for their deeper implications. great precautionary care needs to be applied to bootstrap genetic technologies such as germline editing and engineering, which feedback directly into the process of genetic evolution itself and hence the informational foundation of the biosphere. these technologies have vast utopian potential, and invoke the temptation to make choices which result in an elitist dependence on advanced reproductive technology. they are liable to lead to 'poisoned chalice' dystopias, lacking the resilience to survive over evolutionary time scales. because resplendence is founded on the resilience that natural evolutionary ecosystems have over cosmological time scales and the super-computing power of parallel genetic algorithms in a diverse natural ecology, as a concept it needs to apply a very strong precautionary principle against forms of technology which to bootstrap genetic technologies such as germ-line editing and engineering, which feedback directly into the process of genetic evolution itself and hence the informational foundation of the biosphere. eugenic genetic engineering and/or cloning, or using other genetic reproductive technologies for "brave new world" utopian aims is a key potential threat to long term ecosystemic viability that needs to be avoided, because it is most likely to lead to irreversible loss of characteristics essential to the long-term adaptiveness of both human beings and the species upon which we depend for our future survival. these technologies have vast utopian potential, and invoke the temptation to make choices that result in an elitist dependence on advanced reproductive technology. they are liable to lead to 'poisoned chalice' dystopias, lacking the resilience to survive over evolutionary time scales. use of technologies such as germ-line editing, particularly in humans and the species upon which we depend, thus has to be examined very carefully on a case-by-case basis. . primary threats to evolution and survival: top: hiroshima after the nuclear holocaust. middle: intentional deforestation in indonesia. bottom: genetic technology hold both great promise and great risks, requiring careful ethical assessment to avoid irreversible damage. (left) macaques genetically edited using crispr to alter three genes. right: parthenogenetic and stem-cell generated mice using reproductive genetic technology. crispr, a new gene editing technology based on a key bacterial immune system, has already been shown to be able to make changes in specific genes and yet enable the birth of live geneedited primate offspring, leading to the potential to make selective changes to genes such as those causing diseases in humans. but this technology has to be very carefully assessed. combining it with 'gene drive' techniques, which can selectively result in the edited genes being transmitted to virtually all offspring when an organism containing the edited changes mates and produces offspring, rather than the natural 50-50 ratio, could eliminate a disease such as malaria by precipitating an explosive loss of mosquito fertility, but could also cause irreversible changes to both species and ecosystems. such gene drive mechanisms could continue to cause collateral damage, resulting in the loss of essential characteristics in species upon which depend or even our own species. a decade ago monsanto tried to introduce 'terminator technology' which would cause seeds produced by the company to become genetically infertile in the second generation http://dhushara.com/book/explod/explod.htm http://dhushara.com/paradoxhtm/reprod.htm#anchor-germ-line-47857 http://dhushara.com/paradoxhtm/reprod.htm#anchor-germ-line-47857 http://dhushara.com/paradoxhtm/reprod.htm#anchor-germ-line-47857 dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 202-225 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part iii) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 215 leading to a similar risk of irreversible loss if the natural varieties ceased to be cultivated on an adequate scale by farmers dependent on the technology. resplendence is the natural paradigm successor to religion, in which we cherish and replenish the earth throughout the generations of the diversity of life, no longer seeing through a glass darkly, but now face-to-face, coming into coherence with our sexually-immortal condition, becoming the source of a collective illumination of enlightenment, both scientific and visionary, to flower the future generations and sustain the epoch of paradise on earth. 10. transcendence and the physical universe there is no basis to the cosmological argument for god because there is no meaningful way to mount an initial cause, since space-time begins with the cosmic origin and time does not extend to before but curves to meet itself in much the same way as all the lines of latitude come together at the south pole of the earth. there is thus no meaning to trying to apply linear causal logic that dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 202-225 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part iii) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 216 something beforehand must have made the universe, except as a classical misconception. this problem only gets worse if the universe is part of a larger fractal cosmic inflation process, because it is fundamental to general relativity that the curvature of space-time is shaped by gravity. likewise it is meaningless to talk about a 'final' cause of life a single external defined purpose to which it must converge. just as dark energy suggests the universe will expand forever, so the quantum physics of biology leads to the evolutionary diversity of life and the vision quest of consciousness as open-ended outcomes. in this process we, and the generations of life with us, will discover, ever more deeply, the nature of conscious existence, which is the most inscrutable process in the universe. for this reason we need to protect the evolutionary diversity of life and of conscious existence throughout the generations as a prime purpose in life, while at the same time exploring as deeply as possible the conscious condition. we also have a prime purpose to safeguard the genetic diversity of life in our use of technology. recent research connecting quantum entanglement to space-time and gravity implies that quantum reality, with its spooky wave functions connecting past and future, may define the large scale structure of the universe and hence space-time as well. elapsing time is a feature of an observer inside an entangled state. outside this state, the observer sees space-time extension with no time evolution i.e. eternal existence. it is everything forever alpha to omega. because the conscious brain depends on edge-of-chaos sensitivity and quantum entanglement to anticipate reality and survive in an uncertain world, we can experience both the temporal aspect and the eternal aspect of the existential condition. in the temporal, we witness things change and evolve and we are born and die. in the eternal, everything we have witnessed and will ever witness is encoded in the entanglement of past and future. consciousness and intentional will are a process which enables us to anticipate the immediate future and to act to perpetuate the process in terms of survival. thus the consciousness in every sentient being is subjectively participating in determining the causal destiny of the universe. the universe coming to experience itself is the ultimate interactive consummation of the symmetry-breaking of the forces of nature in the cosmic origin. it is thus fully cosmological the sigma state complementing alpha and omega. cosmological life paradise on the cosmic equator. in the temporal aspect of existence, we are discovering ourselves while discovering nature and collapsing the cosmic wave function so that we all experience a temporal line of world history in the making. from outside the entanglement, this is the universe having come to know itself in paradise on the cosmic equator. http://dhushara.com/paradoxhtm/quant.htm http://dhushara.com/book/bchtm/biocos.htm http://dhushara.com/apoc/apocalypse_files/trans_files/image001.jpg dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 202-225 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part iii) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 217 this knowing is eternal spanning space time so that it is of significance only that it came to pass at all, not when it begins or ends. it doesn't matter if life ends on earth, or even the entire universe meets its heat death, because the experience is eternally encoded in space-time. the eternal aspect of this collective consciousness, spanning the entire history of the universe, is what religious people think of as god generating the universe as a dream, a thought, an intellectual pronouncement, or ultimate cause. let there be life and there was life! vishnu, the sustainer, dreaming the universe out of brahman emerging from a lotus in his navel, lovingly overlooked by lakhsmi. the pauline logos as a demiurge pronouncing the universe into being through his intellect. these worldviews are allegorical myths, not literal accounts. we need to explore the actual mysteries of sentient existence in the first person to validate them, just as good science discovers the natural world by sceptical inquiry. this is a primary responsibility of being a sentient being alongside protecting the diversity of the generations of life. 11. ten clarifications on the nature of existence 1. biogenesis, evolution and consciousness: biogenesis is a cosmological interactive process leading, through biological evolution, to consciousness as the most complete expression of all the fundamental forces of nature in interaction. it is thus the sigma point on the cosmic equator in space-time, standing in consummating relationship to the alpha and omega. 2. transcendence lies in the biota: transcendence is thus manifest principally or exclusively in the biota, and hence in the human vision quest. the messianic quest, the mystical quest, the shamanic vision quest and the quest for enlightenment are thus real, as is the sacredness of sexuality, but worship of deities, including the monotheistic god, is a false vision based on idolatry and bibliolatry. there is no final prophet or messiah, because the mysterium tremendum of existence is manifest in every sentient being. 3. the origin of apocalypse: our conscious awareness of the existential condition during the epochs of human emergence and the development of civilization has led to an awareness of tumultuous future shock converging on the covers being thrown off reality, a phenomenon that has come to be described in religious traditions as apocalypse. 4. transcendence versus deity: transcendence is not manifest in the monotheistic god or other deities, which are projections of human nature and transcendence into imaginary personalities in heavenly and hellish domains. the day of judgment is thus a false morally punishing apocalypse. 5. sexuality, fertility and incarnation: sexual complementarity and fertility is key to the emergence of complex life and consciousness and secures the creative and perennial passage of the generations of life, even though as individual organisms, we suffer a mortal life-span, inescapable in biological life. sexuality is thus integral to the sacred condition and the dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 202-225 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part iii) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 218 immortality of the generations of life. because incarnation is sexual, the idea of reincarnation of individual souls, possibly in different species is a natural fallacy. 6. religion and nature: the purpose of spirituality and religion is to cherish and replenish the planet throughout the generations of life. nature is thus central and pivotal to the sacred condition. 7. religion and morality: the social value of religion is to encourage collective respect for, responsibility about, and action to, protect the living planet and life in the universe. it is neither to worship god, nor to create a dominant culture through morally prescriptive punishing deities and doctrines, nor to repress female reproductive choice, all of which are oppressive worldly instruments of male power. 8. realization and fulfillment: individual realization and collective fulfillment comes through contributing to the future fecundity of life and discovering the inner nature of conscious experience and the natural world and communicating these experiences to others. this is fulfilling the destiny of the universe coming to understand itself in space-time through conscious illumination. 9. conscious autonomy and will: consciousness and intentional will exist to bind together the complementary subjective and objective physical aspects of existential reality in such a way as to enable subjective intentionality to alter the course of physical history and bring about a more blessed and aware world and cosmological condition. we are thus responsible for our actions and their ultimate affects. 10. selfishness and mortality: while free-will can also be used for selfish ends, or to create dominant dystopias, these aims are ignorant and ultimately doomed to mortality because they do not achieve fruition of the immortal condition. the aim of enlightenment is to help everyone see the futility of such selfish manipulative and oppressive actions and to act with joy and vitality to protect the living generations of life. 12. accounting religious apocalypse and its greening in the traditions apocalypse is a cosmological nightmare generated by a patriarchally dominant culture generating religions of conflict and destruction in the name of the male reproductive imperative and its ensuing male mortality anxiety inflated to cosmic proportions in the quest for eternal life and the cosmic war between god and the devil. this is itself a betrayal of faith in both our evolutionary original virtue, which sustained us into this situation, and for believers in the divine, a betrayal of the genuine power and essential goodness of god, by placing him in mortal combat with equally oppressive forces of darkness, which have no place in any cosmological description, outside the all too natural human failings of jealousy, betrayal, anger, contempt, disgust, envy and expedience. the scientific revolution has shown us in astounding ways how the universe actually works and how it comes about, and it does have moral and ethical implications for conserving the diversity dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 202-225 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part iii) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 219 of nature, knowing how long evolutionary time-scales take to generate the living and genetic diversity upon which the robustness of the planet, and our future with it, depends. the unique role of religion, when it is functioning for the human and planetary good, is to bind us together in a paradigm of caring and of moral and ethical goodness and togetherness in which major decisions for the long-term welfare of the planet and its ongoing life may take personal sacrifices on the part of all of us to avoid a tragedy of the commons (hardin) caused by winnertake-all exploitation and greed. this is precisely the theme of the current pope's encyclical to care for the planet, to avoid severe climate change and loss of biodiversity, paralleled by similar responses from the anglicans and a group of muslim scholars which we shall examine in the next section, so it is possible for religion to have a helpful role when it is not oppressive. however, religion also needs to respect female views on contraception and reproduction in an era of peaking and potentially unsustainable human population. its role should be to mitigate human violence with a sense of wisdom and mutual compassion, rather than to invoke homicidal violence and dismemberment through outmoded doctrines and prescriptions, such as stoning for adultery, amputation for stealing, and death for apostasy. as rosemary radford ruether (1982) notes: both the [covenental and sacramental] traditions are marked by a legacy of patriarchalism and must be reinterpreted, if they are to be genuinely affirming of dominated women, men and nature. even then, the question of whether they can be adequately liberated and made liberating will remain. … i assume there is no ready made ecological spirituality and ethic in past traditions. the ecological crisis is new to human experience. this does not mean that humans have not devastated the environment before. but as long as populations remained small and human technology was weak, these devastations were remediable by migration, retreat from top-heavy urban centers, or adaption of new techniques. nature appeared a huge inexhaustible source of life and humans small. only after the bombs of hiroshima and nagasaki did humans begin to recognize the possibility that they could destroy the planet by their own expropriated power. the radical nature of this new face of ecological devastation means that all past human traditions are inadequate in the face of it. many of the ways religions act already encourage compassionate sentiments, in the virtues of charity and love for others, celebrated collectively in rites-of-passage, from birth, through sexual union, to death, and in the festivals of the seasons. they also encourage caring for others in creating a fairer world for all. this is the joy and magic of people coming together in love with a common cause of the fertility of life itself and the part each of us plays in the fabric of existence. we are thus the agents of giving meaning to existence through the meaning we give to life itself, rather than seeking it in subservient worship and unquestioned archaic doctrines. extended to an opportunity for mystical experience as well, provided by the living sacraments completes the cycle in the first person, making the whole process one of confirming reality through personal affirmation, rather than prescriptive belief. we nevertheless need to hold all existing religions to account for their history of violence and deal with them in terms of tough love, resisting all violence and coercion, to avoid them taking dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 202-225 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part iii) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 220 humanity and our very ability to protect our future generations, hostage to their coercive and often violently enforced utopian ambitions. muslims hold muhammad as a sacred perfect being, peace be upon him, under pain of death for his mere depiction, but it is clearly documented that he ordered the summary beheading of 700 jewish men and took their women into sexual slavery by appointing a dying warrior judge over their fate when they had parleyed with the quraysh besieging medina, but had not betrayed the muslims by actually opening their gates in the oasis (armstrong). thus a genocide was committed, even though an actual betrayal had never occurred, or the muslims wouldn't have been in a position to exact such a diabolical punishment. muhammad personally ordered apostates to be killed and women to be stoned for adultery. all people on the planet need to recognise that the prophet's own actions are completely inconsistent with islam's pretence to be a religion of peace. if any religious leader in this day and age were to commit such heinous offences, the international community would hunt them down and put them on trial for crimes against humanity. we need to come to a day of reckoning about those who have committed unconscionable violence in founding a major world religion with utopian aims for world domination, and steadfastly oppose all rights to commit homicidal violence in the name of religion, or scripture. the genocide in the souk of medina (fitna) for this reason i close with a series of abrogations of scripture invoking violence or repression, as possibly the one person on the planet who has declared the need, taken the prerogative, and the had insight to do so, in the spirit of culminating the violent epoch of apocalypse once and for all time to follow, for the liberation of all sentient beings from bondage and religious homicide. but to consummate this process, we need to consider the wider horizon. the world is suffering from a schizophrenic mismatch between the scientific and religious traditions. on the scientific side, paradigm shifts (kuhn) fundamental changes in the description of reality are happening at an accelerating pace, just as albert einstein's quantum theory and relativity formed a new paradigm, generalizing and replacing those of isaac newton. whole new developments, from the theories of fundamental physics, through cosmology and the ultimate origin and fate of the universe, to the human genome project, biological genetics and neuroscience, are completely transforming our understanding of the natural world, using the sceptical principle of accepting only those theories that are confirmed by nature. physicist richard feynman put it this way: in general we look for a new law by the following process. first we guess it. then we compute the consequences of the guess to see what would be implied if this law that we guessed is right. then we compare the result of the computation to nature, with experiment or experience, compare it directly with observation, to see if it works. if dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 202-225 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part iii) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 221 it disagrees with experiment it is wrong. in that simple statement is the key to science. it does not make any difference how beautiful your guess is. it does not make any difference how smart you are, who made the guess, or what his name is if it disagrees with experiment it is wrong. that is all there is to it. by contrast the world's major religions are caught in a sabbatical flat-earth view of existence, in which evolution doesn’t exist, god made the living species in an act of creative manufacture as we make tools, autos and computers, the heavens lie in the clouds and we all wait in fear for the day of judgment. in the middle stands the planet and its biosphere and the human impacts documented by science which could jeopardize the long-term future of planetary life. despite efforts on both sides to paper over the cracks and claim some consistency between science and religion, these two world-views have become fundamentally inconsistent and in a state of conceptual and actual conflict. central to this question is the way religions try to infer the reality of their models by reference to a-priori assumptions, untestable hypotheses and notions invoking supernatural processes transcending any form of human examination. the hellenistic cosmogony of christianity posits a divine ultimate being in turn giving rise to a creator god, who creates the universe as a kind of conscious mental imprint of their own intellect. modern versions of this christian idea see god becoming all things to all men the biblical god of israel invoking jealous wrath in the old testament, the forgiving father god of jesus, who sacrifices his only begotten son, the logoschrist at the beginning and end of the universe, and finally the god imagined to be standing somehow behind the inordinately complex physical universe we have now discovered through science, and in the conscious minds of its diverse inhabitants, along with all the good and beneficent feelings of compassion and awe we can come to express – i.e. god is in everything! despite the us being a developed country with strong scientific and secular traditions, over 42% of people still believe in genesis 1 creationism, sometimes disguised as 'intelligent design', and most, particularly republican christians continue deny human impacts on climate change. http://dhushara.com/apoc/apocalypse_files/image043.png dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 202-225 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part iii) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 222 caught up in this confusion are the endless arguments for the existence of god. the original ontological argument was "that than which nothing greater can be conceived" must exist in the mind; even in the mind of the person who denies the existence of god. the cosmological argument, which we shall consider and refute in detail, is generally in the guise of a notion of the cosmos as a causal process, which thus must be set in motion by a primal first cause claimed to be god. there are fundamental reasons why the cosmogony and cosmology of both the physical universe and conscious sentient existence should apply the standards of sceptical inquiry, only confirming theories which could actually be disproved and for which there is confirming evidence, either objective or subjective. the picture emerging both from quantum theory and the relativistic universe clarifies why positing first causes of this nature are likely to be fundamental misconceptions originating from mental introspection in the classical world, which do not hold in general. quantum theory is stochastic, with deterministic hamiltonian wave functions interleaved with causality-violating processes invoking the probability interpretation, either from the notion of collapse of the wave function and other theories such as many worlds. quantum processes also admit both advanced and retarded solutions, so that implicitly time-reversing properties such as the many versions of the wheeler delayed choice experiment become manifest in diverse forms of quantum entanglement. causality in the physical universe is generally associated with the "arrow of time" in that causes precede their effects, but general relativity invokes the curvature of both space and time, so that for example in the source of the big bang, space and time become rather like the north pole where the lines of latitude come together, with there being no meaning in asking what came before hand, as a primal first cause. ideas of internal symmetries and symmetry-breaking have better explanatory power, although there are also cosmogenic physical theories in which a clash of higher dimensional 'branes', a recurrent bounce from a big crush, or a fractally inflating cosmos, could introduce new big-bang baby universes in the process. likewise the study of conscious experience is better served by empirical discovery than apriori assumptions about transcendence and notions of first-causes, even though subjective consciousness may not conform to the notions of objective replication experimental science usually applies. since we are all subjectively conscious beings, we can each enter into the cosmological spectrum of mental states achievable by the human brain and psyche and into a discovery process, just as shamans and mystics have done since the dawn of human culture. to have veridical validity, this needs to be pursued in the first person rather than surviving thirdhand on doctrines of a priesthood or religious prescription. centrally in terms of the religious pursuit of eternal life in a mortal world, we need to understand that the redemption of mortality lies not the apocalyptic genocide of "a new heaven and earth", but the living immortality of the passage of the generations. complex intelligent life could not have evolved without sexuality providing the almost endless repertoire of viable variations that sexual recombination enables. this leads in turn to the variety of each of us as sentient beings with a common compassionate basis in mortal incarnation as individual organisms. we are thus as individuals, 'emanations' of sexuality and gain our physical immortality in the immortal web of the generations of life. in return we owe it to the passage of the generations to cherish and dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 202-225 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part iii) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 223 replenish it. this is the best of all possible outcomes, not a flawed universe doomed to mortality of the individual. through empathy and compassion we become united in life. the caveat on a-priori assumptions also applies to christogenic theories, such as that of pierre teihlard de chardin, the catholic philosopher/archaeologist who was prevented by the church from publishing his work during his lifetime and produced an evolutionary christology occurring in qualitative 'phase transitions' in which successive phases supplanted one another due to their invoking more efficient and novel forms of emergence, from physical and chemical complexification, through biological evolution from simpler to more successful complex organisms, in turn succeeded by human culture proceeding from primitive societies through early civilizations to democracy and technology, leading to a unitary mind, reminiscent of the 'global village of the world-wide web, culminating in unidirectional causality in the 'body of christ' in love, realizing the hellenistic notion of the cosmic redemption. rosemary radford ruether notes the dark side of this unilateral 'privileged axis', leading to 'sanguine acceptance of extinction of species as the acceptable price of this progress' although it has been widely recognized by scientists for its integrated view of humanity in the universe. chardin's christogenesis model. the idea that there is a beneficent underlying basis for the deeper and deeper integration of conscious experience, which is also a manifestation of the interactive cosmology of the universe is consistent with it being manifest subjectively in the cosmological nature of consciousness itself, which can be experienced in meditation and contemplation. but this is something we need to explore very carefully without preconceptions, because it is the most subtle manifestation of the sentient cosmos. we have no evidence that this will lead to a linear axial christology, rather than an increasing diversity of indwelling mystical insights in a resonating tapestry of living experience, just as we are still trying to determine whether the current physical universe will expand forever, rather than ending in a 'big crunch'. science, as the pursuit of natural knowledge, can tell us the planet is in trouble, but it falls to social activists, such greenpeace, to try to bring human consciousness to bear on the problem, while world leaders dither and argue, urged on by a few more enlightened of their members, often hobbled by conservative forces aligned to business interests who depend for their wealth on the status quo, leading towards a tragedy of the commons. traditionally the complementary role falls to religion to give people a view of reality in which life makes sense, to motivate people to act for the common good, and in which our collective prospects and sense of meaning in life and death are given real hope. science and religion in deeper human history over the last 100,000 years have appealed to complementary aspects of how the human brain has evolved. science is basically an abstraction of the practical natural skills of hunters developing potent arrow poisons and gathers learning the nutrient and medicinal properties of diverse plant species, and potential uses of natural products dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 202-225 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part iii) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 224 to achieve diverse cultural ends. it is the knowledge of how to live in nature successfully. religion plays into our sense of meaning, our togetherness as a people, our sense of moral rightness towards one another in the face of potential betrayal, and the subconscious realms where visionary experiences, our mortal fears and sense of belonging play out in senses of ecstasy and ultimate meaning. it is thus religion that has been the motivating force for the rise and fall of successive cultures and civilizations. the world is in absolutely urgent need of the ability to have paradigm revolutions of its religious traditions, so that humanity can come to constructive engagement with the closing circle of one biosphere. now the tragic fallacy in this equation is that christianity, islam and even buddhism too have set up toxic traps to prevent natural paradigm change. buddha embodies a state of perfection unattainable in the round of birth and death. islam has declared that muhammad is the final prophet, preventing any change to the paradigm under pain of execution. christianity has in many ways set up an even more lethal trap by claiming the only messiah is jesus who will return as avenging lord in the day of judgment, thus not only being the final prophet, but the judge and executioner as well. dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 202-225 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part iii) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 225 correspondence between attitudes to climate change and evolution in us religious groups shows negative attitudes to both are broadly correlated with religious fundamentalism. try to imagine for a moment the relationship between newton and einstein. if jesus, as the historical founder of christianity, is compared to newton, how can an einstein ever come into being in this tradition? no meister eckhart, saint paul, or mother teresa can do it because all are caught in the gilded cage of having to worship the christian doctrinal package, unadulterated by heresy, as good faithful christians. the current pope francis who is a genius about protecting diversity and addressing global warming in his encyclical compiled by world class scientists, and has moved to soften the hard line against divorce, and abortion through forgiveness, is still stuck with claiming that "good weeps" for the victims of church child abuse. what kind of god of creation lurks in the aether, expressing human emotions and "biological" tears for catholic wrongdoings, while genocidal religious war rages in syria and the planet is in ecocrisis? so, is it true that the only way a christian einstein could come about would be by founding a completely new religion, overthrowing the broken paradigm of jesus stuck on the cross bleeding for all eternity? since christianity is the central cultural religious tradition of the western world, this is like saying einstein would have to overthrow science to discover relativity. it is madness pure and simple. it is possible but it would clearly take a huge challenge to the zeitgeist to accept a human innovator daring enough to do a stealth raid as the "thief in the night". the acid test ultimately is universal credibility of the innovation. hence we need to look very carefully at what the natural revolution of this stasis is, in complete honesty and transparency. the answer, in the closing circle of the biosphere, is clearly that the central meaning, raison d'être and purpose of all our human lives is to cherish and replenish the earth throughout the generations of living diversity. there is no other end game, no other unveiling, no other solution this is it! it's not a matter of affirmative belief, such as "i believe in the one god", but the ultimate truth of existential reality itself, and our conscious place in the process. this is what i describe as the way, or tao of the tree of life, the natural successor to christianity in the western tradition. and it comes with two clear implications about nature and fertility, both of which run diametrically opposite to the view of reality pronounced in eden that nature is evil, as the serpent is evil, and that woman is the devil's gateway. the truth is that nature is sacred, sine qua non, as paradise is sacred, and that sexuality is as sacred as nature. reproductive fertility, its underlying genetics and the parental investment of the human female stipulates that female choice reproductively and culturally is at least as sacred as male choice. (continued on part vi) dna decipher journal | june 2016 | volume 6 | issue 2 | pp. 102-106 christianto, v. & umniyati, y., on the plausible implications of gariaev & montagnier’s work: omne vivum ex vivo via crebritudo? issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 102 exploration on the plausible implications of gariaev & montagnier’s work: omne vivum ex vivo via crebritudo? victor christianto *1 &yunita umniyati 2 1 malang institute of agriculture, malang, indonesia 2 swiss german university, tangerang – indonesia abstract recently luc montagnier and his group reported that genetic information might be transmitted to water through applications of electromagnetic field. these experiments seem to confirm what have been done by peter gariaev and his group in the past three decades, i.e., that dna has wave character. however, non-particle view of dna seems to challenge the standard paradigm of dna and biology. in this paper, we briefly explore the non-particle view of dna and consider an extension of the known adage “omne vivum ex vivo” to “omne vivum ex vivo via crebritudo (frequency)”. keywords: dna, genetic information, transmission, gariaev, montagnier, wave character. introduction recently luc montagnier and his group reported that genetical information might be transmitted to water through applications of electromagnetic field [2-3]. these experiments seem to confirm what have been done by peter gariaev and his group in the past three decades, i.e., dna has wave character. however, non-particle view of dna seems to challenge standard paradigm of dna and biology. in this paper, we briefly explore the non-particle view of dna. concluding her review on montagnier’s experiments, laurence hecht wrote [1]: with the results of montagnier, we recognize that the principle, omne vivum ex vivo, still holds, but only on the condition that we adopt a non-particle conception of life. since there are extensive reports since 1980s concerning the possibility of long distance communication between cells, especially using e.m. field, it seems appropriate to consider an extension of the known adage: “omne vivum ex vivo” to “omne vivum ex vivo via crebritudo (frequency)”. * correspondence:victor christianto, malang institute of agriculture, malang – indonesia. url: http://researchgate.net/profile/victor_christianto. email: victorchristianto@gmail.com http://researchgate.net/profile/victor_christianto mailto:victorchristianto@gmail.com dna decipher journal | june 2016 | volume 6 | issue 2 | pp. 102-106 christianto, v. & umniyati, y., on the plausible implications of gariaev & montagnier’s work: omne vivum ex vivo via crebritudo? issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 103 dna & de broglie’s matter-wave hypothesis experiments carried out by montagnier group seem to suggest that genetic information can be transmitted to water via electromagnetic waves. this is very interesting since it challenges standard paradigm in biology [2-3]. this is also related to gariaev’s proposal of dna wave genetics [4-6]. that cell has capability to communicate at a distance may be not surprising, since there are reports indicating that effect [7-8]. but that electromagnetic field can transmit genetic information to water is interesting result which seems to bring us back to an old battle between corpuscular view and wave view of matter, i.e., newtonian corpuscular model vis a vis huygensfresnel’s wave model of matter. louis de broglie seemed to give a hint on that issue by proposing matter-wave hypothesis but it appears that this issue is not solved completely. for clarity, let us put aside objections on einstein’s special relativity and follow de broglie’s argument in his thesis: ,fe  (1) and 2mce  (2) equating (1) and (2) we get: 2mcf  , (3) or . 2c fm   (4) in other words, matter comes from frequency. therefore, it seems possible at least in theory that not only e.m. field can transmit genetic information to water, but also that e.m. frequency can alter genetic code. as a note, although our starting point of using (1) and (2) comes from de broglie’s original proposal, the conclusion is rather different because we do not have to accept his pilot wave model. it seems that equation (4) can give some hints to explain many phenomena related to montagnier and gariaev’s experiments and may plausibly open new ways to treat dna as quantum biocomputer [4]. if this proposition holds true, then it is possible to extend the old adage “all life come from life” (omne vivum ex vivo) to “all life come from life through frequency” (omne vivum ex vivo via crebritudo). this is because genetic information can be altered or transmitted through e.m. field and frequency. in other words, one may use ‘frequentia’, so it becomes: “omne vivum ex vivo via frequentia.” dna decipher journal | june 2016 | volume 6 | issue 2 | pp. 102-106 christianto, v. & umniyati, y., on the plausible implications of gariaev & montagnier’s work: omne vivum ex vivo via crebritudo? issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 104 plausible application of the proposed concept to test the new concept of “all life comes from life through frequency” (omne vivum ex vivo via crebritudo) which challenges the standard paradigm in biology, we suggest the following: let us define f = yield frequency, i.e., frequency where matter becomes wave and a new parameter: , 2c k   (5) then we can write equation (4) as a ratio: .k f m  (6) in other words, from the above equation we may predict that the ratio between a small mass (m) like photon with its yield frequency (f) is always a constant. the small mass here can be extended to neutrino, electron, muon etc. we hope that the above equation may serve as a means to test the proposed concept. one plausible application of this proposition is alternative method of cancer treatment using various frequencies. it is known that some frequencies like 444hz may kill cancer cell without destroying the normal cells. such a method seems worthy to be investigated and developed further [9]. montagnier et al. also use very low frequency such as 7.83 hz, which seems to be closely related to the schumann resonance of 7 hz. whether or not such a 7.83 hz corresponds to ambient frequency of electromagnetic noise in water should be tested with experiments. dna as perturbed sge soliton there are various models of dna, one of them is using solitary wave [10]. its use as a model of phyllotaxis systems including dna has been proposed elsewhere [11-14]. now, we will only consider perturbed sine-gordon equation (psge) as a model of interaction between soliton and external e.m. field. perturbed sge comes in a variety of forms. one common form is a damped and driven sge: [11, p.17] 𝛹𝑡𝑡 + 𝛷𝛹𝑡 −𝛹𝑧𝑧 + sin⁡(𝛹) = 𝐹 (7) in addition, the following two versions of the perturbed sge have been studied in the literature, including: dna decipher journal | june 2016 | volume 6 | issue 2 | pp. 102-106 christianto, v. & umniyati, y., on the plausible implications of gariaev & montagnier’s work: omne vivum ex vivo via crebritudo? issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 105 a. directly forced sge: [11, p.19] 𝛹𝑡𝑡 −𝛹𝑧𝑧 + sin⁡(𝛹) = 𝑀𝑓(𝜔𝑡) (8) b. damped and drived sge: 𝛹𝑡𝑡 −𝛹𝑧𝑧 + sin(𝛹) = 𝑀𝑓(𝜔𝑡) − 𝛼𝛹𝑡 + 𝜂 (9) in the meantime, (2+1)d sge with additional spatial coordinate (y) is defined as: [11,p.21] 𝛹𝑡𝑡 = 𝛹𝑥𝑥 +𝛹𝑦𝑦 − sin⁡(𝛹) (10) in their in-depth review of sge, ivancevic and ivancevic [11] discuss potential applications of sge solitons in dna, protein folding, microtubules, neural impulse conduction and muscular contraction soliton. new insights may be expected in the near future in these biological fields, based on sine-gordon equation soliton. concluding remarks recently luc montagnier and his group reported that genetic information might be transmitted to water through applications of electromagnetic field. these experiments seem to confirm what have been done by peter gariaev and his group in the past 3 decades, i.e., that dna has wave character. concluding her review on montagnier’s experiments, laurence hecht wrote [1]: with the results of montagnier, we recognize that the principle, omne vivum ex vivo, still holds, but only on the condition that we adopt a non-particle conception of life. in this paper, we have briefly explored the non-particle view of dna and consider an extension of the known adage: “omne vivum ex vivo” to “omne vivum ex vivo via crebritudo (frequency)”. acknowledgement: the first authors wishes to express his gratitude to renata wong and prof. akira kanda for discussion and insight. dna decipher journal | june 2016 | volume 6 | issue 2 | pp. 102-106 christianto, v. & umniyati, y., on the plausible implications of gariaev & montagnier’s work: omne vivum ex vivo via crebritudo? issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 106 references [1] laurence hecht. “luc montagnier’s revolution in biology: new evidence for a non-particle view of life.” 21 st century science and technology, winter 2010/2011. url: http://www.21stcenturysciencetech.com/articles_2011/winter-2010/montagnier.pdf [2] luc montagnier, et al. (2011). “dna waves and water.” 5 th intr. workshop dice 2010; journal of physics: conf. series 306 (2011) 012007; [2a] http://arxiv.org/pdf/1012.5166 [3] luc montagnier et al. (2015) “transduction of dna information through water and electromagnetic waves,” arxiv:1501.0162 [q-bio.ot]; see also [3a] luc montagnier, et al. (2009) “electromagnetic signals are produced by aqueous nanostructures derived from bacterial dna sequences.” interdiscip. sci. comput. life. sci. [4] peter gariaev, et al. (2011) “dna as basis for quantum biocomputer,” dna decipher journal, january 2011, vol. 1 issue 1, pp. 025-046. http://www.dnadecipher.com [5] matt pitkanen (2011) “dna & water memory: comments on montagnier group’s recent findings,” dna decipher journal, january 2011, vol. 1 issue 1, pp. 181-190. http://www.dnadecipher.com [6] peter gariaev & matt pitkanen (2010) “model for the findings about hologram generating properties of dna,” url: http://tgd.wippiespace.com/public_html/ [7] ashkan farhadi (2014) “non-chemical distant cellular interactions as a potential confounder of cell biology experiments,” frontiers in physiology, oct. 2014, vol. 5 article 405 [8] a.v. khalyavkin & a.e. gurvich (1978) “role of distant interactions of lymphocytes in the development of antibody formation in vitro,” bull. exp. biol. & medicine, plenum publishing corp. available at www.researchgate.net [9] victor christianto (2015) “a review of cancer electromagnetic frequency therapy: towards physics of cancer,” intr. front. sci. lett., www.scipress.com [10] victor christianto & yunita umniyati (2015) “graphical plot of soliton solution of sine-gordon model of dna,” dna decipher journal, www.dnadecipher.com [11] vladimir g. ivancevic and tijana t. ivancevic. sine-gordon solitons, kinks and breathers as physical models of nonlinear excitations in living cellular structures. arxiv:1305.0613 [qbio.ot] [12] cristiano nisoli (2009) “spiraling soliton: a continuum model for dynamical phyllotaxis of physical systems,” phys. rev. e 80, 026110 [13] ludmila v. yakushevich. nonlinear physics of dna. second, rev. ed. berlin: wiley-vch verlag gmbh & co., 2004 [14] sara cuenda, angel sanchez, niurka r. quintero. does the dynamics of sine-gordon solitons predict active regions of dna? 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register with this site forgot your password? issn: 2159-046x unraveling the tree of life dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 81-103 king, c., the future of christian religion in the genetic age issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 81 opinion the future of christian religion in the genetic age chris king * abstract as we enter the genetic age, where science and technology are providing more and more avenues to play god with our own futures, we need to develop social, ethical, moral and spiritual traditions which are up to the challenge of dealing with the unknown future in a way which preserves human and planetary viability and doesn't subject us to a futile endgame or an apocalyptic armageddon through our own lack of sensitivity and foresight. the western tradition of gentile christianity can only play a part in this future through a revolution of outlook at the most fundamental level. key words: genetic age, science, technology, ethics, morality, spirituality, christian, religion, god. nature, science and religion in the genetic age christianity remains the prevailing religion of western culture, but is it up to the challenge of acting as a spiritual and ethical guardian of human society into a third millennium? while science has flourished and evolved into a unified description of reality and we have become technologically advanced and globally interconnected, world religions remain archaic, divided and involved in partisan utopian struggles, leading towards lethal conflict, possibly on a planetary scale. this is particularly dangerous as we enter an age of human impact, a mass extinction of living diversity and possible human-induced threats to our own viability through climatic tipping points. it is also a manifestly inadequate basis to consider the huge implications of an age of genetic technology which could have vast and irreversible impacts on our future as a species. while science has thrived on the skeptical principles of questioning assumptions and testing theories against the natural evidence, and social systems have moved from autocracies towards egalitarian democracy, in which government is, at least in principle, a dynamic expression of the will of the people, religions, for all their claim to being the sanctuaries of higher spiritual and ethical consciousness remain resistant to change and adamantly opposed to fundamental innovation of the kind that has accompanied the quantum leaps of our scientific revolutions, particularly fundamental renewal of the religious paradigm. to pass any test of validity in our global planetary future, religions need to be able to pass both the kind of natural reality check scientific theories have to, and prove themselves to be a willing and autonomous * correspondence: chris king http://www.dhushara.com e-mail: chris@sexualparadox.org note: this article is based on http://themessiahs-blog.blogspot.com/2011/12/future-of-christian-religion.html http://www.dhushara.com/ mailto:chris@sexualparadox.org http://the-messiahs-blog.blogspot.com/2011/12/future-of-christian-religion.html http://the-messiahs-blog.blogspot.com/2011/12/future-of-christian-religion.html dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 81-103 king, c., the future of christian religion in the genetic age issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 82 democratic expression of the conscious experiences and will of each generation looking towards their own futures and those of their descendants. but for all the tendency to religious belief permeating even the most liberated secular societies, traditional religions seem to be manifestly failing on both these acid tests. in the toxic centre of the cyclone of religious dysfunction, despite being the loved and cherished mainstay, are the central notions of having to have faith and affirmative belief, as the foundation of religious experience, both of which strike at the very heart of natural validity, as they a prioriconfront nature and the universe with unswerving prejudicial conviction. humanity has yet to discover how to come to terms with a sustainable planetary culture and avoid a hard landing caused by our own human impacts on the earth's living environment, which could raise the oceans, deplete non-renewable resources, including energy, chemical resources and natural habitats, and wipe out up to a third of living species, in a triage reminiscent of the bitter waters of revelation. far from being confined to a few natural curiosities, this could cause economic collapse and widespread famine. we are also entering an era where major genetic questions interpenetrate with human survival. is religion, and in particular christian religion, able to cut the mustard to achieve a sustainable future for humanity and the biosphere? monotheistic religions are particularly unsuited to this task, because they are desert religions founded on utopian apocalyptic principles, in free flight towards tumultuous final conflict, the triage of all life, and the victory of one religion or another in a day of judgment in which the whole of the planetary biosphere is conceived as being laid waste in a rapture of the late planet earth. this is about as far from a sustainable future as one can possibly imagine. even in the most technologically and scientifically developed societies of europe and the us, a sizable minority, to a frank majority of people continue to believe in god, hold to religious convictions, and remain in a state of frank denial about basic scientific issues, from biological evolution to the age of the universe. is this a manifestation of the undeniable reality of religion, or is it an archaic throwback from coercive patterns of belief, which people are too dependent on and frightened of any alternative to, to set aside? could it even have a genetic basis in 4000 years of human social selection, in which monolithic religious belief systems have been the strongest single force shaping the military ascendance of dominant societies, driven by their moral suppression of internal conflict? if so, does this verify that religiosity is paradoxically enshrined in evolution, or is it a startling example of how selective breeding can result in insidious and potentially lethal characteristics? in this discussion, there are two complementary threads. one is the innate tendency of people to reach towards religion, and in the christian context, belief in god, as an existential prop to cope with ultimate anxieties about life, death and suffering in the physical world, to give us comfort, even if delusory, and make some ordered sense out of a seemingly chaotic existence of tooth and claw. the other is the specific nature of christianity as a religion, its fundamental tenets, its historical genesis and the degree to which it is founded on real people and historical events, as opposed to fantastic myths dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 81-103 king, c., the future of christian religion in the genetic age issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 83 or contrivances which become less and less credible, as we discover more about nature and the universe around us. if christianity is going to cut the mustard as an influence shaping human destiny into the future, it needs to face acid tests of its validity and capacity to address the changes human culture is likely to face over the third millennium. so how does it stack up? to answer this we need to wind back to the very origins of christianity and understand how this tradition of belief came about. this is going to be a convoluted historical detour, but it is essential to set the groundwork for assessing the christian heritage in the kind of terms necessary to pass the acid tests of authenticity and viability. the nature and mission of jesus in the first instance this comes down to a scrutiny of jesus as the centre of the christian cyclone. we will assume here that jesus is an actual historical figure who walked the earth as an incarnate human, despite conflicting claims to his being god the son by his gentile christian apologists, or merely a figment of myth and fable by some of his detractors. actual records of jesus' life are lean at best, coming principally from three sources, the four orthodox gospels, written long after his life and death by proponents who we have no real evidence actually experienced the events they describe first hand, with manifest religious political agendas; a few gnostic sayings in the gospel of thomas; and a few derogatory remarks in the talmud decrying him as one who led the people of israel astray. even the brief account of jesus in josephus' history is considered to be a later christian insertion to add substance to his historical existence. while he is the son of god to gentile christians, he was a false messiah to orthodox jews. the lexicon talmudicum and talmud babli sanhedrin 106b, 43a, 51a and the toldoth jeshu refer tojeshu-ha-notzri [jesus of nazareth] by mention of the wicked kingdom of edom, since that was his nation... he was hanged on a passover eve... he was near to the kingdom. balaam the lame was 33 years old when pintias the robber [pontius pilate] killed him... they say that his mother was descended from princes and rulers but consorted with carpenters. the personality and divinity of jesus show sharply divided descriptions between the synoptics, mark, matthew and luke on the one hand, the dark and light firebrand semi-gnosticism of john, and the altogether different account in thomas, more that of a paradoxical sage, inducing the reader to fulfill their own discovery of "the kingdom", which 'lies before you but men do not see it'. while the synoptics have peter declare jesus to be the chosen messiah anointed, in thomas he disclaims that he is not the messiah but the catalyst: mark 8:27: and jesus went out, and his disciples, into the towns of caesarea philippi: and by the way he asked his disciples, saying unto them, whom do men say that i am? and they answered, john the baptist; but some say, elias; and others, one of the prophets. and he saith unto them, but whom say ye that i am? and peter answereth and saith unto him, thou art the christ. http://en.wikipedia.org/wiki/gospel_of_thomas http://en.wikipedia.org/wiki/josephus dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 81-103 king, c., the future of christian religion in the genetic age issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 84 thomas 13: jesus said to his disciples, "compare me to someone and tell me whom i am like." simon peter said to him, "you are like a righteous angel." matthew said to him, "you are like a wise philosopher." thomas said to him, "master, my mouth is wholly incapable of saying whom you are like." jesus said, "i am not your master. because you have drunk, you have become intoxicated from the bubbling spring which i have measured out." the fact that many of jesus' sayings in the gospel of thomas are in a root form, which appears to predate the more embellished versions in the synoptics, attests both to its authenticity and to the fact that jesus saw discovering reality in terms of gnosis or 'knowing', rather than belief, particularly the belief in a divine lord and saviour that christianity later became, as noted in elaine pagels' (2003) work "beyond belief". thomas is variously dated to 60 110 ce, with some of the material certainly coming from the first stratum, which is dated to 30 60. the oxyrhynchusfragments date to as early as 130. the sayings which cast thomas as jesus' twin brother, inviting us likewise to be twins with jesus; in 'knowing', convey an atmosphere closer to that of an eastern sage or a nature shaman than an anointed divine lord. the first three sayings of jesus in thomas set out the core of the gnostic path of selffulfillment in knowing in oneself, in the first person, the experiential condition of the all, and that the kingdom is right here in this world, once we come to understand the nature of existence: (1) "whoever finds the interpretation of these sayings will not experience death." (2) "let him who seeks continue seeking until he finds. when he finds, he will become troubled. when he becomes troubled, he will be astonished, and he will rule over the all." (3) "if those who lead you say to you, 'see, the kingdom is in the sky,' then the birds of the sky will precede you. if they say to you, 'it is in the sea,' then the fish will precede you. rather, the kingdom is inside of you, and it is outside of you. when you come to know yourselves, then you will become known, and you will realize that it is you who are the sons of the living father. but if you will not know yourselves, you dwell in poverty and it is you who are that poverty." even when jesus appears to say things which might be interpreted as claiming to be the divine source, we are also one and the same in gnostic awareness, manifest in everything from an overturned stone to a newly split piece of wood: (77) jesus said, "it is i who am the light which is above them all. it is i who am the all. from me did the all come forth, and unto me did the all extend. split a piece of wood, and i am there. lift up the stone, and you will i find me there." on the other side, the synoptics would have him declare that some standing before him would not pass away before the kingdom would come in power, giving the church a claim to being a temporary steward, or guardian, before the lord's return in glory, although the fulfillment of this engagement has receded ever further away, as the centuries have passed unrequited. it is clear in the light of history that the nature of jesus' mission set it apart from the hebrew tradition, http://en.wikipedia.org/wiki/elaine_pagels http://en.wikipedia.org/wiki/gospel_of_thomas dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 81-103 king, c., the future of christian religion in the genetic age issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 85 which led to him being declared a false messiah by the jews, despite having a small following among the hebrew christians under the banner of the desposyni, james the just and jesus' immediate family. among these are blasphemous claims to performing nature miracles, including curing people of maladies, causing 'evil spirits' to enter a herd of pigs who ran in demented horror into the sea of galilee to the consternation of their owners, calming the waters and walking upon them, climaxing in revitalizing lazarus. the nature miracles are not part of the hebrew tradition although some prophets performed them, such as moses mythical parting of the waters of the red sea. profligate miraculous dread is the characteristic of dionysian legend, as the dark god of altered states, who is the original 'true vine' who turned water into wine on the same epiphany, or advent, and in particular dhushara of neighbouring nabatea, at its height in jesus' time, who achieved immortality while wearing a theatrical death mask (glueck 1966). one should also note with caution that these 'miraculous' powers were ephemeral, so that the synoptics note comments like "physician heal thyself" intimating at the lameness mentioned in the talmud, the disciples thinking of deserting him after the episode of the 5000 loaves but having nowhere else to turn, suggesting the performance was less than convincing to them, and his frank failure to perform any convincing good works in his home town of nazareth. the final episodes leading to the crucifixion, including his elaborate advance preparation for the event, including his raising of lazarus, his anointing to his burial, pre-booking a venue for the last supper, riding into jerusalem as the palm king, turning the tables and passing the sop to judas as in a prearranged pact (pagels and king), likewise read as an act of dionysian tragic theatre, raising ultimate questions over his rapid 'demise' on the cross and subsequent medicinal treatment by the women with aloes and spices provided by joseph of arimathea. these ambiguities have led to repeated claims that jesus may have survived the crucifixion (schonfield) and was variously seen in rome (graves ad podro 1957), traveled to india and was buried in kashmir and even that he became a rice farmer in japan and his remains lie in a shrine in aoomori. there is also a continuing series of central events in his mission that read as a classic sacrificial rite of a fertility cult. he was anointed by a woman rather than a high rabbi, as all the other jewish messiahs, from solomon to bar cochbah were, and anointed in a very strange manner for his burial in the manner of kings sacrificed to inana and ishtar, a female anointing without which the title of messiah could not apply. also highly irregular was the dependence of jesus' mission on the support of women 'out of their very substance', followed to his demise by the women who came down from galilee, and later discovered as an apparition in the garden by magdalen, having been privately 'embalmed' with aloes and spices by the women, when the disciples scattered like the sheep of the foolish shepherd of zechariah. both these key aspects of jesus' mission, and the cataclysmic crucifixion, where he is supposed to have been killed, harrowed hell and risen again on the third day, come right out of the fertility religions of sumeria, babylon, and concurrently with his own life, of nabatea. even if we accept that the gospels are mythical accounts written with a hellenistic gloss long after jesus' death, it is very unlikely the misogynistic christian forefathers would have inserted these themes of their own accord. finally we have the vein of pure gold that makes people love god and jesus to this day and that is the completely novel idea that instead of a god of jealousy and retribution, as yahweh is portrayed as being, http://en.wikipedia.org/wiki/desposyni http://en.wikipedia.org/wiki/james_the_just http://en.wikipedia.org/wiki/dhushara http://en.wikipedia.org/wiki/nabatea http://news.bbc.co.uk/2/hi/programmes/from_our_own_correspondent/5326614.stm http://en.wikipedia.org/wiki/bar_cochbah http://www.dhushara.com/paradoxhtm/fall.htm#anchor-genealogy-49575 dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 81-103 king, c., the future of christian religion in the genetic age issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 86 as a totemic deity of the bride israel, abba is deemed by jesus to be a loving, forgiving father, who will even right in the moment forgive us all our sins if we believe in him. this also leads to jesus, reversing rabbi hillel's silver rule "don't do to others what you would not have them do unto you" when asked to recite the torah standing on one foot, to the affirmative and slightly more evangelical golden rule "do unto others what you would have them do unto you". finally we have the command of total forgiveness to turn the other cheek and bless them that curse you. one has to take caution about this, because evolutionary game theory has shown that tit-for-tat, or an eye for an eye, is one of the most effective evolutionary strategies of survival, because it cooperates with cooperators and punishes defectors, but it is prone to cycles of reciprocal retaliation. always cooperate is a lethal sucker's game and one could really only advance this in an apocalyptic belief that the world is transitory and a new kingdom is about to emerge, nevertheless it is infectiously appealing. it is these sayings above all that have led christians, over many centuries of church corruption and diabolical bloodshed against its own people, to continue to believe in god and in jesus as lord and saviour. thus it becomes ever clearer that jesus, in his mission to the lost sheep of israel, had a wider, much more ingenious conception, of generating a root paradigm change, encompassing the wider near eastern religious cosmologies of his time, as well as turning the apocalyptic tables on judaic traditions in the persona of the eschatological son of man coming in power. in this, nabatea plays a key role, as josephus makes clear. in the account of the beheading of john the baptist, in mark (6:14-29), salome dances before the generals in what is clearly a dance of the seven veils of inana, and ishtar, at her mother herodias' behest, claims the baptist's head (as a sacrifice of dumuzzi, or tammuz as he came to be called in the hebrew temple), when herod, as was done to haman in esther, offers her even half the kingdom. this event occurred at macherus on the nabatean border, with herod's generals present, because herod, whom the baptist had accused of marrying his brother philip's wife, and his own cousin, had jilted the princess of nabatea, who ran in fear of her life to her parents aretas iv and shaqilat ii the conjoint king and queen, sparking a war between nabatea and herod in the neighbouring tetrarchy of perea in which herod was defeated. in a strange echo, in supposedly taking up john's mantle, (although the baptist's surviving sabean followers in southern iraq vehemently disclaim jesus teachings), jesus also died anointed to his burial by a woman variously claimed to be mary of bethany and/or magdalen and a 'sinner' caught in adultery. he is also claimed in the gospel of thomas to have come up on salome's bed: (61) jesus said, "two will rest on a bed: the one will die, and the other will live." salome said, "who are you, man, that you ... have come up on my couch and eaten from my table?" and jesus says, "i am he who is from the one, and the things that belong to the father have been given to me." salome replies, "but i am your disciple", and jesus answers, "when the disciple is united he will be filled with light, but if he is divided he will be filled with darkness." the natural founders of the movement following jesus' crucifixion are james the just, peter, and as we shall see in a more subterranean way, mary, martha and salome. http://www.dhushara.com/paradoxhtm/prisoners.htm#anchor-in-46919 http://en.wikipedia.org/wiki/nabatea http://en.wikipedia.org/wiki/john_the_baptist http://en.wikipedia.org/wiki/john_the_baptist http://www.dhushara.com/paradoxhtm/fall.htm#anchor-genealogy-49575 http://en.wikipedia.org/wiki/tammuz_%28deity%29 http://en.wikipedia.org/wiki/esther http://en.wikipedia.org/wiki/aretas_iv_philopatris dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 81-103 king, c., the future of christian religion in the genetic age issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 87 the immediate end result of jesus' blasphemous mission was a small religious following centered around the jewish christians or nazarenes as they were called in jerusalem after jesus' birth place of nazareth. it is clear the nasarenes revered james and the desposyni. the gospel of thomas also asserts jesus appointed james rather than peter to be his successor, in apocalyptically glowing terms: "the disciples said to jesus: we know that you will depart from us; who is it who will lead us?" jesus said to them, "wherever you have come from, go to james the just, for whom heaven and earth came to be." the little we know of james portrays him as a very devout man. hegesippus stated "that he was a lifelong nazirite, abstaining from animal food and strong drink. he neither shaved nor cut his hair, never anointed his body with oil or used the public bath. he never wore woolen, only linen garments, and prayed constantly in the temple for the forgiveness of the people." in 62, immediately before vespasian's attack beginning the siege of jerusalem, he was murdered at the temple variously cast down from the pinnacles at the behest of the high priest ananus ben ananus, or falling from the steps. in eusebius' words they cried: 'o just one, whose word we all ought to obey, since the people are led astray after jesus, who was crucified, tell us what is the gate to jesus?' and he answered shouting out loudly, 'why do you ask me concerning the son of man? he is now sitting in heaven at the right hand of the great power and is about to come on the clouds of heaven.' the christian commentary has seriously injured james cry out: "i beseech thee, lord god our father, forgive them; for they know not what they do." just as luke claims jesus did as lots were cast on his garments. a rechabite priest then shouted: "cease, what do ye? the just man is praying for us," but he is then struck on the head by the club a fuller used to wring out wet garments with. the brief epistle of james does not state it is written by james the just, but simply a servant of god and of the lord jesus christ, to the twelve tribes, although christian writers do attribute it to him. other authors see it as a later pseudo-epigraphical or composite edited work, or a work of wisdom literature in the guise of an epistle. however it does contain a passage which exposes an area of significant conflict with paul's hellenistic teaching, claiming how you actually carry out the eventual acts is the key, and not faith alone the dissonance between salvation and justification: 'what does it profit, my brethren, if a man says he has faith but has not works? can his faith save him? if a brother or sister is ill-clad and in lack of daily food, and one of you says to them, "go in peace, be warmed and filled," without giving them the things needed for the body, what does it profit? so faith by itself, if it has no works, is dead. but some one will say, "you have faith and i have works." show me your faith apart from your works, and i by my works will show you my faith.' peter is equally enigmatic, although he is the 'rock' holding the keys to the golden gate. paul assigns him to leading the mission to the circumcised, but history suggests he taught in antioch and moved to rome where he was martyred by nero. he also undertook a missionary journey to lydda, joppa and caesarea, becoming instrumental in the decision to evangelize the gentiles. the only potentially genuine remnant of his teaching is the brief first epistle of peter, which is notable in suggesting jesus taught the 'imprisoned' in hell. http://en.wikipedia.org/wiki/nazarenes http://en.wikipedia.org/wiki/hegesippus_%28chronicler%29 http://en.wikipedia.org/wiki/nazirite http://en.wikipedia.org/wiki/vespasian http://en.wikipedia.org/wiki/ananus_ben_ananus http://en.wikipedia.org/wiki/eusebius dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 81-103 king, c., the future of christian religion in the genetic age issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 88 even though virtually all we know of jewish christians or nazarenes is sourced through subsequent gentile christian detractors, the little we do know of nazarenes, such as the ebionites, paint a very different picture of the emergence of jesus' following in the first century form the pauline version, he entitled christianity. during the first centuries of the christian era, the ebionites or 'deserving poor' regarded jesus as the jewish messiah and insisted on the necessity of following jewish religious law and rites such as circumcision. the ebionites used only one hebrew gospel, revered james the just and rejected paul as an apostate from the law, as did the elcesaites. epiphanius states (panarion 30.16:9) that some ebionites gossiped that paul was a greek who converted to sadduceean judaism in order to marry the high priest's daughter, and then apostasized when she rejected him. it has to be remembered that the jewish messiah was always considered to be a human, not a god a jewish prophet or king, who was anointed in recognition of bringing about an epoch of long-term future goodness, as solomon did, despite his many strange wives. even with the growth of apocalyptic judaism such as the essene movement, who followed the teacher of righteousness, and the notion of the eschatological son of man, or son of adam, there is no parallel for the messiah being identified with god in the gentile christian manner. the ebionites accepted jesus as the messiah, the greatest of the prophets, but not as the 'virgin born' son of god and considered that he had normal human parentage. by virtue of his righteousness, he was chosen by god to be the messianic "prophet like moses". he became one with god in the baptism and remained so until his crucifixion. they did not view jesus' death as a bloody act of atonement. they rejected christ's pre-existence, divinity, virgin birth, and physical resurrection. one ebionite story does have jesus eating bread with his brother jacob ("james the just") after the resurrection but this can be considered a miraculous happening in line with other prophetic miracles. they practiced a rigorous asceticism and stressed the binding character of the mosaic law. epiphanius stated that they interpreted the eucharist as a memorial of jesus, substituting a chalice of water for the chalice of blood, and became vegetarians, rejecting the temple animal sacrifices, although it has been suggested this applies rather to the elcesaites. of the books of the new testament, the ebionites only accepted an aramaic version of the gospel of matthew, referred to as the gospel of the hebrews, as scripture. this version of matthew, pauline christian critics reported, omitted the first two chapters (on jesus' virgin birth), and started with jesus' baptism by john implying they held an adoptionist view. adoptionists assert that jesus was fully human, born of a sexual union between joseph and mary, and only became adopted as 'god's son', later at his baptism, because of his sinless devotion to the will of god. adoptionism probably arose among early jewish nazarenes seeking to reconcile gentile christian claims that jesus was the son of god with the strict monotheism of judaism, in which the trinity and a divinity in human form was unacceptable, and may date back almost to the time of jesus. after the fall of jerusalem in ad 70, the ebionites settled at pella in transjordan, but remained outside the mainstream of christianity. eusebius summarizes this from his perspective in that they "had poor and mean opinions concerning christ. they held him to be a plain and ordinary man who had achieved http://en.wikipedia.org/wiki/nazarenes http://en.wikipedia.org/wiki/ebionites http://en.wikipedia.org/wiki/elcesaites http://en.wikipedia.org/wiki/epiphanius_of_salamis http://en.wikipedia.org/wiki/adoptionist dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 81-103 king, c., the future of christian religion in the genetic age issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 89 righteousness merely by the progress of his character" (ranke-heinemann 1992 173, wilson i 154, grollier). the hellenistic transformation of jesus into christian deity paul, who had never had direct contact with any of the historical events is the inventor of gentile christianity, as opposed to the jewish practices of the nasarenes. it becomes a hellenistic travesty of hebrew traditions, leading to fantastic notions, from jesus' divinity, and mary's virgin birth, to a rapture in which the elect float up into thin air in the apparent annihilation of the living planet. despite ebionite claims he was a greek apostate, paul was, in his own words, "of the stock of israel, of the tribe of benjamin, an hebrew of the hebrews; as touching the law, a pharisee". he was also saul of tarsus, a roman citizen, persecuting christians. he then claimed , a few years after jesus' crucifixion, that the resurrected jesus had spoken to him on the road to damascus in a great light, and that he was struck blind, but after three days his sight was restored by ananias of damascus. he began to preach that jesus of nazareth is the jewish messiah and the son of god. paul was thus the first born again christian in the modern sense, having no direct connection with jesus' life, except through an apparition similar to marian and other apparitions people occasionally experience today and he carried on his mission and declared his gospel exclusively on the basis of this ephemeral connection. paul asserted that he received the gospel not from any person, but by the direct revelation of jesus christ and assertively claimed almost total independence from the jerusalem community. it was fully three years after his conversion that he first went to jerusalem, where he met james and peter: "then after three years i went up to jerusalem to visit cephas and remained with him fifteen days. but i saw none of the other apostles except james the lord’s brother." he emphasizes this is no lie as if it is somehow scandalous. he claims to have subsequently received their approval for his teachings in a second meeting in jerusalem 11 years later: "when james and cephas and john, who seemed to be pillars, perceived the grace that was given to me, they gave the right hand of fellowship to barnabas and me, that we should go to the gentiles and they to the circumcised. only, they asked us to remember the poor, the very thing i was eager to do." whether this 'poor' means the 'deserving poor' ebionites who decried paul as an apostate remains enigmatic. a vital meeting between paul and the jerusalem church took place some time in the years 48 to 50, often referred to as the council of jerusalem. the key question raised was whether gentile converts needed to be circumcised. it is noted than in john, jesus says "moses therefore gave unto you circumcision; (not because it is of moses, but of the fathers;) and ye on the sabbath day circumcise a man." dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 81-103 king, c., the future of christian religion in the genetic age issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 90 it is claimed it was agreed gentile christians were not obliged to keep most of the mosaic law. according to the account, peter remonstrated "wherefore my sentence is, that we trouble not them, which from among the gentiles are turned to god: but that we write unto them, that they abstain from pollutions of idols, and from fornication, and from things strangled, and from blood." paul claims that at this meeting, peter, james, and john accepted his mission to the gentiles. however it is clear that james remained concerned that paul had not fully kept this agreement, in particular over non-kosher meat from the markets, in their final meeting in jerusalem. however there were continuing tensions over keeping the jewish law, for gentiles who had converted from fertility worship, leading to the incident at antioch: "but when cephas came to antioch, i opposed him to his face, because he stood condemned. for before certain men came from james, he was eating with the gentiles; but when they came he drew back and separated himself, fearing the circumcision party. and the rest of the jews acted hypocritically along with him, so that even barnabas was led astray by their hypocrisy." evidently paul was on the offside, because he left antioch never to return, although catholic tradition claims he and pater eventually taught together in rome. since the pauline letters are the earliest texts in the new testament, dating from around 51, this casts a pall of doubt over the later compilations of the four new testament gospels, which likewise contain a mix of sayings, miraculous claims, frankly implausible divine birth accounts and careful reconstructions of hebrew scripture to make the whole event look like it was prophesied. moreover, as elaine pagels (1995) has made clear, they also contain partisan polemic discrediting the teachings of other groups who had emerged, for example decrying thomas didymus's account as jesus' twin brother in the doubting thomas episode, implying thomas's gnostic teachings didn't fully embrace jesus' divinity and resurrected corporeality. eusebius notes that papias, the second century bishop of hierapolis said that "mark was the interpreter of peter and wrote down carefully what he remembered of what had been said or done by the lord, but not in the right order" (ranke-heinmann 1992 219, graves and podro 1953 37), quoting john the elder (fox r 127), presumably the disciple, suggesting mark contains retellings of accounts witnessed by peter. the earliest hypothetical fragment of mark is the qumran fragment 7q5 dating to 68, but its relationship to mark's gospel is rejected by nearly all authorities. matthew is variously regarded as originating from a jewish-christian source, but has had editorial ornamentation later. the earliest magdalen fragments of matthew are attributed to c 70. both luke and matthew are believed to have derived partly from mark and a hypothetical synoptic sayings source "q", so as they stand are later reconstructions. luke confesses at the outset that he was not present during jesus' lifetime. john claims to be the elusive 'beloved disciple' and is sometimes referred to, along with peter and james in early christian accounts (1 cor 15.3-8). john also contains references to an older compilation of miracles, suggesting it is likewise a redacted compilation and the passage about the woman caught in adultery appears to be a later addition. the rylands fragment of john 18:31-4 dating from c125 ad in egypt confirms the gospel of john's existence by a date of perhaps 90 ad. http://en.wikipedia.org/wiki/7q5 http://en.wikipedia.org/wiki/magdalen_papyrus http://en.wikipedia.org/wiki/q_source http://en.wikipedia.org/wiki/gospel_of_john dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 81-103 king, c., the future of christian religion in the genetic age issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 91 we need to take into account here, that the founding gospels of the new testament do not appear to have envisaged jesus as the divine son of god. the early jewish-christian gospels make no mention of a supernatural birth. rather, they state that jesus was begotten at his baptism. according to the church fathers, the first gospel was written by matthew, called the gospel of the hebrews and was adoptionist in nature. the gospel of the hebrews has no mention of the virgin birth and when jesus is baptized it states, "jesus came up from the water, heaven was opened, and he saw the holy spirit descend in the form of a dove and enter into him. and a voice from heaven said, ‘you are my beloved son; with you i am well pleased.’ and again, ‘today i have begotten you.’ immediately a great light shone around the place". scholars also see adoptionist theology in the gospel of mark. mark has jesus as the son of god, occurring at strategic points, but the virgin birth of jesus has not been developed. the phrase "son of god" is not present in some early manuscripts at 1:1. this omission supports the notion that the title "son of god" is not used of jesus until his baptism, and that mark reflects an adoptionist view. critical parts of mark containing the encounters with the resurrected christ may also be later additions. mark 16:8 stops at a description of the empty tomb, which is immediately preceded by a statement by a "young man dressed in a white robe" that jesus is "risen" and is "going ahead of you into galilee." the last twelve verses are missing from the oldest manuscripts. the theology of adoptionism fell into disfavor as christianity left its jewish roots and gentile christianity became dominant, was declared heresy at the end of the 2nd century, and was rejected by the first council of nicaea. gnostic undercurrents from the earliest times, an exceedingly diverse spectrum of gnostic followings (pagels 1979) also sprang up, from the valentinian groups of alexandria, to the ophites, and phibionites. in trying to reclaim something of the founding tradition, we need to appreciate the diversity of these gnostic cosmologies. the various ophite sects, according to the accounts of christian detractors, believed in the serpent of eden and moses, considering eve worshipped the serpent as the giver of wisdom and new life, and saw jesus as either a pretender to the serpent's power, or an emanation of it. the naassene ophites claimed to have been taught their doctrines by mariamne, a disciple of james the just. the retention of the hebrew form shows that their beliefs may represent the earliest stages of gnosticism. every temple shows by its title that it is intended for the honour of the serpent naas as "the moist essence," of the universe, without which "naught at all of existing things, immortal or mortal, animate or inanimate, can hold together. all things are subject to him, and he is good, and has all things in him ... so that he distributes beauty and bloom to all that exist according to each one's nature and peculiarity, as though permeating all." http://en.wikipedia.org/wiki/valentinus_%28gnostic%29 http://en.wikipedia.org/wiki/ophites http://en.wikipedia.org/wiki/phibionites http://en.wikipedia.org/wiki/naassenes dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 81-103 king, c., the future of christian religion in the genetic age issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 92 they gave to the first principle the names first man and son of man, calling him in their hymns adamas: the first man the fundamental being before its differentiation into individuals. the son of man: the same being after it has been individualized into existing things and thus sunk into matter. thus jesus becomes 'the true gate', through whom the perfect man enters. they represented their "man" as androgynous; and hence one of their hymns runs "from thee, father, through thee, mother, the two immortal names." they declared that "the beginning of perfection is the gnosis of man, but the gnosis of god is perfected perfection." the garden of eden, in the naassene system, is the brain, and paradise the human head. the valentinians envisaged a more complex cosmology than orthodox christianity with the pleroma, 'light or fullness', containing a primal bythos, 'the depth', who after long contemplation emanated sexually dyadic aeons, one of which, sophia suffered from curiosity, leading to the creation of the material world by a demiurge identified with the jewish deity. humanity, possessing both spiritual and material nature, achieves redemption through gnosis (personal spiritual knowledge) rather than worship of a saviour. the valentinians held to a sophisticated ethic which allowed those who had achieved gnosis to waive the strict moral prescriptions of traditional christianity. the gnostics also claimed roots that went back to the women present at the embalming. the gnostic teacher marcellina traveled to rome to represent the carpocratian group,' which claimed to have received secret teaching from mary, salome, and martha. tertullian commented: "these heretical women how audacious they are! they have no modesty; they are bold enough to teach, to engage in argument, to enact exorcisms, to undertake cures, and, it may be, even to baptize!" however , according to occhigrosso, tertullian became a turncoat. montanus led an ecstatic movement rather like pentecostalists today. "many of montanus's followers were women, who were allowed to teach, heal, and exorcise demons. their most famous adherent was tertullian of carthage (c. 203), the great early christian theologian, who first attacked the charismatic movement and then joined it." even non-christian writers in the 2nd century were aware that some tradition existed of secret teachings passed down from "salome the disciple", to sects such as the carpocratians. "there are christian sects named after marcellina, harpocratian christians who trace themselves to salome, and some who follow mariamne and others who follow martha, and still others who call themselves marcionites after their leader, marcion." on another tack, the phibionites were said to engage a form of sexual sacramentalism, including smearing of hands with menstrual blood and semen, and consumption of the same as a variant of eucharist and wee even accused by their detractors of consuming the aborted fetuses of sexual religious rituals. marcion, while not strictly a gnostic held to a docetic view. according to him, the god of the old testament, whom he called the demiurge, the creator of the material universe, is a jealous tribal deity of the jews, whose law represents legalistic reciprocal justice and who punishes mankind for its sins through suffering and death. contrastingly, the god that jesus professed is an altogether different being, a universal god of compassion and love who looks upon humanity with benevolence and mercy. marcion held jesus to be the son of the heavenly father but understood the incarnation in a docetic manner, i.e. that jesus' body was only an imitation of a material body. http://en.wikipedia.org/wiki/montanus http://en.wikipedia.org/wiki/carpocratians http://en.wikipedia.org/wiki/marcion http://en.wikipedia.org/wiki/docetic dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 81-103 king, c., the future of christian religion in the genetic age issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 93 by the time of the burying of the nag hammadi texts (robinson 1990), around 340 for the gospel of thomas, the gnostics had been forcibly suppressed by the conservative bishops, leading to the establishment of christian orthodoxy, which survives to the present in the divided catholic and orthodox churches, and their many protestant and evangelical splinter groups. however, gnosticism was to reappear in the middle ages as a 'spiritual contagion' of the crusades, leading to the violent suppression of the cathars, albigenses and others, along with many christian mystics, assumed witches, and the free spirit movement, in a 600 year inquisition as diabolical as the crusades themselves. the kingdom is a long time coming between the death of the 'saviour' and the immortal kingdom was said to be a prophesied turbulent age called the pangs of the messiah. from jesus' own words, this was meant to take no longer than one generation: mark 9:1 "jesus said unto them, 'verily i say unto you, that there be some of them that stand here, which shall not taste of death, till they have seen the kingdom of god come with power." luke 21:23: "but woe unto them that are with child, and to them that give suck, in those days! for there shall be great distress in the land, and wrath upon this people. and they shall fall by the edge of the sword, and shall be led away captive into all nations: and jerusalem shall be trodden down of the gentiles, until the times of the gentiles be fulfilled. and there shall be signs in the sun, and in the moon, and in the stars; and upon the earth distress of nations, with perplexity; the sea and the waves roaring; men's hearts failing them for fear, and for looking after those things which are coming on the earth: for the powers of heaven shall be shaken. and then shall they see the son of man coming in a cloud with power and great glory." luke 21:32 "verily i say unto you, this generation shall not pass away, till all be fulfilled. heaven and earth shall pass away: but my words shall not pass away. and take heed to yourselves, lest at any time your hearts be overcharged with surfeiting, and drunkenness, and cares of this life, and so that day come upon you unawares. for as a snare shall it come on all them that dwell on the face of the whole earth." matt 24:29 "immediately after the tribulation of those days shall the sun be darkened, and the moon shall not give her light, and the stars shall fall from heaven, and the powers of the heavens shall be shaken." however jesus himself claimed not to know when the son of man would arrive: mark 13:32 "but of that day and that hour knoweth no man, no, not the angels which are in heaven, neither the son, but the father. take ye heed, watch and pray: for ye know not when the time is. ... watch ye therefore: for ye know not when the master of the house cometh, at even, or at midnight, or at the cockcrowing, or in the morning: lest coming suddenly he find you sleeping." this uncertainty of the time is echoed in luke 12:40 and matthew 24:44 as christ coming as a thief in the night: http://en.wikipedia.org/wiki/nag_hammadi_library http://en.wikipedia.org/wiki/cathars http://www.dhushara.com/book/consum/gnosh.htm#anchor270857 http://www.dhushara.com/book/death/death2.htm http://www.dhushara.com/book/consum/free.htm dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 81-103 king, c., the future of christian religion in the genetic age issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 94 "and this know, that if the goodman of the house had known what hour the thief would come, he would have watched, and not have suffered his house to be broken through. be ye therefore ready also: for the son of man cometh at an hour when ye think not." the earliest christian writing is 1 thessalonians, dated circa ad 50. in it paul's message is to wait and not slumber, for the son of man shall come at any time hence, in the rapture in the air 1:10: "and to wait for his son from heaven, whom he raised from the dead, even jesus, which delivered us from the wrath to come." 3:13 "... to stablish your hearts ... at the coming of jesus christ with all his saints ... " 4:16 "for the lord himself shall descend from heaven with a shout, with the voice of the archangel, and with the trump of god: and the dead in christ shall rise first: then we which are alive and remain shall be caught up together with them in the clouds, to meet the lord in the air: and so shall we ever be with the lord. wherefore comfort one another with these words. but of the times and the seasons, brethren, ye have no need that i write unto you. for yourselves know perfectly that the day of the lord so cometh as a thief in the night. for when they shall say, peace and safety; then sudden destruction cometh upon them, as travail upon a woman with child; and they shall not escape. ... therefore let us not sleep, as do others; but let us watch and be sober." this immediate urgency of the kingdom remains central to paul's teaching in 55 ad: 1 corinth 7:25 "now concerning virgins i have no commandment of the lord: yet i give my judgment ... that this is good for the present distress, i say, that it is good for a man so to be. ... but this i say, brethren, the time is short: it remaineth, that both they that have wives be as though they had none; and they that weep, as though they wept not; and they that rejoice, as though they rejoiced not; and they that buy, as though they possessed not; and they that use this world, as not abusing it: for the fashion of this world passeth away." however by the time of the final compilation of the new testament, a threatening heresy had arisen because the end and salvation had not occurred and the pseudo-epigraphical second epistle of peter attempts to finesse the problem, explaining that god has delayed the second coming so that more people will have the chance to reject evil and find salvation. it calls on christians to wait patiently for the parousia and to study scripture. despite his fierce opposition to the gnostic 'heresies' irenaeus remained fully committed to the prophecies of revelation and the belief in the end of days. however origen threw a spanner in the works by claiming the eschatological condition was essentially in the mind occurring only in the souls of believers. this fitted well with the hellenistic imagination of "spiritual progress begun in this world and continued in the next". once the christian church became officially adopted with the conversion of constantine in the fourth century, it became "a powerful and prosperous institution functioning to a well-established routine, and the men responsible for governing it had no wish to see christians clinging to out-dated and inappropriate dreams of a new earthly paradise" (cohn 1957 29). early in the fifth century augustine dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 81-103 king, c., the future of christian religion in the genetic age issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 95 propounded in the city of god that revelation was to be understood as a spiritual allegory, and as for the millennium, that had begun with the birth of christianity and was fully realized in the church. this way it becomes possible for the gentile church to have its cake and eat it too, claiming it is a steward guarding the world for the second coming of the lord, while at the same time never having to relinquish control, because christ is the son of god whom no mere mortal can emulate or become a successor to. irascible squabbles and corruption among the church fathers the orthodox history is equally as bizarre as the gnostic. from the time of paul, christianity ceased being a hebrew religion, or the teachings of jesus, and became a hellenistic religion, with strong pagan motifs, gaining an immense popular following from egypt, through ephesus to greece and rome, appealing to the sentiments and superstitions of cultures involved in polytheistic fertility religions and their mythical heros and heroines. jesus became a heroic man-god fusion and mary became a virgin mother. many of the key festivals, including christmas and easter were effectively hijacked from the solstice of mithras and the festival of the european goddess eostre, noted by the venerable bede, whose ovum remains central to this day, although christians claim this comes down to an egg that turned red when magdalen either saw the risen jesus or declared "christ is risen" to the roman emperor. key elements of the communion were derived from the immensely popular worship of isis, whose archetype as the sacred mother was inherited by mary. rather than the covenantal religion of its hebrew origins, christianity became a sacramental religion, in which the bloodthirsty soma and sangre of the heroic demi-god becomes the eucharist the central communion with the risen saviour, who died to save us from our sins, under the filicidal banner 'without the shedding of blood there is no remission from sin'. having successfully repressed the gnostics, the church fathers then began to indulge in angry disagreements among themselves about the exact nature of jesus as a divine son of god, rather than a prophetic innovator, and argue about his exact relationship with god the father and the holy ghost, who now seems to have also become responsible for mary's pregnancy. these became so vehement that a series of conventions were called to settle the matter of jesus' contradictory corporeality and divinity, driving out docetic notions along with the arian and nestorian theology which then became an heretic anathema. docetic notions shared by marcion and some gnostic teachings (and later the quranic view of isa who was deemed to be taken up by al-llah without suffering, leading to all manner of islamic suicide bombings) center around the idea that jesus was a pure spirit and that his physical body and crucifixion were an illusion. to gnostics who saw matter as evil, it was natural that jesus could not have his eternal spirit tainted with matter, however this contradicted the resurrection of the dead and the intrinsic goodness of god's creation in the orthodox view. but even orthodox notions that differed in minor ways from dominant view became cursed. these contrived notions continued to cause a great deal of friction. http://en.wikipedia.org/wiki/mithras http://en.wikipedia.org/wiki/eostre http://en.wikipedia.org/wiki/bede http://en.wikipedia.org/wiki/isis http://en.wikipedia.org/wiki/docetic dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 81-103 king, c., the future of christian religion in the genetic age issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 96 in arianism the concept of christ is that the son of god did not always exist, but was created by and is therefore distinct from god the father, so although arianism embraces the same entities, it is not truly trinitarian. of all the various disagreements within the christian church, the arian controversy has held the greatest force and power of theological and political conflict, with the possible exception of the protestant reformation. by 325, the controversy had become significant enough that the emperor constantine called an assembly of bishops, the first council of nicaea, which condemned arius' doctrine and formulated the original nicene creed of 325. later the first council of constantinople 381, set out in its most unambiguous form the orthodox party line about creation, god, jesus' divinity and mary's role in the piece: "we believe in one god, the father almighty, maker of heaven and earth, and of all things visible and invisible. and in one lord jesus christ, the only-begotten son of god, begotten of the father before all worlds (æons), light of light, very god of very god, begotten, not made, being of one substance with the father; by whom all things were made; who for us men, and for our salvation, came down from heaven, and was incarnate by the holy ghost of the virgin mary, and was made man; he was crucified for us under pontius pilate, and suffered, and was buried, and the third day he rose again, according to the scriptures, and ascended into heaven, and sitteth on the right hand of the father; from thence he shall come again, with glory, to judge the quick and the dead; whose kingdom shall have no end. and in the holy ghost, the lord and giver of life, who proceedeth from the father, who with the father and the son together is worshiped and glorified, who spake by the prophets. in one holy catholic and apostolic church; we acknowledge one baptism for the remission of sins; we look for the resurrection of the dead, and the life of the world to come. amen". this statement leads to many of the central fallacies in christian teaching as core fundamentals, in conflict with and violation of the natural order. it declares that god, rather than being a unity, is a trinity oddly composed of a male father and son and a holy ghost of undefined gender, while mary, despite being jesus' mother, is somehow just a virgin vessel appendage. from the statement, it appears that mary's pregnancy and jesus' humanity results from fertilization, or direct manufacture, 'made' by the holy ghost. jesus is of one substance with abba and so both are inseparably god although jesus was crucified as an incarnate being. jesus is no longer a prophet, or a wise sage, nor even a demi-god, but consubstantial with god himself. it is easy to understand, in the light of genesis, how god the father is deemed to have created heaven and earth and all things visible and invisible even if we now know nature has taken a more subtle and complex route, but the status of jesus being begotten not made stands at the contradictory nub of his mythical divinity. rejecting the docetic notion, it is clearly stated that jesus' was crucified, suffered and was buried as a physical human being would, who then miraculously on the third day of the beborn sickle moon, ascended into heaven, just as in the older astral religions and is now consubstantial with god. nestorius, in a second heretical conflict with cyril of alexandria, tried to find a middle ground between those that emphasized the fact that in christ god had been born as a man and insisted on calling the virgin mary theotokos "god-bearer", and those that rejected that title because god, as an eternal being, could not have been born. nestorius believed that no union between the human and divine were possible. if such a union of human and divine occurred, nestorius believed that christ could not truly be http://en.wikipedia.org/wiki/arianism http://en.wikipedia.org/wiki/nicene_creed http://en.wikipedia.org/wiki/nestorius dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 81-103 king, c., the future of christian religion in the genetic age issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 97 con-substantial with god and con-substantial with us because he would grow, mature, suffer and die (being transient while god is eternal) and also would possess the power of god that would separate him from being equal to humans. the emperor theodosius ii (401–450) was eventually induced to convoke a general church council, sited at ephesus, itself a special seat for the veneration of mary, where the theotokos formula was popular. the emperor and his wife supported nestorius while pope celestine i supported cyril. cyril took charge of the first council of ephesus in 431, opening debate before the long-overdue contingent of eastern bishops from antioch arrived. the council deposed nestorius and declared him a heretic. but while the council was in progress, john i of antioch and the eastern bishops arrived, and were furious to hear that nestorius had already been condemned. they convened their own synod, at which cyril was deposed. both sides then appealed to the emperor. initially the imperial government ordered both nestorius and cyril deposed and exiled. however, cyril was eventually allowed to return after bribing various courtiers. as if to put the final punctuation on these conflicts the latin church added the filoque "who proceedeth from the father and the son". easterners have argued this is a violation of canon vii of the third ecumenical council, since the words were not included in the text by either the council of nicaea or that of constantinople. specifically canon vii states "when these things had been read, the holy synod decreed that it is unlawful for any man to bring forward, or to write, or to compose a different faith as a rival to that established by the holy fathers assembled with the holy ghost in nicæa. but those who shall dare to compose a different faith, or to introduce or offer it to persons desiring to turn to the acknowledgment of the truth, whether from heathenism or from judaism, or from any heresy whatsoever, shall be deposed, if they be bishops or clergymen; bishops from the episcopate and clergymen from the clergy; and if they be laymen, they shall be anathematized." what has become abundantly clear is that the divine nature of jesus is not a fact or even a valid belief but a product of the imagination of irascible church forefathers. it is not a product of jesus' own teachings, or even of those who witnessed his mission, but a later invention, arising from the pauline view of christ based on his born again conversion, then ornamented into other gentile christian new testament accounts, passing through the gnostic controversies to finally be defined in irascible debates between conflicting orthodox clergy, centuries after his death. original sin and natural virtue the final nail in this eschatological coffin is human fallibility. if jesus was actually a human in flesh and blood, at least until the baptism, how does christianity now view the capacity of others to also take up the challenge of primal innocence in our own visionary nature and thereby replenish the root tradition? one cannot leave this arena without mention of augustine, who formulated the doctrine of original sin that has for centuries left humanity with a pathetic fallacy of intrinsically flawed existence. dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 81-103 king, c., the future of christian religion in the genetic age issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 98 augustine (396-430) took up tertullian's idea of concupiscence (or sexual desire), with all the enthusiasm of a 'twice-born'. he had at first rejected the christianity of his childhood and lived for fifteen years with the first of his two concubines, by whom he had a son and from whom he felt a 'sharp and searing pain' when he had to reject her in order, on his mother's insistence to make a proper (but unfulfilled) marriage. he first espoused manichaeism, a form of iranian gnosticism, which saw light and dark locked in permanent conflict, and the soul, a spark of light, seeking to escape the darkness of the physical world. later ambrose introduced him to christian neoplatonism and the writings of st paul, leading to his conversion in 387. adopting the thesis, that adam and eve had fallen from a state of 'original perfection', augustine insisted that adam, through succumbing to temptation, misused the free will given him by his creator, and as a consequential punishment, had acquired a moral debility, concupiscence, which was transmuted through physical heredity to his descendants, who were thus rendered a massa damnata. death had come upon all human beings by their union with adam, and they also shared in the responsibility for the fall; he thereby denied that humanity had a free moral choice. 'for we were all in that one man ... who fell into sin through the woman who was made from him' (haskins 76, jones 222). the monk pelagius also held that the fall had come about through god's gift of free will, but denied that the sin of adam and eve had been passed on to their descendants and thus rejected st paul's pronouncement in his letter to the romans. "wherefore, as by one man sin entered into the world, and death by sin; and so death passed upon all men, for that all have sinned (5:12 )" pelagius argued that man had free-will and was liable for all his deeds, whether good or evil. augustine disputed with pelagius and claimed that humanity had no free will, but was doomed to transgress because original sin was congenital and universal. to allow man freedom to decide minimized the role of god and the power of the church. two councils of bishops in palestine had declared pelagius orthodox but two in africa, led by augustine opposed them and persuaded pope innocent to support them. the next pope first declared pelagius orthodox and then after 'vehement protests from augustine and the africans' excommunicated him. augustine openly courted the emperor's support, using nubian stallions as bribes. the emperor honorees condemned pelagius ordered him fined, expelled from office and exiled along with his supporters. he died soon after (pagels 1988 129-30). augustine's epiphany was tautological: he was powerless to control the penis because free choice is an illusion. augustine tells us that before the fall, adam had been capable of moving his sexual member with as much control as over a finger. but, infected by original sin, the sexual organs functioned with no regard to their owner, in retribution for their sin of disobedience the curse of sexual arousal. in response to augustine's destruction of pelagius, julian of eclanum challenged augustine back. julian responded that 'natural sin' does not exist. no physically transmitted, hereditary condition infects human nature, much less nature in general. in counter to augustine's reading of pain in childbirth he pointed out naturally that [pagan] village women with good childbirth practice had easy deliveries. elaine pagels (1988 134) comments that augustine denies nature ... for he cannot think of the natural world except as a reflection of human desire and will. julian's greatest feat was to correctly realize that the fall is the existential situation that arises when we fall into the sin of separation from the whole and make the world harsh through our selfishness (pagels 136-8). http://en.wikipedia.org/wiki/augustine http://en.wikipedia.org/wiki/tertullian http://en.wikipedia.org/wiki/manichaeism http://en.wikipedia.org/wiki/pelagius http://en.wikipedia.org/wiki/julian_of_eclanum http://en.wikipedia.org/wiki/elaine_pagels http://en.wikipedia.org/wiki/elaine_pagels dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 81-103 king, c., the future of christian religion in the genetic age issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 99 the paradigm of the fall and the tree of life the purpose and function of religion is not to bring about a messianic apocalypse, or to bring about a scorched earth armageddon in a day of judgment, but to help ensure the survival of humanity and the biosphere over cultural and evolutionary epochs. although many religious believers are coming to understand the necessity for the greening of religion, the current direction of the entire judeo-christianislamic tradition remains targeted towards a dangerous utopian fallacy of a totalitarian rule achieved through competitive scorched-earth violence and ultimate threats to the diversity of life. the fall from eden is a message ingrained in our collective stream of consciousness that shows us that the entire religious paradigm has come about through a falling out of sexual relationship between woman and man, accompanying our retreat from intimacy with nature in our gatherer-hunter origins, in which men have blamed women and cursed them in the name of god out of a fear of female sexuality and female reproductive choice. the invocation that we must all suffer death as a consequence, and that women must go in pain of childbirth, obedient to their husbands commands, cements the patriarchal religious paradigm in place, leading to a retreat from unity with nature and loss of communication with the transcendent as well, as acknowledged in the retreat of the shekhinah, or indwelling feminine manifestation of the transcendent on earth in matrimonial concord. in the unveiling, which apocalypse means, we must all needs come face to face with the reunion of woman and man, and feminine and masculine, in the reality of the tree of life as the vital cord connecting past and future, in sustaining the living planet. the tree of life, hidden since the foundation of the world, in the edenic story, is at once the tree of evolution to ourselves as a conscious sentient species and the tree of biological diversity, in which humanity survives and can survive as a species only by mutual coexistence, and interdependence with our sibling life forms, strengthening the capacity of the planet to sustain itself in the uncertain vagaries of an all too chaotic universe. the evolutionary place of humanity, having come to this point, is to act as guardians of the diversity of ongoing life, both to ensure our own survival as a species and to provide for the emergence of new forms of sentient conscious beings. the role of science and technology is to provide vehicles to make this process as inscrutable and successful as it can possibly be. any form of religion in frank conflict with nature and natural survival or with scientific objectivity is thus a tragic fallacy. the mysterium is a complex phenomenon, not an isolate personality we have already seen in the previous posting "evolution is intelligent design" that the genetic algorithmic processes underlying evolution act as a supercomputer which is more versatile and even more powerful than the fastest computers on the planet, and has been proved capable of generating organismic brains and the human conscious brain over evolutionary time scales. the distributed genetic algorithmic process is thus the root creative process capable of generating the designer and their individual personality aka the conscious brain. http://en.wikipedia.org/wiki/shekhinah http://the-messiahs-blog.blogspot.com/2010/12/pathetic-fallacy-of-intelligent-design.html dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 81-103 king, c., the future of christian religion in the genetic age issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 100 just as christians have made a fundamental error in thinking god created life in a process of so called "intelligent design" analogous to human manufacture, so the very concept of god having an individual personality possessing emotions such as anger or jealousy, analogous to a human or animal organism, is fundamentally flawed. neither is it remotely plausible that god somehow resides in the heavens, the galactic core, black holes, dark matter, or the sweeps of intergalactic space, where the forces of nature do not reach their climax fulfillment, involving gravity, electromagnetism and the strong and weak nuclear forces together forming the complex supra-molecular structures of tissues we find in organisms, and ultimately living conscious brains. moreover if we look to what might complement the physical universe, we find it is consciousness itself. all the evidence points to a cosmology in which sentient consciousness complements biological existence. this is the stuff of religious experience, of heaven and hell and of prophetic visions, and this is consistent with what we know about the hard brain-mind problem in science. it is also consistent with the dilemma of free will and may be an essential property for the universe to resolve the superabundance of the infinite number of parallel universes that arise from quantum reality, the way we find the cat alove or dead, rather than both in schrodinger's cat paradox. in such a cosmology conscious sentience is a collective property of the biota. it is not a single personality acting as a creator or designer, which corresponds only to an individual transient organism. neither, as mentioned, does it correspond to other physical phenomena such as the weather, the interior of stars or black holes because the brains of biota are the most complex and sensitive physical systems in the universe and the only ones we know are capable of subjective consciousness. therefore we need to come to understand the process of conscious life in similar terms to the way we understand the collective power of evolution. that is god consciousness is a collective attribute of subjective consciousness manifest in the biota of the universe across space-time, which is manifest individually in each of us, which we can come to know and understand through exploring our own conscious abyss. one can understand this in terms of the universe evolving conscious sentient life, and through the sentient consciousness of the biota, in our case humanity, the universe becoming able to become more deeply aware itself over space-time. in this sense we are the eyes and ears and a thought in the mind of the cosmic becoming. reproductive sex is sacred. social sex is a human right major religions, including christianity, are centrally concerned with life and death and the ongoing process of life in fertility and reproduction. the judeo-christian heritage has taken a patriarchal position, fallaciously accusing women of being the 'devils gateway' due to eve seducing adam into eating the fruit, to be seen and not heard, to live in pain of childbirth in obedience to their husbands. the basis of this is a deep innate male fear of paternity uncertainty, which lies at the core of attempts to treat women as inferior, and the violent penalties such as stoning for adultery which still plague women in the islamic world. dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 81-103 king, c., the future of christian religion in the genetic age issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 101 this is a fundamental and tragic error, because women are the principal bearers of new life, giving birth to live young, lactating, and being pivotal in early child care. in all mammals, which give birth to live young, the investment of the female in parenting is paramount and female reproductive choice is essential to evolution, while the males are investing in competing sexual fertilization sewing wild oats. humans, despite their cultural emergence, stand at an extreme of sexual polarization biologically, in which human females have a massive and risky out front investment in pregnancy an often difficult childbirth due to the large human head size followed by long years of child nurturing in a very slowly maturing highly social species, and so womens' role in the procreative process needs to be respected as sovereign and sacred. christianity, particularly in its catholic form, has created a distorted sexual environment in which mary continues to be touted as a virgin to god, a couple of centuries after the scientific discovery of the human ovum by karl ernst von baer in 1827, although herophilos (335-280 bc) also lays claim to the discovery. priests are required to be celibate men, resulting in rampant sexual abuse, while for lay folk sex is supposed to be only for procreation and not for sensual pleasure, or social bonding, and is denied as a sacred avenue for spiritual and religious discovery. in an era of frank population explosion in which epidemic diseases such as hiv are rampant the catholic church still takes a self-serving and highly corrupt position banning the most basic forms of contraception and disease protection, on the fallacious basis that sex should be procreative, or abstinence should prevail, even though this has always been a transparent ploy for religious domination through a demographic flood on the part of christians and muslims alike. sexual pleasure and sexual relationship is the glue and foundation of human culture and family life,sine qua non. it is the central social bonding activity in humans essential for keeping the peace. reproductive sexuality is the gateway of new life and consciousness, which humanity and religious and secular society and the diversity of life depend on for our very existence. it is a complete fallacy to infer that sex, even if some of its effects on society are chaotic and stress our emotions of jealousy and fidelity, is evil, or degenerate. the dance of tantra shows us that in a fundamental sense, the entire universe is a sexual union between consciousness and the material universe. nevertheless, even though some 99.9% of sexual engagement is social and only 0.1% actually results in pregnancy, reproductive sex and sexual fertility between a woman and a man. both human society and christian religion is going through a period of reassessing sexual relationship and the rights of same sex couples to engage fully in the social process in terms of civil unions, surrogacy and adoption and taking clerical religions positions. to function as guardians of future generations of humanity, it is essential that we understand the primary and sacred role of reproductive sexuality between a woman and a man as the foundation of the passage of the generations, while having an open view of the right of individuals to chose their sexual partners as they see fit. we thus cannot simply equate social sex with reproductive sex, or union between a woman and a man with same sex unions without reducing the life force from which we all came to an exercise in sensual gratification. http://en.wikipedia.org/wiki/herophilos dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 81-103 king, c., the future of christian religion in the genetic age issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 102 future synopsis we have found that orthodox christianity has dealt us a double edged sword, both deifying jesus without valid cause and crippling humanity with the doctrine of original sin, leaving us no option but to put our faith in god, depend on the teachings of the church and believe in jesus as lord for our salvation, without which we would be helpless like little children. the messianic path, by contrast, is one of coming of age as an adult, taking personal responsibility both for one's incarnation and for the fate of the world in which we live, in cherishing and replenishing the life process. jesus, as the divine son of god, is a pagan hellenistic contrivance, which is neither part of his own teachings, nor is it part of the founding tradition of his followers, but rather an invention of pauline gentile christianity. the concept of the trinity is a corrupt notion in frank violation of any plausible cosmology, which achieved dominance through bribery by cyril of alexandria. likewise the concept of human fallibility in original sin is a corruption of nature, with no genetic basis, again foisted on the tradition by augustine's bribery. if we are going to bring this tradition into any sort of correspondence with reality, in a form which is going have any hope of being a beneficial influence on our planetary future, the tables are going to have to be turned, and things are going to have to change from the bottom to the top. as we enter the genetic age, where science and technology are providing more and more avenues to play god with our own futures, we need to develop social, ethical, moral and spiritual traditions which are up to the challenge of dealing with the unknown future in a way which preserves human and planetary viability and doesn't subject us to a futile endgame or an apocalyptic armageddon through our own lack of sensitivity and foresight. the western tradition of gentile christianity can only play a part in this future through a revolution of outlook at the most fundamental level. three key principles are: 1. sensitivity to nature and scientific knowledge any valid spiritual social movement needs to be sensitive to checking its assumptions against all the tests of nature and physical validity. the standards are thus even higher and more stringent than for scientific discovery, because religion purports not just to discover the nature of reality but to guide humanity. religion cannot afford to confront nature, or attempt to overturn scientific discovery through literal interpretations of ancient scripture as fact. denying evolution as a basis for life's diversity and the emergence of humanity is a tragic error, as is insisting the sabbatical creation is an historical fact, rather than a beautiful metaphorical and mythological account. 2. a democratic living tradition manifest through the personal experience of the participants any valid spiritual social movement needs to be a product of the evolving conscious experiences and wisdom of each generation in which it has an influence, with a view to safeguarding future generations. no pre-existing religious doctrine can validly be imposed on any generation. religious viewpoints need to be a product of the people alive at the time, and not an imposed doctrine based on past messiahs, or dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 81-103 king, c., the future of christian religion in the genetic age issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 103 church fathers. spiritual experience needs to be first hand, through inner meditation, or conveyed directly through the wisdom of a living person's experience, or the veracity of other people's written experiences and accounts, rather than through literal interpretations of scripture, prescriptive rules and taboos, or requiring affirmative belief or unquestioning faith in a past saviour or lord. the first step is bringing jesus down from the cross so that we all can live in freedom from bondage. the natural destiny of sacramental religion is in the use of psychotropic sibling species to facilitate spiritual consciousness, rather than a cannibalistic feast of flesh and blood. 3. respect for the feminine and living fertility the ongoing process of sexual procreation is fundamental to the future of humanity and of the diversity of life sustaining the planet. in this, women play the key role, in providing the continuity of life through pregnancy, live birth, lactation and infant child care. the women in each generation need to retain the sovereignty be able to make the best reproductive choices possible for the children they will bear, without fear of religious threats or penalties devised by males out of their fear of paternity uncertainty, so that both sexes can look to the long term future of the diversity of life, to ensure their offsprings' offspring will also be able to survive. references cohn, norman 1957 the pursuit of the millenium , paladin, granada, london. fox, robin lane 1992 the unauthorized version, alfred a. knopf, ny. glueck, nelson 1966 deities and dolphins, cassel, london. graves r., podro j. 1953 the nazarene gospel restored, cassel, london graves r., podro j. 1957 jesus in rome, cassel & co., london haskins, susan 1993 mary magdalen myth and metaphor, harper collins, london jones, steve 1996 in the blood: god, genes and destiny, harper-collns, london. pagels, elaine 1988 adam eve and the serpent, random house, n.y. pagels, elaine 1979 the gnostic gospels, vintage books pagels, elaine 1995 the origin of satan, vintage books pagels, elaine 2003 beyond belief: the secret gospel of thomas, vintage books pagels, elaine and king karen 2007 reading judas: the gospel of judas and the shaping of christianity, viking press ranke-heinmann, uta 1992 putting away childish things, harper, san francisco robinson, james ed. 1990 the nag hammadi library, harper, s.f. schonfield, hugh 1965 the passover plot : new light on the history of jesus, hutchinson, london. wilson, ian 1996 jesus the evidence, weddenfield and nicholson. login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x dna decipher journal | july 2017 | volume 7 | issue 1 | pp. 38-59 vary, a., origin & modulation of dna life cycles issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 38 article origin & modulation of dna life cycles alex vary * abstract we discuss the origin and modification of dna macromolecules and the negentropic generation and evolution of intelligent life and human consciousness. this paper deals with the conjectured transcendent origin, structure, and encoding of the dna molecule which produced the diversity of species which we observe and study and the instrumentality of consciousness that observes and studies it. keywords: intelligent life, dna encoding, consciousness, cosmos, mesostratum, physiostratum. introduction biologists often describe dna as a primordial high technology structure that contains over a hundred trillion times more information by volume than the most advanced digital information storage device. this self-duplicating, information-storing molecule only ten atoms wide constitutes a form of ultimate technology as yet unmatched by quantum computer science. the dna double helix surpasses richard feynman’s potential encyclopedic information content in a grain of sand in its ability to not only store information but to transmit and transfer it remarkably accurately generation after generation. in his classic lecture there's plenty of room at the bottom, feynman notes, “all this information whether we have brown eyes, or whether we think at all, or that in the embryo the jawbone should first develop with a little hole in the side so that later a nerve can grow through it all this information is contained in a very tiny fraction of the cell in the form of long-chain dna molecules in which approximately 50 atoms are used for one bit of information about the cell.” the dna that spawned and enabled the humanoid species dates back tens of millions of years. that same dna consistently gave astonishing intellectual thinking capacity to humans. evidence shows that the cave man, the neanderthal, possessed intelligence that rivals modern humans. in their primitive, emergent situation, they had no means nor incentive for making microchip-based computers. but they produced ingenious art and invented tools for survival with adroit use of the resources available to them. from the bronze age onward, the technological infrastructure and capabilities of contemporary ‘computing machines’ began to compound exponentially. among ancient computing machines we may include the stonehenge and the egyptian, aztec and mayan pyramids. all humans alive today harbor the same primordial dna and genes which promise continued evolution. it will be argued that the primordial dna and all current modulations and versions of it arose as the result of an synergistic iterative design process governed by a ubiquitous * correspondence: alex vary, phd, retired nasa scientist & independent researcher. email: axelvary@wowway.com dna decipher journal | july 2017 | volume 7 | issue 1 | pp. 38-59 vary, a., origin & modulation of dna life cycles issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 39 universal consciousness which is shared by each individual higher consciousness. in the process of writing the origin of species charles darwin of course had no access to modern genetic science, if he had, he almost certainly would have endeavored to focus on and entitle his monumental work the origin of dna with the subtitle the modification thereof by natural selection and evolutionary biology. this paper deals with the conjectured transcendent origin, structure, and encoding of the dna molecule which produced the diversity of species which we observe and study and which produced the instrumentality of consciousness that observes and studies it. tutorial and recapitulation replication mechanism dna (deoxyribonucleic acid) is a long macromolecule that transfers genetic characteristics in all life forms. it consists of two helical strands coiled around each other. dna is composed of alternating phosphate and deoxyribose units connected by ladder-like rungs composed of purine and pyrimidine bases. the genetic information of dna is encoded in a sequence of bases and is transcribed as the strands unwind and replicate. dna typically includes three billion rungs or bits of a digital code. the rungs that comprise a dna genetic alphabet engage four nitrogenous bases: adenine, thymine, guanine, and cytosine. sugar molecules (ribose or deoxyribose) bind the chemical alphabet while phosphate molecules bind the sugar molecules together to form the double helix. the human genetic message contains a total of 6 billion base pairs, or 12 billion ‘letters’. the dna filaments contained in the nucleus of a human cell wrap around each other several hundred million times and can be stretched out two meters. rna (ribonucleic acid) is a single-stranded molecule transcribed from dna within the cell nucleus. the rna strand is a linear sequence of nucleotide bases that is complementary to the dna strand from which it is transcribed. a nucleotide is any group of molecules linked together as building blocks of dna and rna. messenger rna is a single-stranded molecule of rna that is synthesized in the cell nucleus from a dna template. messenger rna enters the cytoplasm (the substance between the cell nucleus and membrane) where its ‘genetic code’ specifies the amino acid sequence for protein synthesis. the genetic code provides biochemical instructions that translate the particular genetic information that is present. this results in a linear sequence of nucleotides in the messenger rna producing a specific linear sequence of amino acids for the synthesis of particular proteins. then, single enzyme proteins or complexes of two or more proteins operate autonomously as `molecular machines' without immediate reference to the surroundings. these complex enzyme proteins assure that dna and rna function systematically and cooperatively. proteins usually contain amino acid chains between 100 to 500 in length. there are 20 amino acids that are assembled into a variety of over 100,000 functional proteins in humans. the genetic code the recursively complex dna code structure which is common to all species is designed to dna decipher journal | july 2017 | volume 7 | issue 1 | pp. 38-59 vary, a., origin & modulation of dna life cycles issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 40 contain redundancies and similarities. some of these express themselves as ‘vestigial organs’ presumably left over from previous stages of evolution. such organs may appear as superfluous floating hind limbs in whales or the tailbone (coccyx) in humans. these are simply by-products of iterative engineering design protocols. in a similar manner, human designers borrow ideas that have merit in one situation and use them in other situations. these borrowings may be discarded in the final design or may simply become ‘vestigial junk’ or be used in a different way in a successive construction code. apparently, the coccyx was retained in the genetic design code and made part of the human skeletal frame as an important point of muscle attachment required for the distinctive human upright posture the genetic code exhibits the properties of a digital code that derives its significance from prescribed and consistent definitions. a digital language requires context, that is, a lexicon of conventions that are external to the code itself. an effective digital code also demands careful expert design. according to dembski and colson in the design revolution, dna is a dynamic structure that exhibits an underlying design. the nucleotide base pairs are continually vibrating, forming and closing gaps throughout the dna at femtosecond intervals. evidence of design may be inferred because the system remains stable as ‘repair’ enzymes find and correct flaws along vast stretches of the dna. a deliberate redundancy in dna design provides alternative codes that improve its error-correction capabilities. these codes are stored in an integral master plan and are duplicated by a transcription machinery into the working copy rna which is then translated into the instructions from which the amino acids are converted into the necessary protein and enzymes. the transcription enzymes read only the parts of the dna text that code for the construction of proteins and enzymes. these passages are genes which are estimated to represent roughly 3 percent of the human genome. the remaining 97 percent are not read their function is unknown. spread out among the non-coding parts of the text are long repeated 3 to 4 letter sequences, including palindromes ­ that can be read in either direction ­ with no apparent meaning. this apparent gibberish, which constitutes the overwhelming portion the genome is called junk dna. this junk often consists of tens of thousands of repetitious passages. among them is a 300-letter sequence that is repeated a half a million times. these sequences make up a full third of the genome. their meaning is unknown and this has compelled genetic biologists to admit that the vast majority of dna in our bodies does things that we do not presently understand. biologist are not yet privy to the ‘external’ information, plan or lexicon needed to interpret the genetic code woven into the dna molecule. despite the intense efforts being expended in the human genome project to discover the roles of junk dna, the cause of individual differences and many other genetic code-related questions remain unanswered. the creation of these self-replicating entities indicates intricate original programming of dna and goal oriented, deliberate and innovative design concepts. minor experimental and evolutionary tweaking and upgrading do not compare with the landmark appearance of the fundamental dna code that signaled the arrival of the human species endowed with the capacity for intelligent thought. it is altogether reasonable that after 'jump starting' living organisms including microbes and plants the basic dna replication machine was embedded with codes for adaptive self-correction and enhancement: evolutionary tweaking. dna decipher journal | july 2017 | volume 7 | issue 1 | pp. 38-59 vary, a., origin & modulation of dna life cycles issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 41 surely, as the human genome project begins answering these questions, the next objective should be to code and construct a new version of dna. as science discovers more about genomic structure, we will want to re-engineer human dna, perhaps even the dna of other biological organisms. some re-engineering may take the form of cosmetic adjustments, health enhancement, or be dedicated to producing a 'super species' perhaps an intellectually superior species. but all this is may be a form of 'patching' with an awakening knowledge the 'source code' that originated human dna. information transmission and communication the conventional view is that dna information is transmitted in the form of ‘sequential information’ ­ replicated chemokinetically when the cell divides. the information is transcribed as messenger rna and ‘expressed’ by genes. after the messenger rna information is edited and processed, it migrates from the nucleus to the cytoplasm where it is ‘read’ by a specific ribosome that translates it into protein. be the organism a bacteria, a carrot, or a human the dna comprising it does not vary in overall form from one species to another; only the order of words and sentences of the sequential information are modified. it is possible to extract the dna sequence in the human genome containing the instructions for making insulin and splice it into the dna of a bacterium, which will then produce insulin similar to that normally excreted by the human pancreas. ribosome are like cellular machines that assemble the proteins inside the bacterium. they understand the same language as the ribosomes inside human pancreatic cells and use the same 20 amino acids as building blocks. there appears to be something that is beyond purely chemokinetic transfer of information represented by a sequence of chemical words and sentences of the dna molecule. the molecule exhibits the structural properties of an antenna that sends and receives bursts of electromagnetic signals. it is now established that dna emits photons and also responds to photons, it is an information antenna that communicates globally with signals so weak that only recently has equipment emerged that is capable to detect those signals. according to the hypothesis of jeremy narby in the cosmic serpent, there is a link between dna-emitted photons and transmission of genetic information. in general, bio-photon emission is a 'cellular language' a form of communication within cells, among cell colonies and their host organisms. cells and their dna apparently globally broadcast tiny electromagnetic waves wirelessly trans-neuron to direct their own internal reactions as well as to communicate between and among themselves. jeremy narby advances the notion of the role of dna in global information storage and transfer by noting that, in a mere handful of soil, there may be approximately ten billion bacteria and one million fungi. narby writes, “this means that there is more order, and information, in a handful of earth than there is on the surfaces of all the other known planets combined. . . . the information contained in dna makes the difference between life and inert matter. . . . the earth is surrounded by a layer of dna-based life that made the atmosphere breathable and created the ozone layer, which protects our genetic matter against ultraviolet and mutagenic rays . . . the planet is wired dna decipher journal | july 2017 | volume 7 | issue 1 | pp. 38-59 vary, a., origin & modulation of dna life cycles issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 42 with life deep into its crust . . .” accordingly, dna “. . . . proves by its very existence the fundamental unity of life.” . . . and of consciousness [1]. dna and consciousness emergence stuart hameroff and roger penrose in toward a science of consciousness cite as essential for consciousness the cytoskeletal microtubules and related structures within each of the brain's neurons. cytoskeletal structures are clearly the expressions of specific genes that reside in dna. there are particular characteristics of microtubules make them suitable for quantum effects to which hameroff and penrose attribute the emergence of consciousness. these quantum effects depend upon the neuron’s crystal-like lattice structure, hollow inner core, organization of cell function, and structural capacity for information processing. it is inescapable that dna is much more than a chemokinetic mechanism for replication and repair and maintenance of the body and its cells. dna obviously provides for cell differentiation and elaboration into various organs. less obvious, but essential functions of dna are its provisions for communication and interpretation of information not only for survival and communal behavior but also for consciousness which relies heavily upon very special design aspects and expressions of dna genetic codes. in what is thought? eric baum argues that the mind is programmed by dna. he proposes a computational explanation of consciousness. baum maintains that the complexity of mind is simply the outcome of evolution and that to understand the mind we need to understand the evolutionary process that produced it in computational terms. he assumes that evolution ‘discovered’ corresponding ‘subroutines’ and ‘shortcuts’ to speed up its processes and to construct creatures whose survival depends on quickly making right choices. baum concludes that the structure and nature of thought, meaning, sensation, and consciousness emerge naturally from the evolutionary processes. baum ignores evidence that the evolutionary processes appear to have originated spontaneously directed by a focused negentropic phenomenon, as proposed by erwin schrödinger in his classic what is life? baum is undoubtedly right contending that evolution of the brain took place via the ‘organic’ evolution of dna which arguably came after the origination of dna from outside the perimeter of organic evolution. the overall evolutionary process contended by baum should be seen as a consciously-contemplated design iteration and refinement to adapt a primordial dna to earthly chemophysical environments. instead, baum invokes the unprovable notion that all the intricate elements of the dna computer code arose by chance combined with fortuitous coincidences. baum does allow for a vast computer power and resources implied by the emergence of human intelligence and thought. we are tempted to classify eric baum among those who believe that souls are software. but like most evolutionists baum refuses to allow for an outside transcendent originating event or concept. dna has such a conspicuous abundance of symbiotic simultaneous intertwined attributes that it is virtually impossible not to assign its origin and programming to agents that transcend the material world indeed, to spiritual designers that preceded humanity and operate astride the material world. dna decipher journal | july 2017 | volume 7 | issue 1 | pp. 38-59 vary, a., origin & modulation of dna life cycles issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 43 it seems self-evident that the original concept and creation of the self-replicating and intricate programming of dna denotes a deliberate and innovative ‘external’ design process. this is strengthened by the amazingly efficient way that dna structures the neural attributes of cells and organisms react and respond ‘intelligently’ to their environments. more amazing is cell to cell global, non-local, trans-neuron communication. beyond that are the globally diffuse displays of self-awareness and consciousness certainly those displayed by higher organisms. symbiotic tangled entelechy the improbability of abiogenesis and evolution of higher life forms has been compared to the improbability of a tornado sweeping through a junkyard and assembling an airplane. from the modern evolutionary standpoint, while the sudden appearance of cellular and higher life forms are improbable, evolution proceeds nevertheless, slowly, stepwise, stochastically. viewing the human body as a communal super-colony consisting of trillions of differentiated cells moves our attention to an exploration of symbiosis. some symbiotic relationships are obligate in that both symbionts entirely depend on each other for survival. others are facultative, meaning that they can but do not have to live with the other organism. symbiotic relationships include those associations in which one organism lives on another, or where one partner lives inside the other (such as lactobacilli bacteria in humans). strange symbiosis loops prevail wherever life appears, down to the level of individual cells which cannot exist viably without the presence of symbiosis among enzymes, amino acids, cell membranes, and nuclei. one of the most improbable symbiosis loops is described by douglas hofstadter in gödel, escher, bach: an eternal golden braid. hofstadter describes a paradox which he entitles ‘which came first-the ribosome or the protein?’ he writes: “ribosomes are composed of two types of things: (1) various kinds of proteins, and (2) a kind of rna, called ribosomal rna (rrna). in order for a ribosome to be made, certain kinds of proteins must be present, and rrna must be present. for proteins to be present, ribosomes must be there to make them.” hofstadter asks, "which comes first, the ribosome or the protein? which makes which? of course there is no answer because one always traces things back to previous members of the same class, just as with the chicken-and-the-egg question, until everything vanishes over the horizon of time." recapitulation conjecture available evidence indicates that the dna/rna alphabet and its associated codes have remained essentially unchanged throughout the history of the earth. the probability of the specificity and precision having arisen and evolved randomly or by chance is nil. there is accumulating support for declaring that the emergence of life and thinking beings represent a process of information transfer from a universal consciousness to the material world, as discussed later. the result is human intelligence and higher consciousness that transcends material neural systems and the pervasive domain of the dna antennae. dna decipher journal | july 2017 | volume 7 | issue 1 | pp. 38-59 vary, a., origin & modulation of dna life cycles issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 44 we discover an improbably entangled entelechy when we ask: which came first, ‘the ribosome or the protein?’ or ask ‘which came first, the chicken or the egg?’ in the grand scheme of things they are one and the same: an improbable unity. the egg is the chicken, the chicken is the egg, the one is nothing without the other. the egg alone in the universe is meaningless. the yolk without the shell is meaningless. the embryo without the yolk is meaningless. it is senseless for eggs or chickens to exist separately and apart in the cosmos. entelechy as represented by egg/chicken/egg loop is a realization of a potentiality that resides in the mesostratum energetic hyperspace. ribosome-protein and chicken-egg potentiality loops and other loops ostensibly exist simultaneously. we conjecture that our material reality is but a product, a projection, a sequential ontogenetic realization of primordial preordained potentiality loops. the hypothesis illustrated in figure 1 is that the entire life-cycle of the butterfly from egg to caterpillar to chrysalis to butterfly to egg exists holographically, simultaneously, instantaneously in the mesostratum, complete in every essential and minute biological detail. of course, all mesostratum butterfly specifications are encoded in butterfly dna which unravels in the physiostratum as the butterfly is realized stage by stage, sequentially. we see each butterfly illustrated in figure 1 at one specific stage of its life cycle. whether we speak of butterflies, roses, humans, planets, or stars it is apparent that all undergo cycles that are somehow patterned and that each stage of the respective cycle is orchestrated down to the finest detail and mathematical form. we deduce that these implicit designs, patterns, forms, and governing laws exist transcendently, apart from the physiostratum. we argue that these designs reside in the mesostratum which also provides the energetic instrumentalities enabling a primordial consciousness to create, project, and interweave the objective cyclic realities of the physiostratum. the physiostratum putatively provides the venue for sequential ontogenetic realization. accordingly, we contemplate the superstratum of pure thought, as depicted in figure 1 and conjecture that the cosmos (the physiostratum) materialized as a subset of the universe (the dna decipher journal | july 2017 | volume 7 | issue 1 | pp. 38-59 vary, a., origin & modulation of dna life cycles issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 45 superstratum) as a projection of pure thought a supernal consciousness which ideated and assembled and perhaps continues to assemble the chaotic milieu of the cosmos endeavoring to put things into spatiotemporal order extracting, modifying, evolving an objective reality using the energetic signal modalities of an energetic mesostratum. it is a negentropic scenario of a ‘work in progress’ of a supernal consciousness that continues to evolve and reinvent itself. the material realization of a potentiality depicted in figure 1 suggests that a holographic template pre-exists the realization and programming of dna accompanied by a feedback loop by means of which genetic modifications appropriate for diverse species are accomplished. we argue that the genetic modifications are instructed by intellectual entities, namely, memes. in the selfish gene, dawkins urges us to take the idea of meme evolution literally. memes are replicating ideas. not just simple ideas, but quite complex templates that form themselves into distinct units that influence and engender genetic evolution. physiologically, they produce alleles, or alternative genes, that compete with existing genes and when successful, cause hereditary variations. the original genes will attempt to repudiate these newcomers, but after many replications, successful alleles may prevail in a new branch of species evolution. we suggest that memes are informational signals or waveforms in the energetic mesostratum acting as communication media that influence epigenetic modifications and evolution. these speculations and conjectures about life cycles templates and their material realizations still do not explain the origin of dna the ‘backbone’ of life, its replication, and consciousness. our explanation of the origin of the dna molecule invokes the idea of a superstratum~mesostratum~physiostratum triad and a supernal consciousness which incorporates astral agents that not only create and program the dna molecule but the cosmos and planetary habitats and environments suitable for the emergence of life and intelligent beings. superstratum~mesostratum~physiostratum triad mind loop & soul-spirit-body triad it is clear that any discussion of supernal consciousness involves the idea of a mind which transcends material embodiment. the mind as we conceive it spans three strata: (1) the superstratum (the transcendent domain of pure thought), (2) the mesostratum (the mediating domain of information, signals, energetic zpf fields), and (3) the physiostratum (the domain of spacetime and objective material reality) [1]. in this context, the mind is envisioned as extending from the superstratum continuum to the physiostratum discontinuum via signals through the energetic mesostratum interface, as depicted in figure 2. dna decipher journal | july 2017 | volume 7 | issue 1 | pp. 38-59 vary, a., origin & modulation of dna life cycles issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 46 in figure 2 we adopt the notion that each soul-like astral is the superstratum focus of a conscious entity. the dna as represented by the brain/body is the physiostratum focus of a transcendent consciousness. the mind is defined essentially as a loop that unites the astral entity and dna foci via a mesostratum download/upload signal cycle. the challenge is to deduce how astrals employ the zpf (zero point field) and its energetic signal content and the mind upload-download loop to originate dna and consequent biological entities which possess consciousness and intelligence. the physiostratum discontinuum is conceptually a subset of the superstratum continuum. elements of the superstratum and physiostratum commingle in the mesostratum interface. we are aware of the transcendent superstratum and mesostratum indirectly by their ubiquitous influence on the material domain primarily at the quantum level and by their influence on our consciousness and our experience of adjacent realities. adjacent realities the wave function and associated spin, charge, mass describe and define subatomic entities while their particulate nature defines their physical location in spacetime. this may be construed as an imagined wave-particle duality or a pairing of two separate sequential realities. conversely, we perceive adjacent realities, concurrent transcendent and material realities: the wave function is a mesostratum transcendent aspect while the particle is a physiostratum material aspect of a singular entity, for example, an electron or photon. these adjacent realities are combined and form the mind loop which orchestrates our conscious awareness of our tangible particulate objective reality and adjacent wave function signal continuum. retina-consciousness dna education the retina-consciousness relation is inherent to dna structure and coding. consider the retina, a biological photon-detector screen, which undergoes about a trillion photon impingements per square centimeter per second. the neural network associated with the retina processes the chaos of dna decipher journal | july 2017 | volume 7 | issue 1 | pp. 38-59 vary, a., origin & modulation of dna life cycles issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 47 retina-impinging photons and extracts and refreshes information about 'what is out there' an image of the world. but, we do not ‘see’ the constantly refreshed flat image on the retina which is made pixel by pixel, indeed quantum-by-quantum. we ‘see’ what is out there the result of neural processing of the flood of incoming signals. the overall signal information content consists of more than colors in the scene. in concert, the trillions of photons convey information about textures, shapes, topology, inter-relationships, etc. among the emitters of the photons as they reach the retina producing the epiphenomenon of ‘seeing’ the scene ‘out there’ in space in the venue of objective reality. this illustrates how the mind loop and consciousness process the signals supplied by the retina/optic/neural system. consciousness, using information assembled by the mind, orchestrates the chaos of photons from the flat retinal image and extracts and refreshes information about what the image means portrays it as an image of three-dimensional reality. our higher consciousness tells us that objective reality exists ‘out there’ and indeed persists even when unobserved and that our body/brain is part of the reality ‘out there’. this leads to the concept of the mind loop together with consciousness as an orchestrator of informational signals, where the confluence of signal parcels instantiate a physical neural process where an attractor is configured so that everything will be topographically coherent. among the essential features of the mind loop are its metaphysical and contemplative attributes which transcend the neural network and constitute the epiphenomena of consciousness. we consider the ‘mind loop’ as an upload-download modality which is facilitated and sustained by the mesostratum and the energetic zpf subset of the mesostratum. what is illustrated is that the conscious mind constructs and sees an objective reality beyond the flat retinal image we do not see the flat image on the retina we see the objective, indeed 4-dimensional, reality beyond the retina via signals impinging on it. we conjecture that our perception of objective reality informs and influences the dna core of our being that environmental signals select, modify, and regulate gene activity and that our genes are constantly being remodeled in response to life experience. we conclude that our life experience leads to epigenetic shaping and reshaping. we conjecture that our body, neural network, and indeed our dna originated, evolved, and continues to evolve as the tangible reality revealed by our senses that dna is educated by interplay between a higher consciousness and the material world. epigenetic lucy the developing science of epigenetics is revolutionizing understanding of the link between mind and matter and profound effects on our personal lives and the collective life of our species. epigenetics reveals that our genes are constantly being remodeled in response to the objective reality in which we are immersed. at the most elemental level, the cell membrane interacts with its environment and therefore controls the cell’s response it is in a sense the cell’s ‘brain’. we suggest that the cell membrane like a computer chip is programmable and that the programmer is a higher consciousness which transcends the cell. the cell ‘membrain’ exhibits a behavior and epigenetic activity comparable to the information uploaded-download to-from the physical entity (the cell, the neurons/body/brain) via a virtual mind loop. dna decipher journal | july 2017 | volume 7 | issue 1 | pp. 38-59 vary, a., origin & modulation of dna life cycles issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 48 in november 1974, the bones of a prehistoric humanoid were discovered on the slope of a desert channel at hadar located in ethiopia. the small skeleton was a remarkable discovery and a significant link in the search for human ancestors. the discoverer donald c. johanson and his coworkers named the hominid lucy australopithecus afarensis (after the beatles’ song ‘lucy in the sky with diamonds’). lucy was a tiny-brained individual, a little more than 1 meter tall. lucy walked erect on short stubby legs three million years ago. beyond lucy’s epoch of human development, epigenesis prompted brain development, an upright walking stance, and increased hand dexterity through tool use and the need to effectively manipulate the environment. today, many of lucy’s decedents not only walk upright but are tall, slender and have long attractive legs. they stride confidently on stiletto high heel shoes. they still have fairly large vestigial pelvic bones but these are devolving remnants from the past. evidently, we may conclude that lucy and her progeny took a good look at the prevailing reality and via a higher consciousness and associated mind-loop activities induced genetic changes which engendered radical dna reprogramming leading to a more idyllic body. attractors, akasha, and astrals consciousness materialization cycle the tutorial argues that primordial dna and all current modulations and modifications of it arose as the result of a synergistic iterative design process. the dna structure demands the synergistic preexistence and availability of four nitrogenous bases: adenine, thymine, guanine, and cytosine. to form the dna double helix sugar molecules that bind the bases must also be present along with phosphate molecules to bind the sugar molecules. for a ribosome to be made, certain kinds of proteins must be present, and rrna must be present. for proteins to be present, ribosomes must be there to make them. specific dna structural components need to be fabricated abundantly and exist in close proximity prior to assembly of the dna macromolecule and cellular matter containing it. the design and engineering of primordial dna also assumes the preexistence of a life-friendly surroundings and clement climate. the cycle depicted in figure 3 incorporates the notion that our bodies and everything around us did not simply pop out of the energetic zpf substratum but are constructs of a universal consciousness. the process may be seen as a work in progress wherein terrestrial observations are returned for evaluation in an iterative design process. the cycle is derived from the idea that the universal consciousness cannot remain idle and unproductive but needs and makes tangible resources which implement the keppler effect: use of physical stimuli to trigger the formation of new attractors or structural modules. eventually, the cycle may result in the epigenetic re-engineering of various dna structures, substructures, and myriads of genetic components. dna decipher journal | july 2017 | volume 7 | issue 1 | pp. 38-59 vary, a., origin & modulation of dna life cycles issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 49 in figure 3 the brain/mind functions as a detector that filters external electromagnetic stimuli, as when seeing or sensing physical surroundings. for example, the activity pattern on the retina, reproduces the frequency and intensity patterns of the stimuli. these are translated into nerve impulses that result in a characteristic stimulation of the cortex. this stimulation induces phase transitions where disorder becomes order and culminates in an attractor, a highly synchronized and coherent neural activity pattern, the formation and stabilization of which, according to keppler, is orchestrated by the zpf and transmitted to one’s higher consciousness and which is ultimately shared with a universal consciousness. the interplay between the oscillating neural assemblies and the relevant zpf modes results in a zpf information states (a pattern of phase-locked zpf modes) which are comprehended and realized by consciousness. in summary, a physical stimulus triggers a complicated translation process (a cascade of transformations) until it gains access to the fundamental level of reality, via the zpf. keppler elaborates on the zpf substratum which he considers the primary reality from which all the material manifestations emerge as our tangible objective reality. keppler zpf attractors stochastic electrodynamic (sed) theory incorporates the concept that the universal zpf substratum is a fundamental, all-pervasive stochastic energetic field which may be viewed as an ocean of energy that permeates the mesostratum. joachim keppler argues that stochastic modifications of the zpf produce local states of order in the inherently chaotic disordered zpf [2]. the quiescent zpf exhibits no correlations between stochastic individual modes, while the locally coherent zpf exhibits a phase-locked coupling of certain sets of modes. such a phase-locking occurs whenever a mesostratum dynamic system reaches a coherent stable state an attractor whenever a system is in dynamic equilibrium with the zpf. the set of correlated modes depends on the resonance frequencies of the given system, so that dna decipher journal | july 2017 | volume 7 | issue 1 | pp. 38-59 vary, a., origin & modulation of dna life cycles issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 50 the generated modifications (signals or wavefunctions) in the zpf are system-specific information states peculiar to the physiostratum spacetime voxel states [3]. accordingly, specific physiostratum spacetime voxels or groups of voxels (quantumthing gravitational agglomerations) undergo periodic transitions from a disordered chaotic to ordered phase induced by appropriate stimuli such as mathematical objects, strings, wave functions, etc. in the mesostratum zpf substratum. in the ordered phase, the dynamics of loci in the physiostratum plenum assembly become attractors, i.e., the dynamics of an assembly reflects a state of synchronized activity and high coherence. such patterns manifest as quantumthings and quantumthing agglomerations. in the background locus, due to the interaction with the zpf, these activity patterns coalesce to populate the physiostratum milieu. the zpf substrate is therefore an essential component of the mesostratum and fundamental to generating the content of the cosmos. akashic field theory ervin lászló in science and the akashic field posits the akashic field, a field of information, as the substratum of the cosmos. we posit that the akasha resides in the mesostratum the fundamental energy and information-carrying field which includes the zpf and informs not just the universal consciousness (as depicted in figure 2) but our higher consciousness of the past and present. we and lászló believe that the akashic informational field explains why our cosmos appears to be fine-tuned so as to form habitable worlds hospitable to dna and conscious life forms and why dna evolution is an informed, not random, process. the gene machine at this point, lacking empirical demonstration or verification, we imagine a transcendent design process that constructed the primordial dna molecule from resources available on a life-barren planets such as the earth which formed from stellar eruptions and nebular debris strewn about the primordial cosmos which originated and emerged from a cryogenic zpf substratum [4]. such resources necessarily include the organic chemicals needed for constructing the dna molecule as well as a quiescent habitable globular surface and a friendly climate energized by the radiance of a stable star. all this comprises a base of operations that attracts the interest of astrals inclined to populate the cosmos with life wherever feasible. the profound akashic resources of the mesostratum, informed the astrals, our putative designers. the astrals devised genes to carry out a step by step plan for staging cell by cell, organism by organism, establishment of colonies of humanoids on earth and ostensibly elsewhere in the cosmos. iterative procedures are required for goal-oriented biomechanical entities. if our human species or its progenitors were entirely devoid of entelechial or teleological oversight, then the question of intelligent design may be put aside as moot. then gene and her cousins meme, epigene and allele may be granted chance origins arising spontaneously from the dust of stellar debris that settled on earth or some sister planet. it is more likely that her teleological template pre-exited her appearance as a biological entity. we surmise that the gene and her cousins appeared at the behest of creative industrious astrals and straightaway became instrumental in originating species and fostering their evolution in dna decipher journal | july 2017 | volume 7 | issue 1 | pp. 38-59 vary, a., origin & modulation of dna life cycles issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 51 conformance with pre-existing templates in the mesostratum. we argue that the mesostratum, in effect, is a source of holographic templates for genes and derivative biological entities that may be projected into the physiostratum as depicted in figure 1. the gene is a mechanism, a device, that plays a pivotal role not only in human evolution but in the origination of the human and other species. the question of intelligent design reasserts itself because the gene is more than merely a dumb mechanism; it is intelligent, makes choices, provides instructions. some form of the generic ‘gene machine’ has been around for a long time, preceding microscopic plants and critters that first sprung up in the primeval world. the priority of the gene machine’s appearance is needed to prepare groundwork for creating and feeding simple and complex living matter. this leads to the question: ‘what is the origin of the gene, how was it designed and programmed?’ surely, the gene did not design itself. our intimate relationship with the gene, our origin and its origin draws us inevitably into a quandary that demands resolution. we are reluctant to assert that we are here simply by chance. we are evidently here by design even if the design is implemented by the lowly selfish gene simply following a pattern of rules rules that overcome entropy and bring order out of chaos order that finds at least a provisional zenith in the human mind and its intellectual achievements. it is the patent existence of a pattern of rules that inevitably suggests a guiding hand outside the physical realm. that virtual hand reaches out of the mesostratum, as in e. c. escher's celebrated drawing hands each drawing its counterpart suggesting an overseeing creative intelligence such as we assume resides in the superstratum. disquieted and adventurous astrals many, perhaps all, astrals spiritual occupants of the superstratum have a strong desire to assume tangible form as living beings and are therefore inclined to design dna-like molecules which ultimately form the living ambulatory vehicles which the astrals may invest with a higher consciousness, their soul. john, a astral in the superstratum, exclaims in abject desperation, "this ethereal paradise is boring and apparently there's no hope of relief from all this enlightenment and eternal bliss!" sean, another astral, experienced in and having fully enjoyed repeated incarnations, reassures john saying, "your boredom will vanish when you plunge into the world of life and savor mortal existence." john hesitantly says, "i suppose that i could enjoy mortal life, but fear i will then be in the thrall of much abuse, agony and pain interspersed with some pleasure and contentment." "that's just the point, john, you enrich yourself and you contribute a grand work in progress by becoming a self-aware being albeit bound by space and time in one of the many worlds of the cosmos. the pleasure and pain are just part of the deal. you cannot appreciate one without the other. the dynamics of opposites and invigorating conflict allows you to build a repertoire that will amuse your soul as it ultimately idles in boundless blissfulness. you may even want to return to another of the many material worlds to break the tedium you now complain of." dna decipher journal | july 2017 | volume 7 | issue 1 | pp. 38-59 vary, a., origin & modulation of dna life cycles issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 52 "well, sean, i admit i have peeked at various worlds and have gotten glimpses of some entertaining possibilities. perhaps i should participate in worldly affairs, enjoy their occasional ambience, and tolerate any vicissitudes thrust upon me. i should then return to this transcendent paradise with an improved attitude." "more importantly, john, your motivation should go beyond the benefits you glean for yourself. rejoice in the glory of the feedback information and ideas you can deliver as you contribute to our collective life-generating work-in-progress." at this point, jean enters to counsel john who seems still undecided about incarnation in a messy world, "john, there are other options, if you'd rather remain in the spirit world. for example, there are openings in many different types of astral occupations like in the intelligent design or the epigenesis bureau. "john responds languidly, "yes, i'm aware of the job postings. one that grabbed my attention announced the need to expand the staff of the dna genetics bureau. i'm unclear about its exact nature and mission. it sounds highly technical and i am unsure of my qualifications." "no need for concern." jean counsels, "you will be trained as you do the job. remember, you can access inexhaustible intellectual resources and instrumentalities which exist in the mesostratum akasic library. jean continues, "the bureau's main project currently is to continue the original work of evolving the human genome. more human beings worthy of housing astral consciousness and mediating spirits are needed. although some satisfactory progress has been made, on earth for example, there's still a need for lots of fine-tuning to improve the human genome for better communication with our transcendent supernal consciousness. many salutary refinements have come to pass and continue fortuitously, by chance, by natural selection; but there is still too much randomness involved." at this, sean complains, "the whole process of evolution is literally screwed up because human societies have poor breeding practices. they tend to inbreed and remain disgustingly provincial. people often poorly nurture and poorly educate their progeny, they even toss away fetuses that may have great promise. most distressing is that humans do not go about social and genetic engineering systematically and efficiently.” john's imagination is awakened, "i get it! the astrals create, program dna and genetic codes. they redesign and refine all kinds of ancillary, subordinate and intellectually dominant life forms. they build a huge library of successful, time-tested genetic codes. they fine tune the human genome and hope for the best. although astrals can't move mountains, they can easily fiddle with things at quantum, atomic and molecular levels." "but, the rest is up to the sentient creatures they design," sighs jean, "and hopefully each one, each tribe, each colony, each society will contribute to furthering the enlightenment and evolution of the species." john decided to initially incarnate as an eagle so that he could savor a bird's eye view of the earth’s dna decipher journal | july 2017 | volume 7 | issue 1 | pp. 38-59 vary, a., origin & modulation of dna life cycles issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 53 flora and fauna. after studying the remarkable ‘blue planet’ john wondered how it came about and how it became habitable and inviting to life and how it became an appropriate host for dna. dna environment, origin, expression preparing the dna-world stage an astral named atlas is credited with discovering a molten ball of iron revolving around a main sequence star at a distance suitable for habitation. atlas used the energetic resources of the mesostratum and nearby nebular dark matter to cover the ball with a cooler rocky mantel, thus creating earth which now has an outer silicate solid crust, a highly viscous mantle, a liquid outer core, and a solid inner core. the inner core is probably composed primarily of iron and some nickel. it is not necessarily a solid, but behaves as a solid. the thicker crust is continental crust, which is less dense and composed of sodium potassium aluminum silicate rocks, like granite igneous rocks that are relatively rich in elements that form feldspar and quartz and rocks which are relatively richer in magnesium and iron. earth's mantle is the thickest layer of earth. the mantle is divided into upper and lower mantle. the upper and lower mantle are separated by a transition zone. the mantle is composed of silicate rocks that are rich in iron and magnesium relative to the overlying crust composed of elements and compounds suitable for the emergence of living matter based on dna. an astral named gaia is credited for turning the earth’s surface crust into a homoeostatic entity a self-correcting biological system resisting change and to maintaining itself in a state of stable equilibrium. gaia assured that living organisms on earth will affect the nature of their environment in order to make the environment increasingly suitable for life. gaia anticipated that a life-giving planet must regulate its biosphere in such a way as to promote its habitability and the connection between the survivability of species, their evolutionary course, and the symbiosis among species. this includes the thousands of millions of years over which vast oceans formed and coal, oil and gas deposits formed to support populations of diverse living matter and to support the energy needs of advanced civilizations. fossil fuels were formed from plants and animals that lived over 300 million years ago in primordial swamps and oceans. over time the plants and animals died and decomposed under tons of rock and became buried under many layers of mud, rock, and sand. oil and natural gas were created from organisms that lived in the water and were buried under ocean or river sediments. long after the great prehistoric seas and rivers vanished, heat, pressure and bacteria combined to compress and cook the organic material under layers of silt. in most areas, a thick liquid called oil formed first, but in deeper, hot regions underground, the cooking process continued until natural gas was formed. coal formed from the dead remains of trees, ferns and other plants that lived 300 to 400 million years ago. astral gaia established la niña an ocean-atmosphere phenomenon coupled with an opposite phenomenon el niño as part of global climate readjustment pattern. la niña and el niño impact the global climate and influence weather patterns, which occasionally lead to intense storms in some places and droughts in others. el niño is associated with annual weak warm ocean current dna decipher journal | july 2017 | volume 7 | issue 1 | pp. 38-59 vary, a., origin & modulation of dna life cycles issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 54 that running southwards along the coast of peru and ecuador and the warming of the ocean surface or above-average sea surface temperatures in either the central and eastern tropical pacific ocean associated with a band of warm ocean water that develops in the central and east-central equatorial pacific including off the pacific coast of south america. la niña causes mostly the opposite effects of el niño, such as above-average precipitation across the northern midwest, the northern rockies, northern california, and the pacific northwest's southern and eastern regions. an astral named saturn is credited for establishing the food chain which sustains all living matter. saturn set down microbial mats consisting of multi-layered, multi-species colonies of bacteria and other organisms, containing a wide range of chemical environments, each of which favors a different set of microorganisms. each group of mats to differing degrees forms its own food chain and the by-products of each group of microorganisms generally serve as food for adjacent groups. astral saturn anticipated the need to envelope the earth with oxygen for stages of evolution that produced oxygen-breathing mammals and humans. the oxygen is necessary to accommodate the metabolism of food by the post-primordial dna-based creatures. consequently, oxygen became a significant component of earth's atmosphere. there was a significant time interval between the appearance of oxygen-producing organisms and the oxygenation of the atmosphere. oxygen was first produced somewhere around 2.7 billion to 2.8 billon years ago and became 21 percent of the atmosphere around 2.45 billion years ago. this is balanced by roughly 0.04 percent by volume of atmospheric carbon dioxide currently needed to globally sustain green plant life. astral saturn maintained the carbon dioxide level at over 0.20 percent during much of geological history in order to proliferate the plant growth needed to jump start and advance animal life. the astrals assembled a fairly stable and life-friendly environment on the earth despite having to tolerate occasional volcanic eruptions, earthquakes, tsunamis, hurricanes, etc. besetting the planet which has not yet become geologically quiescent. primordial rna and dna after astrals decided to populate globular habitats like the earth with living creatures and humanoids, they immediately assembled and trained spiritual bureaucratic hierarchies and staffs of astral genetic engineers. dormant design processes in the mesostratum akasic library were found and activated. the procedure could not be arbitrary or left to chance; it was organized and systematic. the primordial dna quite literally had to ‘hit the ground running’ and it did after a number of intermediate starts. astrals initially introduced a three-domain biological system that divided primordial cellular life forms into archaea, bacteria, and eukaryote domains. the system emphasized the separation of prokaryotes into two groups, bacteria and archaea. on the basis of differences in their rrna genes, these two groups and the eukaryotes each arose separately from a progenote ancestor with poorly developed genetic machinery. even the simplest members of the three modern domains of life use dna to record their encodement and a complex array of rna and protein molecules to read the encodement for dna decipher journal | july 2017 | volume 7 | issue 1 | pp. 38-59 vary, a., origin & modulation of dna life cycles issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 55 growth, maintenance and self-replication. some rna molecules can catalyze both their own replication and the construction of proteins so that the earliest life-forms were based entirely on rna. these ribozymes initially formed an rna world in which there were individuals but no species. as mutations and horizontal gene transfers occurred the offspring in each generation were likely to have different genomes from those their parents started with. rna was later replaced by dna, which is more stable and therefore can build longer genomes, expanding the range of capabilities a single organism can have. the original ribozymes still remain as the main components of ribosomes, the protein factories of modern cells. rna is quite complex and is not observed to be produced non-biologically. however, some clays, notably montmorillonite, have properties that make them plausible source for the emergence of the primordial rna-based world. they grow by self-replication of their crystalline pattern and they are subject to an analog of natural selection, as the clay species that grows fastest in a particular environment rapidly becomes dominant. moreover, they can catalyze the formation of rna molecules. astrals may have seized on this prebiotic origin of rna to advance towards our dna-based world. dna can be considered as a modified form of rna and the synthesis of dna building blocks from rna precursors is a major astral accomplishment. the ‘first’ organisms with a modified rna that is primordial versions of dna (u-dna and t-dna) were successfully selected against the more primitive organisms of that era. the astrals concluded that the possibility to have a large genome or to repair cytosine deamination could not be realized in that ‘first’ organism and that efficient dna repair and replication proteins able to replicate large dna genomes must be present. in order to solve this problem, the astrals arranged the first appearance of u-dna in a virus, making it the first dna organism resistant to the rna dominance of its host. after dna replication and repair mechanisms were assigned to viruses, enzymes of viral origin were used to correct cytosine deamination and the enzymes were later on transferred to cells, a prerequisite to establish the selective advantage of dna cells over rna cells in term of faithful replication. the transfer of a dna genome from a virus to a cell subsequently eliminated the labile rna genomes. dna origination in viruses leads to dna replication systems which emerged and evolved independently from different lineages of rna viruses. this allows for a long period of dna replication evolution purely in the viral world. the astrals apparently exploited this phenomenon to achieve different version of dna replication proteins. up to now, the study of dna replication has still not revealed the origin and evolution of this pivotal cellular mechanism. the central role of rna in both the origin of life and the mechanism of protein synthesis only partially explains how the astrals achieved these evolutionary constructions. the same is also true for dna transcription. we can tentatively conclude that viruses have played a major role in the origin and evolution of the dna replication proteins and possibly of dna itself. dna as observer and informer our dna-based embodiment is primarily a survival machine, an automaton, with no inherent need for self-analytic consciousness. it is a communal super-colony consisting of trillions of dna decipher journal | july 2017 | volume 7 | issue 1 | pp. 38-59 vary, a., origin & modulation of dna life cycles issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 56 cells. the evolutionary push for evermore complex communities of cells reflects the biological imperative to survive, to control and to make better use of the environment. complexity leads to more awareness, that is, to a greater capability to react and adjust to the environment and thence to improve the probability of survival. when cells band together, differentiate, organize and communicate, there is an exponential increase in the organism’s global self-awareness and ability to adjust to environment and change. over time, this pattern of differentiation the distribution of the workload among the members of the community became embedded in the genes of every cell in the community communicating and significantly increasing the organism’s efficiency and its ability to survive. a command center, the brain, governs the super-colony and its ambulation and responses to chance events, environmental confrontations, and struggles with choices that need to be made. our embodiment our dna-based vehicle of our transcendent consciousness is apparently the product of evolution over millions of earth years adapted and refined to endure, manipulate, and enjoy earthly habitats. our consciousness embodiment perhaps has no inherent human-like consciousness. nevertheless, our survival machines are somehow programmed to respond to and survive their environments, to replicate and evolve, without any urgent need to assume human consciousness or engage in intellectual social intercourse. of course, they possess an operational self-awareness and self-identity. an amoeba or paramecium may well possess these all these attributes but one: the ability to ‘see’ to observe, analyze, and to manipulate and alter parts of the of the objective reality in which it is immersed. as depicted in figure 4 our dna was encoded to differentiate cells that produced an organ for seeing: the eye, retina, optic nerve, and associated neural system. thru our eyes our dna informs itself and, as indicated in figure 3, provides information to the supernal consciousness and to the zpf attractor materialization cycle and the akasic field. we credit the astrals for this adjunct to our higher consciousness. dna decipher journal | july 2017 | volume 7 | issue 1 | pp. 38-59 vary, a., origin & modulation of dna life cycles issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 57 expression of information in the human cell the information and instructions putatively stored in dna is astronomic. we estimate that one human dna molecule contains enough information to fill a million-page encyclopedia. this information is presumed to construct and control the functions of the human body. were one piece of information be read every second, it would take 100 years to complete the process. calculations have revealed that the dna encyclopedia contains some 3 billion different subjects. a molecule of dna a piece of matter that is about 46-50 nm in length and 2 nm diameter and made of protein, fat, and water molecules apparently holds this vast amount of information. it is astonishing that this infinitesimal piece of matter should contain and store so much information. putatively each one of some 100 trillion cells in the human body contains one million pages of information. remarkably, the cell uses this information quite flawlessly, in an exceedingly well-planned and coordinated manner, in the appropriate places, virtually without making errors. moreover, just after conception, the original fetal cell has already begun the process of building the human body. all the cells in the body have the same dna and yet they are not identical, even in the same shared organ. each originates from a common starting point: a fertilized egg. but, each organ cell type is completely dissimilar to that in another organ, and other cells in the same organ, and totally different from the original fertilized egg cell. for example, the retina contains two types of photo receptors, rods and cones some 120 million rods and 6 to 7 million cones which provide the eye's color sensitivity and are concentrated in the central spot known as the macula. theory holds each cell whether a neuron, skin cell, or a photo receptor cell uses genes that it contains differently. all cells have the same set of genes (~20,000 in humans) but it is up to the individual cell whether each gene is turned on or off that is expressed. a gene can be described as a region of dna that can undergo transcription to produce a corresponding rna intermediary, which can then be translated into a specific protein molecule. the proteins determine the activity and function of the cell. the control of protein expression through regulation of each gene is of fundamental importance. by either enhancing or repressing the expression of each gene, a cell can become highly specialized. for instance, a neuron has absolutely no need for rhodopsin, a protein involved in light-sensing. in the photo receptor cells of the retina however, rhodopsin is integral to the cell's function, so its expression will be greatly enhanced. conversely, neurons require very high expression levels of specific ion channels, such as the voltage-gated ion channel, but these genes will be repressed in photo receptor cells. in essence, for each gene in each cell there will be differing levels of expression according to the conditions around the cell, signals received at the cell surface membrane, and the specific cell type (determined during development of the embryo). it is through this process that the function and morphology of each cell is unique. the mesostratum template the human genome project has provided us only with a glimpse into how human biology works. it shows us all of the possible proteins in each cell, but understanding the expression patterns of individual proteins in different cells remains unresolved. as depicted in figures 1, 3, and 4, we conjecture that the mesostratum is the ultimate energetic reservoir and source of dna decipher journal | july 2017 | volume 7 | issue 1 | pp. 38-59 vary, a., origin & modulation of dna life cycles issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 58 information, potentialities, codes, and life cycles templates attributed to dna. in this context, the dna molecule, the genome, the genetic material of an organism is simply the physiostratum realization of a mesostratum encoded superstratum concept drawn from the akashic field and formulated as a zpf attractor. material evolution of the genome is then the result of a design, feedback, and iteration cycle which requires the structuring of an objective material reality and its interaction with a governing supernal consciousness, as represented in figure 3. the dna macromolecule is pivotal as an antenna and transmitter of signals inherent to the process. dna by itself is apparently unable to regulate its own genes. we are finding that at the molecular level the organism is so dynamic, so densely woven and multidirectional in its causes and effects, that it cannot be explained as a purely local process. the cycle depicted in figure 3 explains how dna, which is composed of the arrangement of huge numbers of unintelligent atoms arranged in certain sequences, and enzymes (or rna in rna viruses), working in a harmonious way, is able to organize countless complicated and diverse operations in the cellular structure and dynamics of the body. the wisdom and information is not in the dna molecules or in the cells that contain them, but in the universal consciousness and presumably in the akashic field that brought these molecules into being, programming their life-cycles and guiding them to function as they do. conclusion are we, our habitats, our worlds, satisfactory works in progress functioning as intended by our designers? obviously, we are imperfect beings in an imperfect world and may well be discardable models requiring further iterative design, development, and evolution. the replacement of unwieldy lumbering dinosaurs with emblazoned birds and fish and other land and sea species was probably done upon reconsideration of designs appropriate for earth during its rehabilitation following the devastation wrought by an asteroid millions of years ago. ultimately, we may build beautiful machines, indeed proxy humanoids, that surpass our biological limitations and which our brains, spirits, souls, and consciousness will be eager to occupy [5]. our intimate relationship with dna, our origin and its origin, draws us inevitably into a quandary that demands resolution. we conclude that, although it is pivotal, dna operating alone cannot account for the complexity of living matter, the cycles of life, or their origin. we are evidently here by design and governed by rules that overcome entropy and bring order out of chaos order that finds at least a provisional zenith in the human mind and its intellectual capacity and achievements. it is the patent existence of a pattern of rules that inevitably suggests a guiding hand outside the physical realm. that virtual hand reaches out of the mesostratum, like e. c. escher's celebrated drawing hands with each of two hands drawing its counterpart. as with all art, there is an implicit overseeing non-local creative intelligence. references 1. vary, a., human consciousness as epiphenomenon of primordial consciousness (part i & ii), journal of consciousness exploration & research, september 2016, volume 7, issue 8, pp. 588-598 & pp. dna decipher journal | july 2017 | volume 7 | issue 1 | pp. 38-59 vary, a., origin & modulation of dna life cycles issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 59 599-612. 2. keppler, j. (2016) on the universal mechanism underlying conscious systems and the foundations for a theory of consciousness, open journal of philosophy, 2016, 6, 346-367. 3. vary, a., exploration of mesostratum physics, prespacetime journal, august 2016, volume 7, issue 11, pp. 1473-1483. 4. vary, a., cryogenic origin & nature of the cosmos, prespacetime journal, april 2016, volume 7, issue 5, pp. 899-905. 5. vary, a., informatics and consciousness transfer, journal of consciousness exploration & research, march 2016, volume 7, issue 3, pp. 256-269. dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 43-51 43 pitkänen, m., tgd views on the roles of lithium, phosphate & posner molecule in quantum biology essay tgd views on the roles of lithium, phosphate & posner molecule in quantum biology matti pitkänen 1 abstract in this essay, i compare the work of fisher proposing that phosphate ion and calcium phosphate known as posner molecule are fundamental for quantum neuroscience. phosphate ion show nuclear spin could serve as qubit able to get enzymatically entangled and make possible a transfer of qubits. posner molecule would serve as unit of quantum memory. i describe first what might be called lithium mystery, which served as a motivation of fisher and summarize also the tgd view about the role of lithium. the model of fisher for how phosphate ion and posner molecule could play a central role quantum neural processing is described. i also summarize the tgd view about the situation suggesting that posner molecule might indeed have deep role. what puts bells ringing is that elf radiation at frequencies equal to multiples of 15 hz cyclotron frequency for calcium ion in endogenous magnetic field bend = .2 gauss was found by blackman and others to have effects on vertebrate brain. furthermore, the cyclotron frequency of phosphate ion in endogenous magnetic field bend corresponds to the 11 hz at the top of alpha band defining a fundamental biorhythm. a further interesting observation is that the 6 spin states of phosphate ions could realize genetic code. keywords: lithium, phosphate, posner molecule, quantum biology, tgd. 1 introduction i encountered two years ago fisher’s work [3] (see http://tinyurl.com/hd3t6sr) related to quantum biology. i wrote a short article about it. later i made some interesting additional observations about posner molecules studied by fisher, and this article is an extension of an earlier article containing the additional material. i attach below the abstract of the article of fisher. the possibility that quantum processing with nuclear spins might be operative in the brain is proposed and then explored. phosphorus is identified as the unique biological element with a nuclear spin that can serve as a qubit for such putative quantum processing a neural qubit while the phosphate ion is the only possible qubit-transporter. we identify the ”posner molecule”, ca9(po4)6, as the unique molecule that can protect the neural qubits on very long times and thereby serve as a (working) quantum-memory. a central requirement for quantum-processing is quantum entanglement. it is argued that the enzyme catalyzed chemical reaction which breaks a pyrophosphate ion into two phosphate ions can quantum entangle pairs of qubits. posner molecules, formed by binding such phosphate pairs with extracellular calcium ions, will inherit the nuclear spin entanglement. a mechanism for transporting posner molecules into presynaptic neurons during a ”kiss and run” exocytosis, which releases neurotransmitters into the synaptic cleft, is proposed. quantum measurements can occur when a pair of posner molecules chemically bind and subsequently melt, releasing a shower of intra-cellular calcium ions that can trigger further neurotransmitter release and enhance the probability of post-synaptic neuron firing. multiple entangled posner molecules, triggering non-local quantum correlations of neuron firing rates, would provide the key mechanism for neural quantum processing. implications, both in vitro and in vivo, are briefly mentioned. for earlier work on the possibility of quantum processing in the brain with nuclear spins, please see hu and wu’s work on spin-mediated consciousness theory (see, e.g., https://arxiv.org/abs/quant-ph/ 0208068) 1correspondence: matti pitkänen http://tgdtheory.com/. address: rinnekatu 2-4 a8, 03620, karkkila, finland. email: matpitka6@gamail.com. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/hd3t6sr https://arxiv.org/abs/quant-ph/0208068 https://arxiv.org/abs/quant-ph/0208068 http://tgdtheory.com/ mailto:matpitka6@gmail.com dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 43-51 44 pitkänen, m., tgd views on the roles of lithium, phosphate & posner molecule in quantum biology about two years after writing the first version of this article, i learned about a second article about posner molecules by fisher, swift and van de walle [4] (see http://tinyurl.com/ycyu5bj9) describing a detailed study of posner molecules. the abstract of the article gives idea about what is done. we investigate ”posner molecules”, calcium phosphate clusters with chemical formula ca9(po4)6. originally identified in hydroxyapatite, posner molecules have also been observed as free-floating molecules in vitro. the formation and aggregation of posner molecules have important implications for bone growth, and may also play a role in other biological processes such as the modulation of calcium and phosphate ion concentrations within the mitochondrial matrix. in this work, we use a first-principles computational methodology to study the structure of posner molecules, their vibrational spectra, their interactions with other cations, and the process of pairwise bonding. additionally, we show that the posner molecule provides an ideal environment for the six constituent 31p nuclear spins to obtain very long spin coherence times. in vitro, the spins could provide a platform for liquid-state nuclear magnetic resonance quantum computation. in vivo, the spins may have medical imaging applications. the spins have also been suggested as ”neural qubits” in a proposed mechanism for quantum processing in the brain. i also learned about the finding of m.y. simmons et al [1] (see http://tinyurl.com/ydx6v7xa) about electronic qubits realized with phosphorus atoms serving as donors. this inspires the question whether also electronic qubits might be realized by using the valence electrons of p . about two years after writing the first version of this article i ended up with a model of valence bond [11] (see http://tinyurl.com/ycg94xpl) assuming that the electrons at valence bonds can have nonstandard value of planck constant heff = n × h (the hierarchy of planck constants characterizing dark matter as phases of ordinary matter comes as a basic prediction of adelic tgd [14, 15]). the starting point of the model was the surprisingly weak variation of the bond energy along the rows of the periodic table. the model provides a vision about the role of valence bonds in biology and provides a precise identification for the notion of metabolic energy. the binding energies of bonds decrease with the value of heff/h = n increasing along the rows of the periodic table, and the reduction of the binding energy can be identified as potential metabolic energy liberated in catabolism. the bonds involving atoms towards the right end of the rows of the periodic table have highest metabolic energies, and are indeed the bonds appearing in nutrient molecules. phosphate ion has especially high bond energy so that posner molecules could be also ideal for storing metabolic energy. in the sequel i describe the lithium mystery, which served as a motivation of fisher and also tgd view about the role of lithium. the model of fisher for how phosphate ion and calcium phosphate known as posner molecule could play a central role quantum neural processing is described. i also present tgd view about the situation suggesting that posner molecule might indeed have deep role. elf radiation at frequencies equal to multiples of 15 hz cyclotron frequency for calcium in endogenous magnetic field bend = .2 gauss was found by blackman and others to have effects on vertebrate brain. furthermore, the cyclotron frequency of phosphate ion in endogenous magnetic field bend corresponds to the 10 hz alpha resonance frequency defining a fundamental biorhythm. i will also represent a brief comment about the realization of electronic qubits with p atom serving as a donor. 2 lithium mystery the starting point of fisher was a very interesting finding challenging the hypothesis about life as mere bio-chemistry. already in 1986, scientists at cornell university examined the effects of the two isotopes of lithium on the behavior of rats. pregnant rats were separated into three groups. one group was given li7, one group was given the isotope li6, and the third served as the control group. once the pups were born, the mother rats that received li6 showed much stronger maternal behaviors, such as grooming, nursing and nest-building, than the rats in either the li7 or control groups. li6 therefore as has a positive effect on maternal behaviour unlike li7. the chemistry is exactly the same. according to the popular article, fisher believes that the higher nuclear spin of li6 could give it issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/ycyu5bj9 http://tinyurl.com/ydx6v7xa http://tinyurl.com/ycg94xpl dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 43-51 45 pitkänen, m., tgd views on the roles of lithium, phosphate & posner molecule in quantum biology special role.: in the article he talks about nuclear spin j = 1/2 which cannot be true since the spin must be even. as a matter fact, according to my nuclear physics by howard li7 has nuclear spin of j = 3/2 units whereas li6 has nuclear spin j = 1 so that neither of the above claims is correct. could the bosonic character of li6 nucleus provide an alternative explanation? in any case, the finding strongly suggests that magnetic fields are involved. lithium presumably li6 has also other positive effects. if the positive effects are indeed due to li6 isotope, the dose of lithium could be reduced by using only li6 isotope. i attach here the abstract of the article that i wrote as a reaction to discussions with my friend samppa who told about lithium [9] (see http://tinyurl.com/j44epwp). lithium has been used for more than 50 years as a mood stabilizer in manic depression. during last years lithium has been studied intensively and found that it can be used also in treatment of schizophrenia and many other brain disorders. the effectiveness of lithium is however difficult to understand in the standard framework of biology. in tgd framework organism-environment pair of standard biology is replaced with the triplet magnetic body organism -environment. magnetic body uses biological body as sensory receptor and motor instrument. this suggests that the re-establishment of communications of brain with some level of the magnetic body is how lithium causes its positive effects. magnetic body does not receive information about brain and cannot control it since dark lithium ions and corresponding cyclotron radiation are not present. the disorders caused by the lack lithium and other biologically important ions would therefore be something totally new from the perspective of standard neuroscience. tgd explanation for the effects of lithium relies on the notions of magnetic body and dark large heff = n× h photons, electrons, and ions and relies on cyclotron frequencies as frequencies assignable to the dark photons responsible for the communications between magnetic body and biological body. in this picture the charge of the ion and its total magnetic moment would be relevant rather than only nuclear magnetic moment characterizing also neutral atoms (which could also contribute to the magnetic moment of ion). cyclotron frequencies would replace larmor frequencies. 1. for li6 the cyclotron frequency is about 50.0 hz in the endogenous magnetic field bend = .2 gauss explaining the quantal effects of em fields at elf frequencies on vertebrate brain reported by the pioneers of bio-electromagnetism such as blackman [2] to occur at multiples of cyclotron frequency in this magnetic field for calcium ion and also for other biologically important ions. for ca+2 ion the cyclotron frequency is 15 hz. thanks to the large value of heff = n × h dark photons would have energies above thermal threshold. an attractive hypothesis is that the energies are in the range of bio-photon energies (visible and uv). 2. in the case of li6 the dark photons would make possible communication to and control by the magnetic body relevant for maternal behaviors. magnetic fields oscillating at 50 hz frequency are known to have biological effects [7]. the size of the corresponding magnetic body part would be obtained from the wavelength λ = 2πr (r denotes the radius of earth) of the lowest schumann frequency 7.8 hz as l = (7.8/50) × r = .98 × r. this suggests that dark magnetic flux tubes assignable with earth are involved: not however that the field strength is 2be/5. 3. for li7 the dark photons would have cyclotron frequency about 42.9 hz, which brings in mind the thalamocortical resonance with frequency around 40 hz assigned to consciousness at the time when the use of the word ”consciousness” ceased to be pseudo-science. the more abundant li7 (92.5 per cent) should be also important but could be associated with other kinds of biological functions. 3 phosphate, posner molecule, and cognition fisher as also other quantum biologists tries to understand quantum biology as an improvement of biochemistry. one assumes that standard quantum theory brings in small effects allowing to optimize biological functions. in the case of the avian navigation and also in many other situations the problem issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/j44epwp dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 43-51 46 pitkänen, m., tgd views on the roles of lithium, phosphate & posner molecule in quantum biology is that earth’s magnetic field is only 2 per cent of the minimum magnetic field at which the proposed radical-pair mechanism is found to work [10] (see http://tinyurl.com/jnxvdmf). to my opinion much more radical approach challenging the basics of quantum theory itself is necessary. fisher wants to identify the quantum mechanism behind neural activity assumed to rely on nuclear spins. this is quite a demanding challenge. one should understand long coherence time for nuclear spins representing the qubits, discover a mechanism transporting the qubit through the brain to neurons, identify a molecular scale quantum mechanism entangling qubits, identify a chemical reaction inducing quantum measurement of the qubits dictating the subsequent neuron firing, and understand what happens in nerve pulse transmission from preto post-synaptic neuron at quantum level. 1. fisher assigns fundamental qubit and the ability to develop long lasting quantum entanglement with phosphate ion (see http://tinyurl.com/zgbgtwy). phosphate ion would be qubit transporter. the transfer of phosphate ion from apt to a molecule is fundamental part of metabolism and the tgd proposal is that a transfer of negentropic entanglement (purely tgd based notion involving p-adic physics as correlate for cognition) is in question. 2. enzyme catalyzed qubit entanglement would emerge in the reaction atp→ amp+ppi. ppi is diphosphate ion with entangled phosptate and the reaction ppi→ pi+pi would create two entanglement phosphates. the reaction rate is proposed to depend on whether the 2pi state is spin single or spin triplet. 3. quantum memory is assigned with so called posner molecule [(po4)−3)]6ca+2 9 made of 6 phosphate ions and 9 calcium ions would be the key player. posner molecule belongs to a family of calcium phosphates having as building bricks po−3 4 and ca+2 ions (see http://tinyurl.com/jftjmro). calcium phosphate is the principal form of calcium found in bovine milk and blood. 70 percent of bone consists of hydroxyapatite, a calcium phosphate mineral known as bone mineral. tooth enamel is composed of almost ninety percent hydroxyapatite. posner molecule is neutral since the charges of 9 ca ions and 6 phosphate ions cancel each other: 9 × 2 − 6 × 3 = 0. geometrically posner molecule can be described as a cube with calcium ions at corners and center and phosphate ions at the centers of faces. the nuclear spin of the posner molecule assignable to phosphates is 0, 1, 2, or 3. posner molecule has also reduced rotational degrees of freedom characterized by group z3 giving rise to pseudospin. posner molecule would be a carrier of phosphate qubits giving rise to (working) quantum-memory realized in terms of entangled posner molecules. 4. fisher proposes the notion of quantum entangled chemical reactions. this notion does not make sense if one identifies chemical reactions as processes involving state function reduction as assumed in chemical kinetics. the notion could make sense if chemical reactions are identified as unitary time evolutions for entangled systems such as posner molecules. in tgd framework the notion of entangled time evolutions could make sense in zero energy ontology (zeo). 5. nerve pulse transmission from preto postsynaptic membrane would entangle neurons by entangling posner molecules. biochemistry is complex but to my opinion the proposed model is too complex to be feasible. my view is that the enormous complexity of the description based on biochemical reaction pathways reflects the failure to realize the presence of control level magnetic body. situation would be like trying to understand the functioning of computer program regarding it as mere physical phenomenon without any idea about its purpose. 4 tgd view in the sequel posner molecules are discussed from tgd perspective. the larmor and cyclotron frequencies of phosphate ions are in alpha band for bend = .2 gauss playing a key role as endogenous dark magnetic issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/jnxvdmf http://tinyurl.com/zgbgtwy http://tinyurl.com/jftjmro dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 43-51 47 pitkänen, m., tgd views on the roles of lithium, phosphate & posner molecule in quantum biology field, whose flux tubes carrying dark ions. the 6 phosphate molecules of posner molecule provide a realization of genetic code in terms of qubits. 4.1 larmor and cyclotron frequencies of posner molecule in tgd framework both nuclear spins and angular moment of dark nuclei in the magnetic fields assignable to dark magnetic flux tubes would be important: larmor frequencies would be replaced with the sums of larmor and cyclotron frequencies assignable to (usually) charged particles. it is interesting to look whether the cyclotron frequencies of phosphate and posner molecule could teach something about their possible role. 1. phosphate po−3 4 with mass number 31+4×16 = 95 has cyclotron frequency 9.5 hz in the endogenous magnetic field bend = .2 gauss assumed in tgd model: this is 10 hz in the accuracy with which bend is known. this frequency is in alpha band! for smaller charges -2 and -1 one has frequencies 6.26 hz and 3.13 hz. in tgd framework the transfer of phosphate from atp to the acceptor biomolecule could be at the fundamental level transfer of negentropic entanglement from metabolites [5, 6]. this could reduce to the transfer the ends of the associated flux tubes between the molecules. 2. posner molecule is neutral since the charges of 9 ca ions and 6 phosphate ions cancel each other: 9× 2− 6× 3 = 0. being neutral posner molecule as a whole does not couple to the magnetic field except through its total magnetic moment. tgd proposal that ions form bose-einstein condensates encourages however to consider the possibility that the building bricks of posner molecule form separate bose-einstein condensates. one can ask whether this is possible also more complex calcium phosphates: could bones be much more than just passive building bricks? the simplest possibility is that 3 cooper pairs of fermionic po−3 4 molecules (as is easy to check by noticing that phosphorus and oxygen atoms are bosons and there are surplus 3 electrons: note that phosphorus nucleus is fermion and oxygen nucleus a boson) form a bose-einstein condensate a their own circular portion of flux tube. 9 bosonic ca+2 ions would form similar bose einstein condensate at their own flux tube portion. the value of heff proportional to the mass of the ion by heff = hgr hypothesis. the formation of cooper pairs of phosphate ions would conform with the conjecture of fisher that two phosphate ions can entangle. 3. the value of heff proportional to the mass of the ion if heff = hgr hypothesis is accepted. the formation of cooper pairs of phosphate ions would conform with the conjecture of fisher that two phosphate ions can entangle. these observations put the bells ringing with a frequencies of 10 hz and 15 hz, one might say. unfortunately this frequency is not directly audible, so that i cannot hope that colleagues would hear the ringing! there are however some hopes: also 10 hz and 15 hz can be made audible as difference of frequencies fed to right and left ear! maybe some experimentalist could get interested! 4. a further intriguing observation is that the larmor frequency of p for bend is 10.96 hz. this is marginally in alpha band. this suggests that also larmor frequency of p is indeed important in bio-control by magnetic body. 5. an alternative and more realistic sounding hypothesis is heff = hem. heff = hem would hold true when em interaction becomes non-perturbative. in this case ne would be short ranged and associated with atomic/molecular systems. at this moment one cannot exclude the possibility that only short range ne is involved with living matter. short ranged ne could be associated with dark atoms for which the scale of binding energy behaves like 1/h2eff and is thus reduced for dark atoms [8]. the creation of dark atoms would require metabolic energy. this metabolic energy could also be liberated as dark atoms transforms to ordinary atom. metabolic electrons could be associated with dark atoms and also the dark atoms issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 43-51 48 pitkänen, m., tgd views on the roles of lithium, phosphate & posner molecule in quantum biology in nutrients could provide metabolic energy driving protons through the mitochondrial membrane against potential gradient and transforming adp to atp contains high energy phosphate bond, which would actually correspond to the presence of dark (say hydrogen -) atom. phosphate containing the dark atom would carry the ne or be accompanied by dark magnetic flux tube. the simplest view about photosynthesis would be that the absorption of solar photons excites some atoms to dark states and that nutrients contain these dark atoms as stable enough entities. the contamination of nutrients could mean the decay of these dark atoms to the normal states. 6. the cyclotron frequencies of these bose-einstein condensates would be 9.5 hz resp. 15 hz in bend = .2 gauss. this model could allow to improve the understanding about why the radiation at harmonics of 15 hz has effects on vertebrate brain and also about the realization of alpha rhythm as a control signal from magnetic body. fisher proposes that in nerve pulse transition two posner molecules fuse temporarily and produce a spray of ca+2 ions. this could make sense also in tgd framework. 4.2 a new step of progress after two years roughly two years after writing the first version of this article i ended up with a model of valence bond [11] (see http://tinyurl.com/ycg94xpl) assuming that the electrons at valence bonds can have nonstandard value of planck constant heff = n × h (the hierarchy of planck constants characterizing dark matter as phases of ordinary matter comes as a basic prediction of adelic tgd [14, 15]). the starting point of the model was the surprisingly weak variation of the bond energy along the rows of the periodic table and the observation that the heating of ruthenium leads to a mysterious disappearance of valence electrons known for decades: the interpretation would be that they are transformed to dark electrons [13]. the model provides a vision about the role of valence bonds in biology and provides a precise identification for the notion of metabolic energy. the binding energies of bonds decrease with the value of heff/h = n increasing along the rows of the periodic table, and the reduction of the binding energy can be identified as potential metabolic energy liberated in catabolism. the bonds involving atoms towards the right end of the rows of the periodic table have highest metabolic energies, and are indeed the bonds appearing in nutrient molecules. phosphate ion has especially high bond energy so that posner molecules could be also ideal for storing metabolic energy. posner molecule would be ideal for both control purposes and for metabolism. 1. there are 9 ca2+ ions and 6 po3− 4 ions with cyclotron frequencies of 15 hz and 9.5 hz respectively in the endogenous magnetic field bend = .2 gauss explaining the observations of blackman [2] about the quantal effects of elf em fields on vertebrate brain: thus these molecules are ideal for control by and communication to magnetic body. also the fact that the larmor frequency of p is 10.96 hz and marginally in alpha band, suggests that mb uses spin flips for control purposes. mb could control and coordinate all phosphate containing biomolecules usign this larmor transition of p . this includes atp, dna, rna, the tubulins of microtubules containing gtp and all biomolecules to which phosphate is attached. this would conform with the frequencies in alpha band as a universal biorhythm used by magnetic body to keep metabolism in synchrony in body scale. p nuclei serve as qubits and 6 qubits in posner atom could realize genetic code with 64 code words. could our bone marrow be performing massive quantum information processing?! 2. the 6 phosphates with high energy phosphate bonds are in turn ideal for metabolism: p and o related valence bonds indeed have nearly maximal metabolic energy content in the proposed model of valence bonds based on heff/h = n hierarchy [11] (see http://tinyurl.com/ycg94xpl). issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/ycg94xpl http://tinyurl.com/ycg94xpl dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 43-51 49 pitkänen, m., tgd views on the roles of lithium, phosphate & posner molecule in quantum biology remark: totally unrelated association: the magic number 6 appears also in the structure of cortex: could the six layers represent qubits and realize genetic code? this suggests that bones might also serve as energy storages and of course as nutrients. interestingly, in the evolution of humans the discovery of stones as tools to break down bones of prey animals to get bone marrow has been seen as a critical step leading to the growth of cortex requiring a lot of metabolic energy (to generate large n valence bonds providing ability to generate negentropy). what is interesting that atp molecule the basic metabolic currency has triphosphate with total charge -4 as a building brick. triphosphate is characterized by cyclotron frequency 4.8 hz which is one half of the alpha band frequency. the diphosphate in adp has cyclotron frequency 5.2 hz. note that the cyclotron frequency of fe2+ ion central in oxygen based metabolism is 10.7 hz and in alpha band as also the larmor frequency of p . note that in dna the singly charged phosphates in xmps, x = a, t, c, g, have cyclotron frequency, which is one third of this, that is 3.1 hz. this frequency appears in eeg as a kind of resonance frequency during deep sleep. dna nucleotides as whole have cyclotron frequencies around 1 hz. in microtubules the phosphate of gtp can have three different charge states allowing frequencies 3.1,6.2 and 9.4 hz. i have proposed that these charge states together with two different tubulin conformations give rise to a realization of the genetic code. the proton cyclotron frequency 300 hz has been already earlier assigned with atp and the models for the lifelike properties of a system consisting of plastic balls involved cyclotron frequency of ar+ ion which is same as that of ca2+ ion and cyclotron frequency 300 hz of proton [12] (see http://tinyurl. com/yassnhzb). also the two important frequencies associated with honeybee dance [16] correspond to the cyclotron frequencies of ca2+ and proton (see http://tinyurl.com/ycnst4z5). 4.3 phosphorus electrons as qubits m.y. simmons et al [1] (see http://tinyurl.com/ydx6v7xa) have found that p atoms can serve as donors of electrons giving rise to very long-lived qubits (see http://tinyurl.com/y88d7vhf). i attach the abstract of the article here. substitutional donor atoms in silicon are promising qubits for quantum computation with extremely long relaxation and dephasing times demonstrated. one of the critical challenges of scaling these systems is determining inter-donor distances to achieve controllable wavefunction overlap while at the same time performing high fidelity spin readout on each qubit. here we achieve such a device by means of scanning tunnelling microscopy lithography. we measure anti-correlated spin states between two donor-based spin qubits in silicon separated by 161nm. by utilising an asymmetric system with two phosphorus donors at one qubit site and one on the other (2p1p), we demonstrate that the exchange interaction can be turned on and off via electrical control of two in-plane phosphorus doped detuning gates. we determine the tunnel coupling between the 2p1p system to be 200mhz and provide a roadmap for the observation of two-electron coherent exchange oscillations. a controllable exchange interaction between electron spins is needed for the realization of 2-qubit quantum gate. the valence electron of p atom rather than p nucleus serves as a qubit. the qubits have unexpectedly long relaxation times (measured in seconds) and dephasing times. 2p (2 p atoms) and 1p serve as electron donors. the distance of 2p and 1p is rather long 16±1 nm 1.6 times the p-adic length scale l(151) (p is gaussian prime mg,151 = (1 + i)151 − 1 assignable to neuronal membrane. exchange interaction occurs if there is an overlap between electron wave functions. in tgd framework the electrons donated by phosphorus atoms and forming the qubits could be actually dark electrons with heff/h = n larger than for atoms or normal valence bonds. this would scale up the domain of electron wave functions by n2 and make possible the overlap. this also increases relaxation and dephasing times. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/yassnhzb http://tinyurl.com/yassnhzb http://tinyurl.com/ycnst4z5 http://tinyurl.com/ydx6v7xa http://tinyurl.com/y88d7vhf dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 43-51 50 pitkänen, m., tgd views on the roles of lithium, phosphate & posner molecule in quantum biology remark: in living matter negatively charged phosphate ions for which p atoms have received electrons (negative oxidation number) are important. in the experiment discussed p atom loses electron and becomes a positive ion. references [1] simmons my et al. two-electron spin correlations in precision placed donors in silicon. nature communications. available at: http://www.nature.com/articles/s41467-018-02982-x, 9(980), 2018. [2] blackman cf. effect of electrical and magnetic fields on the nervous system, pages 331–355. plenum, new york, 1994. [3] fisher mpa. quantum cognition: the possibility of processing with nuclear spins in the brain). available at: https://arxiv.org/abs/1508.05929, 2015. [4] fisher mpa swift mw and van de walle cg. posner molecules: from atomic structure to nuclear spins. available at: https://arxiv.org/pdf/1711.05899.pdf, 2017. [5] pitkänen m. macroscopic quantum coherence and quantum metabolism as different sides of the same coin: part i. in bio-systems as conscious holograms. onlinebook. available at: http: //tgdtheory.fi/public_html/hologram/hologram.html#metab, 2006. [6] pitkänen m. macroscopic quantum coherence and quantum metabolism as different sides of the same coin: part ii. in bio-systems as conscious holograms. onlinebook. available at: http: //tgdtheory.fi/public_html/hologram/hologram.html#molephoto, 2006. [7] pitkänen m. quantum model for bio-superconductivity: i. in tgd and eeg. onlinebook. available at: http://tgdtheory.fi/public_html/tgdeeg/tgdeeg.html#biosupercondi, 2006. [8] pitkänen m. criticality and dark matter. in hyper-finite factors and dark matter hierarchy. online book. available at: http://tgdtheory.fi/public_html/neuplanck/neuplanck.html#qcritdark, 2014. [9] pitkänen m. lithium and brain . available at: http://tgdtheory.fi/public_html/articles/ lithiumbrain.pdf, 2016. [10] pitkänen m. can quantum biology really do without new physics? available at: http://tgdtheory. fi/public_html/articles/rpmtgd.pdf, 2016. [11] pitkänen m. does valence bond theory relate to the hierarchy of planck constants? available at: http://tgdtheory.fi/public_html/articles/valenceheff.pdf, 2017. [12] pitkänen m. life-like properties observed in a very simple system. available at: http://tgdtheory. fi/public_html/articles/plasticballs.pdf, 2017. [13] pitkänen m. mysteriously disappearing valence electrons of rare earth metals and hierarchy of planck constants. available at: http://tgdtheory.fi/public_html/articles/rareearth.pdf, 2017. [14] pitkänen m. philosophy of adelic physics. available at: http://tgdtheory.fi/public_html/ articles/adelephysics.pdf, 2017. [15] pitkänen m. philosophy of adelic physics. in trends and mathematical methods in interdisciplinary mathematical sciences, pages 241–319. springer.available at: https://link.springer. com/chapter/10.1007/978-3-319-55612-3_11, 2017. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://www.nature.com/articles/s41467-018-02982-x https://arxiv.org/abs/1508.05929 https://arxiv.org/pdf/1711.05899.pdf http://tgdtheory.fi/public_html/hologram/hologram.html#metab http://tgdtheory.fi/public_html/hologram/hologram.html#metab http://tgdtheory.fi/public_html/hologram/hologram.html#molephoto http://tgdtheory.fi/public_html/hologram/hologram.html#molephoto http://tgdtheory.fi/public_html/tgdeeg/tgdeeg.html#biosupercondi http://tgdtheory.fi/public_html/neuplanck/neuplanck.html#qcritdark http://tgdtheory.fi/public_html/articles/lithiumbrain.pdf http://tgdtheory.fi/public_html/articles/lithiumbrain.pdf http://tgdtheory.fi/public_html/articles/rpmtgd.pdf http://tgdtheory.fi/public_html/articles/rpmtgd.pdf http://tgdtheory.fi/public_html/articles/valenceheff.pdf http://tgdtheory.fi/public_html/articles/plasticballs.pdf http://tgdtheory.fi/public_html/articles/plasticballs.pdf http://tgdtheory.fi/public_html/articles/rareearth.pdf http://tgdtheory.fi/public_html/articles/adelephysics.pdf http://tgdtheory.fi/public_html/articles/adelephysics.pdf https://link.springer.com/chapter/10.1007/978-3-319-55612-3_11 https://link.springer.com/chapter/10.1007/978-3-319-55612-3_11 dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 43-51 51 pitkänen, m., tgd views on the roles of lithium, phosphate & posner molecule in quantum biology [16] pitkänen m. dance of the honeybee and new physics. available at: http://tgdtheory.fi/public_ html/articles/shipmanagain.pdf, 2018. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.fi/public_html/articles/shipmanagain.pdf http://tgdtheory.fi/public_html/articles/shipmanagain.pdf introduction lithium mystery phosphate, posner molecule, and cognition tgd view larmor and cyclotron frequencies of posner molecule a new step of progress after two years phosphorus electrons as qubits untitled dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 210-212 campbell, r., evolution as manifestation of cosmic order issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 210 guest editorial evolution as manifestation of cosmic order robert campbell * abstract during darwin’s time the biblical genesis account was considered by many scholars to be allegorical and various ideas about the transmutation of species were already in circulation, influenced by findings on the beagle trip that embarked in 1831 and by communications with others, including a.r. wallace who had a nearly identical theory, darwin eventually published his famous book on the origin of species. his idea was that small heritable changes over a long period of time can endow a survival advantage in a process of natural selection that can lead to new species. however, the process was regarded as random without plan or purpose. it met with opposition and various amendments until it became generally accepted scientific dogma in the 1930’s and 1940’s. work on genetics was believed to solidly confirm the theory, however very recent dna findings, small rnas and heritable epigenetic factors are currently beginning to call it into question again, quite apart from arguments for creationism or intelligent design. the views of an ardent proponent of the darwinian paradigm will be critically assessed in detail followed by a review of compelling evidence for hierarchical organization as a pervasive feature of the cosmic order, from the physical evolution of the cosmos to biological evolution on the planet earth. key words: charles darwin, alfred wallace, theory of evolution, cosmic order, intellegent direction, spirituality, atheist, richard dawkins. when charles darwin published his famous book the origin of species in 1859, he began a debate that has, if anything, gained in intensity over the years. with modern techniques of probing genes the debate has taken on new proportions. a new breed of biologist, armed with a genetic arsenal, is attempting to reduce the whole of life to the mindless perpetuation of dna sequences. it is intended to be consistent with cosmological implications of the physical sciences. in its passion for unity science reduces life to a meaningless enterprise, an accident without pattern, plan or purpose. this is the grand vision that science offers to lend humanity a sense of cohesion and lead us through the new millennium inspired with hope and direction. on close examination it becomes apparent that there is no hard evidence to support the exclusive interpretations that many biologists place on their findings and new discoveries are exposing flaws in their logic. the mindless claim for the evolutionary mechanism is itself a blind belief lacking in substance. at the same time many of us sympathize with darwin’s disenchantment with the biblical interpretation of the creative process. in the context of his time one can understand his need to reinterpret the evidence that he found in a new, more coherent and intelligent way. so he came up with the idea of accidental mutations which may, in some cases, * correspondence: rober campbell, independent researcher. website: http://www.cosmic-mindreach.com e-mail: bob@cosmic-mindreach.com note: the articles presented in this issue are based on my book “downsizing darwin: an intelligent face for evolution” self-published in 1996 [3]. more information is available at my website [2]. dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 210-212 campbell, r., evolution as manifestation of cosmic order issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 211 endow a greater survival advantage leading to a natural selection of those mutations, and consequently to the emergence and adaptation of new species according to environmental pressures. there is abundant evidence to indicate that life has evolved up through the lower species, and adaptation according to natural selection is surely a part of it. but there is also abundant evidence to indicate that there is intelligent direction implicit in the evolutionary process, unfortunately all of it ignored by science. such questions are forbidden in the halls of science. it seems that mainstream science insists on placing itself in opposition to anything remotely suggesting spiritual overtones. and yet science openly strives to close the book on the whole story of creation, to create a belief system with itself as the only authority, a book it believes must ultimately be accepted by all people for all time. it’s a grand dream that many scientists have. one might even call it an open conspiracy. they would deny us all a spiritual reality, deny there is any transcending basis to values, deny there are any moral issues implicit in experience, and consign us all to oblivion. it is a truly strange phenomenon. to any intelligent impartial observer something is off the rails. we are destroying ourselves through dogma, either the dogma of science or that of religion, and there doesn’t appear to be any way to turn. with these thoughts in mind the following articles are written in two parts. part 1 is a critical review of the most outspoken hard line darwinist’s thinking, as expressed in one of his books (not required reading). richard dawkins is a very high profile figure in the academic community. but it is not enough to ferret out the countless flaws in the thinking that pervades evolutionary biology. one must offer a more credible alternative mechanism consistent with the evidence. it is to this end that part 2 is devoted to an intelligent face for evolution. to simply call it intelligent design is not enough. we must understand how intelligent processes work if an alternate methodology is to find practical scientific application. in short, richard dawkins [4-7] proudly defends darwinism in his popular book river out of eden. a river of genes springing from the blind fortuitous survival of dna sequences is the sole determining factor in the evolutionary process. only dna sequences he insists. but his supporting arguments are riddled with flaws. how strange that the whole of evolutionary biology should be infected with contradictions. blind belief without foundation is flaunted as vigorously as any repressive religion. nor is creationism the only option. the evidence across the broad sweep of time and space confirms that the evolutionary process unfolds in an ordered way that is implicitly intelligent. further, intelligence by its nature spans time and space. it integrates history. it is a living process that may learn by trial and error but reinvests that learning up through hierarchical levels in the long climb toward sentient awareness. left exclusively to genetic linkages, lessons from whole lineages of extinct species spanning eons would be lost forever. even plants display some sentience, from vascular systems that reach for the sky, to flowers that attract pollinating insects, anticipating processes extended in space and time. the invertebrates from flatworms to flies explore an array of sensory-motor systems spanning space and time at accelerated rates. the vertebrates from crocodiles and cows to chimpanzees add conscious reflection of emotional patterns, providing ever higher discretionary capacities to span space and time. lastly, language empowers humans to integrate the whole of space and time through extended ideas. but this leftdna decipher journal | november 2012 | volume 2 | issue 3 | pp. 210-212 campbell, r., evolution as manifestation of cosmic order issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 212 brain capacity invites a right-brain spiritual sense of propriety. and both brains are fueled by an emotional apparatus harnessed to the ancient brains of the crocodile and horse integrated into our cerebral anatomy. we three-brained creatures are specifically structured to span space and time. with anciently rooted aspirations fueled by our animal brothers we are obliged to reach for another rung in evolution’s ladder and grasp the essence of intelligence implicit in the cosmic order. references 1. charles darwin, on the origin of species. london: john murray (1859) 2. alfred r. wallace, on the law which has regulated the introduction of new species, annals and magazine of natural history, including zoology, botany, and geology 16: 184–196 (1855), 3. robert campbell, downsizing darwin: an intelligent face for evolution. mindreach library (1996). 4. http://www.cosmic-mindreach.com 5. richard dawkins, river out of eden: a darwinian view of life. basic books (1996). 6. richard dawkins, the blind watchmaker: why the evidence of evolution reveals a universe without design. w. w. norton & company (1996). 7. richard dawkins, the selfish gene. oxford university press (1990). dna decipher journal | december 2016 | volume 6 | issue 3 | pp. 185-189 185 pitkänen, m., are lithium, phosphate & posner molecule fundamental for quantum biology? exploration are lithium, phosphate & posner molecule fundamental for quantum biology? matti pitkänen 1 abstract in this article i compare the work of fisher proposing that phosphate ion and calcium phosphate known as posner molecule are fundamental for quantum neuroscience. phosphate ion show nuclear spin could serve as qubit able to get enzymatically entangled and make possible a transfer of qubits. posner molecule would serve as unit of quantum memory. i describe first what might be called lithium mystery, which served as a motivation of fisher and summarize also the tgd view about the role of lithium. the model of fisher for how phosphate ion and posner molecule could play a central role quantum neural processing is described. i also summarize the tgd view about the situation suggesting that posner molecule might indeed have deep role. what puts bells ringing is that elf radiation at frequencies equal to multiples of 15 hz cyclotron frequency for calcium ion in endogenous magnetic field bend = .2 gauss was found by blackman and others to have effects on vertebrate brain. furthermore, the cyclotron frequency of phosphate ion in endogenous magnetic field bend corresponds to the 10 hz alpha resonance frequency defining a fundamental biorhythm. 1 introduction i encountered a very interesting facebook link (see http://tinyurl.com/zyy3b4l) to the work of mathew fisher [2] (see http://tinyurl.com/hd3t6sr) related to quantum biology. i attach below the abstract of the article of fisher. the possibility that quantum processing with nuclear spins might be operative in the brain is proposed and then explored. phosphorus is identified as the unique biological element with a nuclear spin that can serve as a qubit for such putative quantum processing a neural qubit while the phosphate ion is the only possible qubit-transporter. we identify the ”posner molecule”, ca9(po4)6, as the unique molecule that can protect the neural qubits on very long times and thereby serve as a (working) quantum-memory. a central requirement for quantum-processing is quantum entanglement. it is argued that the enzyme catalyzed chemical reaction which breaks a pyrophosphate ion into two phosphate ions can quantum entangle pairs of qubits. posner molecules, formed by binding such phosphate pairs with extracellular calcium ions, will inherit the nuclear spin entanglement. a mechanism for transporting posner molecules into presynaptic neurons during a ”kiss and run” exocytosis, which releases neurotransmitters into the synaptic cleft, is proposed. quantum measurements can occur when a pair of posner molecules chemically bind and subsequently melt, releasing a shower of intra-cellular calcium ions that can trigger further neurotransmitter release and enhance the probability of post-synaptic neuron firing. multiple entangled posner molecules, triggering non-local quantum correlations of neuron firing rates, would provide the key mechanism for neural quantum processing. implications, both in vitro and in vivo, are briefly mentioned. 1correspondence: matti pitkänen http://tgdtheory.com/. address: karkinkatu 3 i 3, 03600, karkkila, finland. email: matpitka6@gmail.com. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/zyy3b4l http://tinyurl.com/hd3t6sr http://tgdtheory.com/ mailto:matpitka6@gmail.com dna decipher journal | december 2016 | volume 6 | issue 3 | pp. 185-189 186 pitkänen, m., are lithium, phosphate & posner molecule fundamental for quantum biology? in the sequel i describe the lithium mystery which served as a motivation of fisher and also tgd view about the role of lithium. the model of fisher for how phosphate ion and calcium phosphate known as posner molecule could play a central role quantum neural processing is described. i also present tgd view about the situation suggesting that posner molecule might indeed have deep role. elf radiation at frequencies equal to multiples of 15 hz cyclotron frequency for calcium in endogenous magnetic field bend = .2 gauss was found by blackman and others to have effects on vertebrate brain. furthermore, the cyclotron frequency of phosphate ion in endogenous magnetic field bend corresponds to the 10 hz alpha resonance frequency defining a fundamental biorhythm. 2 lithium mystery the starting point of fisher was a very interesting finding challenging the hypothesis about life as mere bio-chemistry. already in 1986, scientists at cornell university examined the effects of the two isotopes of lithium on the behavior of rats. pregnant rats were separated into three groups. one group was given li7, one group was given the isotope li6, and the third served as the control group. once the pups were born, the mother rats that received li6 showed much stronger maternal behaviors, such as grooming, nursing and nest-building, than the rats in either the li7 or control groups. li6 therefore as has a positive effect on maternal behaviour unlike li7. the chemistry is exactly the same. according to the popular article, fisher believes that the higher nuclear spin of li6 could give it special role.: in the article he talks about nuclear spin j = 1/2 which cannot be true since the spin must be even. as a matter fact, according to my nuclear physics by howard li7 has nuclear spin of j = 3/2 units whereas li6 has nuclear spin j = 1 so that neither of the above claims is correct. could the bosonic character of li6 nucleus provide an alternative explanation? in any case, the finding strongly suggests that magnetic fields are involved. lithium presumably li6 has also other positive effects. if the positive effects are indeed due to li6 isotope, the dose of lithium could be reduced by using only li6 isotope. i attach here the abstract of the article that i wrote as a reaction to discussions with my friend samppa who told about lithium [6] (see http://tinyurl.com/j44epwp). lithium has been used for more than 50 years as a mood stabilizer in manic depression. during last years lithium has been studied intensively and found that it can be used also in treatment of schizophrenia and many other brain disorders. the effectiveness of lithium is however difficult to understand in the standard framework of biology. in tgd framework organism-environment pair of standard biology is replaced with the triplet magnetic body organism -environment. magnetic body uses biological body as sensory receptor and motor instrument. this suggests that the re-establishment of communications of brain with some level of the magnetic body is how lithium causes its positive effects. magnetic body does not receive information about brain and cannot control it since dark lithium ions and corresponding cyclotron radiation are not present. the disorders caused by the lack lithium and other biologically important ions would therefore be something totally new from the perspective of standard neuroscience. tgd explanation for the effects of lithium relies on the notions of magnetic body and dark large heff = n× h photons, electrons, and ions and relies on cyclotron frequencies as frequencies assignable to the dark photons responsible for the communications between magnetic body and biological body. in this picture the charge of the ion and its total magnetic moment would be relevant rather than only nuclear magnetic moment characterizing also neutral atoms (which could also contribute to the magnetic moment of ion). cyclotron frequencies would replace larmor frequencies. 1. for li6 the cyclotron frequency is about 50.0 hz in the endogenous magnetic field bend = .2 gauss explaining the quantal effects of em fields at elf frequencies on vertebrate brain reported by the issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/j44epwp dna decipher journal | december 2016 | volume 6 | issue 3 | pp. 185-189 187 pitkänen, m., are lithium, phosphate & posner molecule fundamental for quantum biology? pioneers of bio-electromagnetism such as blackman [1] to occur at multiples of cyclotron frequency in this magnetic field for calcium ion and also for other biologically important ions. for ca+2 ion the cyclotron frequency is 15 hz. thanks to the large value of heff = n × h dark photons would have energies above thermal threshold. an attractive hypothesis is that the energies are in the range of bio-photon energies (visible and uv). 2. in the case of li6 the dark photons would make possible communication to and control by the magnetic body relevant for maternal behaviors. magnetic fields oscillating at 50 hz frequency are known to have biological effects [5]. the size of the corresponding magnetic body part would be obtained from the wavelength λ = 2πr (r denotes the radius of earth) of the lowest schumann frequency 7.8 hz as l = (7.8/50) × r = .98 × r. this suggests that dark magnetic flux tubes assignable with earth are involved: not however that the field strength is 2be/5. 3. for li7 the dark photons would have cyclotron frequency about 42.9 hz, which brings in mind the thalamocortical resonance with frequency around 40 hz assigned to consciousness at the time when the use of the word ”consciousness” ceased to be pseudo-science. the more abundant li7 (92.5 per cent) should be also important but could be associated with other kinds of biological functions. 3 phosphate, posner molecule, and cognition fisher as also other quantum biologists tries to understand quantum biology as an improvement of biochemistry. one assumes that standard quantum theory brings in small effects allowing to optimize biological functions. in the case of the avian navigation and also in many other situations the problem is that earth’s magnetic field is only 2 per cent of the minimum magnetic field at which the proposed radical-pair mechanism is found to work [7] (see http://tinyurl.com/jnxvdmf). to my opinion much more radical approach challenging the basics of quantum theory itself is necessary. fisher wants to identify the quantum mechanism behind neural activity assumed to rely on nuclear spins. this is quite a demanding challenge. one should understand long coherence time for nuclear spins representing the qubits, discover a mechanism transporting the qubit through the brain to neurons, identify a molecular scale quantum mechanism entangling qubits, identify a chemical reaction inducing quantum measurement of the qubits dictating the subsequent neuron firing, and understand what happens in nerve pulse transmission from preto post-synaptic neuron at quantum level. 1. fisher assigns fundamental qubit and the ability to develop lon lasting quantum entanglement with phosphate ion (see http://tinyurl.com/zgbgtwy). phosphate ion would be qubit transporter. the transfer of phosphate ion from apt to a molecule is fundamental part of metabolism and the tgd proposal is that a transfer of negentropic entanglement (purely tgd based notion involving p-adic physics as correlate for cognition) is in question. 2. enzyme catalyzed qubit entanglement would emerge in the reaction atp→ amp+ppi. ppi is diphosphate ion with entangled phosptate and the reaction ppi→ pi+pi would create two entanglement phosphates. the reaction rate is proposed to depend on whether the 2pi state is spin single or spin triplet. 3. quantum memory is assigned with so called posner molecule [(po4)−3)]6ca+2 9 made of 6 phosphate ions and 9 calcium ions would be the key player. posner molecule belongs to a family of calcium phosphates having as building bricks po−3 4 and ca+2 ions (see http://tinyurl.com/jftjmro). calcium phosphate is the principal form of calcium found in bovine milk and blood. 70 percent of bone consists of hydroxyapatite, a calcium phosphate mineral known as bone mineral. tooth enamel is composed of almost ninety percent hydroxyapatite. posner molecule is neutral since the charges of 9 ca ions and 6 phosphate ions cancel each other: 9 × 2 − 6 × 3 = 0. geometrically posner molecule can be described as a cube with calcium ions issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/jnxvdmf http://tinyurl.com/zgbgtwy http://tinyurl.com/jftjmro dna decipher journal | december 2016 | volume 6 | issue 3 | pp. 185-189 188 pitkänen, m., are lithium, phosphate & posner molecule fundamental for quantum biology? at corners and center and phosphate ions at the centers of faces. the nuclear spin of the posner molecule assignable to phosphates is 0, 1, 2, or 3. posner molecule has also reduced rotational degrees of freedom characterized by group z3 giving rise to pseudospin. posner molecule would be a carrier of phosphate qubits giving rise to (working) quantum-memory realized in terms of entangled posner molecules. 4. fisher proposes the notion of quantum entangled chemical reactions. this notion does not make sense if one identifies chemical reactions as processes involving state function reduction as assumed in chemical kinetics. the notion could make sense if chemical reactions are identified as unitary time evolutions for entangled systems such as posner molecules. in tgd framework the notion of entangled time evolutions could make sense in zero energy ontology (zeo). 5. nerve pulse tranmission from preto postsynaptic membrane would entangle neurons by entangling posner molecules. biochemistry is complex but to my opinion the proposed model is too complex to be feasible. my view is that the enormous complexity of the description based on biochemical reaction pathways reflects the failure to realize the presence of control level magnetic body. situation would be like trying to understand the functioning of computer program regarding it as mere physical phenomenon without any idea about its purpose. 4 tgd view in tgd framework both nuclear spins and angular moment of dark nuclei in the magnetic fields assignable to dark magnetic flux tubes would be important: larmor frequencies would be replaced with the sums of larmor and cyclotron frequencies assignable to (usually) charged particles. it is interesting to look whether the cyclotron frequencies of phosphate and posner molecule could teach something about their possible role. 1. phosphate po−3 4 with mass number 31+4×16 = 95 has cyclotron frequency 9.5 hz in the endogenous magnetic field bend = .2 gauss assumed in tgd model: this is 10 hz in the accuracy with which bend is known. this frequency is in alpha band! for smaller charges -2 and -1 one has frequencies 6.26 hz and 3.13 hz. in tgd framework the transfer of phosphate from atp to the acceptor biomolecule could be at the fundamental level transfer of negentropic entanglement from metabolites [3, 4]. this could reduce to the transfer the ends of the associated flux tubes between the molecules. 2. posner molecule is neutral since the charges of 9 ca ions and 6 phosphate ions cancel each other: 9× 2− 6× 3 = 0. being neutral posner molecule as a whole does not couple to the magnetic field except through its total magnetic moment. tgd proposal that ions form bose-einstein condensates encourages however to consider the possibility that the building bricks of posner molecule form separate bose-einstein condensates. one can ask whether this is possible also more complex calcium phosphates: could bones be much more than just passive building bricks? the simplest possibility is that 3 cooper pairs of fermionic po−3 4 molecules (as is easy to check by noticing that phosphorus and oxygen atoms are bosons and there are surplus 3 electrons: note that phosphorus nucleus is fermion and oxygen nucleus a boson) form a bose-einstein condensate a their own circular portion of flux tube. 9 bosonic ca+2 ions would form similar bose einstein condensate at their own flux tube portion. the value of heff proportional to the mass of the ion by heff = hgr hypothesis. the formation of cooper pairs of phosphate ions would conform with the conjecture of fisher that two phosphate ions can entangle. the cyclotron frequencies of these bose-einstein condensates would be 9.5 hz resp. 15 hz in bend = .2 gauss. this model could allow to improve the understanding about why the radiation at harmonics of 15 hz has effects on vertebrate brain and also about the realization of alpha rhythm as a control signal from magnetic body. fisher proposes that in nerve pulse transition two posner issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2016 | volume 6 | issue 3 | pp. 185-189 189 pitkänen, m., are lithium, phosphate & posner molecule fundamental for quantum biology? molecules fuse temporarily and produce a spray of ca+2 ions. this could make sense also in tgd framework. these observations put the bells ringing with a frequencies of 10 hz and 15 hz, one might say. unfortunately this frequency is not directly audible, so that i cannot hope that colleagues would hear the ringing! there are however some hopes: also 10 hz and 15 hz can be made audible as difference of frequencies fed to right and left ear! maybe some experimentalist could get interested! references [1] blackman cf. effect of electrical and magnetic fields on the nervous system, pages 331–355. plenum, new york, 1994. [2] fisher mpa. quantum cognition: the possibility of processing with nuclear spins in the brain). available at: https://arxiv.org/abs/1508.05929, 2015. [3] pitkänen m. macroscopic quantum coherence and quantum metabolism as different sides of the same coin: part i. in bio-systems as conscious holograms. onlinebook. available at: http: //tgdtheory.fi/public_html/hologram/hologram.html#metab, 2006. [4] pitkänen m. macroscopic quantum coherence and quantum metabolism as different sides of the same coin: part ii. in bio-systems as conscious holograms. onlinebook. available at: http: //tgdtheory.fi/public_html/hologram/hologram.html#molephoto, 2006. [5] pitkänen m. quantum model for bio-superconductivity: i. in tgd and eeg. onlinebook. available at: http://tgdtheory.fi/public_html/tgdeeg/tgdeeg.html#biosupercondi, 2006. [6] pitkänen m. lithium and brain . available at: http://tgdtheory.fi/public_html/articles/ lithiumbrain.pdf, 2016. [7] pitkänen m. can quantum biology really do without new physics? available at: http://tgdtheory. fi/public_html/articles/rpmtgd.pdf, 2016. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://arxiv.org/abs/1508.05929 http://tgdtheory.fi/public_html/hologram/hologram.html#metab http://tgdtheory.fi/public_html/hologram/hologram.html#metab http://tgdtheory.fi/public_html/hologram/hologram.html#molephoto http://tgdtheory.fi/public_html/hologram/hologram.html#molephoto http://tgdtheory.fi/public_html/tgdeeg/tgdeeg.html#biosupercondi http://tgdtheory.fi/public_html/articles/lithiumbrain.pdf http://tgdtheory.fi/public_html/articles/lithiumbrain.pdf http://tgdtheory.fi/public_html/articles/rpmtgd.pdf http://tgdtheory.fi/public_html/articles/rpmtgd.pdf introduction lithium mystery phosphate, posner molecule, and cognition tgd view login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x dna decipher journal | december 2017 | volume 7 | issue 2 | pp. 129-134 129 pitkänen, m., potential ”missing link” in chemistry that led to life on earth discovered essay potential ”missing link” in chemistry that led to life on earth discovered matti pitkänen 1 abstract the phosphorylation of short nucleotide sequences, amino-acid sequences, and lipids making possible formation of small cell membrane like structures is necessary for the formation of larger structures from their building bricks. as noticed, ribozymes catalyze only dephosphorylation. how rna was phosphorylated during rna era or were the amino-acids present all the time? it was recently discovered that an organic molecule known as diamidophosphate (dap) having chemical formula could do the job in presence of water and imidazol. dap could solve several problems simultaneously: how the short sequences of rna (later dna) and amino-acids emerged, and how the predecessors of cell membranes emerged. it is not however whether this process could have been fast enough or whether the slowness only made the first step painful. this problem will be discussed in the sequel. 1 introduction in the attempts to understand pre-biology the basic challenge is to understand how the needed short rna, dna, and amino-acid sequences managed to form. phosphorylation (see http://tinyurl.com/ y732fsd3) is known to be crucial for this process and means energization in standard bio-chemistry. organic phosphate (see http://tinyurl.com/cx9ukv9) possesses somewhat mysterious high energy phosphate bond, which stores energy and makes possible metabolism: in metabolic atp with three phosphates transforms to adp with two phosphates by giving one phosphate with high energy phosphate bond to the acceptor molecule, which is therefore phosphorylated. in the recent biology phosphorylation of various biomolecules such as dna, rna, amino-acid sequences is catalyzed by proteins known as enzymes known as phosphorylases. kinase is one particular enzyme transferring phosphate from atp to the acceptor molecule. proteins consist of amino-acids and would not be present in rna world, which serves almost as a standard model for the prebiotic period. ribozymes are catalysts formed from rna but they catalyze typically only the reversal of phosphorylation. the phosphorylation of short nucleotide sequences and amino-acid sequences, and also lipids making possible formation of small cell membrane like structures is necessary for the formation of larger structures from their building bricks. as noticed, ribozymes catalyze only dephosphorylation. how rna was phosphorylated during rna era or were the amino-acid present all the time? the popular article with the title ”potential ’missing link’ in chemistry that led to life on earth discovered” (see http://tinyurl.com/y9s56xnx) tells about a mechanism allowing phosphorylation during rna era in absence of enzymes. the discovery [2] (see http://tinyurl.com/y9kvgl24) is that an organic molecule known as diamidophosphate (dap) (see http://tinyurl.com/y88vecs2) having chemical formula po2(nh2)−1 2 could do the job in presence of water and imidazol. imidazol (see http://tinyurl.com/y8vgfr42) has chemical formulac3n2h4 and is a molecule possessing aromatic hetero-cycle consisting of 3 c atoms and 2 n atoms. remark: pyrimidine (see http://tinyurl.com/k3vxl9b) in turn is aromatic hetero-6-cycle consisting of 4 c atoms and 2 n atoms and having formula c4n2h4. dna (see http://tinyurl.com/ cpndtse) has as basic building bricks phosphates po− 4 having valence bonds with deoxy-ribose (see 1correspondence: matti pitkänen http://tgdtheory.com/. address: rinnekatu 2-4 a8, 03620, karkkila, finland. email: matpitka6@gamail.com. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/y732fsd3 http://tinyurl.com/y732fsd3 http://tinyurl.com/cx9ukv9 http://tinyurl.com/y9s56xnx http://tinyurl.com/y9kvgl24 http://tinyurl.com/y88vecs2 http://tinyurl.com/y8vgfr42 http://tinyurl.com/k3vxl9b http://tinyurl.com/cpndtse http://tinyurl.com/cpndtse http://tgdtheory.com/ mailto:matpitka6@gmail.com dna decipher journal | december 2017 | volume 7 | issue 2 | pp. 129-134 130 pitkänen, m., potential ”missing link” in chemistry that led to life on earth discovered http://tinyurl.com/qxv9kg8) molecules (containing 5-rings with 4 c atoms and one o). each sugar has valence bond with n of nucleoside c, t, a or g. c and t are pyrimidines with single aromatic 6-ring and a and g are purines obtained by fusing imidazol 5-ring and pyrimidine 6-ring to obtain purine double ring. by replacing one oh of de-oxyribose of dna with h one obtains rna. dap could solve several problems simultaneously: how the short sequences of rna (later dna) and amino-acids were formed, and how the predecessors of cell membranes emerged. it is not however clear to me whether this process could have been fast enough or whether the slowness only made the first step painful. this finding will be discussed in tgd framework. 2 how could the discovery relate to tgd inspired quantum biology? it is interesting to interpret the discovery in tgd framework. the basic question is whether the presence of dark atoms and electrons in bio-molecule distinguish between atomic physics, in-organic chemistry, and organic chemistry. usually organic chemistry is defined to be chemistry of carbon compounds, typically hydrocarbons. could it be that the formation of hydrocarbons involves dark variants of proton and electron identified as heff = n× h variants of ordinary proton and electron? 2.1 from atomic physics to chemistry how could one proceed from atomic physics to atomic physics to chemistry in tgd framework. the basic question is how to understand valence bond: it is not at all clear whether mere schrödinger equation allows to understand it. could the emergence of dark electrons allow their delocalization and formation of valence bonds? it has been known for decades that the heating of rare-earth metals leads to a mysterious loss of some valence electrons and the explanation would be the energy provided by heating kicks them to higher energy states by making some valence electrons dark [9]. the explanation would be in terms of dark electron orbitals for valence electrons which have radii scaled up by factor n2 and are analogous to rydberg states identified as orbitals with large value of principal quantum number and having very large radius. the dark variants of atoms have binding energy scale reduced by factor 1/n2 so that their formation requires energy feed (perhaps radiation at required frequencies). one or more valence electrons of ordinary atom could be dark so that the size of the orbital is scaled up by factor n2. the valence bond central for chemistry in general and in particular for basic biopolymers could contain dark electrons delocalized because of larger value of n than for the non-valence electrons. note that one could be n = n0 > 1 for ordinary atoms making in principle possible atoms with n < n0 with anomalous large binding energy also for the filled shells as the findings of randel mills indeed suggest [6]. surprisingly, dark electrons would be essential in ordinary chemistry thought to reduce to standard model physics! the increase of n reduces binding energy scale and requires energy feed. this would allow to understand why anabolism (see http://tinyurl.com/c8x8avz) that is generation of biopolymers from their building blocks by generating valence bonds requires energy feed and why catabolism (see http://tinyurl.com/cbx99fv) the splitting of biopolymers to their building blocks by splitting the valence bonds liberates energy. the valence bonds would be classified by the value of n and it is quite possible that in organic chemistry the values of n are larger than in in-organic chemistry. could this mean that valence bonds h and c and n and o have higher values in bio-chemistry? also the valence bonds between o and h in water could have larger value of n. to sum up, the transition from atomic physics to ordinary chemistry involved generation of dark electrons associated with valence bonds. the value of n for dark electrons can vary and allow hierarchy of evolutionary steps with increasingly delocalized valence electrons. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/qxv9kg8 http://tinyurl.com/c8x8avz http://tinyurl.com/cbx99fv dna decipher journal | december 2017 | volume 7 | issue 2 | pp. 129-134 131 pitkänen, m., potential ”missing link” in chemistry that led to life on earth discovered 2.2 from chemistry to bio-chemistry what about the step leading to a genuine bio-chemistry involving genetic code? magnetic body (mb) is the basic aspect of biochemistry according to tgd. pollack effect [1] (see http://tinyurl.com/ y8uxocch) leading to the formation of negatively charged regions exclusion zones (ezs) would involve generation of dark protons at magnetic flux tubes of mb with electrons left to the ez possible as ordinary particles [4]. also pollack effect requires feeding of energy, say as irradiation by photons. dna is stable against spontaneous hydration only inside cell membrane. this suggests that the ezs of pollack containing partially dark water molecules satisfying effectively the stoichiometry h3/2o allowed to stabilize dna. therefore ezs are excellent candidates for the predecessors of cell. the tgd inspired proposal is that dna strand for which each phosphate has negative unit charge is companied by dark analog of dna consisting of dark protons such that the states of 3-proton units are in one-one correspondence with dna, rna, trna and amino-acids and the degeneracies of the vertebrate genetic code (number of codons coding for given amino-acid) come out correctly [5] (see http://tinyurl.com/jgfjlbe). a more general picture is that ordinary chemistry is kind of shadow for the dynamics of dark matter at magnetic flux tubes doing its best to emulate it. this would explain also why genetic code has also other variants. it would be the emergence of dark protons with large enough value of n, which would distinguish between ordinary chemistry and bio-chemistry. water is basic element of life and hydrogen bonding is responsible for the formation of water clusters certainly one of the key aspects of bio-chemistry. hydrogen bonds (see http://tinyurl.com/bntn28n) appear between highly electronegative (see http: //tinyurl.com/pbh6r6c) atoms such as o, n, and f (electronegativity is roughly the tendency to attract electrons). what distinguishes hydrogen bond from valence bond is that it is proton rather than electron, which is delocalized. this suggests that the delocalized proton is dark proton at magnetic flux tube connecting the hydrogen bonded molecules. 2.3 the emergence of metabolism in the proposed framework the first basic aspect of life would be the generation of dark electrons and protons using energy feed and their transfer between molecules and their generation by providing the needed energy. 1. metabolism (anabolism) would provide the energy needed to transform ordinary atom (that is electron bound to it) to a dark atom with large value of heff/h = n. this requires energy since the binding energy is proportional to 1/n2 and reduced in the process. this is quite generally true for all dark variants of quantum states. one can say that the increase of the complexity of the system by increasing n characterizing its ”iq” requires metabolic energy (in adelic physics [10, 11] ”iq” has a concrete interpretation as cognitive resources). therefore the first steps of prebiotic life was the emergence of energy feed mechanism making possible the increase of n. 2. i have considered the possibility that the period of prebiotic life preceding the the emergence of chemical storage of energy used dark nucleosynthesis [7] (see http://tinyurl.com/y7u5v7j4) as the source of metabolic energy. the recently discovered life-like properties [3] in a very simple system consisting of negatively charged plastic balls in the plasma of ar+ ions allows to develop rather detailed ideas about this phase of life [8] (see http://tinyurl.com/yassnhzb). 3. a fundamental question is about the step leading to the chemical storage of metabolic energy to valence bonds with non-standard value of n. solar radiation could have generated both negatively charged ezs identifiable as possible predecessors of cell membrane and valence bonded molecules storing metabolic energy. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/y8uxocch http://tinyurl.com/y8uxocch http://tinyurl.com/jgfjlbe http://tinyurl.com/bntn28n http://tinyurl.com/pbh6r6c http://tinyurl.com/pbh6r6c http://tinyurl.com/y7u5v7j4 http://tinyurl.com/yassnhzb dna decipher journal | december 2017 | volume 7 | issue 2 | pp. 129-134 132 pitkänen, m., potential ”missing link” in chemistry that led to life on earth discovered 2.4 about bio-catalysis without bio-catalysis biochemical reactions leading to the formation of biopolymers and cell membrane would be quite too slow. here phosphorylation enters the game. 1. the tgd based model for bio-catalysis relies on the temporary reduction of heff = n×h liberating energy kicking the reactants over potential wall. after this step the catalyst at least in the ideal situation receives the energy and the atom becomes dark again. 2. acid catalyst gives a proton and base catalyst gives an electron. most bio-catalysts are acid catalysts. the tgd based interpretation should rely on the possibility of dark valence electrons and dark protons at flux tubes. since base catalysts are associated with non-organic chemistry, the identification of the electron given by base catalyst as dark electron looks natural. acid catalysts would give dark proton. bio-catalysts are usually activated by phosphorylation and de-activated by de-phosphorylation but there are exceptions to this rule. this can be understood if the catalyst activates a molecule acting as a switch for a reaction. catalysts related to phosphorylation are known as phosphotransferasess (see http://tinyurl.com/y87crqad) and contain kinases transferring phosphate from atp to the acceptor molecules. phosphatases (see http://tinyurl.com/ybf9onba) remove phosphate from the target molecule: they are hydrolases (see http://tinyurl.com/y88zayj7) and use water to remove the phosphate and to hydrate the molecule. 2.4.1 the difference between organic and inorganic phosphates phosphate appears as too variants: organic and inorganic. 1. organic phosphates bound to biomolecules have charge -1. some electrons of organic phosphate ion have transformed to valence electrons and are therefore dark. also some protons one dark proton per dark electron to not affect the observed charge in short scales would be dark and at the magnetic body of the organic phosphate. both dark protons and dark electrons would be present and give rise to somewhat mysterious high energy phosphate bond. 2. free phosphate in water environment appears in ionized variants hnpon−4 4 and is regarded as in-organic and have negative charge 4-n. in inorganic phosphate some dark protons and ordinary electrons giving rise to the negative charge have combined to hydrogen atoms. the larger the number of hydrogens is, the higher the level of inorganicity is. the fractions of variants of free phosphate in water depend on ph characterizing the density of protons present. could ph in fact characterize the fraction of dark protons at magnetic flux tubes? or could it also characterize the fraction of dark hydrogen atoms present. similar question applies to the counterparts of ph for other biologically important ions. 2.4.2 about phosphorylation and the interpretation of dap at chemical level phosphorylation attaches phosphate ion to the hydroxyl group (r-oh) of the acceptor molecule. at deeper level phosphorylation would give dark electron to the acceptor molecule and dark proton to its mb. phosphorylation would increase the quantum coherence length: the formation of short rna, amino-acid sequences and of cell membrane like structures would be a basic example of this. what about the interpretation of the role of dap in this framework? dap has charge -1 as also the phosphate bound to dna and rna have (in atp the outermost phosphate has charge -2). dap is very similar to the phosphate in dna and rna and expected to carry high energy phosphate bond. in tgd framework it would possess both dark valence electrons and dark protons at magnetic flux tubes with issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/y87crqad http://tinyurl.com/ybf9onba http://tinyurl.com/y88zayj7 dna decipher journal | december 2017 | volume 7 | issue 2 | pp. 129-134 133 pitkänen, m., potential ”missing link” in chemistry that led to life on earth discovered only one ordinary electron responsible for the charge of dap. due to the properties of phosphatase the phosphorylation would be very simple process at the level of dark electron and proton. hence dap and imidazole could make possible the phosphorylation. 2.4.3 about dephosphorylation and phosphoryl transfer the scanning of web shows that some sources talk of dephosphorylation and some sources about phosphoryl transfer reactions and it remained unclear to me whether the two terms really have the same meaning. in any case, in tgd framework one can distinguish between these notion. dephosphorylation could mean either phosphoryl transfer (transfer of phosphate between donor and acceptor molecules) or ”dropping” of organic phosphate to water environment and giving it negative additional negative charge (the transfer would be now to water environment) and making it inorganic. 1. phosphoryl would transfer removes po− 4 group and presumably also the associated dark proton from the target and transfers them to the acceptor molecule and its mb. i have proposed that reconnection of flux tubes transforms the flux tubes entering to the donor molecule to that associated with the acceptor molecule so that dark proton is automatically transferred. in atp-adp process the phosphate group and presumably also the dark proton and electron would be transferred to the acceptor molecule from atp. adp is dephosphorylated and acceptor phosphorylated. 2. in ”dropping” the outcome would be in-organic phosphate denoted by pi, which is a mixture of hpo−2 4 and h2po−1 4 . one interpretation is that 1 or 2 dark protons from magnetic flux tubes have transformed to ordinary protons and combined with electrons to form hydrogen atoms. this operation would reduce the number of dark particle and thus the ”evolutionary level” of the system. dephosphorylation is known to lead to a decomposition of the donor molecule to smaller structures, indicating the reduction of heff/h = n and thus of quantum coherence length. in rna world dephosphorylation would be catalyzed by ribozymes and in some important cases also in the recent biology. dephosphorylation would reduce quantum coherence length and lead to the decomposition of structures to smaller ones: mrna splicing is one example of this. catabolism of nutrients and the decay process of dead organic matter provide further basic examples. catabolism (see http://tinyurl.com/cbx99fv) of nutrients and the decay process of dead organic matter suggest what happens. in the first preliminary step of catabolism catalysts are involved. at the second step of catabolism inorganic phosphate is formed, which suggests that the number of dark protons is reduced in the process. this conforms with the reduction of the value of heff/h = n. references [1] the fourth phase of water : dr. gerald pollack at tedxguelphu. available at: https://www. youtube.com/watch?v=i-t7tcmudxu, 2014. [2] gibard c et al. phosphorylation, oligomerization and self-assembly in water under potential prebiotic conditions. nature chemistry. doi:10.1038/nchem.2878, 2017. [3] gogia g and burton jc. emergent bistability and switching in a nonequilibrium crystal. arxiv.org. available at: http://tinyurl.com/ychho4l8, 2017. [4] pitkänen m. pollack’s findings about fourth phase of water : tgd view. available at: http: //tgdtheory.fi/public_html/articles/pollackyoutube.pdf, 2014. [5] pitkänen m. about physical representations of genetic code in terms of dark nuclear strings. available at: http://tgdtheory.fi/public_html/articles/genecodemodels.pdf, 2016. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/cbx99fv https://www.youtube.com/watch?v=i-t7tcmudxu https://www.youtube.com/watch?v=i-t7tcmudxu http://tinyurl.com/ychho4l8 http://tgdtheory.fi/public_html/articles/pollackyoutube.pdf http://tgdtheory.fi/public_html/articles/pollackyoutube.pdf http://tgdtheory.fi/public_html/articles/genecodemodels.pdf dna decipher journal | december 2017 | volume 7 | issue 2 | pp. 129-134 134 pitkänen, m., potential ”missing link” in chemistry that led to life on earth discovered [6] pitkänen m. hydrinos again. available at: http://tgdtheory.fi/public_html/articles/ millsagain.pdf, 2016. [7] pitkänen m. cold fusion, low energy nuclear reactions, or dark nuclear synthesis? available at: http://tgdtheory.fi/public_html/articles/krivit.pdf, 2017. [8] pitkänen m. life-like properties observed in a very simple system. available at: http://tgdtheory. fi/public_html/articles/plasticballs.pdf, 2017. [9] pitkänen m. mysteriously disappearing valence electrons of rare earth metals and hierarchy of planck constants. available at: http://tgdtheory.fi/public_html/articles/rareearth.pdf, 2017. [10] pitkänen m. philosophy of adelic physics. in trends and mathematical methods in interdisciplinary mathematical sciences, pages 241–319. springer.available at: https://link.springer. com/chapter/10.1007/978-3-319-55612-3_11, 2017. [11] pitkänen m. philosophy of adelic physics. available at: http://tgdtheory.fi/public_html/ articles/adelephysics.pdf, 2017. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.fi/public_html/articles/millsagain.pdf http://tgdtheory.fi/public_html/articles/millsagain.pdf http://tgdtheory.fi/public_html/articles/krivit.pdf http://tgdtheory.fi/public_html/articles/plasticballs.pdf http://tgdtheory.fi/public_html/articles/plasticballs.pdf http://tgdtheory.fi/public_html/articles/rareearth.pdf https://link.springer.com/chapter/10.1007/978-3-319-55612-3_11 https://link.springer.com/chapter/10.1007/978-3-319-55612-3_11 http://tgdtheory.fi/public_html/articles/adelephysics.pdf http://tgdtheory.fi/public_html/articles/adelephysics.pdf introduction how could the discovery relate to tgd inspired quantum biology? from atomic physics to chemistry from chemistry to bio-chemistry the emergence of metabolism about bio-catalysis the difference between organic and inorganic phosphates about phosphorylation and the interpretation of dap about dephosphorylation and phosphoryl transfer login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 383-384 383 brief biography graham smetham, b.a., studied mathematics at essex university, england and philosophy of religion at sussex university. during his time at sussex he taught a subsidiary course for scientists on the interconnections between western science and eastern philosophical perspectives and it was through the investigations undertaken during the preparations for this course that he began to have the insights which later developed into wide ranging and detailed explorations contained in his first book quantum buddhism: dancing in emptiness. at sussex he was also part of the religious studies society and at one of its meetings he met the inspirational western theravadin monk ajahn sumedho, then the abbot of chithurst monastry, sussex. ajahn sumedho electrified the audience with his joyful effervescent presence and wisdom. at the time graham was becoming increasingly disillusioned with the western academic practice of endless conceptual juggling with no transformational practice and the contact with the community of chithurst monks and nuns convinced him of the need for both intellectual understanding and transformative meditation practice. although at that time graham had a publisher eager to publish his ph.d. work, illness and increasing disillusionment with western-style academic life led him to abandon an academic career and he gave up working on the ph.d., subsequently he began to lose contact with his intellectual and spiritual roots as he pursued other aspects, ultimately less fulfilling, of life’s pathways. during this time, however, buddhism and the philosophy of science always played a part in the background as he was always drawn to these subjects and somehow ‘knew’ that they were significant for him. he always had a strange feeling that something which had been left behind for the moment was still lingering in the wings. then, some twenty years after leaving sussex university, at a time of extreme personal crisis, graham returned to a serious meditation practice, something that had fallen by the wayside. during one meditation session he was astonished to have a profound meditation vision, like having a cinema screen inside his head, during which he was surrounded by an assembly of manjushris whilst a bowl of orange nectar at his heart radiated channels of orange nectar to the hearts of the surrounding manjushris. graham was further astonished to come across a book a week or two later in which the vision was described as being one of a set used by buddhist practitioner-philosophers prior to writing dharma texts. graham subsequently joined a buddhist community and resumed the researches that he had abandoned twenty years earlier. the result is quantum buddhism: dancing in emptiness–reality revealed at the interface of quantum physics and buddhist philosophy. graham has written three more books: the grand designer: discovering the quantum mind matrix of the universe, quantum buddhist wonders of the universe and quantum buddhism and the higgs discovery: the power of emptiness. further details of these can be found at www.shunyatapress.com. further details of the first book, and some free articles, can be found at www.quantumbuddhism.com. graham is currently working on his fifth book evolution: the greatest illusion on earth, the articles in the current issue are draft chapters from this work. http://www.shunyatapress.com/ http://www.quantumbuddhism.com/ dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 383-384 384 login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x original-review-letter-invited article dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 011-024 gariaev, p. p., friedman, m. j., & leonova-gariaeva, e. a., principles of linguistic-wave genetics issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 11 article principles of linguistic-wave genetics peter p. gariaev*, mark j. friedman & ekaterina a. leonova-gariaeva abstract to create an organism, two genetic programs are required. the first one is geometric, i.e. a scheme, how to design the body. the second program is in the form of a meaningful text which contains instructions and explanations how to use the first program, how to understand and build the organism. these programs exist in the form of “dna video tapes”, which are used by the genetic apparatus, acting like a bio-computer. when the bio-computer reads these video tapes, sound and light images appear that constitute the movie program of the development of the organism. when the creation of a grown-up organism is completed, the movie ends. then the second movie starts, which contains the instructions for maintenance of the organism for indefinitely long time. unfortunately, the videotapes containing information about a perfectly healthy organism, get corrupted with time, errors accumulate (dna mutations). the instructions accumulate errors and the organism gets sick, grows old and dies. it is very likely that these dna video tapes can be renewed and corrected. with this new understanding of how our genetic apparatus works, completely new technologies for healing a person and extending a person‟s life become feasible. and this is the essence of wave genetics and its practical applications to come. key words: dna, genetic program, biological science, crisis, wave genetics. 1. genetics and its problems “central dogma” of genetics the genetic apparatus of every organism on earth, including humans consists of chromosomes, where all genetic information of an organism, such as dna or rna, is stored. the paradigm or “central dogma” of genetics and molecular biology states that: 1) the genetic apparatus operates as a purely material structure. 2) all the functions of genetic control of an organism are localized in approximately 2% of dna, the so called coding dna of an organism. the remaining 98% of the *correspondence author: peter gariaev, ph.d., academician russ.acad. natur.sci and russ. acad. med./tech. sci., director of quantum genetics inst. address: russia, maliy tishinskiy per. 11/12 25, moscow 123056, russia. email: gariaev@mail.ru mark j. friedman, ph.d., professor, mathematical sciences department university of alabama, huntsville, al 35899. http://www.math.uah.edu/friedman/ e-mail: friedman@math.uah.edu ekaterina a. leonova-gariaeva, ph.d. mailto:gariaev@mail.ru http://www.math.uah.edu/friedman/ mailto:friedman@math.uah.edu dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 011-024 gariaev, p. p., friedman, m. j., & leonova-gariaeva, e. a., principles of linguistic-wave genetics issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 12 geneticapparatus code nothing, and are garbage or junk dna, which mainly represents a graveyard of virus dna. the 2% coding dna code proteins and rna. note however that genes of a human or genes of a fly or genes of a warm or genes of a plant are almost indistinguishable. the biologists and geneticists use the language of analogies and metaphors to explain how genetic apparatus operates. the genetic apparatus consisting of 46 chromosomes is viewed as a library consisting of 46 volumes or books. each book (a chromosome), contains a text (instructions of how to build an organism) which consists of sentences (dna) consisting of words (genes). and each word (a gene) consists of 4 letters (certain “chemical letters”), i.e. the “genetic alphabet” consists of only 4 “letters”. the material realizations of the dna molecules are famous double helixes, consisting of segments which are genes. in essence, genetic apparatus operates as follows. the texts, written in the “dna language”, are first translated by the organism into the “rna language” and then into the “protein language. and proteins are the stuff that we are mostly made of (not counting water). proteins perform two principle functions in the organism: they metabolize substances that we eat and participate in the morphogenesis, i.e. development of the spatial-temporal organization of an organism. here texts are 2% coding dna, which are matter and matter only, like a physical book. and the analogy with a book ends here. what genetics currently cannot explain we point here to some important well established facts within genetics which “central dogma” of genetics cannot explain. as everyone knows, huge biological differences between different species are transmitted from parents to children. in other words, there are huge genetic differences between different organisms. at the same time, genes and proteins are practically the same for different species. hence can think about proteins as a set of “bricks” that can be used to build and maintain all kind of “houses”, i.e. organisms: plants, animals, humans. an unresolved problem: how to explain huge differences in the morphogenesis, i.e. in the development of an organism from an embryo, between different species? genome (total sum of all genetic material) of an organism cannot consist of 98% of garbage. this is nonsense from the perspective of evolution, which throws away anything unnecessary. geneticists and embryologists discovered existence of special proteins which determine the shape and size of particular parts of an embryo, i.e. a hand, an ear, etc. however, this description contains a key unresolved problem, namely, some of these proteins are synthesized in one place of an organism, while their action in the form of a command is immediately expressed in another place of the embryo separated from the first one by hundreds of cells. there is no explanation for this immediate distant transmission of the command. dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 011-024 gariaev, p. p., friedman, m. j., & leonova-gariaeva, e. a., principles of linguistic-wave genetics issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 13 2. experimental data questions “central dogma” of genetics and the paradigm of life sciences some critical experimental data have been rapidly accumulating over the recent decades. this data unambiguously points to significant gaps and inconsistencies in “central dogma” of genetics. moreover, this data challenges us to find courage in ourselves to rethink and revise the whole premises of our understanding of the nature of life. we summarize here the highlights of this data. dna phantom effect a quartz cuvette with a dna sample is moved from one location to another. and a trace, a phantom, is left in the air in the original location of the sample. this phenomenon was registered using the laser spectroscopy method by p. gariaev in 1984 in russia and by the group of r. pecora in 1990 in the u.s.a. gariaev also investigated the stability of the phantom and he found the following. after blowing the phantom away by the gaseous nitrogen, it comes back in 5-8 minutes. and the phantom disappears completely after 1 month. we remark that sound waves radiated by the dna molecules were registered in these experiments. dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 011-024 gariaev, p. p., friedman, m. j., & leonova-gariaeva, e. a., principles of linguistic-wave genetics issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 14 dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 011-024 gariaev, p. p., friedman, m. j., & leonova-gariaeva, e. a., principles of linguistic-wave genetics issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 15 phantom dna effect. appearance of a “dna phantom” when using a correlation laser spectroscopy (spectrometer "malvern") method. 1 st figure, top: the background spectrometer readings before introduction of a water solution of a dna sample. 2 nd figure from the top: dna sample in the form of a water solution (3ml, 1mg/ml in a quartz cuvette) is inserted into the spectrometer. the dynamical spectrum of fluctuations of dna molecules is registered. 3 rd figure from the top: the cuvette with the dna sample is removed from the spectrometer. and one would naturally expect to see the background spectrometer readings, like at the 1 st figure. however, instead the spectrometer registers presence of certain fine structures, a “dna phantom”, in the same location where the cuvette with the dna sample initially was. 4 th figure from the top: the spectrometer readings in 10 minutes after the removal of the cuvette with the dna sample. after the cuvette part of the spectrometer was cleared by gaseous nitrogen, the spectrometer started giving the background readings, like in the 1st figure above, but in 5-8 minutes a “phantom” was registered again. this procedure was repeated many times, and each time a “dna phantom” would return. approximately in one month the “phantoms” gradually disappeared, or ceased to be registered, shifting beyond limits of sensitivity of the spectrometer. in 2005 a group of p. gariaev in russia performed the following experiment. dna samples were exposed to electromagnetic fields in certain frequency ranges. as a result, various luminous dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 011-024 gariaev, p. p., friedman, m. j., & leonova-gariaeva, e. a., principles of linguistic-wave genetics issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 16 wave structures were created in the air nearby. they were recorded on film. these amazing phantom structures were found to move along complicated trajectories. moreover, they mimicked the shape of the dna sample and some objects surrounding it. effect of multi-replication of the dna sample and of some objects surrounding it. a dna sample from a cow‟s spleen in the form of an air dried preparation is placed in a cell made of aluminum foil. the sources of the excitation em (electromagnetic) fields in the range from ultra-violet to infra-red ranges are placed above the preparation. on the left: the control, the sources of the em fields are switched off. on the right: the experiment, the sources of the em fields are switched on. several luminous wave patterns are visible. they are replicas of the dna, of the light sources, and of the equipment used for the dna excitation. all the replicas initially move to the right. however, once the dna preparation is touched mechanically, the replicas start moving to the left, and then disappear in 5-8 seconds. phantom leaf effect in 1975 v. adamenko in russia performed the following experiment. after a part of a living leaf was cut and the remaining part was placed into a high frequency electromagnetic field, a visual image of the whole leave appeared. in other words, a phantom image of the cut part appeared which lived for 10-15 seconds and could be recorded on film. the experiment was reproduced by the gariaev group and many other laboratories in the world. dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 011-024 gariaev, p. p., friedman, m. j., & leonova-gariaeva, e. a., principles of linguistic-wave genetics issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 17 dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 011-024 gariaev, p. p., friedman, m. j., & leonova-gariaeva, e. a., principles of linguistic-wave genetics issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 18 cytopathic (cell pathological) “mirror” effect during the period from 1980 to 1990 a group of v. kaznacheev in russia performed a series of experiments to investigate the following phenomena. two identical cell cultures were placed into hermetically sealed glass containers separated from each other by a quartz barrier. a pathology was introduced into one of those cultures. within 2-3 days the second cell culture displayed the same pathology. distant interaction between embryos in 2000 v. burlakov in russia discovered the following phenomena. two embryos of certain fish in different embryonic stages of their development were placed into hermetically sealed glass containers separated from each other by a quartz barrier. after several weeks the embryos started to display malformations. and what is even more interesting, the types of malformations were dependent on the differences in embryonic stages of development between the two embryos. in particular, for the same embryonic stage of one embryo, different embryonic stages of the other one induced different malformations for the first one. according to the established embryogenethis theory, and biology, in general, any distant interaction between embryos is impossible. holographic transmission and programming of the morphogenic information in 2000 v. budakovski in russia performed the following experiment. he recorded a fragment of a tissue of a raspberry plant on a hologram using a red laser and then transmitted the hologram to a raspberry plant tumor (callus). and after several months the callus developed into a raspberry plant. the plant science cannot explain these results. wave genes heal diabetes in rats these are more advanced experiments than those described before, and they are based on the principles and technology of wave genetics (see section on wave genetics below). three series of experiments with identical protocol were conducted by the groups of p. gariaev in 2000 in moscow russia, in 2001 in toronto, canada, and in 2005 in nizhni novgorod, russia. the goal of the experiments was to test new technology for regenerating damaged pancreas. pancreas is an endocrine gland which has several important functions, the major one being production of insulin, a hormone responsible for sugar metabolism. a control group of rats was injected a lethal dose of a poison called alloxan which destroys pancreas, the hormone responsible for insulin production in an organism. as a result, all the rats in the control group developed type 1 diabetes (high blood glucose concentration level) and died within 4-6 days. then the same lethal dose of alloxan was injected to another group of rats. and when the rats in this second group reached the critical condition, they were exposed to a healing wave information. as a result of that exposure, the sick rats got healed: their blood sugar level got normalized and their pancreas got regenerated. this healing wave information was produced by a laser bio-computer when the laser beam scanned the healing matrix. and this healing matrix was created when the bio-computer read information from the pancreas and spleen which were dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 011-024 gariaev, p. p., friedman, m. j., & leonova-gariaeva, e. a., principles of linguistic-wave genetics issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 19 surgically removed from healthy newborn rats of the same species as those used in the alloxan experiments. one can explain the results of the experiment using the following analogy. the pancreas gland contains dna-movies with information about healthy condition of the pancreas in its genetic apparatus. and this video morphogenic information programmed the stem cells of sick rats to regenerate their pancreas gland. combined statistics for all 3 series of experiments is as follows. altogether, around 90% of all the rats had their pancreas gland restored and their health recovered. in some of the experiments the bio-computer was modified to allow successful transmission of the healing information to sick rats at the distance of up to 20 kilometers. note, that no known physical fields have the capability to transmit such extremely week signals with such unbelievably powerful results. blood glucose concentration over time as a function of the alloxan injection and the consecutive laser bio-computer treatment by the wave information. day of the experiment the healing effect of the treatment of sick rats by the wave information produced by a laser biocomputer. in this experiment, the distance from the healing matrix, scanned by the laser beam, to the sick rats was 1cm. dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 011-024 gariaev, p. p., friedman, m. j., & leonova-gariaeva, e. a., principles of linguistic-wave genetics issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 20 3. a new paradigm for life sciences the experimental data presented above represents critical evidence that forces us to conclude that some key elements are missing in our current understanding on life. in other words, our western scientific paradigm is incomplete. and we now articulate an extended paradigm which provides a natural and simple conceptual framework to account for those experiments. of course, many researchers made contribution in this area and we do not claim originality. we hope that our emphasis on connections to experimental data will stimulate research in this new and exciting area. we are guided by a famous principle in philosophy of science known as occam‟s razor principle. this principle says that one should always make the simplest possible or “minimal” theoretical assumptions to account for new knowledge being incorporated into an existing theory. we remark that the wave genome theory, being developed by the group of p. gariaev, is one of the first examples of a scientific theory emerging within this new paradigm. and it will be outlined below. postulates of the new paradigm 1) all living organisms consist of two substances: the material substance and the energy informational (ei) (or subtle) substance. 2) the key property which distinguishes the ei substance, and the corresponding to it ei field, from all substances and fields known in modern physics is that the ei substance is omnipresent, i.e. it is present simultaneously at eat each point in space of our three dimensional material world. this means, in particular, that the distance between ei substances of any two material objects in our three dimensional world is always zero, no matter how far are they located physically from each other. 3) in agreement with postulate 1), we assume that each living organism exists at two levels: the material level and the ei level. 4) the two levels of an organism are intimately linked with each other and affect the condition of each other as well as reflect the condition of each other. moreover, the ei level is the leading one. 5) we define life as a dynamic exchange of energy and information between a physical organism and its ei (or subtle) counterpart. application of the new paradigm to explain the anomalous experimental data we illustrate here that our extended paradigm can easily account for the experiments descried in section 2. dna phantom effect. this experiment can be interpreted as follows. in the process of taking the laser spectroscopy measurements, a laser ray was sent to the dna sample. during that time dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 011-024 gariaev, p. p., friedman, m. j., & leonova-gariaeva, e. a., principles of linguistic-wave genetics issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 21 some information and energy was transmitted from the dna sample to its counterpart at the ei level. after the (material) dna sample was removed, the process of transmission of information and energy was reversed. specifically, the dna sample at the ei level was still at the same place, and it started sending information and energy back to the same physical location from which the material dna sample was removed. and as result, a dna phantom was detected at the same physical location. distant interaction between embryos. this experiment can be interpreted as an exchange of information and energy along the following chain (the first embryo at the material level) -> (the first embryo at the ei level) ) -> (the second embryo at the ei level) -> (the second embryo at the material level). obviously the directions in the chain can be reversed. wave genes heal diabetes in rats. this experiment can be interpreted similarly to the previous one. one difference would be the following. to explain transmission of the healing information to sick rats at the distance of 20 kilometers without energy expenditure, we need to take advantage of postulate 2), which in this case says that the distance between ei pancreatic dna recording in the wave bio-computer and the ei pancreatic dna of sick rats is zero, and hence we do not need energy to transmit the information. 4. wave genetics brief historical perspective the concept of biological field has been developed by a number of researchers. due to very limited space, we only mention two names. a. gurvitch in russia around 1920 pointed to a necessity to introduce the concept of biological field of a chromosome, as complimentary to genes, to account for special organization of an organism. according to r. sheldrake, uk, creation may be viewed as a living organism. this ancient concept challenges the notion of the universe as a mechanism with god as the great mechanic. his theory of "formative causation" implies a non-mechanistic universe, governed by laws which themselves are subject to change. the hypothesis of morphic resonance and morphic fields that he has developed is as an alternative to mechanistic thinking in biology. the concepts of wave genetics of gariaev and his group have been nurtured by the existing tradition that has facilitated their breakthrough in both experimental and theoretical directions. basic principles of wave genetics 1) 98% garbage dna is not actually “garbage dna”, but is a supercode, and this code (or codes) are of a higher level than those coding rna and proteins. this “higher level” is the “wave level”. 2) genome is a quasi intelligent system. 3) the function of the wave level of genetic coding is to program the spatial-temporal organization of an organism. dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 011-024 gariaev, p. p., friedman, m. j., & leonova-gariaeva, e. a., principles of linguistic-wave genetics issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 22 traditionally, genetics talks about dna, rna and proteins‟ speech and texts only. the standard linguistic structures of genome are realized at the material level in the form of sequences of “chemical letters” in a dna chain consisting of the 2% coding dna. in wave genetics the texts are realized at the material level in the form of sophisticated dynamic holograms (gene-holograms) in liquid crystals of the chromosome continuum. dna wave bio-computer short term information on gene-holograms is the result of interference recording on the intercellular water structures of spatial light and sound images of the current condition of cells. and these images are read by the light and sound radiations of the chromosomes, transmitted to the neighboring cells informing them about the condition of the cell sending the information. such an operation is performed by each cell in the organism, and there a billions of those. thus all the cells in the organism form a combined unified informational space, which functions like a dna wave bio-computer. this bio-computer processes, in real time, information about metabolic processes in cells. another type of bio-holographic information is of morphogenetic nature, and therefore it is fixed for a particular organism. it changes in time very slowly in the process evolution of bio systems and is inherited. the dna wave bio-computer a quasi intelligent system, which operates with its own languages, similar to human ones, which we are only beginning to understand. the linguistic structures of genome at this level are true speech and true texts. by this we mean that quasi intelligent decisions are made regarding regulation of the structure and functions of an organism and its parts. genome: a quasi intelligent system classical genetics has discovered experimentally that genetic rna texts contain ambiguous words (homonyms) which may have more than one meaning, and the choice of the meaning is determined by the context. the significance of this discovery which was missed by genetics, is as follows. these words (homonyms) code critically significant molecules: proteins. if such a word-code has two meanings, and one of them is wrong for creation of a particular required protein, this will result in a biochemical accident and death of the organism. so, for example, the word 'ring' can code two different meanings: „a circle’ and „a place of competition’ of boxers. in order to give the precise and unique meaning to a homonym, the genetic apparatus must first „comprehend’ the meaning of the rna text and only then make a decision, what precise meaning to give to a word-homonym. this example clearly illustrates that the genetic apparatus has quazi-intelligence and is capable to quazi-thinking at the molecular level and at the level the genome-biocomputer. wave genetics explains some puzzling real life phenomena telegony. this is a phenomenon known to occur among both animals and humans which cannot be explained from the perspectives of classical genetics. it consists in that when a female has her first sexual intercourse and then years later gives birth to a child from another male, her child dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 011-024 gariaev, p. p., friedman, m. j., & leonova-gariaeva, e. a., principles of linguistic-wave genetics issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 23 may have genetic characteristics of her first sexual partner. for example, a white woman who had originally sexual intercourse with a black man, may later in her life give birth to a mixed race baby from a white man. the wave genetics considers this as a real life example of dna phantom effect, and views it as a striking confirmation of wave genetics principles. in this case the first male leaves his wave signature i.e. he “imprints” his dna phantom in the genetic apparatus of the female. it appears that this phantom is more powerful than dna phantoms of other males. abortion. a similar explanation is apparently valid in the case when a woman after an abortion experiences something like birth contractions at the ninth month of pregnancy. such sufferings, as well as some other negative health phenomena, may follow the woman for years. a possible explanation would be that that killed embryo leaves its phantom in the mother‟s womb. perspectives we now have a paradoxical situation in genetics, molecular biology, and medicine, in general, that is both grave and promising at the same time. long ago, science decided to investigate the genetic codes of human beings. science has recently completed the 10 years long effort, called the genome, of mapping the dna sequences of humans. all the letters and sequences of the dna codes of humans are known by now. thanks to these results, the forces of trans-genetic engineering have been gathering momentum. already, scientists have introduced artificial gene sequences into sets of plants, animals, and bacteria, which are being used as carriers of these artificially introduced genes. such experiments have been thought to hold great potential in human health applications, promising possible cures for many diseases and disabilities, and in the creation of disease resistant food stuffs, promising a greater abundance of food. paradoxically, the more success we have in such genetics and molecular biology technologies, the farther we seem to be from understanding the actual foundational principles, the inner workings, of the genetic codes. so far, successes in this direction have mainly been concerned with functions of particular gene sequences that act to fabricate various proteins, which are building materials for cells. these particular gene sequences comprise only 2% of the genetic memory found in the chromosomes. the other 98%, the major part of the chromosomes, is not understood by genetics, and has for some odd reason been labeled as "junk" dna. many hypothesis have been brought forward to attempt to account for the reasons for the existence of this "junk" dna; ranging from considering that this 98% majority of the dna might be acting as "assistants" for the primary dna sequences; to explaining that this 98% majority of dna arises as a "cemetery of viruses", a rather difficult notion. to ignore, or to, so critically, underestimate the role of 98% of the human genome, is an appreciable error. moreover, whether we correctly see the true role of the genetic information represented by the known 2% of the dna, is still an open question, especially in the situation where the remaining 98% of the dna is presently "terra incognita", an unknown terrain. presently, our understanding of dna is very limited. with our present understanding, we cannot cure cancer, we cannot resist aids, we have not defeated tuberculosis, nor can we at present dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 011-024 gariaev, p. p., friedman, m. j., & leonova-gariaeva, e. a., principles of linguistic-wave genetics issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 24 prolong significantly the lives of people. initial promises of bright future, based on creations of trans-genetic research, have actually turned out to be only dangerous trans-genetic foodstuffs, hazardous to the biosphere on which our very lives depend. the cloning of animals has produced only ugly and useless creatures, or animals that grow old and die abnormally rapidly, as in the well-known case of the cloned sheep, dolly. and it is quite natural that these results cause alarm within the scientific community. a large group of swedish scientists has recently produced the following example: http://www.psrast.org/defknthe.htm. how are we to escape from this condition of an abundance of flawed and dangerous experiments, where many inconsistent and hazardous results are caused by lack of proper understanding of 98% of the dna sequences, and a dramatic deficiency in understanding the true foundational principles of the operations of dna, the chromosomes, and the human genome? this same group of swedish scientists has pointed that one of the principle directions for improving our understandings of dna is represented by developments such as http://www.scribd.com/doc/37302424/the-dna-wave-biocomputer the essence of our ideas, which have already found some practical applications, is the following. we proceed from very simple strategic reasoning. for success in our attempts to treat various medical problems and to sharply slow down the processes of human aging, it is clearly necessary to understand the languages by which cells communicate with each other. we have managed to accomplish this, to some extent. it appears that the languages we were looking for, are, in fact, hidden in the 98%, "junk" dna, contained in our own genetic apparatus: http://www.wavegenetic.ru/petr_gariaev.pdf the basic principle of these languages is similar to the language of holographic images http://www.wavegenetics.jino-net.ru/zip/new_tec-7-2007.zip based on principles of laser radiations of the genetic structures, http://www.wavegenetics.jino-net.ru/zip/teleport.zip which operate together as a quasi-intelligent system. it is particularly important to realize that our genetic devices actually perform real processes which supplement the triplet model of the genetic code. at what stage of development is this new knowledge and what can it bring us? we are making the first steps in investigating the mechanisms of the relevant physical processes and developing mathematical descriptions of the informational processes, which occur in genetic structures. we have produced some laboratory equipment that allows us to accurately model the informational functions of the living cell and its dna. such devices represent the first quantum bio-computers. these devices have allowed us to carry out distant multi-kilometer transfers of some genetic/metabolic information; the introduction of this information into a bio-system-acceptor; and has allowed us to perform strategic management functions of bio-systems, biochemical systems, and actual physiological conditions: http://www.wavegenetics.jino-net.ru/zip/new_tec7-2007.zip in particular, we have found that it is possible to restore endocrine glands in animals, and the same approach seems to be promising to considerably slow down the aging process in humans. http://www.psrast.org/defknthe.htm http://www.scribd.com/doc/37302424/the-dna-wave-biocomputer http://www.wavegenetic.ru/petr_gariaev.pdf http://www.wavegenetics.jino-net.ru/zip/new_tec-7-2007.zip http://www.wavegenetics.jino-net.ru/zip/teleport.zip http://www.wavegenetics.jino-net.ru/zip/new_tec-7-2007.zip http://www.wavegenetics.jino-net.ru/zip/new_tec-7-2007.zip login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 56-73 56 pitkänen, m., on the correspondence of dark nuclear genetic code & ordinary genetic code exploration on the correspondence of dark nuclear genetic code & ordinary genetic code matti pitkänen 1 abstract the basic problem in the understanding of the prebiotic evolution is how dna, rna, aminoacids and trna and perhaps even cell membrane and microtubules . the individual nucleotides and amino-acids emerge without the help of enzymes or ribozymes but the mystery is how their polymers emerged. if the dark variants of these molecules served as templates for their generation one avoids this hen-and-egg problem. the problem how just the biomolecules were picked up from a huge variety of candidates allowed by chemistry could be solved by the resonance condition making possible metabolic energy transfer between biomolecules and dark nuclei. simple scaling argument shows that the assumption that ordinary genetic code corresponds to heff/h = n = 218 and therefore to the p-adic length scale l(141) ' .3 nm corresponding to the distance between dna and rna bases predicts that the scale of dark nuclear excitation energies is .5 ev, the nominal value of metabolic energy quantum. this extends and modifies the vision about how prebiotic evolution led via rna era to the recent biology. unidentified infrared bands (uibs) from interstellar space identified in terms of transition energies of dark nuclear physics support this vision and one can compre it to pah world hypothesis. p-adic length scale hypothesis and thermodynamical considerations lead to ask whether cell membrane and microtubules could correspond to 2-d analogs of rna strands associated with dark rna codons forming lattice like structures. thermal constraints allow cell membrane of thickness about 5 nm as a realization of k = 149 level with n = 222 in terms of lipids as analogs of rna codons. metabolic energy quantum is predicted to be .04 ev, which corresponds to membrane potential. the thickness of neuronal membrane in the range 8-10 nm and could correspond to k = 151 and n = 223 in accordance with the idea that it corresponds to higher level in the cellular evolution reflecting that of dark nuclear physics. the energy quantum of ordinary josephson radiation is below the thermal energy for photons but the notion of generalized josephson junction saves the situation. for massive particles associated with flux tubes the thermal energy t/2 is below the potential energy defined by action potential and that of metabolic energy quantum. also microtubules could correspond to k = 151 realization for which metabolic energy quantum is .02 ev slightly below thermal energy at room temperature: this could relate to the inherent instability of microtubules. also a proposal for how microtubules could realize genetic code with the 2 conformations of tubulin dimers and 32 charges associated with atp and adp accompanying the dimer thus realizing the analogs of 64 analogs of rna codons is made. keywords: dna, rna, genetic code, dark, ordinary, prebiotic evolution. 1 introduction the idea about the realization of genetic code in terms of dark proton sequences giving rise to dark nuclei is one of the key ideas of tgd inspired quantum biology [24]. this vision was inspired by the totally unexpected observation that the states of three dark protons (or quarks) can be classified to 4 classes in which the number of states are same as those of dna, rna, trna, and amino-acids. even more, it is possible to identify genetic code as a natural correspondence between the dark counterparts of dna/rna codons and dark amino-acids and the numbers of dnas/rnas coding given amino-acid are same as in the vertebrate code [24]. what is new is that the dark codons do not reduce to ordered products of letters. 1correspondence: matti pitkänen http://tgdtheory.com/. address: rinnekatu 2-4 a8, 03620, karkkila, finland. email: matpitka6@gamail.com. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.com/ mailto:matpitka6@gmail.com dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 56-73 57 pitkänen, m., on the correspondence of dark nuclear genetic code & ordinary genetic code during years i have considered several alternatives for the representations of genetic code. for instance, one can consider the possibility that the letters of the genetic code correspond to the four spin-isospin states of nucleon or quark or for spin states of electron pair. ordering of the letters as states is required and this is problematic from the point of view of tensor product unless the ordering reflects spatial ordering for the positions of particles representing the letters. one representation in terms of 3-chords formed by 3-photon states formed from dark photons emerges from the model of music harmony [22]. by octave equivalence the ordering of the notes is not needed. 1.1 insights the above observations inspire several speculative insights. 1. the emergence of dark nuclei identified as dark proton sequences would relate to pollack’s effect in which irradiation of water generates in presence of gel phase bounding the water what pollack calls exclusion zones (ezs). ezs are negatively charged and water has effective stoichiometry h1.5o. ezs deserve their name: somehow they manage to get rid of various impurities: this might be very important if ezs serve as regions carrying biologically important information. the protons of water molecules must go somewhere and the proposal is that they go to the magnetic body of some system consisting of flux tubes. the flux tubes contain the dark protons as sequences identifiable as dark nuclei. 2. since nuclear physics precedes chemistry, one can argue that prebiotic life is based on these dark biomolecules serving as a template for ordinary biomolecules. to some degree biochemistry would be shadow dynamics and dark dynamics would be extremely simple as compared to the biochemistry induced by it. in particular, dna replication, transcription, and translation would be induced by their dark variants. one can even extend this vision: perhaps also ordinary nuclear physics and its scaled up counterpart explaining ”cold fusion” are parts of evolutionary hierarchy of nuclear physics in various scales. 3. nature could have a kind of r&d lab allowing to test various new candidates for genes by using transcription and translation at the level of dark counterparts of the ordinary basic biomolecules. 1.2 conditions on the model the model must satisfy stringent conditions. 1. both the basis a, t, c, g and a, u, c, g as basic chemical building bricks of rna and dna must have emerged without the help of enzymes and ribozymes. it is known that the biochemical pathway known as pentose-phosphate pathway (see http://tinyurl.com/y9akkwok) generates both ribose and ribose-5-phosphate defining the basic building brick of rna. in dna ribose is replaced with de-oxiribose obtained by removing one oxygen. pyrimidines u, t, and c with single aromatic ring are are reported by nasa to be generated under outer space conditions (see http://tinyurl.com/y7sh9zk4). carell et al [3] (see http: //tinyurl.com/z65kpyo) have identified a mechanism leading to the generation of purines a and g, which besides pyrimidines a,t (u) are the basic building bricks of dna and rna. the crucial step is to make the solution involved slightly acidic by adding protons. tgd inspired model for the mechanism involves dark protons [25] [8]. basic amino-acids are generated in the miller-urey type experiments (see http://tinyurl.com/ 4q2arv). also nucleobases have been genererated in miller-urey type experiments [4]. therefore the basic building bricks can emerge without help of enzymes and ribozymes so that the presence of dark nuclei could lead to the emergence of the basic biopolymers and trna. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/y9akkwok http://tinyurl.com/y7sh9zk4 http://tinyurl.com/z65kpyo http://tinyurl.com/z65kpyo http://tinyurl.com/4q2arv http://tinyurl.com/4q2arv dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 56-73 58 pitkänen, m., on the correspondence of dark nuclear genetic code & ordinary genetic code 2. genetic code as a correspondence between rna and corresponding dark proton sequences must emerge. same true for dna and also amino-acids and their dark counterparts. the basic idea is that metabolic energy transfer between biomolecules and their dark variants must be possible. this requires transitions with same transition energies so that resonance becomes possible. this is also essential for the pairing of dna and dark dna and also for the pairing of say dark dna and dark rna. the resonance condition could explain why just the known basic biomolecules are selected from a huge variety of candidates possible in ordinary biochemistry and there would be no need to assume that life as we know it emerges as a random accident. 3. metabolic energy transfer between molecules and their dark variants must be possible by resonance condition. the dark nuclear energy scale associated with biomolecule could correspond to the metabolic energy scale of .5 ev. this condition fixes the model to a high extent but also other dark nuclear scales with their own metabolic energy quanta are possible 1.3 vision the basic problem in the understanding of the prebiotic evolution is how dna, rna, amino-acids and trna and perhaps even cell membrane and microtubules . the individual nucleotides and amino-acids emerge without the help of enzymes or ribozymes but the mystery is how their polymers emerged. if the dark variants of these molecules served as templates for their generation one avoids this hen-andegg problem. the problem how just the biomolecules were picked up from a huge variety of candidates allowed by chemistry could be solved by the resonance condition making possible metabolic energy transfer between biomolecules and dark nuclei. simple scaling argument shows that the assumption that ordinary genetic code corresponds to heff/h = n = 218 and therefore to the p-adic length scale l(141) ' .3 nm corresponding to the distance between dna and rna bases predicts that the scale of dark nuclear excitation energies is .5 ev, the nominal value of metabolic energy quantum. this extends and modifies the vision about how prebiotic evolution led via rna era to the recent biology. unidentified infrared bands (uibs) from interstellar space identified in terms of transition energies of dark nuclear physics support this vision and one can compre it to pah world hypothesis. p-adic length scale hypothesis and thermodynamical considerations lead to ask whether cell membrane and microtubules could correspond to 2-d analogs of rna strands associated with dark rna codons forming lattice like structures. thermal constraints allow cell membrane of thickness about 5 nm as a realization of k = 149 level with n = 222 in terms of lipids as analogs of rna codons. metabolic energy quantum is predicted to be .04 ev rather near to action potential .05 ev. the thickness of neuronal membrane in the range 8-10 nm and could correspond to k = 151 and n = 223 in accordance with the idea that it corresponds to higher level in the cellular evolution reflecting that of dark nuclear physics. the energy quantum of ordinary josephson radiation is below the thermal energy for photons but the notion of generalized josephson junction saves the situation. for massive particles associated with flux tubes the thermal energy t/2 is below the potential energy defined by action potential and that of metabolic energy quantum. also microtubules could correspond to k = 151 realization for which metabolic energy quantum is .02 ev slightly below thermal energy at room temperature: this could relate to the inherent instability of microtubules. also a proposal for how microtubules could realize genetic code with the 2 conformations of tubulin dimers and 32 charges associated with atp and adp accompanying the dimer thus realizing the analogs of 64 analogs of rna codons is made. 2 a model for dark nuclei as dark dna to make progress one must construct a concrete model for the dark nuclei. the basic idea [23] is that cylindrical variants of ezs discovered by pollack [2] give rise to the dark counterparts of dna, rna, and issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 56-73 59 pitkänen, m., on the correspondence of dark nuclear genetic code & ordinary genetic code amino-acids as dark proton sequences. trnas would be analogs of tritium and 3he. 2.1 option i consider first the option, which i christen as option i. 1. the tgd based model leads to the proposal for a formation of this kind of dark nuclear strings such that the distance between protons is rather precisely electron compton length le ' .4×10−12 meters explains ”cold fusion” in terms of dark nucleosynthesis which should have preceded ordinary nucleosynthesis by heating the material to the temperature required by it [27] [19]. dark nucleosynthesis would have produced part of heavier nuclei outside stars. the binding energy scale for dark nuclear physics would be scaled down like 1/length and 2.6 mev binding energy per nucleon for 3he of the ordinary nuclei would be scaled down by a factor 2−11 to 1.3 kev. note however that it is excitation energies of order 1 mev what matters and would scale down to .5 kev. this level does not yet correspond to biology as we know it but could be one step in the evolutionary hierarchy leading from nuclear physics also based on nuclear strings to biology involving increase of planck constant heff/h = n identifiably as the dimension of algebraic extension of rationals characterizing the complexity of the dynamics. 2. these dark nuclei have heff/h = n = 211 (or near to it) and cannot be those responsible for the dark variants of biomolecules since the distances of dark protons given by electron compton length are much smaller than the distance between dna nucleotides about .34 nm, which is roughly 142 times the electron compton length 2.4× 10−3 nm. a scaling of n by 27 would give l(141) = .3 nm scale to be compared with .34 nm so that the p-adic length scale le(k) would correspond to p-adic length scale l(k) with k = 141. the value heff/h = n = 218 predicts nearly correct distance between nucleotides. the excitation energy scale about 1 mev would scale down to .5 ev, which corresponds to the nominal value of the metabolic energy quantum and the bond energy of hydrogen bond. remark: the p-adic length scale associated with a system is defined to be l(k) if the size of the system is in the half open interval [l(k), l(k+1)). one can also consider the possibility that p-adic length scale corresponds to the upper end of [l(k − 1), l(k)). 3. the negative charge of dna and rna assignable to one oxygen of phosphate combining with ribose and dna/rna base could come from the tubular ez formed in the formation of dna. the negative charge of phosphates and the positive charge of dark protons could guarantee the stability of pairs of dark proton sequences and ordinary rna and dna. (a) dna strand has radius of r = 1 nm. le(141) = .3 nm is considerably shorter than r. the debye length rd of dna gives rough idea about the scale above which the negative charge of dna nucleotides associated with the phosphates screened. rd should be longer than r: otherwise it is possible to speak about charge of dna only atomic length scales. one should have rd > r: otherwise it does not make sense to assign negative dna charge except in atomic length scales. le(141) < r requires that the dark codons are pancake like structures. remark: the rough estimates depend on how one identifies p-adic length scale. for the identification as l(k) = √ 5le(k) motivated by the mass formula for electron, one would have l(k) = √ 5le(k) giving l(141) = 0.67 nm. with this interpretation the estimate for the screening radius would be still shorter than r. (b) pancake structure suggests that the dark codons are separate horizontal units of dark quarks having length about 3le(141) = .9 nm, which is still slightly shorter than r. a possible solution of the problem is that dark codons correspond to flux tube loops at the magnetic issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 56-73 60 pitkänen, m., on the correspondence of dark nuclear genetic code & ordinary genetic code body of dna codon carrying three quarks. in this case the transversal size scale of dark codon could be much longer. this kind of flux loops are assigned also with the ordinary nuclei. remark: scaled up hadron physics would be associated with flux tubes of the magnetic body of the codon at which one would have nucleons as 3-quark color singlets. i have already earlier proposed that scaled variants of hadron physics [9] appear in tgd inspired biology. one motivation comes from honeybee dance [1]! 4. what could force the decomposition to 3 dark proton units in 1-1 correspondence with the codons? pancake model suggest that dark nucleus consisting in a well-defined sense of dark nuclei represented as nuclear strings, which are 3-proton analogs of tritium and 3he and protons themselves contain dark quarks at horizontal flux loops. many-sheeted space-time allows to consider this possibility and i have considered this already in the original nuclear string model for ordinary nuclei: in this case 4he with very large binding energy could define one this kind of sub-units. dark codons as genuine dynamical units would make natural the correspondence with ordinary codons. the pairing dark amino-acids with positive charge with ordinary amino-acids might lead to problems since 16 amino-acids are neutral. the only charged amino-acid residues are lys (+), arg (+), asp (-) and glu (-). 1. the formation mechanism for dark proton sequences gives for dark amino-acids a large positive charge. amino-acids are however not accompanied by negatively charged phosphate ions. does charge neutrality require that the dark bonds between dark proton has negative charge so that one has effectively neutron? dark weak interactions correspond to large value of n [27] so that in dna length scale their proceed as fast as electromagnetic interactions (weak bosons would behave like massless particles below scaled up weak scale). this could make possible β decays changing the charges of the bonds between dark protons or dark neutrons [27] and lead to a stability by β emission. 2. proteins in water environment have a charge due to protons or electrons attaching to them. this charge depends on ph and becomes negative above certain critical ph. one might think that the limit of very large ph (no protons) corresponds to the situation in which the electrons of ez attach to amino-acids. dark codons do not have decomposition to letters whereas ordinary codons have. in a well-defined sense one could say that dark code is holistic whereas the ordinary code is reductionistic. 1. this brings in mind western written language in which words decompose to letters. in some eastern languages the symbols of written language correspond to entire words. do these differences correspond at deeper level to ordinary and dark genes. could the analytic and holistic aspects of cognition relate to the differences between ordinary and dark code. 2. one cannot exclude the entanglement between codons and evolution as emergence of entanglement even suggests this. could this kind of entanglement give rise to basic units of dna, in particular genes and introns. could the decomposition of gene into coding regions and introns could correspond to a decomposition to unentangled products of internally entangled pieces. this would increase exponentially the degrees of freedom involved and explain why organisms with practically the same code can be at so different evolutionary levels. in the splicing process when intronic portions are cut out from dna sequence. do the remaining pieces of rna get entangled or does the decomposition of dark rna to unentangled pieces have some meaning? note that also ordinary rna would be entangled or entangled. could introns provide the means for decomposing the coding rna to unentangled pieces. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 56-73 61 pitkänen, m., on the correspondence of dark nuclear genetic code & ordinary genetic code 3. the most natural possibility is that entanglement contains superposition of codon sequences in which each sequence codes for the same amino-acid. the chemical codons appearing in the superposition have different masses and chemical properties but in zero energy ontology (zeo) this is possible. situation would be like for a superconductor in which coherent state means superposition of states with different numbers of cooper pairs and thus different fermion number in standard ontology but in zeo this problem disappears. 2.2 option ii option i is not exact scaling up of nuclear physics since entangled 3-proton states are basic units: this is not the case in ordinary nuclear physics. also neutrons are absent. could one have direct correspondence of nucleon states with the letters a, t, c, g so that the letters of the codon would not entangle? their ordering would be however important. for option ii this is possible: nucleon has two spin states and two isotopic spin states in one-one correspondence with a, t, c, g in suitable order. this kind of correspondence between spin-isospin states of quarks and a, t, c, g was actually the original proposal discussed in [7]. this would give rise to a realization of genetic code at the level of letters. 1. could dark nuclei be formed as a pile of unentangled dark nucleons with size scale of order l(141) and with vertical distance equal to that between rna bases. for dna and rna would have dark proton sequences. for amino-acids, which are not always charged one would have also neutrons. this does not conform with the idea that pollack effect is involved. 2. now roughly one half of the dark letters are neutral so that rna and dna would have negative charge, which is one half of its charge in the scale le(141). the tgd view about nuclear strings could come in rescue here [12]. the bonds between nuclei correspond to flux tubes with charge 0, +1, or -1. ordinary nuclear physics do not predict them but tgd does. if the dark neutrons are connected to the next nucleon by a flux tube with charge +1, charge neutrality is achieved without losing the identity of nucleon as neutron. 3. the mechanism generating ezs favors dark proton sequences and the negative charge associated with phosphates could stabilize these sequences: this favors option i. 4. there is also now a difference to ordinary nuclear physics in that in ordinary nuclear physics the order of letters formed by the spin states of p and n is not believed to matter. now it matters and would be essential for the genetic code: if the order does not matter, one has only four codons! one can however ask whether the ordering of ordinary nuclear strings is actually matters but our measurement technology is not able to distinguish between the different orderings of nucleons. for instance, the energies of different nucleon orderings could be very nearly the same. 5. the correspondence of the letters of genetic code with dark nucleon states is natural for unentangled code. if the dark nucleons of the codon are allowed to entangle as the idea about evolution as generation of entanglement suggests, one obtains more complex structures than for dark protons. for codons formed from dark protons only 8 codons are possible. also it seems that if dark code with unentangled letters existed, its evolution to a code with entangled letters is not plausible since it would suggest that the generation of entanglement induced also the entangled of the letters a,t,c,g of the ordinary code. this view is in conflict with the physical intuition. it would seem that ordinary dna codons must be just product states of their letters and entangle as a whole to dark codons. some concluding remarks are in order. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 56-73 62 pitkänen, m., on the correspondence of dark nuclear genetic code & ordinary genetic code 1. option ii predicts only genetic codons but not the difference between dna, rna, amino-acids and trna like option i. neither does it predict genetic code as the mapping of codons to amino-acids. thus option ii does not look promising. the idea about the evolution of genetic code is however too attractive to be given up. perhaps ordinary nuclear physics and n = 211 dark counterpart correspond to steps in the evolution for which the codons had 1 and 2 letters, perhaps entangled for 2-letter code. the 4 letters could have been spin states of nucleons for ordinary nuclear physics. at this level one cannot speak about dna, rna, trna, and amino-acids. one can also imagine entanglement of the letters of 2-letter codon: maybe this could emerge at n = 211 level. at this level one could have simple analogs of the basic biomolecules. codons would be dark proton analogs of deuterium. 2. the fact that dna has forms a coil of thickness about le(151) = 10 nm suggests that also higher padic length scales and maybe even higher level dark nuclear physics are involved. also the thickness of neuronal membrane has upper bound le(151) to be contrasted with the thickness of ordinary cell membrane given by le(149) = le(151)/2. 3. genetic code could have emerged from a simpler code [10]. if only dark protons are allowed, the unentangled product states would have only two letters giving rise to 8 codons if 3 dark protons serve as a unit. i have proposed that 2-letter and 1-letter codes preceded the 3-letter code and fused to 3-letter code. 2-letter code would have had 4 unentangled codons and 1-letter code 2 unentangled codons. 3 tgd view about the emergence of chemical life consider first the basic assumptions. 1. dark dna, rna,... emerged before chemistry and serve as templates for ordinary dna, rna,... the replication, transcription, and translation for ordinary dna, rna,... are induced by the corresponding processes for their dark counterparts. 2. dark proton sequences are associated with tubular ezs in water generated by pollack effect. 3. the amount of entanglement measured by entanglement negentropy (having a well-defined meaning in adelic physics [29]) is expected to increase gradually during evolution. hence one expects generation of more and more entangled sequences of dark nucleons. at the bottom perhaps ordinary nuclear physics one would have the product states of dark nucleons. perhaps dark nuclear physics with n = 211 came next. after that came n = 218 dark nuclear physics. but which came first: dark variants amino-acids, trna, rna, or dna and their chemical counterparts? and could one see even genes as entangled codon sequences coding for the same protein? 3.1 the quantum vision about the prebiotic evolution the following vision about quantal prebiotic evolution beginning from amino-acids suggests itself. the basic idea is that all processes took place at dark level and induced the processes for ordinary biomolecules in water environment. even the enzyme and ribozyme actions essential in recent biology would be replaced with corresponding actions at dark level and biochemistry would reduce to shadow dynamics. 1. amino-acids are easiest to produce (as miller-urey experiment demonstrated (see http://tinyurl. com/4q2arv)) requiring no enzymatic action and there is just single chemical amino-acid per dark rnas coding for it. therefore the pairs of amino-acids and their dark variants could have emerged first. note that proteins were not yet present. remark: vivo-vitro difference could mean that dark partner of biomolecule is present in vivo and missing in vitro. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/4q2arv http://tinyurl.com/4q2arv dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 56-73 63 pitkänen, m., on the correspondence of dark nuclear genetic code & ordinary genetic code 2. dna requires cell membrane. this requires rna emerged after amino-acids. this implies that dark variants of dark trna, their pairing with trna and the pairing of dark rna with rna emerged next? this picture supports that the old tgd inspired idea about the role of trna during rna era. dark trna would have made possible the replication of dark rna sequences (rather than the translation of rna to amino-acid sequence) during this era. the dark amino-acid of dark trna would have served as a catalyst inducing the addition of dark rna codon to the growing rna sequence. no chemical transcription machinery nor dna was needed at this stage. this would solve one hen-or-egg problem. 3. after that a revolution would have occurred. for some reason dark amino-acids began to attach to the growing sequence of amino-acids and dark rna codon was left alone. what prevented dark rna codon to attach to the growing dark rna sequence? was it the emerging entanglement between dark codons giving rise to genes as entangled pieces of dna that made this impossible. this means entanglement also between the ordinary codons, which makes sense only in zeo. if possible at all this entanglement should respect genetic code so that entangled superposition would involve only codons coding for the same amino-acid so that the translation to a single amino-acid sequence rather than their quantum superposition is possible. if more general superpositions are allowed the translation process would be like state function reduction to amino-acid sequence. 4. at this step the replication of both dark and ordinary rna was lost and it seems that dark dnadna pairs replicating dark dna and transcribing it to dark rna and inducing corresponding process at the level of chemistry must have emerged at the same time. the emergence of dna requires also the emergence of cell membrane. could the emergence of cell membrane relate to the emergence of dark nuclei in the p-adic length scale l(k), k = 151 and could the double layered structure of cell membrane serve as an analog for that of dna double strand? could lipid layers correspond to 2-d analogs of dna strand with lipids taking the role of codons? 5. could the full genetic code emerged in step-wise manner as proposed earlier [7, 16]? genetic code can be seen in a good approximation as a fusion of 16-letter code and 4-letter code. this might be understood if the entanglement of dark codons emerges first as entanglement of only two first letters. what gave rise to the correspondences between dark dna, rna, trna, amino-acids and their dark variants? how the amino-acids and nucleotide bases were selected? 1. the basic principle would be the condition that metabolic energy can be transferred between chemical and dark levels. this is possible if there identical transition energies in the spectra of biomolecules and their dark variants making possible resonance. 2. metabolic energy quantum in the range .4-.5 ev could correspond to the energy scale of dark k=141 nuclear physics if 1 mev is taken as the estimate for a typical nuclear binding energy. hydrogen bonds also corresponds to this energy scale but this might be just what is needed to give rise to coherent metabolic activity. to sum up: for dna,rna, and trna the emergence of entanglement would have created the chemical counterparts of quantum superpositions: zeo is necessary since in positive energy ontology superpositions are highly implausible. there are some questions to ponder. 1. why the decomposition into triplets? does resonance condition for the metabolic energy transfer select triplets as basic units and also the rna-amino-acid correspondence? do also intronic regions have triplets as basic units? issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 56-73 64 pitkänen, m., on the correspondence of dark nuclear genetic code & ordinary genetic code one ends up to a prediction of vertebrate genetic code also from a model of music harmony [22]. in fact, the model explains also its slight variation and the 2 additional amino-acids. could this help to understand why the triplet code is so unique. 2. could one imagine that also quarks and antiquarks were involved? could dark nucleon pair with dark quark with same spin and isospin and color confinement forces dark proton triplets? dark quarks indeed define a representation for a,t,c, g. in the model of topological computation [7, 16]. i have actually speculated with the possibility that dark quarks and antiquarks are paired with ordinary dna codons. 3. could dark conjugate protons or their triplets of parallel dark dna strands form cooper pairs or does pairing of dark protons triplets (their conjugates) with dark quarks (anti-quarks) give rise to bosonic states? 3.2 unidentified infrared bands as a test for the proposal unidentified infrared bands (uibs) are an ill-understood phenomenon associated with radiation coming from interstellar space. there are also other analogous phenomena having no explanation in terms of molecular transitions [5] and one can ask whether they could be seen as signatures of dark nuclear physics. 1. uibs are observed around bands around ir energies e ∈ {.11, .20, .375} ev. 2. poly-aromatic hydrocarbons (pahs) (see http://tinyurl.com/atx4t9a) are known to generate uibs [5]. therefore the uibs from interstellar space could originate from pahs. 3.2.1 tgd based models for uibs tgd suggests several explanations for uibs involving new physics related to the p-adic length scale hypothesis and heff/h = n hierarchy. 1. for years ago i discussed a model for uibs based on p-adic length scale hypothesis [5]. the idea was that protons ”drop” from atomic space-time sheet with k = 137 to a larger space-time sheet to k1 > 137 space-time sheet and the difference of zero point kinetic energies is liberated as radiation [5]. the proposal was that the zero point kinetic energies give rise to a hierarchy of metabolic energy quanta. second possibility is phase transition in which the size of the k = 137 space-time sheet increases to k1 > 137 and liberates the difference of zero point kinetic energy. for the third option energy preserving phase transition increasing heff/h = n by a factor (k1 − k)/2 followed by a phase transition reducing the value of heff back to the initial one but without change of the size of the space-time sheet would liberate the difference of zero point kinetic energies. 2. also dark nuclear transitions could explain uibs. for k = 141 as the p-adic length scale of dna letters would give nuclear energy scale e = .5 ev equal to the metabolic energy quantum by scaling 1 mev for the ordinary nuclei. this is too high an energy but there are of course also smaller energies possible for the nuclear excitations possibly explaining the uibs. the challenge is to explain not only the presence of these separate bands but also the band structure. local wave functions for dark protons are localized in scale of .34 nm (dna). estimate for the energy scale associated with local excitations is obtained from particle in box model. the scale of these excitations is roughly (l(137)/l(141))2 = 2−4. these excitations could be generated thermally. 3. what about hydrogen bonds? the strength of hydrogen bond essentially the bond energy is in the range .4-.5 ev -, which as such does not correspond to the average uib energy, which come issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/atx4t9a dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 56-73 65 pitkänen, m., on the correspondence of dark nuclear genetic code & ordinary genetic code approximately as three lowest powers of two. the range of bond energies is .1 ev is smaller than the smallest uib energy .11 ev. uibs can be associated with hydrogen bonds if there are states of bond with higher bond energy. they could correspond to higher values of n = heff/h for the de-localized dark proton associated with the bond (analogous to de-localized valence electron). for instance, if the energy of the bond corresponds to the cyclotron energy of proton in a magnetic field associated with the bond, it is proportional to n. the photon energies come approximately as powers of 2. if the favored values of n are in bands around n = 2k favored by the p-adic length scale hypothesis, one has hopes of understanding the band structure in terms of transitions reducing the value of k. membrane potential (see http://tinyurl.com/chylvs9) plays a key role in metabolism and one can wonder whether uibs might relate to the potential energies defining energies ej = zev of josephson photons associated with membrane if it acts like josephson junction like structures associated with the prebiotic lifeforms. 1. membrane potential energy varies in the range (.04, .08) ev (cell interior is negatively charged). excitable cells (able to generate action potentials) include neurons, muscle cells, endocrine cells, and some plant cells. the average value for them is around .06 ev and further depolarization makes these cell more excitable. this suggests that the instability is caused by thermal radiation with nearly the same energy. the threshold for the generation of the action potential eact is in the range (.050, .055) ev. interestingly, during ageing neurons become more hyperpolarized and therefore less excitable. in photoreceptors the resting potential energy can be as low as .03 ev making them very sensitive to light. 2. in tgd inspired quantum biology axonal membrane can be seen as a generalized josephson junction [13, 14, 15] decomposing nanoscopically to josephson junctions defined by cell membrane proteins. the protein as junction would correspond to a magnetic flux tube along which various charged particles with heff = n × h flow possibly as supra currents. as a special case cell membrane acts like an ordinary josephson junction. in this case the increment of the electrostatic energy of the cooper pair over membrane given by ej = 2ev defines the energy of the smallest quantum of josephson radiation. the intensity of thermal radiation at temperature t as function of photon energy e has a peak at e ' 3t , which for room temperature about t = .03 ev gives emax = .09 ev. the energy zev of cooper pair should be larger than emax. for critical action potential one has eact = 0.1 ev, which is slightly above emax = .09 ev so that the action potential has minimal value and thus minimizes metabolic energy costs and implies quantum criticality with temperature as a critical parameter. note however that for energies below emax the intensity of thermal radiation decreases so that also these energies might serve as josephson energies: this and the fact that incoming photons have intensity higher than termal background at this energy could explain why some photoreceptors can have ev = .03 ev. 3. could also josephson radiation relate to uibs? the josephson energy of cooper pair for the membrane potential is around ej = 0.1 ev, which corresponds to the lowest uib band, which could thus correspond to action potential .05 ev of excitable membrane. the higher bands would correspond roughly to two octaves suggesting that the action potentials in these case are roughly .1 ev and .2 ev. quantum criticality would suggest that temperatures scale like the energies of the bands slightly higher than emax ' 3t . metabolic energy transfer between magnetic body and biological body (defined in very general sense for any system) is possible if the spectra of transition energies share common transition energies. therefore issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/chylvs9 dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 56-73 66 pitkänen, m., on the correspondence of dark nuclear genetic code & ordinary genetic code the spectrum of transition energies assignable to hydrogen bonds could have many transition energies common with that assignable to dark nuclear transitions and second and third explanation could be consistent with each other. 3.2.2 model for hydrogen bond the explanations of uibs in terms of hydrogen bonds encourages to consider a concrete model for the hydrogen bond as flux tube. this suggests a connection with metabolism at cellular level involving transfer of protons through cell membrane against potential gradient assumed to take place as dark protons carrying the metabolic energy and providing it to adp-atp process after their return. 1. the simplest model for the proton inside flux tube is as particle in 1-d flux tube with magnetic field. unless the magnetic field strength and/or n is very large, the kinetic energy in the direction of flux tube dominates and phase transition would change the scale of kinetic energy proportional to n2 for fixed flux tube length. for n = 2k this would give too strong dependence of photon energies on k. 2. on the other hand, if the flux tubes are flux loops of the magnetic body of molecule their lengths naturally scale as n and the longitudinal kinetic energy is not affected in the transition. the cyclotron energy proportional to n would change and for n ∼ 2k one obtains qualitatively correct behavior. for proton in magnetic field of bend = .2 gauss the cyclotron frequency is 300 hz and corresponds to ec(bend) = 1.2× 10−12 ev. the identification of ec(b) = .5 evs would give ec(b) = n(b/bend)× ec(bend) = ec(b) = .5 ev. an estimate for b for the flux tube of hydrogen bond comes from flux quantization: ebs = 1 holds true for unit quantum of flux and for flux tube radius of one angstrom this would give b/bend ∼ 5 × 108. this gives the estimate n ∼ 108 ∼ 227. the rather large value conforms with the general vision for the values of n for dark protons whereas dark electrons of valence bonds would have much smaller values. the emergence of dark protons could be seen as the transition from chemistry already involving n as characterizer of valence bonds [28] to bio-chemistry. 3. the identification of the metabolic energy quantum in terms of cyclotron energy could apply also in the case of cellular metabolism. the model for the generation of atp from adp assumes that protons are pumped by the energy coming from nutrient molecules against the membrane potential. the membrane potential correspond to energy of .05 ev but metabolic energy quantum is 10 times larger. this looks like an inconsistency, which in thermodynamical approach is resolved by introducing of chemical potentials. in genuine quantum approach the introduction of thermodynamics quantities is not allowed. the general vision about metabolic energy as a tool to increase heff/h = n defining kind of molecular iq suggests that the transformation to dark proton at magnetic flux tube along which proton can travel through the membrane is responsible for the most of the energy needed for pumping. after the dark proton has returned through cell membrane it transforms to ordinary proton and liberates the metabolic energy and makes possible adp-apt transformation. the above model assumes that the lengths of hydrogen bonds as flux loops scale like n. this makes possible the reconnection of flux loops coming from opposite sides of the membrane to pair of flux tubes along which dark protons can flow. similar picture applies also to other biologically important ions. the general view about superconductivity in tgd universe [13, 14] suggests that reconnection can give rise to a cooper pairs of protons with members at separate flux tubes. also cooper pairs of electrons and biologically important ions could form by the same mechanism. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 56-73 67 pitkänen, m., on the correspondence of dark nuclear genetic code & ordinary genetic code 3.3 pah world hypothesis from tgd point of view the so called pah world hypothesis (see http://tinyurl.com/ycxm9zes) has been proposed as a prebiotic era preceding rna world. as a matter of fact, pah world hypothesis inspired more a detailed development of tgd based model for dark nuclei. let us first list some properties of poly-aromatic hydrocarbons (pahs) (see http://tinyurl.com/ atx4t9a). 1. pahs consist of aromatic rings glued together along sides. by definition aromatic rings have delocalized electrons. in benzene, which is the classical and simplest example of pah, the electronic state is quantum superposition of states in which bonds and double bonds alternate along the ring but are shifted by 60 degrees with respect to each other. naphtalene has two aromatic rings and anthracene and pnenanthtrene have 3 rings. 2. pahs are very stable non-charged non-polar molecules and are very common in earth. they are found in coal and tar deposits and produced in an incomplete combustion of organic matter. pahs are poisonous. for instance, tobacco smoke contains pahs with carcinogenic effects. the stability of pahs motivates the belief that a large fraction of carbon in the interstellar space consists of pahs. 3. benzene in difficult to detect in in the interstellar space since the rotational symmetry does not allow to detect rotational transitions. recently however nitrobenzene was detected so that benzene and more complex pahs presumably exist in interstellar space (see http://tinyurl.com/yap9ksrg). benzene and more complex pahs can give rise to more complex aromatic by hydrogenation, oxidation, carboxylation, and nitrogenation and led also to the basic building bricks of dna and amino-acids and pahs are proposed to have played important role in prebiotic life. 1. pah world hypothesis states that the polymer like sequences of pahs serve as scaffoldings for the formation of rna like polymers (see http://tinyurl.com/ycxm9zes). the key motivation is that the distances between pahs are same as between rna and dna bases: 3.4 nm. the proposal is that during pah era rna nucleosides a, u, c, g were attached to pahs by hydrogen bonds. 2. second hypothesis is that formaldehyde molecules [(h2c)=o] formed valence bonds with rna bases and with each other giving rise to sequences analogous to the phosphate-ribose backbone of rna. the sequence of disjoint co=:s was replaced with the sequence ..(c-r)-o-(c-r)-o-.. with r denoting the rna nucleoside. after this hydrogen bonds were split and the predecessor of rna was detached from the pah scaffolding. later the pre-rna strands were folded to form double prerna strands similar to ribozymes. the problem is to understand how the formaldehyde backbone was replaces with more stable phosphate-ribose backbone. in tgd framework dark nuclei would serve as scaffolding, which however does not detach from the corresponding biomolecules. the distances between dark variants of biomolecules would explain why the two distances are the same. very many molecules, including pahs, can attach around dark rna/dna and the periodic structure would be reflect the properties of dark nuclei. this could explain uibs as emission bands of both dark nuclei and hydrogen bonds essential for the pairing and the transfer of metabolic energy between ordinary and dark biomolecules. also in dna double strand hydrogen bonds could serve similar function. if thermal radiation excites higher energy states of nuclei, the emission of uibs depends on temperature. perhaps this could be tested. uibs could therefore serve as a direct signature of dark nuclear physics. if dark nuclei are not associated with pahs in vitro or in an environment not containing water, uibs would be absent. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/ycxm9zes http://tinyurl.com/atx4t9a http://tinyurl.com/atx4t9a http://tinyurl.com/yap9ksrg http://tinyurl.com/ycxm9zes dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 56-73 68 pitkänen, m., on the correspondence of dark nuclear genetic code & ordinary genetic code 4 some reckless speculation about higher level variants of dark genetic code a hierarchy of dark nuclear physics with hierarchy of n = heff/h = n coming as certain powers of two so that the corresponding length scales correspond to p-adic length scales is so attractive idea that i cannot avoid the temptation to speculate about it and i have done it already earlier [11]. 4.1 could cell membrane correspond to dark nuclear physics for k > 141? cell membrane consisting of two lipid layers (see http://tinyurl.com/h9a2hsq) is binary structure as also dna double strand. dnas replicate as would do also rnas during rna era. also cells and therefore also cell membranes replicate so that the analogy might make sense. since processes like translation and transcription do not occur, cell membrane should be seen as analog of rna: the counterpart of rna era would prevail at these levels. could cell membranes correspond to a fourth level in the hierarchy of nuclear physics? or could there be entire hierarchy coming assignable to certain p-adic length scales? one motivation for these speculations is that the gaussian mersenne primes mg,k=(1 + i)k − 1 for k ∈ {151, 157, 163, 167} define p-adic length scale l(k) ∝ 2k/2 between 10 nm assignable to the double membrane in mitochondria and 2.5 µm assignable to cell nucleus: so many gaussian mersenne in so short length scale range is a number theoretical miracle. remark: i have claimed in earlier publications that the lipid double layer defining cell membrane has thickness le(151) = 10 nm: actually the thickness is le(149) = 5 nm for ordinary cells and 8-10 nm roughly le(151) for neuronal membranes. the double cell membrane associated with mitochondria has thickness 22 nm and corresponds to le(153): the thickness of the two membranes is about 7 nm. this observation allows to understand in what sense neurons and mitochondria are above ordinary cells in the evolutionary ladder. 1. the thickness of ordinary cell membrane corresponds roughly to le(149) = 5 nm whereas the coiling associated with the cell membrane corresponds to le(151). also neurons correspond to le(151). could k = 149 resp. k = 151 define levels of ordinary cell resp. neuron in the hierarchy of dark nuclear physics? remark: one can argue that cell membrane in particular neuronal membrane is highly dynamical unlike rna. in zeo however dynamical evolutions of space-time surfaces as preferred extremals correlates for behaviors replace 3-d static patterns as basic entities so that the emergence of cell membrane might mean dark genetic code for dynamical patterns analogous to deterministic computer programs defining predetermined dynamical patterns. in central nervous system nerve pulse patterns coded by dark rna could provide similar coding of behavioral patterns. 2. cell membrane consists of lipid bilayer. the lipid layer has three parts (see http://tinyurl.com/ h9a2hsq). the totally hydrated layer nearest to water is hydrophilic head group, which in the case of phospholipids contains negatively charged phosphate. this phosphate layer has thickness .7− 1.0 nm. below it is a partially hydrated layer of thickness .3 nm, which corresponds to l(141): this of course puts bells ringing! hydrophobic lipid tail layer below it is dehydrated. the thickness of single lipid layer is 1.25-1.75 nm and would correspond to the p-adic length scale le(145) = 1.2 nm. 3. the phosphate layer analogous to phosphate-ribose backbone and the thickness l(141) of partially hydrated layer suggests that it corresponds to ez created in pollack effect so that there would be parallel dark rna sequence along axon (possibly helical as for microtubules). in the case of cell issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/h9a2hsq http://tinyurl.com/h9a2hsq http://tinyurl.com/h9a2hsq dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 56-73 69 pitkänen, m., on the correspondence of dark nuclear genetic code & ordinary genetic code membrane would have lattice like system formed from dark protons, and maybe even dark neutrons (as an analog for the neutron halo in some nuclei). 4. if the recent biology is the analog of rna era for k > 141 codes, their manifestations could be seen as analogs of rnas and the number of different lipids associated with the cell membrane could give some idea about their number. cell membrane could be seen as a 2-d analog of rna polymer. cell division implying membrane replication would correspond to rna replication (proposed to be catalyzed by trna at rna era). even the analogs of trna and amino-acids but not proteins should be present if one takes the analogy very seriously. could one identify pairs of lipids and some molecules analogous to proteins appearing in cell division? 5. both sides of the lipid bilayer would contain cylindrical lattices of dark rna codons. in the case of axon one could have the analog of dark rna strand extended to a cylinder containing bundles of these strands at its surface. lipid layers would be 2-d analogs of 1-d dna strands in this case. lipids would be analogs of rna codons and dark rna codons would code for them: this predicts 64 different lipids in cell membrane. single dark rna would correspond to the size scale of single lipid given by l(143) = 2l(141) = .625 nm so that the dark nuclear physics would correspond to k = 143 and n = 220. the number n of parallel dark rna strands is roughly the circumference of the axonal lipid layer divided by the size of single lipid about l(143) = .625 nm given by n ∼ 2π × le(167)/le(143) = π × 224 ∼ 5× 106. remark: the flux tubes connecting the dark dna sequences above lipid layer to those associated with dna could make possible to realize topological quantum computation [7, 16] in terms of braiding induced by the 2-d liquid flow induced by nerve pulse patterns at nuclear membrane. flux tubes might be associated with cytoskeleton and define analog of central nervous system. a rough estimate for the numbers of codons for human dna of length about 1 m and the number of codons allowed by the surface of the nuclear membrane are of order 109 so that the proposal might make sense. could this totally irresponsible speculation about p-adic hierarchy of dark nuclear physics and genetic codes survive thermodynamical constraints? 1. the condition that metabolic energy quantum is not below thermal energy at physiological temperatures suggest that scaling factors λ larger than λ = 16 in n = heff/h for n = 218 associated with dna and rna cannot be allowed. single lipid layer would correspond to le(145) = 4le(141) = 1.25 nm and λ = 4. single lipid layer with hydrophilic layer included corresponds to le(147) = 8le(141) = 1.25 nm and λ = 8. 2. the value of heff/h = n would be n = 222 ∼ 4×106 for k = 149 and scaling factor would be λ = 16. the value of the metabolic energy quantum is now around .04 ev whereas the action potential is around .05 ev. as explained, in tgd universe the cell membrane can be seen as josephson junction decomposing in an improved resolution to membrane proteins acting as josephson junctions [13, 14]. josephson energy of cooper pair is twice this that is ej = 0.1 ev slightly above the maximum emax = 3t = .09 ev of the thermal distribution at physiological temperature. 3. for k = 151 the metabolic energy quantum would be scaled down to .02 ev (as noticed earlier, the membrane potential for some photoreceptor is .03 ev). the energy at which the intensity of thermal radiation at temperature of 300 k is emax = .09 ev. the potential energy gain over cell membrane for a cooper of charged particles would be ej = .045 ev, which is roughly one half of of the energy of thermal photon at the maximum emax = 3t = .09 ev of the thermal distribution. the intensity of the thermal radiation is reduced only by a factor .69 for e = emax/2 so that there seems to be a real problem. 4. as far metabolic energy quantum and josephson radiation are considered, for k = 149 membrane would be a quantum critical system. quantum criticality would give rise to instability making issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 56-73 70 pitkänen, m., on the correspondence of dark nuclear genetic code & ordinary genetic code possible the generation of nerve pulses. during nerve pulse the dark protons at the dark spacetime sheet would return to the neuronal membrane and destroy the ionic equilibrium. also the temperature criticality of consciousness manifesting itself as the generation of hallucinations during fever could be understood. for k = 151 the situation would be overcritical and will be discussed separately. for k = 151 josephson energy of cooper pair is scaled down to ej = .045 ev considerably below emax = .09 ev. does this mean that josephson radiation cannot carry information? or could nature have found the means to overcome this problem? the notion of generalized josephson junction central in tgd inspired theory of eeg as communications from brain to mb [15, 6] could save the situation. 1. for the generalized josephson junction the energy of quantum of josephson radiation is e = ej + ∆ec, where ∆ec is the difference of cyclotron energies at the two sides of the membrane. ec is proportional to heff = n× h and large enough value of n guarantees that ec is above emax ' 3t irrespective of the value of the membrane potential. the variations of the membrane potential modulate josephson frequency, and are proposed to provide a coding of sensory data defined by nerve pulse patterns communicated to mb. 2. heff = hgr = gmm/v0 hypothesis [21, 20] guarantees the spectrum of cyclotron energies is universal and does not depend on the mass m of the charged particle being in the range of visible and uv energies of photons (this allows to deduce information about the values of mass m and velocity parameter v0 < c): bio-photons would be produced in energy conserving phase transitions transforming dark photons to ordinary ones [17, 18]. 3. if mb itself (a structure which has size scale of earth at eeg frequencies around 10 hz) has low enough temperature, this would allow to overcome the limitations caused by the thermal masking of the ordinary josephson radiation so that the frequency modulations by nerve pulse patterns could code for the sensory data. heff = hgr = gmm/v0 hypothesis indeed allows very large values of heff for which ordinary cyclotron energies proportional to heff would be ridiculously small for the ordinary value of h. what about the situation for massive particles like proton? now maxwell-boltzmann (gaussian) distribution is a good approximation and for effectively d-dimensional system the value of distribution is reduced by 1/e at thermal energy ecr = dt/2. one could argue that above this energy thermal masking can be avoided. for d = 1 at magnetic flux tubes this would give ecr = t/2 = emax/6. at tphys = .03 ev one would have ecr = 0.15 ev. metabolic energy quantum would be above ecr for k = 151. even k = 153 possibly assignable to mitochondrial double membrane can be considered but represents an upper bound at physiological temperatures. remark: in tgd view about information processing in brain [26] active linear neuron groups relate to verbal cognition and 2-d neuronal groups relate to the geometric cognition associated with the decomposition of perceptive field to objects. at cellular level dna and cell membrane could perhaps be seen as counterparts for these structures. in tgd framework neuronal membrane is proposed to be a constructor of sensory representations communicated to the magnetic body (mb) using generalized josephson radiation whereas motor control by mb has been assumed to take place via dna [10]. 4.2 microtubules as quantum critical systems also microtubules (see http://tinyurl.com/y8km9vve) are 2-d structures having a strong resemblance with the lipid layers of cell membrane. could a higher level representation of genetic code similar to the one proposed for lipid layers make sense for them. 1. microtubules are hollow cylinders with outer resp. inner diameter equal to 24 resp. 12 nm (the scales differ by factor 2) so that their thickness is 12 nm is same as the inner radius and would issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/y8km9vve dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 56-73 71 pitkänen, m., on the correspondence of dark nuclear genetic code & ordinary genetic code correspond to l(151) = 10 nm. they decompose to 13 parallel helical filaments consisting of 13 tubulin proteins having size scale of order le(151). 2. tubulins are dimers of α and β tubulin and the pairs are oriented along the helical filament. one can estimate the size of α and β tubulin by diving the circumference of 24 nm of the microtubule with the number of filaments, which is 13. this gives for the size scale of tubulin the estimate rtub ∼ 12 nm not far from l(151). this supports the view that p-adic length scale l(151). the size scale of the transversal volume associated with lipid is roughly .62 nm that is l(143) = 2l(141) so that they could correspond to k ∈ {141, 143}, presumably k = 141. therefore one could see microtubules as scaled up variants of cell membrane with scaling factor 2(151−141)/2 = 25 = 32. similar scaling would take place for the value of n = heff/h giving n = 223 so that microtubules would represent a higher level of evolution identified as increase of n. microtubules have indeed emerged after cell membrane. 3. it has been proposed that the α and β conformations of tubulin give rise to bit or even qubit. if this were the case, single helical filament rotating one full turn would have 213 states and carry 13 bits of information. 13 independent filaments would have 226 ' 64× 106 states and carry 26 bits of information. one could also think of codon as sequence of 13 filaments with the states of filaments representing 213 letters of the code. 4. microtubular surface has rather high charge density and is polarized: the almost stationary end has negative local charge density roughly equal to that of dna whereas the growing end has lower surface charge density. one manner to control the charge of the tubulin dimer is in terms of the charge states of gdp and gtp by ionization of the phosphates. maximal negative charge for tubulin dimer would be 5 units. microtubules are highly dynamical objects with inherent instability and have varying length: one might say that microtubules are quantum critical objects. quantum criticality and thus instability might relate to the fact that the metabolic energy quantum is very near to thermal energy at room temperature. the dynamics for the length of microtubule could be induced from the dynamics of ez involving the flow of protons between microtubule and its magnetic body defined by dark dna. the gradient in charge density would make possible positive net charge density at the growing end of the microtubule. in zeo it looks reasonable to argue that the dynamical patters are coded by a generalization of genetic code just as computer programs code for deterministic dynamical patterns. 5. what could the dark code behind the dynamics be? the αand β tubulins of tubulin dimer involve gtp (see http://tinyurl.com/ybtjluaf) resp. gdp (see http://tinyurl.com/y8uok7kq). in the case of dna one has xmp , x = a, t,c,g. the analogs of dark rna sequences would contain mere g and the information coded by the tubulin would be determined by the conformation of the tubulin dimer giving 1-bit code. this looks somewhat disappointing. if the charge states of the phosphates of gdp and gtp can vary and all charge combinations for phosphates are possible, one has 23 charge states for gtp and 22 charge states for gdp. together with the bit associated with the tubulin conformation this would give 26 states and realize 6 bits of the ordinary genetic code! one would have 2-d realization of the genetic code analogous to that proposed for the lipid layer with the state of tubulin analogous to rna codon. this coding together with thermal criticality would make microtubule a dynamical object since the deviation of the tubulin charge from -1 units would spoil charge local charge neutrality of tubulin-dark rna pair. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/ybtjluaf http://tinyurl.com/y8uok7kq dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 56-73 72 pitkänen, m., on the correspondence of dark nuclear genetic code & ordinary genetic code i have proposed that flux tubes connecting tubulins to the lipids of the axonal lipid layer could give rise to topological quantum computation [7, 7]. the size scale of lipid is about le(141) and that of tubulin about le(151) = 32le(141), and the the radius of axonal membrane is by two orders of magnitude larger than microtubular surface. hence this proposal does not look realistic unless one assumes that sub-structures of cell membrane with size scale of order le(167)/le(151) = 28 larger than tubulin size represented as space-time sheets with cell nucleus size l(167) have flux tube connections to tubulins. this kind of map would give rise to a kind of abstraction about what happens at the level of axonal membrane integrating out un-necessary details. this abstraction is natural since microtubules would indeed correspond to a higher level of cognitive hierarchy. roughly n = 216 lipids would contribute to the information received by single tubulin. could nerve pulse patterns can induce braiding of the flux tubes in this scale? references [1] shipman b. the geometry of momentum mappings on generalized flag manifolds, connections with a dynamical system, quantum mechanics and the dance of honeybee. available at: http://math. cornell.edu/~oliver/shipman.gif, 1998. 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[18] pitkänen m. comments on the recent experiments by the group of michael persinger. in tgd based view about living matter and remote mental interactions. online book. available at: http: //tgdtheory.fi/public_html/tgdlian/tgdlian.html#persconsc, 2013. [19] pitkänen m. cold fusion again. in hyper-finite factors and dark matter hierarchy. online book. available at: http://tgdtheory.fi/public_html/neuplanck/neuplanck.html#cfagain, 2014. [20] pitkänen m. criticality and dark matter. in hyper-finite factors and dark matter hierarchy. online book. available at: http://tgdtheory.fi/public_html/neuplanck/neuplanck.html#qcritdark, 2014. [21] pitkänen m. quantum gravity, dark matter, and prebiotic evolution. in genes and memes. online book. available at: http://tgdtheory.fi/public_html/genememe/genememe.html#hgrprebio, 2014. [22] pitkänen m. geometric theory of harmony. available at: http://tgdtheory.fi/public_htm/ articles/harmonytheory.pdf, 2014. [23] pitkänen m. pollack’s findings about fourth phase of water : tgd view. available at: http: //tgdtheory.fi/public_htm/articles/pollackyoutube.pdf, 2014. [24] pitkänen m. about physical representations of genetic code in terms of dark nuclear strings. available at: http://tgdtheory.fi/public_htm/articles/genecodemodels.pdf, 2016. [25] pitkänen m. one step further in the understanding the origins of life. available at: http:// tgdtheory.fi/public_htm/articles/purineorigin.pdf, 2016. [26] pitkänen m. artificial intelligence, natural intelligence, and tgd. available at: http:// tgdtheory.fi/public_htm/articles/aitgd.pdf, 2017. [27] pitkänen m. cold fusion, low energy nuclear reactions, or dark nuclear synthesis? available at: http://tgdtheory.fi/public_htm/articles/krivit.pdf, 2017. [28] pitkänen m. does valence bond theory relate to the hierarchy of planck constants? available at: http://tgdtheory.fi/public_htm/articles/valenceheff.pdf, 2017. [29] pitkänen m. philosophy of adelic physics. available at: http://tgdtheory.fi/public_htm/ articles/adelephysics.pdf, 2017. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.fi/public_html/tgdeeg/tgdeeg.html#biosupercondi http://tgdtheory.fi/public_html/tgdeeg/tgdeeg.html#biosupercondii http://tgdtheory.fi/public_html/tgdeeg/tgdeeg.html#pulse http://tgdtheory.fi/public_html/genememe/genememe.html#dnatqccodes http://tgdtheory.fi/public_html/genememe/genememe.html#dnatqccodes http://tgdtheory.fi/public_html/tgdlian/tgdlian.html#biophotonslian http://tgdtheory.fi/public_html/tgdlian/tgdlian.html#biophotonslian http://tgdtheory.fi/public_html/tgdlian/tgdlian.html#persconsc http://tgdtheory.fi/public_html/tgdlian/tgdlian.html#persconsc http://tgdtheory.fi/public_html/neuplanck/neuplanck.html#cfagain http://tgdtheory.fi/public_html/neuplanck/neuplanck.html#qcritdark http://tgdtheory.fi/public_html/genememe/genememe.html#hgrprebio http://tgdtheory.fi/public_htm/articles/harmonytheory.pdf http://tgdtheory.fi/public_htm/articles/harmonytheory.pdf http://tgdtheory.fi/public_htm/articles/pollackyoutube.pdf http://tgdtheory.fi/public_htm/articles/pollackyoutube.pdf http://tgdtheory.fi/public_htm/articles/genecodemodels.pdf http://tgdtheory.fi/public_htm/articles/purineorigin.pdf http://tgdtheory.fi/public_htm/articles/purineorigin.pdf http://tgdtheory.fi/public_htm/articles/aitgd.pdf http://tgdtheory.fi/public_htm/articles/aitgd.pdf http://tgdtheory.fi/public_htm/articles/krivit.pdf http://tgdtheory.fi/public_htm/articles/valenceheff.pdf http://tgdtheory.fi/public_htm/articles/adelephysics.pdf http://tgdtheory.fi/public_htm/articles/adelephysics.pdf introduction insights conditions on the model vision a model for dark nuclei as dark dna option i option ii tgd view about the emergence of chemical life the quantum vision about the prebiotic evolution unidentified infrared bands as a test for the proposal tgd based models for uibs model for hydrogen bond pah world hypothesis from tgd point of view some reckless speculation about higher level variants of dark genetic code could cell membrane correspond to dark nuclear physics for k>141? microtubules as quantum critical systems dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 438-475 smetham, g. p., soul dust or a matter of mind: the mindless ideas of nicholas humphrey issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 438 article soul dust or a matter of mind: the mindless ideas of nicholas humphrey graham p. smetham * abstract the ideas presented by nicholas humphrey in his book soul dust and elsewhere are an excellent example of the kind of ridiculous and logically incoherent accounts of the mindless evolution of matter into ‘illusory’ mind which are penned by materialist advocates of primordial mindlessness. humphrey’s approach relies on often clearly incoherent, and sometimes almost childish, speculations, with little attention to evidence and scant regard for logical rigor. according to humphrey consciousness is just so remarkable that an unwary brain might be tempted to think consciousness is really real. according to humphrey, however, consciousness is an illusion generated by matter mattering to itself, and is ultimately ontologically non-existent. both direct phenomenological investigation and modern science show that, contrary to humphrey’s materialist desires, consciousness “has its own intrinsic degrees of freedom” and is a fundamental dimension of reality. ultimately we are not the result of the evolution of an “original dollop of physical matter”. keywords: materialism, consciousness, mindless evolution, mindless matter, quantum revolution, darwinism. in his 2008 paper ‘getting the measure of consciousness’ nicholas humphrey opens with the assertion that: no one doubts that our experience of phenomenal consciousness the felt redness of fire, the felt sweetness of a peach, the felt pain of a bee sting – arises from the activity of our brains. 1 this is not true, and this glaring untruth would seem to indicate that humphrey does not bother to actually examine the views, or the evidence presented by, other researchers in the field of the investigation of the nature of consciousness and its relationship to the brain. in the previous year the important work irreducible mind: towards a psychology for the 21 st century was published. this work begins: the central contention of this book is that the science of the mind has reached a point where multiple lines of empirical evidence, drawn from a wide variety of sources, converge to produce a resolution of the mind-body problem along lines sharply divergent from the current mainstream view. 2 * correspondence: graham smetham, http://www.quantumbuddhism.com e-mail: graham.smetham@gmail.com http://www.quantumbuddhism.com/ mailto:graham.smetham@gmail.com dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 438-475 smetham, g. p., exploring mindless materialist visions of the mindless evolution of minds from mindless matter issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 439 the “current mainstream view”, of course, refers to exactly that claimed by humphrey to be incontrovertible – the activity of the brain is the ultimate generator of consciousness. the authors of irreducible mind, in this extensively researched and exhaustively referenced work, bring together a wealth of evidence indicating the falsity of the ‘naturalistic’ view which humphrey considers to be unquestionable and inviolable. the authors of im, examine in extensive and painstaking detail the evidence from phenomena which include such aspects as psychosomatic medicine, placebo effects, psychic healing, stigmata, multiple personalities, the exploits of yogis, physiological effects in hypnosis, automatism, near death experiences, the nature of genius, and meditation. all these topics are presented with reference to thoroughly researched and validated, exhaustively referenced, phenomenon that are accepted by leading authorities in the various fields covered. as one reviewer concludes: “the topics that i have some knowledge of … were covered with more than sufficient thoroughness and accuracy to support the point that consciousness, including subliminal consciousness, can produce physical effects and is not a mere epiphenomenon as proposed by philosophical materialists.” 3 humphrey’s approach, in contrast to the extensiveness, depth and rigor of im, however, relies on rather dubious and often clearly incoherent, in some cases almost childish, speculations, with little attention to evidence and scant regard for logical rigor. the just so stories for little children, which were written by british author rudyard kipling, are described by wikipedia as “highly fantasized origin stories” 4 so it is very appropriate that humphrey, described on wikipedia as “an english psychologist, based in cambridge, who is known for his work on the evolution of human intelligence and consciousness” 5 entitled his 1982 new scientist article ‘consciousness: a just-so story’. the story of the evolution of consciousness he presents in this article is pure fantasy. according to wikipedia the term ‘justso-story’ also has an ‘anthropological sense’: just-so story, also called the ad hoc fallacy, is a term used in academic anthropology, biological sciences, social sciences, and philosophy. it describes an unverifiable and unfalsifiable narrative explanation for a cultural practice, a biological trait, or behaviour of humans or other animals. the use of the term is an implicit criticism that reminds the hearer of the essentially fictional and unprovable nature of such an explanation. 6 as we shall see, this characterization is highly appropriate for humphrey’s work. the stories, or fairy tales, told around the camp fires of mindlessness in materialist strongholds regularly involve obvious nonsense, but in the academic corridors of materialism it doesn’t seem to matter! a central piece of such absurdity is the notion that consciousness is said to have ‘evolved’ from an absolute lack of consciousness or mind within the context of the materialist darwinian paradigm. this means that at some point in the far mists of time there must be a point when there is absolutely no consciousness within the universe at all. and this further means that dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 438-475 smetham, g. p., soul dust or a matter of mind: the mindless ideas of nicholas humphrey issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 440 at some point consciousness, an aspect of reality which has qualities which are entirely absent from ‘matter’, must magically arrive on the evolutionary scene without any causal mechanism. at least the materialist account of darwinian evolution of the natural world supplies a causal mechanism, random mutation and natural selection, even though it turns out to be unviable. the notion that consciousness is purely and nothing more than magical arrangements, patterns and machinations of mindless matter means that there must have been some point at which there was absolutely no consciousness, but only mindless matter mutely mattering away to itself. and then, suddenly, the light, albeit only a glimmer, a feeble spark of internal awareness, suddenly takes hold within a magically complex bit of, heretofore mindless and unconscious, jelly. presumably such feeble sparks of awareness were not continuous. surely matter did not manage to turn the full light of awareness on all at once for all time. so one might ask what evolutionary advantage the occasional feeble spark of awareness taking place within a primordial piece of organic jelly could possible confer, surely the organism in question could hardly have been conscious of them! according to humphrey’s article consciousness: a just-so story: …once upon a time there were animals ancestral to man who were not conscious. that is not to say that these animals lacked brains. they were no doubt percipient, intelligent, complexly motivated creatures, whose internal control mechanisms were in many respects the equals of our own. but it is to say that they had no way of looking in upon the mechanism. they had clever brains, but blank minds. their brains would receive and process information from their sense organs without their minds being conscious of any accompanying sensation; their brains would be moved by, say, hunger or fear without their minds being conscious of any accompanying emotion; their brains would undertake voluntary actions without their minds being conscious of any accompanying volition ... and so these ancestral animals went about their lives, deeply ignorant of an inner explanation for their own behaviour. 7 so these ancestral animals were kind of organic robots, without any glimmer of internal lighting so to speak, their brains are blank. but although their brains are utterly blank and devoid of internal glimmer or spark of any awareness, at the same time we are told that they process information, and they do so without sensation, or without being conscious of the sensation, for the moment which of these depictions is the one humphrey has in mind is not clear. furthermore they were “were no doubt percipient, intelligent, complexly motivated creatures, whose internal control mechanisms were in many respects the equals of our own.” so they were, in fact, what in modern western philosophical parlance is termed “zombies.” according to humphrey, for such internally blank creatures “it was their behaviour itself, not their capacity to give an inner explanation of it, that mattered to their biological survival.” a question which this vision begs, of course, is why a blank, organically but mindlessly functioning lump of organised matter wants, needs, is moved, or whatever, to survive biologically. for dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 438-475 smetham, g. p., exploring mindless materialist visions of the mindless evolution of minds from mindless matter issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 441 humphrey and others of his persuasion, it is taken as a given that matter, although completely mindless and devoid of intentionality, for some mindless reason ‘wants’, for want of a better word, to club together to keep a blank organism in the survival race, unaware of course of any rewards. so at this point in time these zombies: as the occasion demanded … acted hungry, acted fearful, acted wishful and so on, and they were none the worse off for not having the feelings which might have told them why. it is difficult to lend credence to such a simplistic view and there is absolutely no evidence for it. these creatures, according to humphrey’s vision of this time of abject mindlessness, have internal material machinations of their brains which trigger some kind of internal ‘flag’ which indicated ‘hunger’ for example, but they did not experience ‘hunger’ at all, there was no internal sensation, no consciousness of hunger, no hunger pangs, the brain just knew, in an unconscious unknowing manner, that the organism needed an intake of food in order not to eventually drop dead. presumably if these creatures did not manage to get the necessary sustenance they would start to exhibit behaviour of distress, all the time not actually feeling distress. this obviously follows from humphrey’s vision that “they acted hungry, acted fearful, acted wishful and so on” indicating that such zombie creatures acted in the same way as we do without the same sensations that we have. but then one must ask why would such creatures need to show distress behaviour, they are actually not in any conscious distress, so why did not the blank brain just register the severe lack of food without generating distress behaviour? presumably it’s just something matter cannot help doing when it gets hungry, it starts exhibiting distress behaviour even though it’s not in any distress. the section heading for this fantasy is ‘percipient but not conscious’, a heading which indicates the employment of the usual materialist slight of mind in order to produce the illusion of the mindless becoming mindful. the technique is to use a word which generally indicates the presence of consciousness, in this case ‘percipient’, which means ‘having the ability to perceive,’ with the claim that the manner in which the word is being employed does not require the presence of consciousness. then the implied presence of consciousness is used as a means to bring consciousness onto the evolutionary scene in a way which some unsuspecting people, and there are a lot of them, find quite natural. the story humphrey is going to try and foist on us in his ‘just-so-story’, indeed as if we were children, is that these poor zombies, endowed with “clever brains, but blank minds”, perhaps could have just carried on perceiving in complete and utter blankness and unconscious unknowingness but it just got too much for them, or they discovered that turning consciousness on was more fun. the absurdities of language use which often accompanies this deception is so laughable that it is difficult not to wonder whether the people who fall for the intellectual fraud are not actually dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 438-475 smetham, g. p., soul dust or a matter of mind: the mindless ideas of nicholas humphrey issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 442 zombies, mechanically processing the meanings of words without employing consciousness. here is humphrey’s next step in the delusional story: nonetheless, these animals were the ancestors of modern human beings. they were coming our way. though their lives may once have been comparatively brutish and relatively short, as generations passed they began to live longer, their life-histories grew more complicated, and their relationships with other members of their species became more dependent, more intimate, and at the same time more unsure. sooner or later the capacity to explain themselves and to explain others to take on, if it’s not too grand a word, the role of a natural “psychologist”, capable of under-standing and predicting their own and others’ behaviour within the social group – would become something they could no longer do without. at that stage would not their lack of consciousness have begun to tell against them? it is vital to bear in mind that there is not one shred of evidence for these putative zombie ancestors of ours who, according to humphrey, are “coming our way”. they are conjured in the vivid, if simplistic, imagination of humphrey’s brain, rather like the consciousness that humphrey hopes to persuade us must be conjured from the mindless and unconscious matter making up his increasingly social zombie creatures, which are now, we are told, desperately in need of the light of consciousness. they can’t be fully social without it! apparently humphrey’s zombies, who please always bear in mind have “clever brains” but not a glimmer of consciousness or awareness, are not doing too badly in their darkness. humphrey tells us that “their life-histories grew more complicated, and their relationships with other members of their species became more dependent, more intimate.” so they were managing a degree of intimacy within their abject darkness. furthermore they were living longer and more complicated lives, all without experiencing any passage of time or experiencing any complications of course. however, according to humphrey’s story there is a problem. despite the fact that up until now his zombies have been happily (without experiencing any happiness of course) perceiving away in complete darkness, satisfying their hunger without experiencing hunger, exhibiting wishing behaviour without wishing and so on, suddenly a degree of unsureness comes on the scene, presumably without them actually experiencing unsureness. where it comes from or why it arises we are not told, it arrives unannounced without reason, except perhaps that things have got complicated because the zombies are living longer and getting more intimate without experiencing any intimacy. it should be clear by now that the way that this story is being set up means that the zombie creatures are constantly experiencing without experiencing and the story is being concocted to give the appearance that they cannot continue like this. it’s all getting too much for them. they need consciousness otherwise they will not be able to become ‘natural psychologists’ who are dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 438-475 smetham, g. p., exploring mindless materialist visions of the mindless evolution of minds from mindless matter issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 443 “capable of understanding and predicting their own and others’ behaviour within the social group.” the important issue which humphrey will conveniently leave out of the story, however, is that, if the stuff that makes up the bodies and brains of his increasingly “social” zombies is the kind of material stuff beloved by all staunch materialists, the ultimately solid extended matter-stuff with no extra, added, included free of charge ‘mind’ or ‘consciousness’, then, no matter how dire the circumstances, there is nowhere that consciousness can possibly arise from, it is simply not included in the definition of matter. humphrey, however, doesn’t rush to get consciousness onto the evolutionary scene he decides to soften his readers resolve to maintain some consciousness of coherence by subjecting them to a bizarre sequence of incoherent claims under the enigmatic section heading ‘watch your brain working’. in answer to his question “would not their lack of consciousness have begun to tell against them?” humphrey answers: not necessarily. at least not at first, and not to the extent that all that’s said above implies. for inner explanations are not the only kind of explanations of behaviour. debarred as our unconscious ancestors may have been from looking in directly on the workings of their brains, they could still have observed behaviour from outside: they could have observed what went into the internal mechanism and what came out, and so have pieced together an external, objectively based explanatory model. “why am i (humphrey) looking in the larder?” not, maybe, “because i’m feeling hungry”, but rather “because it’s five hours since humphrey last had anything to eat” or “because humphrey has shown himself to be less fidgety after a snack”. in short, while our ancestors lacked the capacity to explain themselves by “introspection”, there was nothing to stop them doing it by the methods of “behaviourism”. the first thing i am forced to observe here is that, having read and pondered many such materialist fairly stories, i am convinced that very, very rarely do readers actually subject them to rigorous logical analysis. one would have thought that if a reasonably intelligent person were to subject humphrey’s claim here, and in many other places, to logical and conceptual analysis then they could only have a laughing fit! yet humphrey has given lectures along these lines to various collections of supposedly academic worthies and there is not a glimmer of a titter. once again it is vital to bear in mind that consciousness has not made an entrance onto the fairytale scene yet so all is blankness inside the “clever brains” of humphrey’s zombies. it is because of this inner ‘blankness’ which is due to the absence of consciousness that humphrey says that the zombies cannot manage ‘inner explanations.’ it seems that humphrey equates consciousness with an inner “watching” of the “brain working”. there is, of course, absolutely no evidence that this is what consciousness is, but, what the hell, by humphrey’s own admission this is a ‘just-so-story.’ now fortunately for the mindless zombies, although they do not have a clue about their own inner states, they can concoct ‘behaviourist’ type explanations of their own dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 438-475 smetham, g. p., soul dust or a matter of mind: the mindless ideas of nicholas humphrey issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 444 behaviour. they could, in the midst of complete, absolute and utter internal blankness, answer the question “why am i looking in the larder?” without experiencing themselves asking the question, with a behaviourist-style explanation, without experiencing the explanation as an explanation it’s all blank inside. the story humphrey has concocted is simply incoherent, the terms employed are simply inappropriate in a situation where the zombie creature really are all robotically blank inside. robots would not be puzzled about their behaviour unless programmed to. the desire to have explanations is an aspect of the world of consciousness, not utter mindless blankness. try to seriously picture what humphrey is suggesting here. we have the poor hungry and internally blank zombie. the zombie is hungry but does not experience itself as hungry or consciously know that it is hungry because of internal blankness. the brain somehow decides to deal with non-experienced hunger by going to the fridge. but the zombie does not know that it is going to the fridge because it is hungry because it does not experience itself as being hungry. it is therefore puzzled, without experiencing itself as being puzzled, and the only explanation it can come up with, without experiencing the explanation, is a behaviourist one. if you are not laughing yet you’ve got no ‘soul dust’ (the title of humphrey’s latest book), the notion of explaining one’s own behaviour to yourself in behaviourist terms because of a complete inner blankness whilst not actually experiencing the explanation because of the inner blankness is beyond the ridiculous. and yet this was published in new scientist! in the next phase humphrey refers to the behaviourist admiration of the ‘objective’ elimination of subjectivity: “the behaviourist,” wrote one of its first modern champions, j. b. watson, “sweeps aside all medieval conceptions. he drops from his scientific vocabulary all subjective terms such as sensation, perception, image, desire, purpose, and even thinking and emotion.” and who better placed to follow this recommendation than an unconscious creature for whom – such conceptions could not have been further from his mind? actually, of course, at this point in the story humphrey’s “unconscious creatures” do not have ‘minds’, remember “it’s all blank inside” – you have keep very alert when dealing with materialists, they constantly try to sneak mind on the scene as if it were a concoction of matter, when actually it’s just a sneaky use of words. we need to be quite clear that, according to humphrey’s story, the zombies have no trace, jot or glimmer of “sensation, perception, image, desire, purpose, and even thinking and emotion.” furthermore it’s not that they just don’t have the “conceptions”, obviously they do not have the conceptions, how could they? it’s all blank inside. they actually have no trace, jot or glimmer of “sensation, perception, image, desire, purpose, and even thinking and emotion.” these unconscious zombie creatures are all matter and no mind and no experience. you have to be very stringent with materialists because given just a smidgen of a chance they will sneak mind into their matter without you noticing. dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 438-475 smetham, g. p., exploring mindless materialist visions of the mindless evolution of minds from mindless matter issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 445 humphrey next employs an observation by another behaviorist which is useful for his cause: in fact, it is we conscious human beings who have trouble being hardheaded behaviorists: it is we who, as that other great behaviorist b. f. skinner has lamented, “seem to have a kind of inside information about our behaviour. we have feelings about it. and what a diversion they have proved to be!” feelings have proved to be one of the most fascinating attractions along the path of dalliance.” why, then, when ignorance of the inner reasons for behaviour might have been bliss, did human beings ever become wise? and it is at this point that humphrey abandons logical integrity. our mindless zombies are made of pristine ‘matter’ with no trace of added mind. and full blown hard-core matter, the kind of matter which materialists consider to be the primary ontological stuff of reality does not have mind qualities or the qualities of consciousness. humphrey’s zombies, by his own words, have no trace, jot or glimmer of “sensation, perception, image, desire, purpose, and even thinking and emotion.” this means that, according to humphrey’s own story it is impossible for “human beings ever become wise”, by which humphrey means acquire consciousness. but it is clear that humphrey has no intention of conforming to conceptual and logical coherence; it’s just a just-so-story, and it’s a conceptually incoherent and misleading just-sostory: what tempted him was a leap in the complexity of social interaction, calling in its turn for a leap in the psychological understanding of oneself and others. suddenly the oldtime psychology which was good enough for our unconscious ancestors, which is still apparently good enough for watson and for skinner, was no longer good enough for their descendants, behaviourism could take a natural psychologist only so far. and human beings were destined to go further. we need to quite clear that on the basis of materialism, a materialism which has led to the evolution of humphrey’s mindless zombies, who supposedly acted in lots of ways which made them look as if they had minds and experiences whereas in reality all was blank inside, no level of complexity of social interaction could call forth the new ontological realm of consciousness in order to provide “a leap in the psychological understanding of oneself and others”. if, as materialists maintain, matter is absolutely and completely non-conscious and has no glimmer of potentiality for consciousness, then no new modes of complex social interactions could possibly cause it to excrete a new ontological dimension of reality, no matter how powerfully humphrey’s zombies were “tempted”, without being aware of temptation of course. the notion that for the first part of the evolutionary process there is absolutely no glimmer of mind, absolutely no activity of consciousness, no trace of awareness, but only the mute and utterly dark and blank machinations of matter, and then suddenly, because of some adventitious and random requirement of getting along more intimately with one’s neighbours, or needing greater insight to their previously non-existent ‘minds’, blank evolution concocts a radically new dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 438-475 smetham, g. p., soul dust or a matter of mind: the mindless ideas of nicholas humphrey issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 446 quality of reality, a quality which just was not around before the magical point of consciousness creation, is quite simply ludicrous. and yet this is the incoherent picture regularly advanced by materialist ‘philosophers’ and ‘thinkers.’ and this absurd evolutionary picture is also inconsistent with other ‘just-so-stories’ indulged in at other points in time by humphrey. but expecting consistency from materialist story tellers is a vain hope, as vain as the hope of turning mindless matter into mind. humphrey is nothing if not grandiose in his belief in the efficacy of his just-so-stories. so in 2000 we find him publishing a paper in the journal of consciousness studies entitled ‘how to solve the mind-body problem’. this paper is extraordinarily insightful, although not in a way that supports humphrey’s materialist cause. in this paper he quotes with approval the statement by the eighteenth century french philosopher denis diderot that “all phenomena, whether of weight, elasticity, attraction, magnetism or electricity, are all aspects of a single state.” he then tells us that: …contemporary physicists are still uncertain whether such a theory of everything is possible even in principle. but within the narrower field that constitutes the study of mind and brain, cognitive scientists are increasingly confident of its being possible to have a unifying theory of these two things. they – we – assume that the human mind and brain are, as diderot anticipated, aspects of a single state – a single state, in fact, of the material world, which could in principle be fully described in terms of its microphysical components. … every instance of a human mental state is identical to a brain state … meaning that the mental state and the brain state pick out the same thing at the microphysical level. 8 now this is a very interesting insight, an insight which actually undermines humphrey’s materialist position. why so? because the ground level microphysical level is the quantum field which is immaterial. as a recent book on quantum theory explains: now, from a philosophical point of view, this is rather big stuff. our whole manner of speech … rather naturally makes us think that there is some stuff or substance on which properties can, in a sense, be glued. it encourages us to imagine taking a particle and removing its properties one by one until we are left with a featureless ‘thing’ devoid of properties, made from the essential material that had the properties in the first place. philosophers have been debating the correctness of such arguments for a long time. now, it seems, experimental science has come along and shown that, at least at the quantum level, the objects we study have no substance to them independent of their properties. 9 so it would seem that, if we take the evidence of the physical sciences seriously, and as humphrey considers himself to be a scientist of sorts there should be no reason for him not to, it seems that a unification of the material stuff of the brain and the realm of the mental is indeed metaphysically possible. but the common substrate, the quantum field, is entirely immaterial, although it does give rise to the fleeting realm of the apparent particles which appear to make up dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 438-475 smetham, g. p., exploring mindless materialist visions of the mindless evolution of minds from mindless matter issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 447 a ‘material’ world. as the physicist robert oerter says in his excellent book the theory of almost everything: the standard model, the unsung triumph of modern physics: in nineteenth-century physics, the universe contained two things, particles and fields. particles were tiny and hard, like small billiard balls. fields were elastic and spread throughout space. particles produced fields according to their electric charge and their motion, and particles responded to the fields of the particles around them. relativistic quantum field theory completely eliminates the distinction between particles and fields. matter (the electrons and positrons) and forces (the photons) are both described in the same way by quantum fields. quantum fields combine particle nature and field nature in a single entity. the quantum field spreads out through space, just like classical field, but it is quantized: when you try to measure the field you always find a whole particle, or two particles, or none. you never detect half an electron or a fractional photon. if fields were peanut butter, classical fields would be smooth and quantum fields would chunky. 10 a materialist may be tempted to grasp at quantum straws, hoping that the chunky nature quantum field could resurrect a semblance of their beloved ‘matter’. however, it is the field aspect that is primary and the ‘particle’ aspect comes into being “when you try to measure the field.” according to humphrey a significant advance in understanding the nature of his putative “mindbrain identity” requires the recognition that: …there can be no hope of scientific progress so long as we continue to write down the identity in such a way that the mind terms and the brain terms are patently incommensurable. the problem will be especially obvious if the dimensions do not match up. humphrey elucidates this claim with the example of dimensional analysis of mathematical equations. any mathematical equation must reduce down to the same combination of dimensions on each side. the fundamental dimensional units are mass (m), length (l) and time (t). so if we reduce an area to its fundamental dimensional form it is l 2 because it consists of a length multiplied by a length, volume is l 3 because it consists of a length multiplied by a length multiplied by a length, and speed is lt -1 which is a length divided by time. now consider the einstein’s famous equation: e = mc 2 in dimensional terms both e and mc 2 reduce to ml 2 t -2 so both sides have the same combination of fundamental dimensions. humphrey next extends this important insight this to conceptual analysis in general: but what is true of these dynamical equations is of course just as true of all other kinds of identity equations. we can be sure in advance that, if any proposed identity is to have even a chance of being valid, both sides must represent the same kind of thing. indeed we can generalise this beyond physical dimensions, to say that both sides must have the dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 438-475 smetham, g. p., soul dust or a matter of mind: the mindless ideas of nicholas humphrey issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 448 same conceptual dimensions, which is to say they must belong to the same generic class. so, if it is suggested for example that mark twain and samuel clemens are identical, mark twain = samuel clemens, we can believe it because both sides of the equation are in fact people. or, if it is suggested that midsummer day and 2lst june are identical, midsummer day=2lst june, we can believe it because both sides are days of the year. but were someone to suggest that mark twain and midsummer day are identical, mark twain=midsummer day, we should know immediately this equation is a false one. but what happens next in humphrey’s materialist thought process is, contrary to his own important insight, entirely conceptually incoherent, although he tries to cover over this fact: now, to return to the mind-brain identity: when the proposal is that a certain mental state is identical to a certain brain state, mental state, m = brain state, b, the question is: do the dimensions of the two sides match? the answer surely is, yes, sometimes they do, or at any rate they can be made to, provided cognitive science delivers on its promise, it should soon be possible to characterise many mental states in computational or functional terms, i.e. in terms of rules connecting inputs to outputs. but brain states too can relatively easily be described in these same terms. so it should then be quite straightforward, in principle, to get the two sides of the equation to line up. “sometimes they do”! “provided cognitive science delivers on its promise”!! “it should soon be possible”!!! this is classic materialist obfuscation and avoidance of the truth of things. the famous twentieth century philosopher of science sir karl popper called this kind of thing “promissory materialism,” in other words what is being said by humphrey is that the identity is by no means evident or established, but humphrey tells us he is sure ‘cognitive science’ will get around and prove it sometime in the future. however this is nothing more than blind faith in the face of a great deal of contrary evidence. but why not just do a proper conceptual analysis, just like a mathematical dimensional analysis. in order to do this, however, we need to decide whether we can validly reduce mind and consciousness to anything simpler. and an important first step in this task is to consider where and why the fundamental dimensions of physics mass, length and time come from. we tend to think of these as fully ‘objective’ entities which exist independently of us “out there” in an independent structure reality. but it is worthwhile considering the famous twentieth century physicist john wheeler’s admonishment that quantum physics has shown us that: the universe does not ‘exist, out there,’ independent of all acts of observation. instead, it is in some strange sense a participatory universe. 11 if you ponder the issue of why mass, length and time are taken to be fundamental, the reason is clearly that these are aspects of our experience which appear within our immediate experience of the world to be fundamental, in the sense of being irreducible within first order experience, and independent of each other. for instance: is it possible in experience to straightforwardly, which is to say without convoluted conceptual elaboration, to experientially reduce mass to length? the answer is clearly no. mass is related to the direct experience of obstructive contact and the direct dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 438-475 smetham, g. p., exploring mindless materialist visions of the mindless evolution of minds from mindless matter issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 449 experience of the ‘weightiness’ of objects, length is a measure of our direct experience of extension in space, and time is a measure of extension in, well, time. none of these can be directly in the immediacy of experience reduced to one of the others. i can, of course, connect these aspect in certain ways by conceptual elaboration, but within first order direct experience they are separate and irreducible to each other. so what about mind or consciousness, can it be reduced, within direct experience, to any of the others. of course, amongst many western philosophers of mind and researchers within the field of consciousness studies it is held that consciousness is a great mystery, a ‘hard’ problem, as the philosopher of mind david chalmers has characterized it, something absolutely intractable to the mind! this view, if you think about it, is basically making the claim the consciousness has absolutely no comprehension of its own nature, which, also if you think about it, is very odd. but this view only arises because western philosophers, like humphrey, in general are convinced, without any evidence whatsoever, that consciousness must be reducible to matter. but this is in no way indicated within direct experience, and, as indicated above, the fundamental aspects of ‘physical’ reality are derived originally from our direct experience. in fact in direct experience consciousness, which is the immediately experienced clear field of awareness within which phenomena, both inner (feeling, thoughts) and outer (phenomena which appear as external entities) are experienced, is the ground of awareness within which all phenomena have an appearance. experientially consciousness is the ground of awareness which provides the possibility for the other dimensions of experience. so within direct experience of the primary phenomenological features of reality consciousness is the primary amongst primary constituents. and, remarkably this primacy is now emphasized by the fact that consciousness has been found to be entangled in an intimate way at the quantum level, which is why the quantum physicist eugene wigner said: when the province of physical theory was extended to encompass microscopic phenomena, through the creation of quantum mechanics, the concept of consciousness came to the fore again; it was not possible to formulate the laws of quantum mechanics without reference to consciousness. 12 and quantum cosmologist andre linde has been prompted to ask the question which is indicated by the quantum situation: is it possible that consciousness, like space-time, has its own intrinsic degrees of freedom and that neglecting these will lead to a description of the universe that is fundamentally incomplete? what if our perceptions are as real as (or maybe, in a certain sense, are even more real) than material objects? 13 so both direct phenomenological investigation and modern science show that, contrary to humphrey’s materialist desires, consciousness “has its own intrinsic degrees of freedom” and is a fundamental dimension of reality. at this point our fundamental dimensions of reality must be mass, length, time, and consciousness. dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 438-475 smetham, g. p., soul dust or a matter of mind: the mindless ideas of nicholas humphrey issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 450 in his discussion of the dimensional analysis of equations humphrey tells us that because of the dimensional analysis of e = mc 2 : by the same token, if anyone were to propose e = mc 3, we would know immediately that something was wrong. now, by the same token, we know that if anyone were to propose, such as humphrey does, that “mental state, m = brain state, b” we would know immediately that something was wrong. why is this? well according to humphrey’s materialist perspective when we do a dimensional analysis we have: brain state, b → is of dimension m (‘material’ neurons) mental state, m → is of dimension c (consciousness) but we cannot have m = c because the dimensions do not match. but what, then, can we say about humphrey’s breezy and confident assertion that it is easy to establish the identity of brain states and phenomenal experience within consciousness: …this part of the task may be just as easy as in the case of cognitive states such as remembering the day. we do an experiment, say, in which we get subjects to experience contour sensations, while again we examine their brain by mri. we discover that whenever someone has a red sensation, there is activity in cortical area q6. so we postulate the identity: phantasm of red = activity in q6 cortex. so far, so good. as humphrey himself indicates on the very next page, the assertion of identity is actually a hypothesis, as yet unproven, but which he is sure will be proven at some future point, of a correlation. again humphrey makes the assumption that at some point in the future his faith will be vindicated, he does not bother to look at evidence available today which indicates that this is very, very unlikely. at this point it is relevant to take a detour and recall humphrey’s just-so-story concerning blank zombie creatures “on the way” to having full human-type consciousness. this story is actually incompatible with humphrey’s assertion of confidence in the ultimate identity of brain states and phenomenal conscious experience. figure 1a and 1b illustrate, in an appropriate light-hearted manner, the situation prior to, and subsequent to, the pressing need for the zombies to develop the inner light which enabled them to become “natural “psychologist(s)”, capable of understanding and predicting their own and others’ behaviour within the social group”, and thus abandon their zombie condition. but if were accept this account then we must also accept that evolutionary social pressures are capable of actually transforming the actual nature of the ontological ‘stuff’ of the material world. the brain stuff in figure 1a must be adopting all the right states for making our zombie mimic being hungry or wishing etc. but in humphrey’s justso-story it is certainly not producing the experiential-phenomenal accompaniment! so the kind of matter in 1a and 1b must be very different! but humphrey does not mention this deep ontological transformation. instead he implicitly maintains the view that the stuff of 1a and 1b is dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 438-475 smetham, g. p., exploring mindless materialist visions of the mindless evolution of minds from mindless matter issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 451 exactly the same except that in 1b the ‘same’ stuff does something dramatically different. again this is incoherent. figures 1a and 1b humphrey was led to the idea that it might have been possible at some point in evolution for a human ancestor to have been doing all, or at least most, of things that we humans now do without any accompanying phenomenal consciousness by the phenomenon of blindsight. this is the ability of some people who are visually blind, which means they have no sensations of seeing the world, to be able to ‘perceive’ some features of reality. as humphrey points out this is a “kind of unconscious vision,” 14 which has now been demonstrated in many cases. this led humphrey to make the radical suggestion that ‘perception’ can occur without an accompanying ‘sensation’. it follows from this that there can logically be a philosophical-zombie, functioning exactly like a human being but without any accompanying ‘sensations,’ which for normal human beings seem to be part and parcel of ‘perception.’ humphrey, however, disagrees with this view. according to his vision, all perception actually takes place entirely in the dark as in blind sight, and also as in the zombie situation of figure 1a. the light of phenomenal consciousness or awareness (figure 1b) is an added extra which is not essential to perception. in order to explain his viewpoint humphrey uses the image shown in figure 2, i have added the images from figure 1 to indicate how they correspond. humphrey explains: the external object, a, transmits a stimulus to the sense organ, a`. the subject creates a sensation, b, as an active response to it a personal evaluative response. this response is not designed to be a copy of the stimulus. but, just in so far as it is s's response to the particular stimulus, it carries potentially a wealth of information about the stimulus, both as to what the stimulus is as a physical event and as to how the subject feels about it. s's reading of this information, p(b), can be put to several uses …; but the one thing it is not used for is as the raw material for the perception of the world. perception has its own quite separate channel, p(a), beginning over again with the stimulus. 15 this is indeed a radical, and bizarre, proposal which has produced, rightly, incredulity in some quarters. and it is easy to see serious flaws in its structure. according to this proposal the actual perception, the ‘real’ perception so to speak, takes place via route a`→ p(a), and it takes place in dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 438-475 smetham, g. p., soul dust or a matter of mind: the mindless ideas of nicholas humphrey issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 452 blankness. in other words the subject perceives without having a sensation, which means that they must perceive without ‘knowing’ that they perceive. figure 2 (16) according to humphrey the sensation, the ‘inner light’ of phenomenal awareness, is generated via a completely different mechanism which is “active response” on the part of the subject, it is “a personal evaluative response” and “not designed to be a copy of the stimulus.” humphrey’s personal evaluative ‘sensation’ also has amazing qualities, apart from the glow of phenomenal conscious-awareness. this is because, although the ‘sensation’ is “not a copy” and is only a subjective response, it also, says humphrey, has “potentially a wealth of information about the stimulus.” but this is logically impossible! if all the perception gets done on route a`→ p(a), which according to humphrey’s proposal must be the case because he makes an absolute division between the ‘perception’, which he conceives of as completely unconscious and mechanically blank, and the ‘subjective’ ‘glow’ of the ‘sensation’ which is added on, then the completely subjectively added on ‘sensation’ cannot contain information about the object, it’s all subjective. and the fact that it’s all ‘subjective’ produces a huge problem for humphrey’s materialist perspective. if we allow that the real perception route is a`→ p(a) is all mechanically materialist, no new added extra immaterial ingredient of awareness is secreted from brain neurons along the way. dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 438-475 smetham, g. p., exploring mindless materialist visions of the mindless evolution of minds from mindless matter issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 453 on the other route to the ‘sensation’, however, it’s a different matter because an immaterial subjective bit gets projected on. humphrey, of course would claim it is all material machinations of the neurons, but this simply does not fit well with humphrey’s description of this extra added qualitative sensation as a ‘subjective’ “personal evaluation.” ‘personal evaluations’ are the stuff of consciousness, but here humphrey wants us to believe that a completely blank brain carries out a “personal evaluation” and then generates a completely new kind of ‘stuff’ of reality, the phenomenal glow of conscious awareness, and sticks it on to the entirely blank perception. furthermore this extra bit actually carries no aspect of the perception because it is all subjective and the perception is an ‘objective’ yet unconscious perception. none of this makes sense. when materialists write this kind of nonsense they generally assume what they should be trying to prove, i.e. that matter produces consciousness. they have to; it cannot do anything of the kind. and one does not have to do experiments to know this; this fact is contained in the definitions of ‘matter’ and ‘consciousness’. ‘matter’ is defined to be all solid and extensive stuff lacking any conscious qualities and ‘consciousness’ is immaterial knowing ‘stuff’ (using this term very loosely). because of quantum physics we now know that this kind of matter does not exist. nevertheless, it is this kind of non-existent ‘matter’ which is generally held in high esteem in the brains of materialists. as we shall see, the fact that the materialist version of ‘matter’ does not exist, reality is in fact all quantum ‘dream-stuff’ as quantum physicist wojciech zurek indicates, allows us to create a clear, coherent and comprehensive account of consciousness and the appearance of matter. once realize that the physical properties of the quantum field contains the potentialities for the production of the appearances of the material world and the knowing awareness of consciousness all becomes very easy to understand because the ontological ground of reality, the quantum field, contains the potentialities for both kinds of production, the appearance of matter and experience of consciousness. materialists, however, claim that the ontological ground of reality is devoid of all traces of mind and consciousness, devoid of any glimmers of awareness or any glimmer of the potentiality for consciousness, and then start to propound deeply ridiculous, contradictory, incoherent and absurd claims such as daniel dennett’s claim that: an impersonal, unreflective, robotic, mindless little scrap of molecular machinery is the ultimate basis of all the agency, and hence meaning, and hence consciousness, in the universe. 17 and here is humphrey’s less dramatic version: consciousness is made of a certain kind of physical activity inside the subject’s head. and this activity, we can assume, has been designed by natural selection, using nothing other than the resources of a biologically evolved nervous system. 18 dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 438-475 smetham, g. p., soul dust or a matter of mind: the mindless ideas of nicholas humphrey issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 454 and, because they place themselves in such an absurd intellectual position, they are forced then to resort to conceptual deception in their works. presumably they are deceiving themselves as well as their readers, i cannot think of any reason why someone would engage in such a profoundly mistaken course of intellectual deception knowingly, but i could be wrong. however the deception is fundamentally the same in all materialist advertising campaigns, it simply involves using language in a manner which relentlessly suggests the presence of consciousness, awareness and conscious intentionality whist pretending that it is not there. as soon as they want to produce the new magical ingredient in their description of process of reality they simply make what is implicit in the consciousness-saturated language used to describe the putatively mindless material machinations explicit. an unwary reader, or a reader already sympathetic to the materialist cause, doesn’t notice the trick and they impute the illusion, generated by the language use, to the process of reality, even though in reality the trick is impossible. humphrey’s use of the notion of one bit of the brain suddenly carrying out a subjective personal evaluative response to the perception is example of assuming the presence of consciousness whilst in the midst of supposedly accounting for the generation of consciousness is an example of this strategy. the notion that, once have performed the personal evaluation, the unconscious brain neurons somehow ‘subjectively’ excrete a glob of consciousness to stick on to the perception is just silly, but such silliness is regularly indulged in during materialist advertising campaigns. remarkably, in his ‘how to solve the mind-body problem’ paper humphrey actually admits that his method involves a bit of linguistic skullduggery: our task was to recast the terms on each side of the mind-brain identity phantasm, p = brain state, b, so as to make them look more like each other. what we have done so far is to re-describe the left hand side in more concrete terms. thus the phantasm of pain becomes the sensation of pain, the sensation of pain becomes the experience of actively paining, the experience of actively paining becomes the activity of reaching out to the body surface in a painy way, and this process becomes self-resonant and thick… 19 in this absurd sequence humphrey is actively and painfully trying to re-describe phenomenalconsciousness of the “phantasm of pain” so that it looks or sounds more like ‘matter’ being “selfresonant”. the implausibility of the desperately forced links is painful, and this is not a matter of “reaching out to the body surface in a painy way” (i’ve just made my pain worse by requoting this gibberish!). even more depressingly painful is the fact that such ideas are entertained as worthy of consideration by many in the academic community. in the final section of this paper humphrey presents another version of his evolutionary vision of how mind is generated from mindlessness which he says he will do “in cartoon form” as if what had gone before did not have a certain cartoon quality. we are asked to return to the “earliest of times and imagine a primitive amoeba like animal floating in the ancient sea.” the boundary of this animal is important because: dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 438-475 smetham, g. p., exploring mindless materialist visions of the mindless evolution of minds from mindless matter issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 455 …everything within it is part of the animal, belongs to it, is part of “self”, everything outside it is part of “other”. the boundary holds the animal’s own substance in and the rest of the world out. the boundary is the vital frontier across which exchanges of material and energy and information can take place. 20 notice the blurring of the conceptual boundaries between the material stuff of the animal and its realm of “self”. humphrey is about to tell us that this animal is in no way “mentally aware of what is happening” and yet he has imputed a “self” in order to allow the further imputation of intentionality to what he claims is purely mindless mechanistic processes. what follows makes one wonder whether humphrey might have been better off writing children’s bedtime stories: now light falls on the animal, objects bump into it, pressure waves press against it, chemicals stick to it. no doubt some of these surface events are going to be a good thing for the animal, others bad. if it is to survive it must evolve the ability to sort out the good from the bad and to respond differently to them reacting to this stimulus with an ow! to that with an ouch! to this with a whowee! thus, when, say, salt arrives at its skin it detects it and makes a characteristic wriggle of activityit wriggles saltily, when red light falls on it, it makes a different kind of wriggle: it wriggles redly. these are adaptive responses, selected because they are appropriate to the animal's particular needs, wriggling saltily has been selected as the best response to salt, while wriggling sugarly, for example, would be the best response to sugar, wriggling redly has been selected as the best response to red light, while wriggling bluely would be the best response to blue light. all this is supposed to be totally mechanical with no component of any kind of mentality, although, in conformity with a general procedure within materialist descriptions, implications of mentality are contained within some of the language employed, the animal responds with “an ow!” or “an ouch!” or “a whowee” (i did say that many of humphrey’s elucidations border on the childish). also note the use of the descriptions that the animal, in response to various stimuli, “wriggles saltily”, “wriggles redly” and so on. now in this context this terminology is supposed to be describing purely material-mechanical, non-mental reflexes. however if you go back to the quote on page 81 where humphrey talks of the need to describe “phantasms”, which are phenomenalsensations involving consciousness, more like brain-states one find that he has identified the experience of pain as “the activity of reaching out to the body surface in a painy way.” he has replaced, for his own convenience, what should be experience within consciousness with a seemingly mechanical description. this of course paves the way for identifying what should be a purely mechanical “wriggling redly” with the experience of red! this is in line with humphrey’s ‘theory’ that: …sensations derive their characteristic phenomenology from the fact that they are – in evolutionary origin – a kind of bodily action, involving reaching back to the stimulus at the bodily surface with an evaluative response. 21 dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 438-475 smetham, g. p., soul dust or a matter of mind: the mindless ideas of nicholas humphrey issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 456 but it is not a “fact” that sensations are “in evolutionary origin a kind of bodily action.” and “evaluative responses” are the kind of processes minds engage in, not bodies. humphrey constantly presupposes what he is supposed to be demonstrating. and the primary technique he employs amounts to smoke and mirrors linguistic deception. in an lse public lecture promoting his book soul dust: the magic of consciousness humphrey once more reiterates his simplistic and incoherent ‘theory’ that ‘sensations’, the immediate awareness within a person’s field of perception, are nothing more than a species of bodily “performances” with some wonderful, and deeply deceptive for those not up to the task of seeing the illusion, conceptual perfidy. in this book humphrey tells us that consciousness is a “magical mystery show” “put together” by evolution, using nothing other than material components, of course. now the term “magic show” is, of course, not a precise technical description of the phenomenon of consciousness, it is an evocative metaphor. but humphrey treats his vague and suggestive metaphors as if they were precise links in rigorous demonstration. if consciousness is a “show”, he says, then it must have been a “show” at the outset and “sensations have indeed always involved a kind of performance”. this is because, according to humphrey, “sensation originated in evolution as a kind of active response to stimulation, a bodily expression of what was happening to the animal and how it felt about it.” 22 the outrageously dubious nature of the links that humphrey employs here should be obvious to anyone with an ability to do a bit of conceptual analysis. we begin with the vague metaphorical assertion that consciousness is a “magic show”; and the question that humphrey wants to answer is: how can purely material evolution create this magic show of consciousness, which appears to be entirely different in qualitative nature to the material realm? well, a “show”, asserts humphrey, is a kind of “performance” and his theory that sensation is actually nothing more, or was originally nothing more, than a “bodily action involving reaching back to the stimulus at the bodily surface with an evaluative response” is a kind of “performance” therefore it follows that this “bodily action” is the “magic show” of consciousness. hence the “performance” of the “magic show” of consciousness is the same as the “performance” of the “bodily action” of sensation. it’s all so easy when you misuse language! no wonder a member of the audience asked at the end of the lecture “isn’t your presentation a linguistic and intellectual illusion.” at least one member of the audience saw through the illusion of humphrey’s magic show. at this point in the lecture humphrey recounts his just-so-story of the floating pre-cambrian animal non-mentally responding with “an ow!” or “an ouch!” or “a whowee” to various stimuli. in this way the stimuli are “assessed” and the animal responds with some kind of “wriggle” of “acceptance” or “rejection” accompanied by a “smile” a “scowl” a “grin” at “the level of a very primitive organism.” and all this is supposed to happening with absolutely no dimension of mentality, no glimmer of consciousness. “however,” says humphrey: suppose that the animal should actually want to know what was happening to it, and form a mental representation of that stimulus its responding to. well a neat solution dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 438-475 smetham, g. p., exploring mindless materialist visions of the mindless evolution of minds from mindless matter issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 457 would be for the animal to monitor its own response because the reflex behaviour carries lots of information about the stimulus… 23 how can an absolutely mechanical organism, which is completely devoid of any trace glimmer or spark of consciousness or mentality, “want to know what is happening to it?” and, then, furthermore, come up with “a neat solution!” however, according to humphrey: …our ancestors soon discovered that they could represent what was happening at their body surfaces by monitoring what they themselves were doing about it. 24 and now humphrey has simply slipped in the realm of consciousness and intentionality as if it were the most natural thing in the world, even though there has been no demonstration of how a purely material-mechanical stimulus-response organism could exude this realm of awareness, ‘wanting’ and intentionality. later, humphrey tells the audience, as the animal becomes more sophisticated it is not happy with this state of affairs and ‘wants’ a more sophisticated tracking mechanism. so “what can it do?” the answer is “for the responses to become internalized where they can be still monitored.” “sensory responses have become what” humphrey “calls ‘privatized.’ figure 3 is humphrey’s image of this process, with a small addition (the faces). as i said humphrey should have been a children’s writer, there is absolutely no evidence for his absurd cartoon concoction, it is indeed an incoherent private fantasy, which should be met with laughter and derision for its childish implausible incoherence. figure 3 (25) in the third of the cartoons of figure 3 we are supposed to imagine that the ‘privatized’ response causes a “self-resonant and thick” feedback loop within the material of the emerging ‘brain’ of the primitive creature. as with many materialist fantasies humphrey considers that if the matter of the brain can be imagined into performing some kind of really complicated and almost mystical feat of internal self-referencing then its material stuff must be then capable of producing dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 438-475 smetham, g. p., soul dust or a matter of mind: the mindless ideas of nicholas humphrey issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 458 the illusion of consciousness. the ‘wriggles’ on the body surface are now internalized into the stuff of the brain, and because our brains are now tying themselves up into convoluted wriggling knots it is no wonder that they start excreting this strange illusory magic show of consciousness: it has been true all along, ever since the days when sensory responses were indeed actual wriggles at the body surface, that they have been having feedback effects by modifying the very stimulation to which they are a response. in the early days, however, this feedback circuit was too round-about and slow to have had any interesting consequences. however, as and when the process becomes internalized and the circuit so much shortened, the conditions are there for a significant degree of recursive interaction to come into play. that’s to say, the command signals for sensory responses begin to loop back upon themselves, becoming in the process partly self-creating and self-sustaining. these signals still take their cue from input from the body surface, and still get styled by it, but on another level they have become signals about themselves. to be the author of such recursive signals is to enter a new intentional domain. 26 again we are in the realm of smoke and mirrors, there is absolutely no reason why “recursive signals” should conjure up “a new intentional domain”. humphrey next reveals another of his ridiculous hunches, these internal brain knots require more than four dimensions: …my hunch is that re-entrant circuits in the brain are creating complex attractor states that require more than the usual four dimensions to describe them and that it is this that makes these “states of mind” seem to have immaterial qualities. but you do not need to understand what i have just said to get the message. creating something that gives the illusion of having weird and wonderful properties need be no great shakes, certainly much easier than creating something that actually has them… 27 but this is just another indication that the complex “re-entrant circuits” in humphrey’s brain must be short-circuiting. for if the “complex attractor states” (humphrey supplies the picture shown in figure 4) are exemplified in the material of the brain then how can they possibly “require more than the usual four dimensions,” within the four-dimensional matter of the brain, humphrey makes no mention of subtle atomic structures or quantum physics. as far as i can see humphrey is not referring to abstract “re-entrant circuits”, he is taking about the crude neuronal ‘stuff’ of the brain. this is certainly suggested by humphrey’s remark that: we can surely assume that the kind of development i have sketched above will not have happened accidentally. it must be the result of natural selection favouring genes that underwrite the specialised neural circuits whatever they turn out to be – that do indeed sustain the illusion of qualia, giving rise to the magical mystery show for the firstperson. 28 we should surely conclude from this that it is the “specialized neural circuits” which are more than four-dimensionally convoluted into “complex attractor states.” one can find research into how the various subtle neuronal activities produce some kind of multiple-dimensional informational states generated by electrical-informational fields as when a research paper refers to “integrator circuit models characterized by multiple dimensions of slow firing-rate dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 438-475 smetham, g. p., exploring mindless materialist visions of the mindless evolution of minds from mindless matter issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 459 dynamics,” 29 but this is not what is suggested by humphrey’s elucidations, if elucidations they can be called. indeed the very reference to “the usual four dimensions to describe them” would suggest that humphrey is indicating three spatial dimensions and time. which would further suggest that he thought the brain could create new dimensions of spacetime whilst remaining thoroughly ‘material’. figure 4 – a differential attractor 30 humphrey writes that “you do not need to understand what i have just said to get the message”. but unfortunately this is not true. what is true that his attempted explanations here are “confused and confusing” as the new statesman reviewer raymond tallis says: he claims to have solved “the hard problem” of consciousness: how it is that a piece of matter such as a human organism (or its brain) can have conscious experiences, items that do not seem of a nature that can be conjured out of matter alone. his “explanation” is confused and confusing, not the least for his conclusion that consciousness is “a magical mystery show that you lay on for yourself”, a “self-created entertainment for the mind”, staged by one part of the brain to influence another part of the brain. 31 there is, indeed, no talk of subtle ‘consciousness fields’ in humphrey’s attempted explanations, it seems always to be a matter of one bit of jelly laying on a show for another bit of jelly. is any of this at all plausible? but suppose we give humphrey the benefit of the doubt and accept for a moment that he might have thought in terms of the brain exuding subtle multidimensional consciousness fields which produce the qualitative aspect of consciousness. in this case we are back with the problem that this means that, prior to the remarkable shift from zombie status to fortunate ‘magic show’ status, the brain would not have been exuding such consciousness fields. and this means that the very material stuff of the brain changed very, very radically at some point. again such a notion is beyond implausibility. when his ideas are analyzed with any precision there are so many huge problems one can only conclude that many people do not bother to really make an effort to investigate. this is often the case in the materialist camp. dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 438-475 smetham, g. p., soul dust or a matter of mind: the mindless ideas of nicholas humphrey issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 460 in the concluding remarks to his paper on how to solve the mind-body problem humphrey says regarding his linguistic massaging to make brain-states look identical to phenomenalconsciousness: to return to our identity equation: we needed a certain set of features on the brain side. we could have invented them if we were brave enough. but now, i submit, we actually have them handed to us on a plate by an evolutionary story that delivers on every important point. 32 a rigorous analysis of his various fantasies, however, clearly indicates that, indeed, the truth of humphrey’s “evolutionary story” is that he did invent it! in his essay ‘consciousness: the achilles heel of darwinism? thank god, not quite’ inadvertently exposes the absurdity of the materialist case; and the fact that he does this, and the manner in which he does it, also exposes the deficiencies in his own intellectual acuity. the apparent existence of the phenomenon of consciousness, with its remarkable immaterial qualities, he indicates, might be thought to require some kind of ‘super-intelligent design.’ however, we know with absolute confidence, he implies, that: living beings, remarkable as they are, are nonetheless physical mechanisms made of purely material substance. and even if there are some puzzles about what’s gone into their evolutionary design (and there really are not many such puzzles left), biology has progressed so far that we can see in just about every case how the living machinery operates. many scientists would predict it will soon be in every case but one. and, yet this one hard case is so central to our world and of such personal importance that it may be enough to call the whole scientific enterprise into question. the problem case is human consciousness. consciousness … is unquestionably a phenomenon apart. most of this is just fallacious. are living beings “made of purely material substance?” no, if one believes the findings of modern physics then everything is made of quantum ‘stuff’. and quantum ‘dream-stuff’, as zurek calls it, is not material, if we are using this term with the connotation that humphrey is employing. the next issue is that biology has not progressed as far as humphrey claims. there is one huge problem of our understanding of “evolutionary design”, which is how “living machinery” arose in the first place from utterly dead, non-conscious matter. with reference to this, the general and mistaken image of the origin of life from utter, blank lifelessness is brilliantly described by simon-conway morris: …images of warm ponds, seething volcanic springs, and massive thunderstorms rumbling across a deserted yet pregnant landscape are used to feed the imagination. at this stage, life has yet to exercise its peculiarly specific grip, its spinning of the genetic code, it’s weaving of biochemical complexities; …the nascent processes of darwinian dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 438-475 smetham, g. p., exploring mindless materialist visions of the mindless evolution of minds from mindless matter issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 461 selection are already winnowing and reaping … metaphorically the molecules slug it out by tooth and claw. cycles develop, life emerges… but this is pure fantasy, despite much misreporting to the contrary it is the case that: …something is missing, life cannot be created in the laboratory, nor is there any clear prospect of it happening. 33 there is no compelling evidence for this overused fantasy. the announce-ments of the test tube creation of life are wildly overstated and one of the chief exponents of this research, stanley miller, was candid enough to say that: the problem of the origin of life has turned out to be much more difficult than i, or most, people envisioned. 34 and there is growing evidence that the quantum level of the process of reality is likely to be fundamental in the development from apparent lifelessness to the first glimmers of life and consciousness. the claim that just about all evolutionary biological mechanisms are understood is absurd bluster. humphrey’s assertions about evolutionary biology being pretty much sown up were made in 2006; the following report is from the new york times july 7 th 2007: the $73.5 billion global biotech business may soon have to grapple with a discovery that calls into question the scientific principles on which it was founded. last month, a consortium of scientists published findings that challenge the traditional view of how genes function. the exhaustive four-year effort was organized by the united states national human genome research institute and carried out by 35 groups from 80 organizations around the world. to their surprise, researchers found that the human genome might not be a “tidy collection of independent genes” after all, with each sequence of dna linked to a single function, such as a predisposition to diabetes or heart disease. instead, genes appear to operate in a complex network, and interact and overlap with one another and with other components in ways not yet fully understood. according to the institute, these findings will challenge scientists “to rethink some longheld views about what genes are and what they do.” biologists have recorded these network effects for many years in other organisms. but in the world of science, discoveries often do not become part of mainstream thought until they are linked to humans. with that link now in place, the report is likely to have repercussions far beyond the laboratory. the presumption that genes operate independently has been institutionalized since 1976, when the first biotech company was founded. in fact, it is the economic and regulatory foundation on which the entire biotechnology industry is built. 35 and, furthermore, the evo-devo revolution has seriously upset the canonical mainstream darwinian perspective, although committed materialist darwinists are trying to cover over the cracks. dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 438-475 smetham, g. p., soul dust or a matter of mind: the mindless ideas of nicholas humphrey issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 462 did humphrey care that he had promulgated an utter falsehood in an ‘academic’ paper? of course not, it is an entrenched and seemingly accepted feature of current western academic practice that established figures can perpetuate absolute falsehoods with impunity. to a large extent in many university departments the accepted ethos is not the pursuit of truth but the pursuit of academic careers and ego enhancement, and as a result: philosophers of mind appear to have arrived, today, at less-than-satisfactory solutions to the mind-brain and free will problems, and the difficulties seem, at least prima facie, very closely connected with their acceptance of a known-to-be-false understanding of the nature of the physical world, and of the causal role of our conscious thoughts within it. 36 this leads us to the final odd assertion contained in humphrey’s observation, which is that the phenomenon of consciousness “may be enough to call the whole scientific enterprise into question.” the truth is that the quantum revolution opens up a new territory wherein consciousness becomes a natural quality of the quantum ground of reality, and because of this science is expanded. as the physicists rosenblum and kuttner have recently pointed out, reinforcing the insights of penrose, stapp, mensky and many others: consciousness and the quantum enigma are not just two mysteries; they are the two mysteries; first, our physical demonstration of the quantum enigma, faces us with the fundamental mystery of the objective world ‘out there;’ the second, conscious awareness, faces us with the fundamental mystery of the subjective, mental world ‘in here.’ quantum mechanics seems to connect the two. 37 these issues do not impinge upon humphrey’s blank brain because he operates in an academic environment wherein showing a few paradoxical pictures serves as an argument that consciousness is an illusion created by the ultimately blank ‘material’ brain. but where was all this ‘material’ at the moment of the big bang, when all was quantum potentiality? no matter! let’s not bother with scientific details, it’s all a matter of matter and, according to humphrey, a few paradoxical pictures will help to prove the point (see figure 5). referring to william paley’s argument from design, proposed in 1800, involving a traveller finding a watch and concluding the existence of a designer, humphrey employs this example in the context of consciousness: but suppose now we were to come across an object … that, so far as we can see, does not belong to the world of normal physical phenomena. something whose nature lets not say what it is yet is such that we cannot understand it as a mechanism or see how it could have been put together to function as it does. in short, something seemingly impossible to make. suppose, for illustration, we were to stumble on the object in this picture. surely the inference would be inevitable that we were confronted not merely by evidence of an intelligent designer but of a designer with august supernatural powers. dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 438-475 smetham, g. p., exploring mindless materialist visions of the mindless evolution of minds from mindless matter issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 463 humphrey’s “object” here is, of course, consciousness. according to humphrey consciousness is just so remarkable that an unwary brain might be tempted to think consciousness is really real and must have been “designed”. however, according to his simplistic and dogmatic viewpoint, the fact that it is possible to draw paradoxical pictures is meant to lend support to his claim that consciousness must be an illusion. another image humphrey has resorted to as part of his campaign to claim that consciousness can be easily thought of as being an illusion is that of the impossible triangle shown in figure 6. such examples, humphrey seems to think, are entirely appropriate for demonstrating that consciousness, when seen from a “third person point of view,” whatever that might possibly mean, can be easily seen to be a “trick”. humphrey says about this: now, no one wants to think that consciousness is likewise some kind of trick … but let us nonetheless see where the analogy may lead. the standard philosopher's example of how hard the problem is, is the case of what it is like to see red. so, now, suppose you were to be looking at a ripe tomato: what might you want to explain about the extraordinary qualia-rich red sensation that you are having? since the qualia are indeed so up-front and remarkable, and since no one knows what this is really about, we are all, most probably, going to start off by asking what may be a bad question: “how can we explain the existence of these qualia as we experience them?” so here again it will only be if we undergo a radical shift in perspective and realise that the “qualia as we experience them” could be a mental fantasy, that we shall move on to asking what may be the good question: “how can we explain why we have the impression that such fantastic qualia exist even if they do not?” but, now, here is why it is likely to be so difficult to make this move: in the case of consciousness we cannot simply turn over the page to see the solution. we are all innocents, no one has ever seen qualia from a different viewpoint, we are stuck with the first-person perspective. so, the result is we persist with questing for the qualia as such. 38 dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 438-475 smetham, g. p., soul dust or a matter of mind: the mindless ideas of nicholas humphrey issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 464 figure 5 (39) figure 6 (40) let us consider these remarks for a few moments. consider the situation where someone is looking at a red tomato. the situation is one in which it is indeed the case that the actual experienced phenomenon of redness within the field of consciousness of the observer does not dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 438-475 smetham, g. p., exploring mindless materialist visions of the mindless evolution of minds from mindless matter issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 465 exist externally as a film of ‘redness’ glued, so to speak, on to the surface of the tomato. at the level of analysis of atomic structure photons of light are falling upon the atomic structure of the tomato and, because of the nature of that atomic structure, red wavelength photons are emitted into the eyes of the observer. now at this point in time, as humphrey indicates, we have very little in the way of detailed knowledge of how the atomic processes within the brain give rise to the direct and immediate experience of ‘redness’, “extraordinary qualia-rich red sensation”, which is experienced by the observer. this is why consciousness is supposed to be such an immense problem. humphrey is quite aware of the deficiency in our knowledge. he says clearly that “the qualia are indeed so up-front and remarkable, and since no one knows what this is really about.” in other words, the actual first-hand experience is impressive and we do not know the mechanism by which it arises. but then humphrey claims something which is entirely incoherent, without support and absurd. because the experience is so “up-front and remarkable”, so powerfully present as something which seems very real, in fact the very basis of any experience of reality, humphrey actually claims that the question as to how this remarkable and very real looking phenomenon comes into existence is a “bad question” and, astonishingly, humphrey asks his readers to accept that the correct approach is ask how it doesn’t come into existence. if we were to adopt this as a scientific or philosophical principle then this would mean that the more real a phenomenon appeared to be the more we must suspect that we are being deceived, and the more determined we must be in resisting the temptation to account for its reality and, to the contrary, must diligently search for highly implausible explanations for why it does not exist. a corollary to this seems to be, amongst crude materialists like humphrey, that the more unreal a phenomenon has been shown to be the more we must pretend it is real. for, as stapp has pointed out with reference to the belief that the ‘matter’ of the brain is ultimately ‘real’stuff: …no such brain exists; no brain, body, or anything else in the real world is composed of those tiny bits of matter that newton imagined the universe to be made of. 41 the stuff of reality is all ultimately made up from insubstantial “dream-stuff.” humphrey, adding insult to injury, then tells us that it is not possible to have a third person point of view of qualia. in the case of consciousness we cannot turn the page over to see the impossible triangle shown to be an illusion. the kind of simplistic illusions that humphrey employs as support for his case, however, are entirely inappropriate. this is easily seen. when the solution to how the ‘impossible triangle’ trick is revealed there is no shock at the way that the trick is carried out, we are not amazed that the “solid wood” that the triangle is constructed out of can be formed into the shape required to perform the trick but, as we have seen, humphrey himself thinks ‘matter’ is going have to perform amazing self-referential convolutions of multidimensional interconnections in order to get what he considers to be the illusion of consciousness off the ground. the two situations are incommensurate and in the case of consciousness there is a yawning gap of credibility between the basis of the illusion and the illusion. to put it as crudely dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 438-475 smetham, g. p., soul dust or a matter of mind: the mindless ideas of nicholas humphrey issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 466 as humphrey’s materialism, there is no apparent difference in the kind of stuff, the “solid wood,” that is involved in the two perspectives. in the case of consciousness, however, the kind of stuff involved appears to be dramatically different. humphrey, however, assumes that he knows without a doubt, despite the contrary evidence of physics, that everything that can and does exist must be ‘material’: …in consciousness we find ourselves right at the centre of something which if we were not already conscious would be far beyond what we could imagine. let’s not deny this or try to explain it away as an illusion. the paradoxical features of consciousness are precisely the features with which scientific understanding has to begin. nonetheless, even though we should not try to explain it away, this doesn't mean we must assume that consciousness is not an illusion. our starting assumption as scientists ought to be that on some level consciousness has to be an illusion. the reason is obvious. if nothing in the physical world can have the features that consciousness seen to have, then consciousness cannot exist as a thing in the physical world. so, while we should concede that as conscious subjects we do indeed have a valid experience of there being something in our minds that the rules of the physical universe don't apply to, this has to be all it is – the experience of something in our minds. as usual with humphrey there are a few extraordinarily incompetent, yet entertaining, observations and formulations. the fact that comments such as consciousness presents us with a phenomenon which “if we were not already conscious would be far beyond what we could imagine” are not met with howls of laughter by more acute colleagues is as mysterious as consciousness itself is supposed to be. if “we were not already conscious”, of course, we would not be able to imagine anything whatsoever! humphrey, however, seems to think that it is possible for there to be a non-conscious type of life-form which can, indeed, imagine away to its heart’s content. the following piece of fantastic nonsense is from humphrey’s brief article ‘seeing red: a postscript’: let’s stipulate, then, that the theory of consciousness has to be comprehensible to a scientist from mars an individual in many ways not unlike ourselves, highly intelligent, perceptive and even capable of self-reflection, but who nonetheless has never evolved into the kind of being who has sensations. suppose we could explain to this martian what happens in the brain of a human being who is engaged, say, in smelling a rose. and suppose he could thereby arrive at the entirely novel (to him) conclusion that it must be like something to be this human being, and indeed like this: “i am feeling this thick, sweet, olfactory sensation in my nostrils”. it’s a tall order; but, still, it’s what the theory ought to do. is a theory which could bring this off a possibility even in principle? since the theory must employ only such concepts as the martian can make sense of at the outset, we need to consider what kind of pre-theoretic notions he brings with him. given that as yet he knows nothing about sensations, will he have other essential concepts on which to build? dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 438-475 smetham, g. p., exploring mindless materialist visions of the mindless evolution of minds from mindless matter issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 467 the answer for any kind of being with a normal brain and normal consciousness and with a modicum of non-martian intelligence, of course, is that without consciousness there is no basis for any kind of conceptuality, as humphrey indicated in his other just-so-stories, without consciousness its all utter blankness. here, however, he now wants us to believe, with no evidence and on the basis of incoherent arguments, of the ‘existence’ of a type of consciousness (martian) which has absolutely no phenomenal-sensational-awareness. but this is just making things up on the spur of the moment for the convenience of materialist storytelling, or fantasyspinning. the materialist tendency to inappropriately impute consciousness and capacities derived from consciousness, for their convenience, to martian zombies for example, really makes me see red! humphrey has begun this particular section (the quote before last) with a degree of incoherence that he is determined to consistently maintain, for he next tells us that we must not explain the phenomenon away but we must show it to be an illusion. showing something is an illusion is explaining it away! and, he attempts to explain, the reason is “obvious.” according to humphrey the ‘physical’ world is material and has no qualities of consciousness, so consciousness cannot exist. although it does have a ghostly and illusory semi-existence! a final example of humphrean incoherence that is worth considering is from his short article placebo effect. he accepts that the effect has been scientifically proven and then writes: how do these changes in what a patient thinks (particularly) or feels (more generally) about his ailment activate the physiological mechanisms that lead to recovery? and, then, the deeper question about the evolutionary design: what biological advantage can there be in having mind control the bodies healing systems in this way? in this article humphrey constantly indicates that it is the sphere of mind which is able to intervene and have leverage upon the realm of the physical, which is to say the ‘material’ realm: “how does the mind talk to the body’s healing systems in such specific ways?” humphrey does not offer a materialist explanation and the article gives the impression that, when not having to present a contrived materialist advertising spiel for an academic audience, humphrey quite naturally thinks in terms of mind as being a significant and effective ontological aspect of reality. indeed the concluding paragraph reads: and so, today, the very prospect of medical attention the patient’s belief in it works its magic for the simple reason, … that for most of human history, once a sick person has had cause to think that he will soon be safe and well, he has had just the excuse he needs to bring on his own recovery as fast as possible. this is an observation which seems to indicate quite forcefully the power of mind to have a dramatic effect upon the physical realm. such effectiveness of mental intentionality is completely incompatible with humphrey’s assertion that the realm of sensation, consciousness and mentality is just an ultimately non-existent illusory trick of matter performing magical machinations. dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 438-475 smetham, g. p., soul dust or a matter of mind: the mindless ideas of nicholas humphrey issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 468 humphrey, however, seems completely oblivious to this glaring inconsistency. perhaps he really does have only a blank brain after all! there is, however, one huge significant insight in humphrey’s new, “radical” perspective which is contained in his latest book soul dust: the magic of consciousness, an insight which is totally undermined by humphrey’s dogmatic and unscientific materialism. this insight is that consciousness has an intrinsic value, or even may be a significant part of the intrinsic value of the process of reality: …consciousness makes life more worth living, conscious creatures enjoy being phenomenally conscious. they enjoy the world within which they are phenomenally conscious. and they enjoy their selves for being phenomenally conscious. but “enjoy” is too weak a term. in the case of human beings at any rate, it would be truer to say that they revel in being phenomenally conscious. they love the world in which they are phenomenally conscious. they esteem their selves for being phenomenally conscious. moreover,…for conscious creatures there is real biological value in all this. the added joie de vivre, the new enchantment with the world they live in, and the novel sense of their own metaphysical importance has, in the course of evolutionary history, dramatically increased the investment that individuals make in their own survival. 42 and in a remarkable turn of affairs for a materialist humphrey indicates an intense appreciation of the remarkable qualities of consciousness and its importance in personal growth and even spiritual growth: it is our good fortune … that other types of researchers of recognized this all along. we might call them the “alternative natural historians of consciousness: on one side are painters, poets and musicians; on the other, followers of meditative religious traditions such as buddhists. 43 however, it is better not to get too excited because, although humphrey appears to be a great appreciator of the qualities of consciousness, indeed the book contains many long quotations which indicate how humans have always valued sense-perception and consciousness, this does not undermine his fervent and unshakeable belief that this remarkable aspect of reality ultimately does not exist. so, the issue is, then, if consciousness does not ultimately exist, how and why did it come to at least to appear to exist, or have an illusory ‘existence’. well the answer humphrey offers goes something like this. evolution, for some mystical reason that no materialist has yet offered any explanation for, after a few billion years managed to get non-conscious zombie-type organic beings wandering pointlessly around planet earth in complete internal blankness, no internal glimmer at all. because this blank existence was no fun, although why completely non-conscious organic zombies should require fun is, again, a mystery, these zombie beings did not have much in the way of incentive to keep surviving, there was nothing much in it for them. without the internal light of phenomenal consciousness they felt, in their blank unaware type of zombie nondna decipher journal | july 2013 | volume 3 | issue 4 | pp. 438-475 smetham, g. p., exploring mindless materialist visions of the mindless evolution of minds from mindless matter issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 469 feeling mode, that they might just as well be non-surviving ‘matter’ just lying around doing nothing much except being non-conscious matter, at least they wouldn’t have to make an effort. evolution needed to come up with a solution to this block to getting more complex organic zombies lumbering around the planet. again, why ‘evolution’ wanted to do this is a mystery; in the end, according to materialists, it’s all a matter of unconscious matter mattering to itself. but evolution has its random purposes. anyway it needed some way of motivating its reluctant zombie ‘survivors’. then, as if by magic, in the way evolution generally manages to keep evolving, a solution came into being. evolution figured out that if it could trick its zombies into thinking that they were not zombies but had an wonderful internal glow of sensation, although at this moment in time of course these zombies were not capable of thinking or sensing anything, but that’s a minor issue, then they could be tricked into surviving on their own account. the pressure would be off of evolution. the evolving survivors could slug it out for survival on their own account! you can see why materialists value evolution so highly; it’s very crafty, almost intelligent! in his essay consciousness: ‘the achilles heel of darwinism? thank god, not quite’ humphrey explains his vision as follows: we can see, then, how it might have been within the power of natural selection to design human minds to experience consciousness the way they do. but there remains of course a crucial proviso. the basic premise of darwinism is that natural selection selects for traits that are biologically adaptive leading to greater success in reproduction. so natural selection will only have designed human minds to experience consciousness this way if, in the history of our species, individuals who harboured this experience made out especially well in the struggle for survival. and how could that be? why should our particular take on being conscious bring us biological good fortune? to answer this, the most important question, we must look objectively at what the encounter with the magically rich features of consciousness actually does for us – how, if at all, it changes human lives. … without the experience of being conscious we would simply not have the sense we have that there is something substantial at the centre of our psychical existence, something it's like to be us. but once we do experience it, the self is there for us. a self that has this at its centre is a self to be reckoned with, a self worth having. and such a self bursts with the potential to become the principle around which we organize our private mental lives. this could be true not only for human beings but animals as well. perhaps whales, dogs, monkeys maybe all mammals, all birds have comparable experiences of consciously being there. but for human beings it evidently goes much further. for in our case we now have a self that seems to inhabit a separate universe of spiritual being. and this is dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 438-475 smetham, g. p., soul dust or a matter of mind: the mindless ideas of nicholas humphrey issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 470 something else. as the subjects of something so mysterious and strange, we humans gain new confidence and interest in our own survival, a new interest in other people too. we begin to be interested in the future, in immortality, and in all sorts of issues to do with co-consciousness and how far consciousness extends around us. this feeds right back to our biological fitness, in both obvious and subtle ways. it makes us more fascinating and more fascinated, more determined to pursue lives wherever they will take us. in short more like the amazing piece of work that humans are. lord byron said that “the great object of life is sensation to feel that we exist, even though in pain.” that's the raw end of it. but, at a more reflective level, what keeps us going, gives us courage, makes us aim high for ourselves and our children is the feeling that as human selves we have something very special to preserve. matters might rest there. but in the context of writing about intelligent design, i want to leave you and tease you with one further idea about how consciousness can change our view of things, for which we have the evidence right before our noses. the novelist thomas mann, when asked to contribute his thoughts to ed murrow’s 1950s radio program this i believe, came out with the following: “in my deepest soul i hug the supposition that with god’s ‘let there be,’ which summoned the cosmos out of nothing, and with the generation of life from the inorganic, it was man who was ultimately intended, and that with him a great experiment is initiated, the failure of which because of man’s guilt would be the failure of creation itself, amounting to its refutation. whether that be so or not, it would be as well for man to behave as if it were so.” mann had earlier written, in the magic mountain, “consciousness, then, was simply a function of matter organized into life; a function that in higher manifestations turned upon its avatar and became an effort to explore and explain the phenomenon it displayed a hopeful-hopeless project of life to achieve self-knowledge. hopefulhopeless it may always be. but … it is reflection on the mysteries of consciousness our very failure to see how consciousness “fits in” that is the chief inspiration for the belief in special creation that mann hugged to his soul. now, as mann hints, this belief whether true or not may be a significant life-force in its own right. for if we can indeed believe that we owe our lives to a beneficent creator who (presumably having some choice in the matter) deliberately arranged that the world he created would come to contain human beings, then this can and arguably ought to encourage us to make it our cause in life to honour the very cause of life, by living up to our creator’s plan so, here's the irony. belief in special creation will very likely encourage believers to lead biologically fitter lives. thus one of the particular ways in which consciousness could have won out in evolution by natural selection could have been precisely by encouraging us to believe that we have not evolved by natural selection. anyone for “natural creationism”? dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 438-475 smetham, g. p., exploring mindless materialist visions of the mindless evolution of minds from mindless matter issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 471 i have quoted this at length because this extraordinary passage is so replete with magnificent nonsense which, when investigated and corrected, leads to deep and significant insight! the first sentence indicates how materialists regularly use language which imputes intelligence and intentionality to their beloved “natural selection”, which is supposed to be blind, random and entirely unintelligent. humphrey tells us that natural selection has the “power” to “design human minds to experience consciousness the way they do.” however, given that according to the materialist cause ‘matter’ is entirely devoid of all glimmer or potentiality for the manifestation of the qualities of consciousness, “natural selection” would need the supernatural power for the creation from absolute nothingness of a new ontological aspect of reality to accomplish this. this is one of the central absurdities of the materialist worldview. humphrey next tells us that natural selection would only deploy this intentional power if it endowed the favoured species endowed with the new capacity a biological advantage. this means that according to this vision prior to the deployment of the new ontological aspect of reality, or illusory ontological aspect, there was absolutely no trace or tiny spark of consciousness, or the illusion of consciousness, then suddenly ‘natural selection’ deploys its power to create an illusion of sentience in order to give a biological-mechanical advantage. we suddenly think and feel that we have ‘selves’ which we, mistakenly, think are “worth having” and “begin to be interested in the future, in immortality, and in all sorts of issues to do with co-consciousness and how far consciousness extends around us,” furthermore an apparently ‘spiritual’ dimension seems to open before the amazed illusory minds which humans, and perhaps some animals, have been tricked, by the power if natural selection, into thinking that they have. in reality, according to this ridiculous vision, none of this is real; everything is blind, blank, mindless organic mechanism. when the physicist john bell heard about the ‘many-worlds’ interpretation of quantum theory he said that if one were to take such a proposal seriously then it would not be possible to take anything seriously ever again. the same can be said of these kinds of materialist visions, which dissolve into cartoon-like laughable nonsense when examined with logical rigor and precision. if ‘matter’ is entirely devoid of the qualities of consciousness and awareness there is absolutely no way it could produce even the illusion of consciousness and awareness, no matter how powerful humphrey and his materialist compatriots fantasize ‘natural selection’ to be. as mary midgley writes in her review of soul dust: inert stuff could never have produced the crystals, the galaxies, the volcanoes and, above all, the living things that have evolved out of our original dollop of physical matter. and after all those achievements, why should it seem surprising for matter to have topped things by adding consciousness. 44 whilst midgley is quite correct in asserting that inert stuff could not produce living beings, it is unfortunate that the criticism does not go far enough. for ultimately we are not the result of the dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 438-475 smetham, g. p., soul dust or a matter of mind: the mindless ideas of nicholas humphrey issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 472 evolution of an “original dollop of physical matter”, as hawking and mlodinow point out in their recent book the grand design: new answers to the ultimate questions of life: we are the product of quantum fluctuations in the very early universe. 45 just understanding this one obvious fact, that, to parody dennett: the ground quantum field is the ultimate basis of all the agency, and hence meaning, and hence consciousness, in the universe, renders the materialist cause hopeless. it is because of this central scientific fact, established by physics, that the quote from thomas mann, who of course lived before quantum discoveries, that “consciousness, then, was simply a function of matter organized into life” is wrong and irrelevant. the notion that somehow ‘natural selection’ is able to magically produce entirely new qualitative aspects of reality, even ‘illusory’ ones, from primal stuff which has no trace of, no glimmer of, no tiny spark of, no potentiality to manifest those qualities, is nothing but illogical, irrational and incoherent nonsense. furthermore it is entirely unscientific, even though humphrey and his materialist cohorts puff themselves up with imagined scientific pride (here in fact is an illusion generated to produce an illusory self-importance’). at the end of humphrey’s attempted explanation of the manner in which ‘natural selection’ “designed” consciousness in order to encourage the poor deluded sentient beings in the, essentially blank, meaningless and purposeless, evolutionary rat race of survival, he asks: anyone for “natural creationism”? for anyone who takes the evidence of science seriously, which materialists seldom do, the answer has to yes! this is because the most recent scientific accounts of the ‘birth’ of the universe, including everything which subsequently evolves within it, require that: …the universe appeared spontaneously, starting off in every possible way. most of these correspond to other universes …. some people make a great mystery of this idea, sometimes called the multiverse concept, but these are just different expressions of the feynman sum over histories. 46 this quantum scenario, which is essentially the view proposed by the famous twentieth century physicist richard feynman, indicates a spontaneous creative burst, emerging from a vast pool of potentiality, which creates the multiverse of possible worlds, which are in a state of quantum superposition. this means that there is no ‘matter’ to be found in this realm of vast potentiality. there is, however, the potentiality for everything which can come into manifestation. nothing can later come into being, or evolve, which is not a potentiality within the quantum realm hovering at the edge of time. a hugely significant feature of this presentation is the fact that the “observers are part of the system” 47 and: the histories that contribute to the feynman sum don’t have an independent existence, but depend on what is being measured. we create history by our observations, rather than history creating us. 48 in other words the observers, or what another famous twentieth century physicist john wheeler called ‘observer-participants,’ are able to weed out possible universes, and thereby select those dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 438-475 smetham, g. p., exploring mindless materialist visions of the mindless evolution of minds from mindless matter issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 473 which remain in the possibility mix, even backwards in time. thus one of the central chapters in the grand design is entitled ‘choosing our universe’: the idea that the universe does not have a unique observer-independent history might seem to conflict with certain facts that we know. there might be one history in which the moon is made of roquefort cheese. but we have observed that the moon is not made of cheese, which is bad news for mice. hence histories in which the moon is not made of cheese do not contribute to the current state of our universe, though they might contribute to others. this might sound like science fiction but it isn’t. 49 here hawking and mlodinow are reiterating wheeler’s assertion that: directly opposite to the concept of universe as machine built on law is the vision of a world self-synthesized. on this view, the notes struck out on a piano by the observer participants of all times and all places, bits though they are in and by themselves, constitute the great wide world of space and time and things. 50 and this viewpoint clearly requires, and shows that consciousness is an internal aspect of the process of reality, it is the driving force which unfolds and manifests the quantum potentialities within the quantum realm. if, then, one accepts the most up to date findings of physics, which humphrey and other crude materialists simply ignore, a deep and non-individuated level of consciousness-awareness is a fundamental ontological aspect of the process of reality. it is a great pity that some of the people who were asked to review humphrey’s book soul dust did not seem to be aware of the current state of physics and therefore were not able to fully indicate the extent to which humphrey’s fantasies are grossly unscientific. thus midgley wrote that: humphrey … still rules that this everyday consciousness is an illusion. he seems not to notice that illusions are impossible unless somebody conscious is there to be deluded. he sees his problem as simply one of fitting the unreal entities that we think we see and hear into the only real world, which of course, the world as science reports it. 51 and later in the review she refers to “the core error” which “is a common but shockingly obvious one: the suggestion that nothing is real except what the physical sciences tell us.” 52 such a view, however, indicates a lack of knowledge of what physics does tell us, which is, as stapp points out: we live in an idea-like world, not a matter-like world.’ the material aspects are exhausted in certain mathematical properties, and these mathematical features can be understood just as well (and in fact better) as characteristics of an evolving idea-like structure. there is, in fact, in the quantum universe no natural place for matter. this conclusion, curiously, is the exact reverse of the circumstances that in the classical physical universe there was no natural place for mind. 53 the majority of significant physicists: schrödinger, planck, heisenberg, wheeler, hawking (if he takes his own writings in the grand design seriously), linde, penrose, wigner, zurek, to dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 438-475 smetham, g. p., soul dust or a matter of mind: the mindless ideas of nicholas humphrey issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 474 name just a few, come down on the side of stapp’s evaluation of the ultimate nature of the process of reality as being mind-like. as stapp evaluates the kind of ideas presented by humphrey’s fantastic and incoherent mindless materialist meanderings: …the re-bonding [between mind and the appearance of matter] achieved by physicists during the first half of the twentieth century must be seen as a momentous development: a lifting of the veil. ignoring this huge and enormously pertinent development in basic science, and proclaiming the validity of materialism on the basis of an inapplicable-in-this-context nineteenth century science is an irrational act. 54 indeed! 1 humphrey, n. (2008) ‘getting the measure of |consciousness’: http://www.humphrey.org.uk/papers/2008gettingthemeasure.pdf, 264 2 kelly e. f., kelly e. w., crabtree a. & gauld a. (2009), 1 3 kennedy, j. e. journal of parapsychology, 2006, volume 70, 373-377 4 http://en.wikipedia.org/wiki/just_so_story 5 http://en.wikipedia.org/wiki/nicholas_humphrey 6 http://en.wikipedia.org/wiki/just-so_story 7 new scientist, 19 august 1982 8 humphrey, n, 2000, “how to solve the mind-body problem,” journal of consciousness studies, 7, 5-50. 9 allday, jonathan (2009), 493 10 oerter, robert (2006), 132 11 dolling, l.m.; gianelli, a. f. & statile, g. n. (eds) (2003) p491 – john a. wheeler (1978): ‘the ‘past’ and the ‘delayed choice’ double-slit experiment.’ 12 quoted in stapp, henry (2007), 162 13 barrow, john d., davies, paul c. w., harper, charles l. (eds.) (2004), 451 14 humphrey, n. (2006), 47 15 humphrey, n. (2006), 50-51 16 humphrey, n. (2006) 17 dennett, daniel (1991), 27 18 humphrey, n. (2006), 75 19 humphrey, n. (2000), ‘how to solve the mind-body problem’, 14 20 humphrey, n. (2000), ‘how to solve the mind-body problem’, 15 21 humphrey, n. ‘a self worth having’ – http://www.edge.org/conversation/a-self-worth-having. 22 soul dust lecture lse http://www.youtube.com/watch?v=drljsnubun8 23 soul dust lecture lse http://www.youtube.com/watch?v=drljsnubun8 24 soul dust lecture lse http://www.youtube.com/watch?v=drljsnubun8 25 http://www.humphrey.org.uk/papers/2000mindbodyproblem.pdf 26 humphrey, n. (2000), ‘how to solve the mind-body problem’,19 27 humphrey, n. (2008) ‘getting the measure of |consciousness’: http://www.humphrey.org.uk/papers/2008gettingthemeasure.pdf, 266 28 humphrey, n. (2008) ‘getting the measure of |consciousness’: http://www.humphrey.org.uk/papers/2008gettingthemeasure.pdf, 267 29 ‘spatial gradients and multidimensional dynamics in a neural integrator circuit.’ 30 http://www.humphrey.org.uk/papers/2008gettingthemeasure.pdf dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 438-475 smetham, g. p., exploring mindless materialist visions of the mindless evolution of minds from mindless matter issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 475 31 http://www.newstatesman.com/books/2011/02/mind-self-consciousness-brain 32 humphrey, n. (2008) ‘getting the measure of |consciousness’: http://www.humphrey.org.uk/papers/2008gettingthemeasure.pdf, 266 33 conway morris, simon (2003), 46 34 conway morris, simon (2003), 48 35 http://www.nytimes.com/2007/07/01/business/yourmoney/ 01frame.html?pagewanted=all?_r=1 36 stapp, henry: ‘philosophy of mind and the problem of free will in the light of quantum mechanics’, 19 37 rosenblum, b. and kuttner, f. (2006), 179 38 humphrey, n. (2008) ‘getting the measure of |consciousness’: http://www.humphrey.org.uk/papers/2008gettingthemeasure.pdf, 268 39 http://www.humphrey.org.uk/papers/2006consciousness.pdf 40 http://www.humphrey.org.uk/papers/2008gettingthemeasure.pdf 41 stapp, henry (2007), 139 42 humphrey, n. (2012) 43 humphrey, n. (2012) 44 http://www.guardian.co.uk/books/2011/feb/05/nicholas-humphrey-soul-dust-review 45 hawking & mlodinow (2010), 139 46 hawking & mlodinow (2010), 136 47 hawking & mlodinow (2010), 135 48 hawking & mlodinow (2010), 140 49 hawking & mlodinow (2010) 50 barrow, john d., davies, paul c. w., harper, charles l. (eds) (2004) p577 – wheeler, j a (1999) ‘information, physics, quantum: the search for links.’ in feynman and computation: exploring the limits of computers, ed a. j. g. hey, p309 (314). cambridge, ma: perseus books. 51 http://www.guardian.co.uk/books/2011/feb/05/nicholas-humphrey-soul-dust-review 52 ibid. 53 stapp, henry (2004), 223 54 stapp, henry: ‘quantum interactive dualism’, 18 dna decipher journal | july 2022 | volume 12 | issue 1 | pp. 90-96 90 pitkänen, m., water oxidation & photosynthesis in tgd framework exploration water oxidation & photosynthesis in tgd framework matti pitkänen 1 abstract water oxidation in which water splits into 4 electrons, 4 protons and oxygen molecule o2 is the first step of photosynthesis. the catalytic mechanism behind water oxidation remains rather poorly understood. the total binding energy of h2o is about 75 ev and the catalyst should provide this energy to temporarily overcome this barrier. zero energy ontology (zeo), which is behind the tgd based quantum measurement theory, predicts that ”big” (ordinary) state function reductions (bsfrs) involve time reversal. the time reversal of water oxidation occurs spontaneously in a reversed time direction and second bsfr establishing the original arrow of time makes it possible to achieve water oxidation. this mechanism involving two bsfrs applies quite generally to catalysis. the function of the catalyst is to make possible the bsfr and the natural expectation is that the description of catalysis as a process with apparently standard arrow of time is possible. the reduction of the value of heff for cyclotron states of dark particles at magnetic flux tube liberates energy assignable to cyclotron states of dark particles and could kick the reactants over the potential wall making the reaction extremely slow otherwise. 1 introduction these comments were inspired by an interesting article ”isolating an elusive missing link” (https:// cutt.ly/dng7my6) about water oxidation. it came as a surprise to me that water oxidation is still a poorly understood piece of biochemistry. bio-chemists believe that they understand various aspects of the reaction reasonably well with one exception, which is the formation of the o2 molecule in water oxidation and the article tells about progress in this respect. the water oxidation reaction (wor) is one of the most important reactions on the planet since it is a key step in photosynthesis and is also the source of nearly all the atmosphere’s oxygen. what is so beautiful is that both photosynthesis as a chemical storage of the solar energy and water oxidation producing oxygen essential for aerobic respiration to utilize the stored energy, are parts of the same process. understanding the intricacies of wor can hold the key to improve the efficiency of the reaction which could be utilized to produce hydrogen. as the article tells, the reaction’s chemical mechanisms are complex and the intermediates highly unstable. this makes their isolation and characterisation extremely challenging. to overcome this, scientists are using molecular catalysts as models to understand the fundamental aspects of water oxidation particularly the oxygen-oxygen bond-forming reaction. wor (see https://cutt.ly/jng72r8 and https://cutt.ly/ang781b) forms an essential part of photosynthesis (https://cutt.ly/tng77r4). what happens in wor is that two water molecules split 4h+,4e−, and o2. the reaction mechanism is not completely understood. somehow the solar radiation induces the process in which two h2o molecules split to 4h+, 4e−, and o2. the 4 electrons are utilized in photosynthesis in the kok cycle. in the sequel a general mechanism of catalysis inspired by zero energy ontology (zeo) [6] is discussed. in this approach biocatalysis involves two ”big” state function reductions (bsfrs) changing the arrow of time. the first bsfr induces time reversed time evolution leading from the final of a sub-reaction kicking the reactants over the potential wall preventing the reaction from occurring. after the second bsfr the time evolution continues from the initial state of time reversed time evolution in standard time 1correspondence: matti pitkänen http://tgdtheory.com/. address: rinnekatu 2-4 a8, 03620, karkkila, finland. email: matpitka6@gamail.com. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://cutt.ly/dng7my6 https://cutt.ly/dng7my6 https://cutt.ly/jng72r8 https://cutt.ly/ang781b https://cutt.ly/tng77r4 http://tgdtheory.com/ mailto:matpitka6@gmail.com dna decipher journal | july 2022 | volume 12 | issue 1 | pp. 90-96 91 pitkänen, m., water oxidation & photosynthesis in tgd framework direction. the catalytic process takes place spontaneously and the role of the catalyst is to make the spontaneous occurrence in the reversed time direction possible and probable enough. quantum coherence in long scales is necessary and the identification of dark matter as heff = nh0 phases implied by adelic physics predicts it [4]. 2 basic facts about photosynthesis and water splitting photosynthesis involves two parts. the first part does not involve photons and leads to the splitting of water producing from two water molecules 4 protons and 4 electrons plus o2 molecule. the second part involving photons stores their energy chemically. the first part occurs in oxygen evolbing complex (eoc), known also as water splitting complex, and acting as a cofactor of photosystem ii enzyme in which the photosynthesis proper takes place. 2.1 oxygen evolving (water splitting) complex (oec) oec is the cofactor of photosystem ii enzyme. oec has an inorganic core obeying the empirical chemical formula mn4ca1ooxcl12(hco3)y core. core is surrounded by 4 protein subunits of photosystem ii at membrane-lumen interface. oec functions as follows. 1. the extraction of 4 electrons and and hydrogen ions from 2 water molecules produces o2 molecule as a kind of waste. 2. 3. oce transfers 4 electrons, one at a time, to photosystem ii via a tyrosine residue in the reaction center. photosystem ii must store the energy of 3 photons before the fourth one provides sufficient energy for water oxidation. kok theory states that oec can exist in 5 states s0, ..., s4. s4 since oec has lost 4 electrons. s0 is the most reduced. s4 is unstable to reset to ground state s0 and reacts with water producing free oxygen. oec receives the 4 electrons and returns to state s0. 4. after that photons from photosystem ii drive the system from s0 to s4. the electrons from oec are transferrred to photosystem ii one-by-one. photons from photosystem ii energize electrons which are driven through the a variety of coenzymes and cofactors to reduce plastoquinone to plastoquinol. 5. the 4 hydrogen ions are used to create a proton gradient. this means that they are driven against the membrane potential gradient and gain potential energy liberated later as the protons return back and provide electrostatic energy used to by atp synthase to transfrom adp to atp. 2.2 the energetics of photosynthesis consider first the energetics of photosynthesis (https://cutt.ly/tng77r4). 1. as far the energetics is considered, the process of photosynthesis is equivalent to co2+ 2h2o +γ → ch2o + o2 + h2o. what happens to the 4 electrons and protons produced in the splitting of water? 2. co2 loses one o and co combines with two protons and electrons to form ch2o. this requires a catalyst to temporarily kick out o from co2. this energy is returned to the catalyst when two electrons and protons combine with o to form h2o. the binding energy of c=o bond and h=o bond are indeed nearly the same. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://cutt.ly/tng77r4 dna decipher journal | july 2022 | volume 12 | issue 1 | pp. 90-96 92 pitkänen, m., water oxidation & photosynthesis in tgd framework 3. water splitting requires energy e = 4eb(o − h) + 4eb(e − p)= 4 ×(5.15 + 13.6) = ev. the formation of o = o provides energy eb(o = o) = 5.13 ev. in the formation of h2o 2 × (5.15 + 13.6) ev is returned to the catalyst but this energy has been already taken into account and compensates for the energy needed to split co2. therefore the energy e1 = 4(eb(o−h)+eb(e− p))−eb(o = o)= [4 × (5.15 + 13.6) 5.13] ev needed from catalyst must correspond the energy liberated in the formation of ch2o. this is true assuming that the binding energy of e and p associated in the o-h valence bond is the sum of atomic binding energy and o-h bond energy. the formation of ch2o involves combination of 2 protons and electrons to form two hydrogens, the atomic binding energy 2eb(e-p)= 2×13.6 ev is liberated in the formation of ch2o and compensates the same energy appearing in e1. hence the atomic binding energies can be forgotten in the energy budget and it is enough to compare only the molecular binding energy e2 in e1 with eb . the molecular contribution to e1 is e2 = 4× 5.15− 5.13 ev = 15.48 ev. 4. the formation of ch2o means a generation of molecular binding energy which is approximately the sum of o=ch2 binding energy and c-h binding energies. besides this atomic binding energy of two hydrogen atoms is liberated. the liberated molecular binding energy is eb(ch2o) = eb(o = ch2) + 2 × eb(c − h)= (7.75+2× 4.28) ev= 16.31 ev. the amount of the liberated molecular binding energy is eb(ch2o) = 16.31 ev and is by .83 ev larger than e2 = 15.48 ev. one must drive 4 protons against a potential gradient and this requires energy 4 × .07ev = .28 ev which is smaller than this energy. 4 photons are used and if their energies are about 2 ev they provide 8 ev. 5. this estimate does not take thermodynamics and second law into account. since pressure and temperature can be assumed to stay constant in the process, the thermodynamical approach using gibbs free energy g = e + pv − ts as thermodynamical function is natural. dg = v dp − sdt +∑ i µidni reduces to dg = ∑ i µidni if pressure and temperature are constant. 6. the overall process can be written as 6co2 + 6h2o + light → c6h12o6 + 6o2. this form corresponds to a polymerization of 6 ch2o molecules to form sugar c6h12o6. 7. several separate steps are involved with photosynthesis besides the splitting of water; there are 4 steps corresponding to the transfer of electron decomposing to substeps related to the photosynthesis proper. each of this steps involves catalysis. that two water molecules are involved in the basic process, could also be essential. the hydrogen bond between the water molecules or its dark variant could play some role. 3 tgd view about water photosynthesis and water oxidation tgd provides a new view about bio-catalysis in which the magnetic body (mb) acts as a controller. one might hope that at this level the description of the biocatalysis is much simpler than at the level of biochemistry. therefore one can ask whether a simple overall view based on the energetics and the notion of mb carrying dark matter at its flux tubes could help. since 5 different kinds of valence bonds must be temporarily split in the overall reaction, a catalyst providing the needed energy to temporarily break the valence bonds is needed. there are many other steps involving catalysis and the actual situation taking into account reactions involving photons is extremely complex. from the foregoing it is clear that the splitting of water requires 75 ev energy. most of this energy is related to the ionization of hydrogen atoms. note however that valence electrons in the valence bonds are approximated as ordinary atomic electrons. unless quantum tunnelling is involved, this energy must be provided by some source. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 1 | pp. 90-96 93 pitkänen, m., water oxidation & photosynthesis in tgd framework 3.1 does time reversal provide a general mechanism of bio-catalysis? in the tgd framework one can consider 3 general mechanisms of biocatalysis and both mechanisms could be involved. the basic problem in the understanding of catalysis is to identify the mechanism kicking the reactants over the potential wall making the reaction extremely slow. how to get over this potential wall is even rid of it? zero energy ontology (zeo) [6, 4, 8] suggests a completely general mechanism of biocatalysis. 1. zeo is behind the tgd inspired quantum measurement theory and makes it possible to resolvin the basic paradox of standard quantum measurement theory and gives rise to a quantum theory of consciousness. the new element is that the arrow of time changes in ordinary (”big”) state function reduction (bsfr), whereas it remains unchanged in ”weak” measurements, ”small” state function reductions (ssfr). in zeo, bsfr creates a superposition of time reversed deterministic classical time evolutions analogous to bohr orbits and leading from the final state to the geometric past. the findings of minev et al [1] support the notion of bsfr [3]. 2. bsfr has far reaching implications. since water splitting has turned out to be very difficult to understand, a natural question is whether bsfr could explain it. if water splitting occurs as bsfr, it would correspond to a spontaneously occurring process 4e+4p+ o2 → h2o in reversed time direction requiring no catalysis. second bsfr would mean a return to a moment of geometric time where one as 4e+4p+o2. 3. bsfrs could be involved also with the other steps involving the splitting of chemical bonds and make it possible to kick the reactants over the potential wall. in a reversed time direction this process would take place spontaneously and lead from free atoms to their bound states by generation of atomic and molecular bonds. 4. bsfr is especially natural in the situations in which the reverse process occurs spontaneously meaning that only the process but not its reversal involves potential wall. this seems to be the case in bio-catalysis. in nuclear reactions the situation is different since both the process and its reversal involve overcoming of a coulomb wall. the zeo based vision provides only a general idea about what is involved with a given catalytic step of a given step of say photosynthesis but tells nothing of its chemical details, in particular of the role of mb and dark particles at it. the chemistry of water oxidation catalyst oxygen evolving complex is extremely complex but a general principle might considerably facilitate its understanding. 3.2 how to model the reverse time evolution behind catalysis as ordinary time evolution? the most plausible option is that water oxidation and also other steps involving liberation of atoms from bound states take place via bsfr. the zeo based view about biocatalysis does not however exclude the modelling of the time reversed process as occurring in the standard direction of time and being based on some catalytic mechanism. the presence of the catalyst would make the bsfr possible. this kind of modelling would help to characterize the catalyst and the superposition of time reversed time evolutions leading to the final state as time evolutions with standard time direction. 1. the first mechanism involves a reduction of heff for a magnetic flux tube liberating energy temporarily kicking the system over the potential wall. that energy is liberated follows from the fact that energies in general increase with heff . the reduction of the cyclotron energy proportional to heff of the charged particles at the flux tube would liberate the needed energy. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 1 | pp. 90-96 94 pitkänen, m., water oxidation & photosynthesis in tgd framework this mechanism might make sense in the case of molecular binding energies of order few ev which is the energy scale for the cyclotron energies in the magnetic field bend = .25 ev for heff = hgr = gmm/v0. this mechanism could apply to the catalytic steps of photosynthesis separately. if it applies to water oxidation, the energy 75 ev provided by flux tubes would be returned gradually to the catalyst (shortened magnetic flux tube) during photosynthesis proper as electrons and protons bind to the hydrogen atoms of coh2 and h2o during the process. 2. second, much more speculative (even in tgd framework), mechanism would be a phase transition increasing the thickness of a magnetic flux tube liberating magnetic and volume energy [9] suggested to be behind the proposed rather rapid expansion of the earth increasing its radius by factor 2 and leading to cambrian explosion. this transition would scale up the value of heff for valence electrons by factor of 2 and reduce the bond energies by factor 1/4 and also the energy of electron of hydrogen atom. this mechanism could be behind the proposed model of quantum tunneling innuclear reactions [5]. the quantum tunnelling would involve bsfr as a phase transition increasing the value of heff and size scale of the colliding nuclear strings. these dark nuclei would have dramatically reduced binding energy and increased spatial scale making it possible to overcome the coulomb barrier. the reactions would proceed fast in the dark phase and the second bsfr would transform dark nuclei to ordinary nuclei. ”cold fusion” would rely on this mechanism except that now the protons would be transformed to dark protons by the analog of pollack effect, and there is no need to break nuclear bonds as in ordinary nuclear reactions [2, 7]. also in the case of nuclear quantum tunnelling the phase transition would be scaling of flux tubes. the basic objection is that the phase transition would reduce the energy scale of valence electrons of all atoms involved. this does not look realistic. 3.2.1 shortening of flux tubes by a reduction of heff how could the bio-catalysis assisted by mb proceed? mb should provide the energy needed to split the bonds of various molecules. could the reduction of heff for cyclotron states at dark magnetic flux tubes liberate cyclotron energy of charged particles at them proportional to heff? 1. the magnetic cyclotron energy ec = ~effzeb/m is large for large ~eff . magnetic energies for heff = h are rather small. also for relatively small values of heff > h assignable to valence bonds, the cyclotron energies for proton and electron are much smaller than atomic binding energies for reasonable values of the magnetic field. 2. the basic proposal which led to the heff vision is that in tgd framework large values of heff allowing cyclotron energy in an endogenous magnetic field bend ' .2 gauss to be in visible and uv range are possible. the value of heff/h of order 1014 is needed. nottale hypothesis ~eff = ~gr = gmm v0 , one has v0 = 1/2 in the simplest model implying that gravitational compton length equals to the schwartschild radius rs ' 1 cm of the earth implies that cyclotron energies do not depend on the mass of small particle, in particular they are same for all charged particle with given charge if the value of b is same. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 1 | pp. 90-96 95 pitkänen, m., water oxidation & photosynthesis in tgd framework 3. dark protons at magnetic flux tube are a basic building brick of tgd inspired quantum biology. could the liberation of cyclotron energy for dark protons (or for dark ions) allow to break o-h bonds and ionize hydrogens? could some dark protons (or ions) transform temporarily to ordinary protons and liberate their cyclotron energy propto hgr so that mb could act as a bio-catalyst. 4. the general view of bio-catalysis suggests that the eventual formation of the final state molecules liberates energy, which increases the value of heff of dark flux tubes to its original value. note that the energy of the final state is by .83 ev smaller than that of the initial state so that dissipative losses are possible even if the entire energy of the photon is stored as metabolic energy. 3.2.2 could the thickening of flux tubes liberate energy and reduce atomic binding energy scale? although this option does not look realistic, it deserves a more detailed treatment. 1. the phase transition, which increases the radius of magnetic flux tubes by a power of 2 (by p-adic length scale hypothesis), liberates energy and could induce an increase of heff at the level of valence electrons and reduce the binding energy scale of the valence electrons proportional to 1/h2eff by a factor 1/22k. this mechanism was discussed in [9]. 2. the energy of 75 ev would be reduced to about 75/22k ev. k = 1 would give 18.8 ev and k = 2 would give 4.7 ev. the reduction of the binding energy would be due to the energy liberated in the thickening of the magnetic flux tubes. water would be special in the sense that these phase transitions could occur for the magnetic flux tubes assignable to water and explain its multiphase character responsible for its numerous thermodynamic anomalies. 3. what is the scale of the flux tubes involved? suppose that a flux tube portion of radius l and roughly the same length is involved. if the energy e of is of order e ∼ ~eff/l, the length scale would be about l = (h/heff ×1.6 nm. for heff = h, the length scale corresponds to cell membrane thickness. the outcome of this process would be a reduction of the scale of valence electron binding energies and of bond energies. in this phase the required reactions could proceed easily. received june 8, 2021; accepted july 22, 2022 references [1] minev zk et al. to catch and reverse a quantum jump mid-flight, 2019. available at: https: //arxiv.org/abs/1803.00545. [2] pitkänen m. cold fusion, low energy nuclear reactions, or dark nuclear synthesis? available at: http://tgdtheory.fi/public_html/articles/krivit.pdf., 2017. [3] pitkänen m. copenhagen interpretation dead: long live zeo based quantum measurement theory! available at: http://tgdtheory.fi/public_html/articles/bohrdead.pdf., 2019. [4] pitkänen m. quantum self-organization by heff changing phase transitions. available at: http: //tgdtheory.fi/public_html/articles/heffselforg.pdf., 2019. [5] pitkänen m. solar metallicity problem from tgd perspective. available at: http://tgdtheory. fi/public_html/articles/darkcore.pdf., 2019. [6] pitkänen m. some comments related to zero energy ontology (zeo). available at: http:// tgdtheory.fi/public_html/articles/zeoquestions.pdf., 2019. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://arxiv.org/abs/1803.00545 https://arxiv.org/abs/1803.00545 http://tgdtheory.fi/public_html/articles/krivit.pdf http://tgdtheory.fi/public_html/articles/bohrdead.pdf http://tgdtheory.fi/public_html/articles/heffselforg.pdf http://tgdtheory.fi/public_html/articles/heffselforg.pdf http://tgdtheory.fi/public_html/articles/darkcore.pdf http://tgdtheory.fi/public_html/articles/darkcore.pdf http://tgdtheory.fi/public_html/articles/zeoquestions.pdf http://tgdtheory.fi/public_html/articles/zeoquestions.pdf dna decipher journal | july 2022 | volume 12 | issue 1 | pp. 90-96 96 pitkänen, m., water oxidation & photosynthesis in tgd framework [7] pitkänen m. could tgd provide new solutions to the energy problem? available at: http: //tgdtheory.fi/public_html/articles/proposal.pdf., 2020. [8] pitkänen m. negentropy maximization principle and second law. available at: https:// tgdtheory.fi/public_html/articles/nmpsecondlaw.pdf., 2021. [9] pitkänen m. updated version of expanding earth model. https://tgdtheory.fi/public_html/ articles/expearth2021.pdf., 2021. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.fi/public_html/articles/proposal.pdf http://tgdtheory.fi/public_html/articles/proposal.pdf https://tgdtheory.fi/public_html/articles/nmpsecondlaw.pdf https://tgdtheory.fi/public_html/articles/nmpsecondlaw.pdf https://tgdtheory.fi/public_html/articles/expearth2021.pdf https://tgdtheory.fi/public_html/articles/expearth2021.pdf introduction basic facts about photosynthesis and water splitting oxygen evolving (water splitting) complex (oec) the energetics of photosynthesis tgd view about water photosynthesis and water oxidation does time reversal provide a general mechanism of bio-catalysis? how to model the reverse time evolution behind catalysis as ordinary time evolution? shortening of flux tubes by a reduction of heff could the thickening of flux tubes liberate energy and reduce atomic binding energy scale? sidorov1 – dnadj dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 177-205 sidorov, l., & chen, k., biophysical mechanisms of genetic regulation: is there a link to mind-body healing? issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 177 article biophysical mechanisms of genetic regulation: is there a link to mind-body healing? lian sidorov * & kevin chen abstract over the past several decades, pioneering biophysics work has shown that living tissues interact with electric and magnetic fields in unexpected and dramatic ways. from initial anecdotal accounts of enhanced healing under electromagnetic stimulation, research in this field has progressed to a sophisticated arsenal of investigative tools and theoretical models which include polarized light microscopy to study the liquid crystal properties of living cells and laserexcitation of dna to induce hybridization through non-molecular information transfer. in almost all cases, the results point to a set of remarkable properties of living tissues, and in particular of genetic material: the emerging picture is that of biosystems as sources and domains of coherent electromagnetic fields, which account for practically instantaneous inter-cellular communication and a highly efficient mechanism of energy utilization, and which seem to reflect very closely the developmental and patho-physiological state of the organism. in addition, a wide spectrum of genetic mechanisms now appears to be under the influence of surrounding electromagnetic fields. at the same time, an impressive number of studies in the areas of parapsychology and mindbody medicine converge to show that conscious intent can affect practically every single type of genetic program, as well as many physiological parameters [1]. these studies also show that such effects can be produced from great distances, and that occasionally they are accompanied by unusual energy signatures. is there a correlation between the effects of electromagnetic fields and those of mental intent on genetic regulation and living tissues? this paper will discuss the major experimental evidence and proposed mechanisms of these interactions, as well as the principal obstacles lying in the way of a viable, comprehensive theory. at the same time, we will attempt to formulate several preliminary hypotheses based on this evidence and to sketch some possible directions for future research in this field. key words: genetic control architecture, emfs, coherence, liquid crystals, interference grids, photon polarization, psycho-physiological remodeling, nonlocal communication, topological geometrodynamics. * correspondence: lian sidorov, dds. http://emergentmind.org e-mail: liansidorov@gmail.com note: this paper is based on a presentation made at the first international conference on the science of whole person healing, march 28-30, 2003, washington dc, and was originally published in journal of nonlocality & remote mental interactions, vol. 4, issue 1, april 2006. http://emergentmind.org/ mailto:liansidorov@gmail.com dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 177-205 sidorov, l., & chen, k., biophysical mechanisms of genetic regulation: is there a link to mind-body healing? issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 178 introduction the history of mind-body medicine in the modern era has been one of continuous struggle against both the derisive attitudes of a scientific mainstream firmly embedded into a reductionist, materialistic mind frame and the conceptual difficulties of studying something as elusive as the contents of consciousness. while gradual correlations with general factors such as stress have lead to the acceptance of psychoneuroimmunology as a legitimate field of study, there is very little material in the medical literature about other, more specific effects that mental intent might have on the body. this unfortunate state of affairs, we hope, is about to change. over the past decade, thousands of studies have been conducted all over the world, looking at the interactions between conscious intent and living systems from biomolecules and single celled organisms to human beings and describing statistically significant effects in very concrete, histological and physiological terms. these studies, reported in the scientific parapsychology literature as well as in some physics and biomedical publications, are part of a rapidly growing body of "human potential science" projects frontier programs funded by governments such as japan and china to look at exceptional human abilities and harness their implications. similar studies have also been carried out in the us, russia, germany and other western countries, unfortunately under less supportive conditions which are generally reflected by their more conservative protocols. a large proportion of this material is now available in abstract format through english-language publications such as d. benor's "spiritual healing: scientific evidence of a healing revolution" (vision publications, 2001 edition) and the qigong institute's database cd-rom, updated yearly. in another paper [1], we have reviewed the main classes of studies described in this literature, with a focus on genetic functions showing how practically every major genetic program (from dna replication and cell division rates to gene-specific transcription, translation and mutagenesis, to cell differentiation and apoptosis) can be modulated by intent under experimental conditions. in this follow-up article, we would like to take the discussion one step further and begin to look at a possible mechanism that might account for these startling experimental findings. the present model of genetic control, based on chemical messengers, transcription factors, molecular feedback loops, enzyme conformation, promoter regions and other forms of cis-/trans modulatory regulation is restricted to describing these all-important programs at a primarily intra-cellular level which fails to fully account for the astounding degree of synchronization between the billions of cells comprising the human body. it has been shown that on average four to eight different transcription factors service each gene's regulatory module and that many hundreds to thousands of genes must be coherently expressed in order to create any given tissue or multicellular structure [2 p. 9]. thus higher-level aspects of growth and development, as well as pathological and healing processes, such as the differential spatio-temporal expression of dna in specialized cells and the emergence/loss of complex architecture during embryogenesis or malignant growth, are still a matter of heated debate and speculation [3,77]. how does the dna material in each cell respond to its variable environmental circumstances in a way which dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 177-205 sidorov, l., & chen, k., biophysical mechanisms of genetic regulation: is there a link to mind-body healing? issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 179 reflects the cell's lineage, internal clock and also the activities of thousands of cells in its immediate vicinity? are chemical messengers sufficient to account for the speed and accuracy of this large-scale orchestration, or are there higher levels of genetic control architecture yet to be discovered? we believe that sufficient evidence has already accumulated to support the existence of such nonlocal, non-molecular controls. we also believe, along with a growing number of biophysical research scientists, that the key to the most effective preventive and therapeutic health interventions lies in the understanding of genetic regulation at the top levels of the control hierarchy that is, in the way cells communicate with each other, their environment and, possibly, with the poorly-understood physical correlates of mental intent. we have therefore divided this article into several parts: in the first section we will try to challenge the strict biomolecular approach to medicine by presenting a number of studies which clearly demonstrate that electromagnetic fields play a major role in genetic expression; the second part will briefly review the main characteristics of mind-matter interactions with respect to living systems; finally the discussion will attempt to draw parallels between the biophysical and consciousness-mediated mechanisms and point to theoretical models that might account for the effects of intent on targeted biological structures in a nonlocal framework. i. the effects of weak em fields on genetic programs a. cell differentiation in adult, embyonic and malignant states the work of rose and becker (1940s-1970s) observing that three major characteristics of malignant cells (cell simplicity, mitotic speed and metabolic priority) were also typical of embryonic growth and regeneration, in 1948 meryl rose conducted a landmark experiment designed to test whether the physiological environment of regeneration could take over the controls of tumor cells. after transplanting pieces of frog kidney tumor to the limbs of salamanders and watching them grow, he amputated the leg just below or, in some cases, right through the tumor mass. as opposed to controls, where the tumor metastasized and ended up killing the host, these specimens demonstrated a remarkable phenomenon: the tumor cells dedifferentiated more fully as the blastema formed, then redifferentiated along with the blastema thus proving that "the regeneration's guidance system could control cancer, too" [4 p. 217]. furthermore, replicating experiments conducted in 19621963 by f. seilern-aspang and k. kratochwil at the austrian cancer institute showed that, in cases where the primary tumor was in the tail, amputation of the tail below that level (i.e. leaving the primary tumor intact) resulted in total disappearance of both the primary mass and all its distant metastases as the tail regenerated [4 p. 220] thus complete healing of two aetiologically-distinct injuries. although this result was obtained only when the amputation was close to the site of the primary tumor, it demonstrated beyond doubt that the key to such "spontaneous remission" was a shift in the tumor's immediate environment most probably the electrical currents in the neuroepidermal junction, which becker would later prove were the initiators of regeneration. dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 177-205 sidorov, l., & chen, k., biophysical mechanisms of genetic regulation: is there a link to mind-body healing? issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 180 in 1961, becker and his team found that applying a very weak current (in the order of a billionth of an ampere) to a culture of nucleated frog red blood cells induced complete dedifferentiation in the cells, which reactivated their nuclei, lost all hemoglobin and became primitive (unspecialized) in the space of four hours [4 p. 143]. these changes, which were later found in the rbcs of fish and other reptiles, suggested a reactivation of the dna for once the staining characteristics of the nucleus shifted, the process continued even if the current was interrupted. all the changes involved paralleled those found in the salamander limb blastemas, demonstrating that the process of regeneration was initiated by an endogenous "current of injury". applying this knowledge to wound healing in mammals, in 1971 beckers's team stimulated the bone marrow of rats' amputated forelegs with a 1 nanoampere current and managed to obtain partial regeneration of the limb, including new, well organized bone, cartilage, muscle, blood and nerve tissue: at least ten types of cells had differentiated from the blastema, and some specimens even demonstrated the rudiments of finger cartilage. [4 p. 153] what is the nature of this endogenous current which preoccupied becker for over three decades? far from being restricted to areas of injury, as originally believed, becker showed in a series of ingenious experiments that the entire body of a living organism was permeated by a weak dc current, which furthermore appeared to reverse its polarity as the organism's state of consciousness changed from awake to deep sedation/anaesthesia. by demonstrating the hall effect in the leg of a salamander as it regained consciousness [4 p. 101], becker showed that this dc potential was a semiconductor current in other words, that the carriers were electrons in a semiconducting lattice. but to admit the existence of a semiconductor current permeating and regulating the brain-body continuum, one must be ready to look for an appropriate substrate. semiconduction requires an ordered molecular structure, such as crystals, in which electrons can exist in a delocalized fashion and flow coherently across large distances with minimal dissipation of energy a very different model from the type of conduction associated with neurons. in the wet, warm, perpetually-fluctuating environment which is the living organism, what could possibly constitute a proper matrix for this type of phenomenon? b. interactions between emfs and dna evidence from bioelectromagnetics labs (1990s-2003) before addressing the nature of semiconduction in living tissues, let us review a few more interesting studies which look at the effects of electromagnetic fields on dna regulation. in a 2002 study, tofani et al.. found a statistically significant inhibition of tumor growth (40%) and increase in survival time (31%) when mice bearing a subcutaneous human colon adenocarcinoma (widr) were exposed to 70min/day 5.5mt magnetic fields with 50 hz modulation for 4 weeks; a decrease in tumor cell mitotic index and proliferative activity and increase in apoptosis were also observed with no adverse or abnormal effects [5] dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 177-205 sidorov, l., & chen, k., biophysical mechanisms of genetic regulation: is there a link to mind-body healing? issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 181 in a similar study reported by simko et al.. [6], extremely-low frequency emfs (0.1-1mt, 50hz) applied continuously for 48-72 hrs resulted in increased micronucleus formation and apoptosis in transformed cell lines (human squamous cell carcinoma scl ii), but no adverse effects in normal, non-transformed cells. cell death induction consistent with apoptosis was also reported in two transformed cell lines (widr human colon adenocarcinoma and mcf-7 human breast adenocarcinoma) that were exposed to 1mt magnetic fields modulated by 50hz elfs). cells with daily exposure of 70 min. for 4 weeks showed significant tumor growth inhibition (up to 50%) by the end of treatment. no toxic morphological changes were observed in renewing, slowly proliferating or static normal cells. [7] zhou et al. [9] have shown that a 72 hr exposure of hl60 cells to 50hz, 0.1-0.8 mt magnetic fields resulted in an increased transcription level for tumor necrosis factor receptor p75 and interleukin il-6ralpha mrna expression. zhao [10] examined the promotion of dna synthesis in pdl fibroblasts under exposure to 0.14t magnetic field for 10, 40, 60, 120 min/day x 1week, comparing these to similar treatments every other day. remarkably, he found that the cellular dna contents increased proportionally with exposure time in the daily-treated samples, while no significant changes were found if the treatments occurred on alternate days. he concluded that the magnetic field had a cumulative, threshold-dependent and time-delayed effect on dna synthesis. eichwald & walleczek [11] found that elf (extremely low frequency) emfs controlled calcium uptake regulation in t lymphocytes: a bi-phasic response (stimulation / inhibition) was identified depending on the degree of cellular activation. the authors also noted that this, in turn, may affect other cellular processes that are ca dependent – i.e. dna synthesis. sontag & dertinger [12] reported that human promyelocytes (hl-60) exposed for 5 minutes to an amplitude-modulated, 4000 khz interferential current (25, 250 and 2500 microa/cm^2) showed windows of significant stimulation and depression in intracellular camp within the range of frequencies studied (0-125 hz). in a study by kubinyi et al.., t-rna synthetase activity isolated from the brain and liver of mice exposed to microwave radiation (2.45 ghz) during gestation showed a decrease after continuous wave exposure, and an increase in activity after amplitude-modulated irradiation [13]. it is interesting to note that many of these studies specifically report finding no adverse effects on normal cells exposed to the same em fields. finally, blank and soo [14] reviewed evidence that em fields interact with the activity of the cell membrane enzymes na,k-atpase and cytochrome oxidase in a frequency-dependent manner but argued that, in addition, large electron flows known to exist within the stacked base pairs of dna could interact directly with em currents and lead to gene activation [15]. one finding that supports this contention is that dna transcription in cell-free solutions can be activated by electromagnetic fields [16]. dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 177-205 sidorov, l., & chen, k., biophysical mechanisms of genetic regulation: is there a link to mind-body healing? issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 182 c. endogenous coherent fields: biosystems as dynamic holograms evidence from the international institute of biophysics (1970s-2003) all living systems emit light spontaneously: these ultra-weak emissions range from a few up to several hundred photons per second per square centimeter of surface area. the distribution spectrum ranges from infra-red to ultra-violet and is nearly flat, which indicates that the energy is emitted from a wide range of excited molecules and stored in a delocalized manner within the system. based on the characteristics of these emissions, popp and others [17, 18] have shown that the source of the biophotons is a coherent photon field within the organism. the dominating role of source and sink for the biophoton field is the dna molecule [17, 24] (in fact the mammalian red blood cells, which do not have active chromatine, are the only cells which do not emit biophotons). photon fluxes play a remarkable number of biological roles as either carriers of information (in enzyme activation, phototropism, photomorphogenesis, phototaxis, regulation of gene expression, vision) or as a driving energy for biological processes [21]. furthermore, it is known that both the intensity and the spectrum of the biophoton emission are strongly correlated with the physiological and developmental state of the organism: for example, [22, 23, 25] report significantly higher levels of photon emission from surgically removed tumors compared to normal tissues, a non-linear correlation between bpe and growth rate, and further correlations between the ultra-weak light from the fingertips of patients and their age and certain physiopathological states. these findings offer ample support to the thesis that biophotons are intimately related to the regulation of critical biological functions. noting correlations between optical properties of molecules and their carcinogenic activity, popp has suggested that cancer induction is related to the loss of coherence of a photon field in the living tissues, originating from excited states of dna [26, 27]. growth regulation is based on the death rate of cells, with sudden cell death and mitosis having to balance each other perfectly. with 10^7 cells dying every second in the human body, this information has to travel a distance of at least 10^-3 cm in 10^-7 seconds, which is much faster than the velocity of messenger molecules, approaching the velocity of sound. if it is assumed that the message is holistic and "communicated" to the entire body, then the scale becomes 1 meter, and the speed of transmission reaches electromagnetic values. thus cancer can be seen as an imbalance between cell growth and death due to a deterioration of intercellular and full-body communication systems [17] and indeed, research has shown [25] that the characteristics of biophoton emission curves are different for normal versus tumor tissues. the spatio-temporal coherence of biophoton fields means that complex electromagnetic (em) interference patterns are created throughout the organism: the more coherent the light, the sharper the interference patterns. it has been suggested by popp, gariaev and others that these patterns may be the basis of morphogenesis and structural/biochemical regulation of the organism throughout its life an em blueprint guiding the development, repair and even social behavior of organisms. the phase information within and between cells is hypothesized to act as a biological control parameter regulating the growth and differentiation of cells, with constructive interference domains intra-cellularly and destructive interference in the extradna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 177-205 sidorov, l., & chen, k., biophysical mechanisms of genetic regulation: is there a link to mind-body healing? issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 183 cellular matrix [24]. experimental evidence such as the phantom leaf effect [28], the delayed luminescence function of tumor cells and the distribution of daphnia larvae [29, 30, 18] certainly seem to support this hypothesis. one of the most remarkable findings to shed some light on the possible mechanism of biophoton control comes from ho's laboratory: in 1993, she and lawrence discovered that, under polarized light microscopy, the extraordinary level of molecular coherence makes organisms appear crystalline. this dynamic coherence is a continuum that extends from intracellular molecules to the cytoplasm, extracellular matrix and the connective tissues throughout the organism [18]. the lipids in cellular membranes, the cytoskeletal and muscle proteins, collagen and other connective tissue macromolecules, as well as the dna in chromosomes all these essential and ubiquitous molecules of living systems are liquid crystals [31, 32]. consequently, the organism may be seen as a solid state possessing many of the physical characteristics of these highly interesting materials. liquid crystals (lcs) are mesophases states of matter between the solid and liquid phase. while they possesss long range orientational order, they are highly mobile and responsive, undergoing orientation changes (phase transitions) when exposed to a wide variety of stimuli, including electromagnetic fields, temperature and pressure changes, hydration, ph, concentrations of inorganic ions and other psysico-chemical parameters [31, 32]. lc can convert information about minute changes in pressure, temperature and light into electrical currents (they are piezoelectric, pyroelectric and photoelectric). finally, they are permanently modified (sensitized) by the passage of electrical currents so as to facilitate the future passage of such currents [4 -p. 257). considering these arguments, mae-wan ho suggests that the lc matrix may act as a quantum holographic medium which records interference patterns between local events and the global body field an idea which finds full agreement with gariaev's experimental work [33]. d. evidence from the russian academy of sciences gariaev's dna-wave biocomputer (1990s-2003) since the early '90s, peter gariaev's team has been developing a new theoretical and experimental approach to the study of genetic material encoding and expression. in a pioneering series of papers [28, 34, 35, 36, 37, 38], he and his colleagues challenge the limits of the genetic code triplet model and propose instead a dual, substantive/wave basis for the encoding and expression of genetic material. the wave-like, non-local aspect of genetic regulation is recorded at the polarization level of dna-associated photons, and the genome is seen as a quasi-hologram of light and radio waves which creates the background necessary for the appropriate expression of genetic material. some of the experimental evidence cited in support of this new model is listed below: dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 177-205 sidorov, l., & chen, k., biophysical mechanisms of genetic regulation: is there a link to mind-body healing? issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 184 1. the existence of homonymous-synonymous ambiguities of genetic texts; 2. the virus-like strain specificity of prions in the absence of nucleic acid material; 3. the role of introns: statistical analysis using the zipf-mandelbrot law reveals that dna noncoding sequences, which account for 95-98% of the genome, have more in common with natural languages and demonstrate more long-distance correlations than coding sequences; this, according to the authors, is a strong indication that non-coding areas are the basis for one or more biological languages and represent "a strategic informational content of chromosomes"; 4. the ability of dna and chromatin in vitro to be pumped as a laser-active medium for subsequent laser light generation; 5. dzang kangeng's experiments: successful wave transmission of genetic information from donor biosystem to an accepting one via split laser beams fed repeatedly through the opticallyactive donor biosystem, then delivered to the receiving biosystem in early developmental stages. mixed characteristics of these non-molecular hybrids (seeds and chicks) were transferred to the next generation without need for further irradiation. (although kangeng provides no theoretical interpretation of the operational device, the authors' previous work with laser mirrors closely parallels his protocol, leading them to conclude that the polarized laser beam split into orthogonal waves which, by repeated passing through the optically active donor dna and multiple interference with itself, lead to the phenomenon of photon field localization and information recording); 6. the authors' similar experiments with polarization-laser-radio-wave (plrw) spectroscopy, whereby they used orthogonally polarized em beams to repair the genetic information of old radioactively-damaged seeds from the chernobyl area (1987). the authors argue that the genome emits light and radio-waves whose delocalized interference patterns create calibration fields (blueprints) for a system's space-time organization. this holographic-type information is being constantly and simultaneously read in billions of cells, accounting for the quick coordinated response typical of living systems. gariaev and his team suggest that the genome operates like a "complex multi-wave laser with adjustable frequencies", able to produce light and radio waves which regulate the biosystem's space and time organization. this complex background is the basis for the correct expression of genetic material (peptide codes) during embryogenesis and adult life, accounting for the elusive self-regulation and specificity of dna function in various tissues and under various conditions. various solitons (optical, acoustic, conformational, rotable-oscillating, etc) excited in polynucleotide areas, and transmitted over large distances significantly exceeding the hydrogen-bond length, "become the apparatus for continual (non-local) reading of context rna sequences on a whole". on the basis of this model, the authors suggest that the activation of oncogenes and xenobiotic hiv sequences is dependent on genome holographic processes and therefore that future research in these high-profile areas should focus on the factors modulating such em field characteristics (such as external artificial modified fields) in addition to local, molecular biology approaches. dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 177-205 sidorov, l., & chen, k., biophysical mechanisms of genetic regulation: is there a link to mind-body healing? issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 185 given that the expression (onset) of oncogenes and retroviruses such as hiv is known to vary widely among individuals and be largely context-specific, the authors suggest that external artificial modified fields may, in the future, help us modulate this apparent cellular context (environment) and thus keep such noxious genetic material dormant for indefinite periods of time. another interesting suggestion made by gariaev is that phenomena such as cellular apoptosis might be connected with an abnormal compression of photons by cell nuclei, which are accumulated to a maximal value and then destroy the nuclei. since apoptosis has been frequently demonstrated in healer-treated cancer cultures, and unusual electromagnetic signals are also commonly observed during spiritual healing sessions, we would like at this point to re-direct our attention and discuss some of the major experimental evidence and current conclusions with respect to this phenomenon. ii. the effects of healers' intent on living tissues in an earlier paper [1] we have described a series of experiments which demonstrate that human intentionality can produce a statistically significant effect on the following genetic programs: 1. cell division, reflecting dna synthesis and mitotic rates 2. transcription rates and dna conformation 3. gene specific translation rates 4. cell differentiation 5. mutagenesis 6. apoptosis, or programmed cell death. furthermore, conscious intent has been shown capable (at statistically significant levels) of producing the following structural and physiological effects: 1. conformational changes in cell membrane, chromatin, proteins [1, 78] 2. distant influence on a target's eeg, heart rate, galvanic skin response, finger blood volume, blood pressure, as well as fish orientation and algae motility [40, 41, 42 p. 336] these controlled, randomized and typically (but not always) blind studies have been extensively discussed in our previous paper – however we shall briefly summarize these results in order to highlight certain parallels with the effect of weak emfs on living tissues, as described earlier. dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 177-205 sidorov, l., & chen, k., biophysical mechanisms of genetic regulation: is there a link to mind-body healing? issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 186 accelerating or decelerating the growth of biological subjects this is one of the most commonly documented effects of conscious intent on living organisms in both the eastern and western literature. the studies reported under this category include the acceleration of seed germination and plant growth rate [79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89]; a directional increase/decrease in the growth rate of in-vitro cancer cell cultures like human nasopharyngeal carcinoma cell line (cne-2), human breast cancer cell lines, lung cancer cells (spc-a1), liver cancer cell line (bel-7402), erythroleukemia (k562), promyelocytic leukemia, cne-2, sgc-7901 gastric adenocarcinoma, spleen cells of mice and lung tumor cell line (la795), etc. [90, 91, 92, 93, 94, 1]; bi-directional effects on the growth of bacterial cultures such as e-coli [95,96] and salmonella typhimurium [97]; and inhibition of in-vivo tumor growth in mice [94, 98, 99]. the typical in-vitro study involved randomly dividing laboratory-prepared cancer cells or other cultures into groups with at least one group being treated with intention or external bio-energy (like external qi), plus one or two control groups. sometimes, one group was treated by a sham healer (person without training in bioenergy healing). in vivo-models most commonly used mice inoculated with cancerous cells, which were then randomly divided into various groups with one group being treated by external qi or other spiritual healing method for a set period of time. the control group could be either non-treatment or sham treatment. then tumor size and the survival time were measured as the outcomes. related to this type of study are experiments in which human intent was applied to revitalize fully denatured seeds and accelerate sprouting, producing measurable plants within minutes. one particularly gifted subject, ms. chulin sun, has worked with dozens of scientists world-wide and been involved in hundreds of successful replications of this phenomenon over the past 16 years. some of these studies involve revitalization of fried peas or cooked peanuts [100, 101, 102] while others report a statistically significant acceleration in the sprouting of peas [103], wheat [104], corn, watermelon seed, bean, flower seed and peanuts [101, 105]. transcription/translation and differential gene expression chien et al. [106] looked at the bi-directional effects of external qi on fs-4 human fibroblasts and found that "facilitating" qi produced a 1.8% increase in cell growth rate in 24 hrs, 10-15% increase in dna synthesis and 3-5% increase in cell protein synthesis in a 2 hr period. with "inhibiting" qi, cell growth decreased by 6% in 24 hours, while dna and protein synthesis decreased respectively by 20-23%, 35-48%. zhang et al. [107] studied the effect of emitted qi on the nucleic acids of chick red blood cells and found a two-fold increase in dna and 12-fold increase in rna content. dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 177-205 sidorov, l., & chen, k., biophysical mechanisms of genetic regulation: is there a link to mind-body healing? issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 187 related results include the ability of emitted qi to increase nk cell and k cell activities [108] and to enhance the number of active osteoclasts and the quality and quantity of both fibrous and bony callus tissue in laboratory rabbits [109]. these studies suggest that conscious intent may act by increasing the rate of cell-specific transcription/translation responsible for specialized functions, as well as possibly stimulating cell differentiation and/or recruitment. structural changes caused by intent or mental power d. y. chu of peking university tested more than 20 qigong healers in controlled studies to explore the effects of eqt on the conformation of bio-molecules [110]. in her study, a circular dichroism (cd) spectrum was used to monitor the conformation of various bio-molecules, such as poly-glutamic acid, poly-lysine, metallothionein, and some rnas. after more than a hundred trials were repeated with different healers and controls, she found that the cd spectra of biomolecular samples were changed significantly after exposure to eqt in comparison with both controls and the baseline. in general, the changes of the cd characteristic elliptisity were over 110 x 103 dgr×cm2×dmol-1, and the maximum was 93.9 x 104 dgr×cm2×dmol-1. the change of elliptisity could be positive or negative depending on the intent of the qigong healer. these findings were successfully replicated when she visited the us in 2000 [111]. rein and mccraty [112] reported a 250% change in dna conformation, directly correlating with the intent of a healer from a distance. the directional winding/unwinding of dna under specific intent has been repeatedly demonstrated by rein and his team over a number of years and experimental set-ups, with some samples showing more denaturation than could be obtained via normal heating or mechanical means [113]. similar changes in the conformation of dna and rna samples have been found under the effect of conscious intent (external qi) by lu zuyin [114] and sun et al. [115] as indicated by changes in the samples' ultraviolet absorption curve. in addition, statistically significant effects on erythrocyte cell membranes were documented by braud et al. [116, 117] and sun et al. [118]. these include the ability of healers and/or ordinary persons to decrease the rate of rbc hemolysis; to increased fluidity of the erythrocytic membrane; and to suppress activity of na+, k+ of rbc membrane. changes in cell colony architecture were also documented by chen x. et al [119] and by chen [120,121], correlating with a change in the types of glycoproteins expressed on the cell membrane surface so this effect may also be a result of alterations in the specific genes expressed under the effect of external qi. intent-induced mutation nash [122] randomly assigned 60 ordinary subjects (not known to be psychically gifted) into three groups: one group mentally promoted mutation of lac-negative strains of e-coli to lacdna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 177-205 sidorov, l., & chen, k., biophysical mechanisms of genetic regulation: is there a link to mind-body healing? issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 188 positive strains in three test tubes, one group mentally inhibited mutation in three test tubes, and the rest 20 subjects worked as control. all tube conditions were carefully blinded to the lab technicians. he found that the mutation ratio of lac-positive to total bacteria was greater in the promoted tubes than that in the inhibited tubes (p < .005); and less in the inhibited tubes than in the control (p < .02). there are many more studies in this area that we will not discuss in detail here. for example, liu et al [123] applied eqt as mutagenesis for micromonospora echinospord, and found that eq has the ability to kill micro-organisms and change strains properties. pei et al [124] reported that mutation of e-coli c311 occurred after exposure to eqt. shan et al [125] also used the intent of the qigong healer as mutagenesis to select various antibiotic-producing strains in the pharmaceutical production, and had some success. bai et al. [103] reported that the seeds mentally induced to germinate rapidly were apparently genetically altered with significant differences in dna extraction and polymerase chain reaction. morphological alterations and cell differentiation electron microscopy studies of malignant tissue extracted from laboratory animals treated with external qi have repeatedly shown clear histological signs of apoptosis and/or reversal of cancer features, when compared to controls. for example, in their study of the inhibitory effect of eqt on human hepatocarcinoma in mice, chen et al [126] found morphological alterations including nuclear condensation, nuclear fragmentation, decreased ratio of nucleus and cytoplasm, swollen mitochondria with poorly organized mitochondrial cristae (some vacuolated) and many apoptotic bodies in the extracellular space. shao et al. [127] looked at qigong-treated mice with implanted s180 sarcoma and reported that the averaged diameters of cells and nuclei, the ratio of nucleus to cytoplasm and the number of tumor cells division phase and ag-nor counts in nuclei in the sarcoma of eqt treated mice were all much less than those in the controls (p < 0.001). they also found that in the eqt treated mice a great number of sarcoma cells showed atrophy, degeneration, and pyknosis or karyolysis, while some membrane structures such as mitochondria appeared to be injured. finally, li et al. [128] studied the effects of emitted qi on g422 neurogliomas implanted in mice, finding that mitotic rates were reduced and the differentiation of the glioma cells tended to be reversed and the activity of nk and k cells was increased significantly compared to the tumor control. these several hundred studies, conducted over the past 3 decades by a large number of university and independent laboratories in countries like the us, england, china, japan, russia, germany and others, represent a pioneering body of work whose importance cannot be overstated. although not all of them have been conducted under ideal methodological conditions of blindness and control, and the reporting style is far from consistent across the field (see [42] for an outstanding synopsis and analysis of experimental quality in these different categories), the overall evidence is much too compelling and significant to ignore. replicating these studies under proper, uniform academic standards is of course a necessary first step. however, many of the results obtained by independent laboratories appear to reinforce each other, to a degree that dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 177-205 sidorov, l., & chen, k., biophysical mechanisms of genetic regulation: is there a link to mind-body healing? issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 189 certain general observations about the effect of mental intent on biological targets can already be drawn. a. specificity of intent the effect of intentionality appears to be directional and target specific. for example, achterberg and rider showed that training patients in cell-specific visualization of either t lymphocytes or neutrophils resulted in statistical increase in cell blood levels correlating with the type of imagery employed [43]. becker used hypnotized subjects to demonstrate that they could decrease or increase the dc potential of specific areas of the body depending on the suggestion given (a suggestion of numbness in the left arm resulted in no response to a pinprick stimulus and a drop to zero in the dc potential, while the pinprick response/dc potential remained almost unchanged for the right arm; the change in voltage was "exactly the same as that seen in standard chemical nerve block" [45 p 90-91]. many of the studies described above also reflect such a directional effect (see, for example, 129, 41, 113, 47). b. electromagnetic windows of healing and intent studies by zimmerman and beck show that healers' hand and brain frequencies measured during active "healing states" sweep a 0.3-30 hz range, with most activity in the 7-8 hz area. these frequencies, which show an uncanny consistency across a remarkable number of cultures and healing traditions, appear to closely overlap the electromagnetic specificity windows used in clinical and laboratory applications to enhance neural regeneration (2 hz); bone growth (7 hz); ligament healing (10 hz) and capillary and fibroblast proliferation (15, 20 and 72 hz) [48]. both local and distant mental interactions have been shown to produce unusual em signatures. magnetic signals up to 105nt were found by wu et al. during qi emission by qigong practitioners [49]. unusually high static charges (up to 221 volts) from the bodies of healers and psi-gifted people were reported by watkins, hochenegg, shallis and green [42 p157]. nakamura measured an increase in biophoton emission intensity from the hands of practitioners in the qigong state [50]. wallace found that human biophoton emissions could be increased by subjects at will and measured up to 100 times stronger emissions from the hands of gifted subjects compared to controls [51]. high surges in the magnetic field surrounding healers, or significant effects on distant magnetic sensors, have been published by ullman, watkins, puthoff and targ, zimmerman and ostrander and schroeder, sergeyev, (52; 42 p 168; 39]. photographic film exposure in association with healing or clairvoyance experiments has been demonstrated in independent studies by watkins, turner and zhao yong-jie [42 p 157, 169]. radin reports that the background ionizing radiation could be decreased in accordance to task instructions (p<0.05), only to suddenly increase above control levels 20 seconds after the dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 177-205 sidorov, l., & chen, k., biophysical mechanisms of genetic regulation: is there a link to mind-body healing? issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 190 treatment period [53]. in a series of experiments involving therapeutic touch practitioners and their subjects, gamma radiation levels significantly decreased in 100% of the subjects and at every body site tested [54, 55]. finally, we should also ask ourselves what such capabilities tell us about the healer's metabolic status. we know, for example, that advanced practitioners of qigong can enter a special state (bigu) in which they can subsist for weeks, sometimes months, on only 2-300 calories per day, while carrying on with normal activities. [56, 57] this "super-efficient state", as prof. roy has described it, has been shown to be metabolically different from that of normal fasting which suggests that the body somehow switches over to a different way to process and conserve energy. is there a link between bigu and the energetic phenomena described above? c. distant mental interactions with living systems (dmils) dmils include a wide range of variables, from physiological parameters like eeg and galvanic skin response [40, 58, 59, 60] to the denaturation of dna in solution [42, 61] to affecting the morbidity and mortality rates of hiv/aids patients by remote prayer groups [62]. typically in these experiments the sender is isolated from the experimental group by distances ranging from a few meters (an adjacent room) up to thousands of kilometers and the subjects are blind to the sending period, so that a comparison can be made with the "non-influence" windows. the statistical significance of these remote effects across dozens of independent studies is highly consistent despite the subjects' inability to consciously "guess" the sending window. some studies have shown a lag time to onset of effect in the order of seconds [59,60], while in others, paradoxically, an anticipatory effect has been demonstrated [58] consistent with decades of parapsychological retro-pk evidence, but a clear challenge to our current concept of information flow and causality. such evidence of space and time non-locality is probably the single greatest reason for which spiritual healing continues to encounter major resistance as a legitimate research subject from the scientific establishment. and yet at a physics theoretical level there is nothing that prohibits such effects from taking place: indeed, if there is one salient observation to be made on the basis of our foregoing discussion, it is that modern medicine seems to have almost entirely disassociated itself from the biophysical bases of life: current thinking appears to stop mysteriously at the biomolecular level, completely oblivious to the physics that lie beneath. our challenge is to take this next step and place the current, biomolecular understanding of genetic regulation into a broader context hoping that some of the answers which have eluded us so far, such as the onset criticality and reversal of malignant programs, will become more obvious at this level of the control hierarchy. dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 177-205 sidorov, l., & chen, k., biophysical mechanisms of genetic regulation: is there a link to mind-body healing? issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 191 iii. a new perspective on the genetic code a. a hierarchy of genetic regulatory mechanisms: even a brief survey of the literature, such as we have undertaken, suggests that there are at least three main levels of control mechanisms dictating the unfolding of genetic programs: 1. the biochemical level: this includes, but is not limited to, the triplet genetic code and the newly discovered histone code; mechanisms such as the availability of cellular chemical messengers, molecular feedback loops and cis-/ trans-regulation work on this level, controlling to at least some degree the sequence of different genes' expression. 2. the biophysical level: this can further be divided into local and non-local effects. 2a. local control refers to the conformational effects of electromagnetic fields on chromatin, enzymes and cell membranes which in turn affect the exposure of given genes and the rate of transcription/translation, plus possibly the rate of dna synthesis and cell mitosis. 2b. non-local effects include endogenous field coherence, electromagnetic interference grids, superconduction, photon localization phenomena and the possibility of nonmaterial, wave-based genetic hybridization and regeneration, as demonstrated by the experiments of gariaev and kangeng. 3. the conscious level. as we suggested before, it is difficult to tell at this point whether consciousness and mental intent act both locally and non-locally, although the existence of dmils and anticipatory effects is a strong indication that we need to look beyond simple electromagnetic entrainment between healer and patient. once we recognize that genetic programs are continuously modulated by all these different parameters, we need to ask ourselves a new set of questions. for example: 1. what is the correct order of these elements in the hierarchy? 2. how do level 1 and 2 mechanisms interface with conscious intent? (em or other physical substrate?) 3. how do coherent biophoton fields interact with environmental emfs? 4. how does conscious intent modulate endogenous emfs? 5. what is the power/frequency/polarization profile of biophoton emissions under different states of consciousness and how does it vary with various intentions or forms of visualization? dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 177-205 sidorov, l., & chen, k., biophysical mechanisms of genetic regulation: is there a link to mind-body healing? issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 192 6. what is the basis of target specificity and bi-directional effects in controlled healing/pk studies? 7. how is information transmitted non-locally? b. preliminary framework to begin addressing these questions, it is important to re-emphasize the biophysical perspective on living tissues emerging from the works cited above. according to this view, the coherence of endogenous em fields and liquid crystal properties of biomolecules account for:  nonlocal communication throughout the organism/ tissue/population o -synchronized behavior of billions of cells o exquisite sensitivity and specificity to weak stimuli o highly efficient energy utilization  possible brain-body electromagnetic continuum and tuning regulatory mechanism for tissue-level interference effects c. working hypotheses 1. intent-driven chromatin decondensation as a factor in transcription? it is generally accepted that the conformation of the chromatin fiber must change reversibly in processes that require the access of regulatory proteins and enzymes to the dna template (such as in transcription, replication and repair). van holde and zlatanova have suggested [63, 64] that one of the major conformational changes that occurs during dna compaction is a collapse of the angle made between three consecutive nucleosomes (internucleosomal angle), probably mediated by electrostatic changes in histone interactions with linker dna. could such a change in angle be partly controlled by the electromagnetic hologram grid nodes postulated by gariaev, popp and others? if electrostatic interactions are responsible for chromatin folding/unfolding, it would be easy to see how changes in the frequency or polarization angle of dna-associated biophotons could alter the locus of action of such pretranscriptional decondensation. the demonstrated ability of conscious intent to produce winding/unwinding of in-vitro chromatin and to directionally influence transcription becomes highly significant in this context. one other supporting piece of evidence is the published experiments of yan xin [65] in which he repeatedly demonstrated the ability of external qi to dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 177-205 sidorov, l., & chen, k., biophysical mechanisms of genetic regulation: is there a link to mind-body healing? issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 193 alter the polarization of targeted he-ne laser beams from distances ranging between 7-2000 km. the change in polarization occurred within an hour of the external qi emission, as repeated sharp fluctuations averaging 6-7 degrees and 10-12% change in intensity of the normal beam, compared to baseline. no difference was recorded in the controls. 2. meditation as psycho-physiological remodeling we propose that qigong and other meditative techniques work by progressively increasing the overall coherence ("qi flow"?) of the body's liquid crystal matrix via conscious mental driving, in a way not dissimilar to laser pumping or the gradual orientation of ferromagnetic particles in an em field. meditation frequencies could engage the thalamic silent periods (as oschman has suggested) and possibly other frequency-window pacemakers, and thus drive the configurational states that the body naturally cycles through, to sensitize its lc matrix to particular frequencies. moreover, the semiconductor nature of living tissues suggests that, with repeated passage of an em current through them, their sensitivity to subsequent signals should increase a property which, we believe, is critical to the understanding of long-term physiological changes seen in meditators [66, 67]. the maintenance of a mentally-driven, permanent tighter-than-average molecular coherence would, in our model, lead to a gradual increase in tissue liquid crystallinity, more efficient signal detection/transmission and hence greater perceptual sensitivity, energy efficiency (bigu) and ability to correct local em "contextual errors". 3. do specific intents translate into characteristic brain-body wave forms? as we have seen earlier, becker has shown that an organism's somatic dc field correlates in very specific ways with its state of consciousness: using salamanders for test subjects, becker found that under anesthesia, their peripheral voltages dropped to zero, and even reversed in very deep stages [4 p. 111]. similar instances of reversal in body polarity are reported as occurring in human subjects monitored during deep trances induced in preparation for remote viewing. in spiritual healing, benor reports on a study by rein and laskow which found that four different intentions by the same healer produced different body magnetic emissions which correlated with different biological effects on tumor cell cultures [42 p. 159]. as we have seen earlier, the bi-directional effect of intent on living targets is also mirrored, remarkably, by the bi-phasic response of tissues to specific em frequency windows (section ib). furthermore, it is highly interesting to note the close parallel between the genetic-level effects of healing intent as described in [1] and those of weak electromagnetic fields as discussed earlier in this paper (i.e. altered levels of mrnas and proteins, increased enzyme activities, decrease in tumor growth and cell mitotic index, tumor cell alterations in shape and membrane discontinuity, increased apoptosis, accelerated differentiation as well as seed revitalization and hybridization dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 177-205 sidorov, l., & chen, k., biophysical mechanisms of genetic regulation: is there a link to mind-body healing? issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 194 with the gariaev/kangeng techniques). the fact that many of these bioelectromagnetic studies found no adverse emf effects on normal cells also seems to parallel the regulatory influence of healing intent [42, 78]. is there a link between effective mental healing intent, or the altered state of consciousness required to produce it, and these unusual em emissions? are characteristic frequencies/spectra required for particular healing effects? and do these unusual em signals play an active role in healing (perhaps by entrainment and frequency synchronization with the patient, as oschman suggests) or are they merely by-products of a deeper interpersonal communication mechanism we have yet to discover? based on the evidence presented in this paper, we tend to agree with suggestions by beck, oschman and becker that healers produce characteristic electromagnetic frequencies which can exert specific biological effects on their target. however, we would like to qualify this statement by adding the following observations: 1. frequency may not be the only parameter involved in modulating the em signal. in view of popp's and gariaev's data, we have reason to believe that the phase and polarization of endogenous fields are also under the effect of conscious intent, which may be self-generated or transmitted non-locally by a healer. thus the specificity of guided imagery may be the result of unique windows of frequency/ polarization excited at the level of the cerebral cortex, then spreading globally along neural and perineural pathways. it is also possible that concentration on complex sensory modalities (i.e. the vividness of imagery) synchronizes larger areas of the cortex, resulting in a more powerful signal. gariaev's contextual holographic paradigm further suggests that a pathologic em environment may be less stable than that of healthy tissue, and thus more easily modified. finally, we could also make an argument that stress, or other chronic emotional disturbances, represent a possible source of de-synchronization with partial loss of endogenous field coherence. 2. another point that cannot be overemphasized is that the presence of electromagnetic signatures associated with intent does not necessarily imply an em transmission mechanism (i.e. via proximal frequency, entrainment or coupling to the schumann resonance, as previously discussed by oschman, becker and sidorov) but simply that these ubiquitous em signals may be produced as a secondary, local effect of the primary interaction. while em coupling cannot be excluded in some situations, we need to realize that the nonlocal characteristics of mental healing (target specificity, distance and time independence) require more than a classical communication framework (see below). 4. distant information transfer one of the most remarkable features of distant mental interactions with living and inert systems is that they affect only the target samples, leaving other (control) samples which are within the dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 177-205 sidorov, l., & chen, k., biophysical mechanisms of genetic regulation: is there a link to mind-body healing? issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 195 same radius, statistically unchanged [49]. this strongly suggests that we are dealing with some form of entanglement between healer and target, rather than a classical, isotropic field-mediated process. however, it has been repeatedly pointed out by dossey, walach, pitkanen and others that in such cases the definition and exact mechanism of quantum entanglement would have to be expanded to account for the insertion/extraction of intelligent information and for the notorious problem of decoherence in complex quantum systems. one comprehensive model that happens to contain such an extended concept of entanglement (together with numerous testable predictions which are supported by gariaev's spectra and the presence of em signatures at the target) is pitkanen's topological geometrodynamics an 8dimensional cosmology which is the product of 4-d minkowskian space-time and the su(3)/u(2) projective space of two complex dimensions [68, 69, 70, 71]. the geometrization of all basic interactions in tgd means that classical fields and matter form a pseudo-feynman diagram in which the lines representing matter are replaced by spacetime sheets and virtual bosons are replaced by topological light rays ("massless extremals", mes). mes generate geometrical supracurrents which serve as a source of coherent photons and act as geometrical correlates of entanglement between distant material space/time sheets (the vertices of the pseudofeynman diagram). one of the predictions of tgd is that focused mental intent produces topological field quanta form-specific mes which act as non-dissipative entanglement bridges between sender and target and which create characteristic ionic and electromagnetic signatures at both ends by their interaction with local magnetic flux tubes. thus the solution proposed by pitkanen appears to elegantly connect all the major observations we have discussed in our paper up to this point: a distant healer's conscious intent can be seen as generating form-specific geometrical currents which "propagate" non-dissipatively across arbitrarily large distances and which interact with the intended target by producing characteristic, coherent photon signatures. in turn these photons interact with the organism's endogenous electromagnetic field to modulate specific frequency or polarization parameters as described by popp and gariaev, thus altering interference patterns, regulating inter-cellular communication and the contextual environment of dna/rna expression inside cells. of course, at this point it is difficult to fill in all the details, or indeed feel confident of the absolute validity of such a model. on the other hand, tgd opens experimental possibilities that have generally not been available with other theories of nonlocal healing. in [70] we have made a number of proposals regarding the types of tests that could be conducted as a preliminary verification of tgd predictions. together with additional replications of the gariaev experiments and of the major histo-molecular healing studies reviewed in this paper, we believe these ideas are well-worth pursuing as part of a future research program in complementary and alternative medicine. as opposed to previous mind-body research proposals, all these suggested protocols are remarkably concrete, objective, quantifiable and compatible with our need to construct a consistent physical theory. since only innovative experimentation will be able to select the most promising theoretical models, and since in the absence of such models we cannot begin to incorporate this valuable body of evidence into our overall therapeutic strategy, we feel it is imperative that the nih and other potential sponsors treat these proposals with the attention they deserve. dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 177-205 sidorov, l., & chen, k., biophysical mechanisms of genetic regulation: is there a link to mind-body healing? issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 196 conclusions where do we go from here? the first step, of course, should be a well-coordinated experimental program replicating the major classes of mental interactions described in these two papers. protocols could be set up to study the biophysical basis of differential response in normal and abnormal cell populations (target specificity/normalization); to compare the effect size, replicability, side effects and long-term response for biophysical and mind-body therapeutic approaches in specific pathological models; to study the ability of normal human populations to learn and effectively implement such mental techniques (clinical studies); and to investigate the interactions between external em fields and endogenous currents with respect to genetic regulation. finally, given the common challenge that nonlocal communication presents to researchers in physics, parapsychology and mind-body medicine, we strongly advocate the establishment of interdisciplinary teams to collaborate on innovative new protocols capable of extracting meaningful conclusions about this fundamental aspect of reality. from an applications point of view, we should start identifying the most effective meditation protocols for specific effects i.e. enhancement of immune function, expression of specific genes, and suppression of pathogens or reversal of malignant cell behavior/induction of apoptosis. it is also important to start designing and standardizing teaching programs, perhaps through the use of biofeedback methods to evaluate the effectiveness of teachers' and students' meditation on specific biological parameters. understanding the interactions between mind-body interventions and conventional treatment modalities (such as the demonstrated increase in drug uptake and reduction in chemotherapy side effects with concurrent qigong practice) is another long-term goal, which should allow us to eventually integrate such multi-modality therapies for optimal results with minimal iatrogenic trauma to the organism. finally, we would like to take a step back and end this presentation with a philosophical observation. for more than a century, the common assumption in parapsychology research has been that the brain is the primary detection organ for subconscious/ anomalous cognition. however, in spite of this experimental focus, there is a remarkable lack of evidence supporting this contention in fact we now know that certain peripheral responses to anomalous stimuli, such as the galvanic skin response, are highly consistent in the absence of any conscious awareness of these stimuli. is the brain the only conceivable transducer of nonlocal information? indeed, the literature shows that psi function manifests across the full taxonomic continuum, from humans to animals [41, 58, 73, 74, 77] to plants and individual cells [72, 42]. since such consistent features are generally attributed to a very successful adaptive mechanism, and pitkanen's tgd predicts a fractal hierarchy of biological emitters/receivers for nonlocal communication, could it be that the exquisite sensitivity of genetic material (dna, rna, protein) to mental intent may in fact reflect a deep evolutionary principle? for these first forms of life, devoid of what we would call a sensory system, chemical and electromagnetic interactions with the environment would have been one, albeit purely random, type of "orientation" response. however, the complex behavior of organisms starting from the very bottom of the taxonomic tree (see virus and prion dynamics, dna repair and transcription, etc) strongly suggest that behavioral adaptations were set in place, which clearly reflect a directional, dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 177-205 sidorov, l., & chen, k., biophysical mechanisms of genetic regulation: is there a link to mind-body healing? 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(1994). preliminary observation of the effect of external qi on the e-coli (c311). chinese journal of somatic science. 4(2): 83-85. dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 177-205 sidorov, l., & chen, k., biophysical mechanisms of genetic regulation: is there a link to mind-body healing? issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 205 125. shan ly, sun y, zhang ly, hu yj, li sp, sun my et al. (1990). studies on the selection of antibiotic producing strains by treatment with qigong. 3rd nat acad conf on qigong science, guangzhou, china. 1990: 20. 126. chen xj, li yq, liu gc & he bh, (1997). the inhibitory effects of chinese taiji five element qigong on transplanted hepatocarcinoma in mice.” asian medicine, issue 11 (1997): 36-38. 127. shao xm, liu gc, zhou qj, yu f, xu hf, xue hl, et al (1990). effect of qigong waiqi (emitted qi) on the growth and differentiation of implanted tumor cells (in mice); 3rd nat acad conf on qigong science, guangzhou, china. 1990: 85. login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 380-382 issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 380 references abbott d., davies, p. c. w. & pati, a. k. (eds.) (2008), quantum aspects of life, imperial college press. al-khalili, jim (2003), quantum: a guide for the perplexed. weidenfield and nicolson, new york. allday, jonathan (2009), quantum reality: theory and philosophy. crc press. asher, r. j. (2012), evolution and belief: confessions of a religious paleontologist. cambridge university press. baggott, jim (2005), a beginner's guide to reality. penguin books. baggott, j. (2012), higgs: the invention and discovery of the 'god particle', oxford university press. barrow, john d. & tipler, frank j. (1986), the anthropic cosmological principle, oxford paperbacks. barrow, john d., davies, paul c. w., harper, charles l. (eds.) (2004), science and ultimate reality. cambridge university press. bohm, d (2002), wholeness and the implicate order (first published: routledge & kegan paul, 1980; routledge classics, 2002) bohm, d. (2003), the essential david bohm, (ed. by nichol, l.), routledge, london. brockman, j. (ed.) (2006), intelligent thought: science verses the intelligent design movement, vintage. carroll, sean, b. (2006), endless forms most beautiful. weidenfield & nicolson. carroll, s. (2012), the particle at the end of the universe, dutton. chandrakirti and jamgon mipham (2002), introduction to the middle way: chandrakirti’s madhyamakavatara with commentary by jamgon mipham. translated by the padmakara translation group. boston: shambhala publications. conway morris, simon (2003), life’s solution: inevitable humans in a lonely universe. cambridge university press. coyne, j. (2009), why evolution is true, oxford university press (2010 edition). d’ espagnat, b. (2003), veiled reality, westview press. d’ espagnat, b. (2006), on physics and philosophy, princeton university press. davies, paul (2007), the goldilocks enigma. penguin books (first published 2006:allen lane) davies, paul & gregersen, niels henrik (eds.) (2010). information and the nature of reality: from physics to metaphysics. cambridge university press. dawkins, r. (1995), river out of eden: a darwinian view of life, phoenix, orion books ltd (2004 reissue). dawkins, r. (2005), the ancestor’s tale: a pilgrimage to the dawn of life, phoenix, orion books ltd (first published 2004). dawkins, r. (2006), the blind watchmaker. new edition – penguin (first published 1986) dawkins, r. (2006a), the god delusion. black swan. dawkins, r. (2010), the greatest show on earth: the evidence for evolution, black swan, (first published 2009 bantum books). dembski w. a. (2002), intelligent design: the bridge between science and theology, inter-varsity press, us. dennett, daniel (1991), consciousness explained, the penguin press. http://www.amazon.co.uk/s/ref=ntt_athr_dp_sr_1?_encoding=utf8&field-author=abbott%20derek%20et%20al&search-alias=books-uk&sort=relevancerank dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 380-382 issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 381 dobzhansky, th. (1937), genetics and the origin of species. columbia university press, new york. (2nd ed., 1941; 3rd ed., 1951). dolling, l.m.; gianelli, a. f. & statile, g. n. (eds.) (2003), the tests of time: readings in the development of physical theory. princeton university press. fodor, j. & piattelli-palmarini, m. (2011), what darwin got wrong, profile books. feynman, richard (1988), qed: the strange theory of light and matter. princeton university press. ghirardi, g. (2005), sneaking a look at god's cards: unraveling the mysteries of quantum mechanics, revised edition, princeton university press. 1 st ed – 1997, il saggiatore, milano. goswami, a. (2008), creative evolution. quest books. greene, brian (2004), the fabric of the universe. allen lane. gribben, john (2009), science: a history. penguin books. hawking, s. (2011), a brief history of time: from big bang to black holes, bantum. hawking, stephen & mlodinow, leonard (2010). the grand design: new answers to the ultimate questions of life. transworld publishers – bantum press. humphrey, n. (2006), seeing red: a study in consciousness, harvard university press. humphrey, n. (2012), soul dust: the magic of consciousness, quercus. isaacson, w. (2008), einstein: his life and universe, pocket books. jones, s. (2000), almost like a whale: the origin of species updated, black swan. kelly e. f., kelly e. w., crabtree a. & gauld a. (2009), irreducible mind: toward a psychology for the 21st century, rowman & littlefield publishers lockwood, michael (2005). the labyrinth of time: introducing the universe. oxford university press. mcfadden, johnjoe (2002). quantum evolution: how physics weirdest theory explains life's biggest mystery. norton & co. meyer, s. c. (2010), signature in the cell: dna and the evidence for intelligent design, harperone. oerter, robert (2006), the theory of almost everything, pi press. penrose, roger (1995), shadows of the mind. oxford university press:1994, random housevintage. penrose, roger (2005), the road to reality: a complete guide to the laws of the universe. vintage. randall, l. (2012), higgs discovery: the power of empty space, the bodley head ltd. rosenblum, b. and kuttner, f. (2006), quantum enigma: science encounters consciousness. oxford university press, u.s.a. schlosshauer, m. (ed.) (2011), elegance and enigma: the quantum interviews, springer: the frontiers collection. schrödinger, e. (1944), what is life? cambridge university press. sheldrake, rupert (2009), a new science of life (revised edition), icon books. smolin, lee (2002), three roads to quantum gravity. perseus. sober, e. (2008), evidence and evolution: the logic behind the science, cambridge university press. dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 380-382 issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 382 stapp, henry (2004), mind, matter and quantum mechanics. springer-verlag berlin heidelberg 1993, 2004 (frontiers collection). stapp, henry (2007), mindful universe. springer-verlag berlin heidelberg (frontiers collection). tallis, r. (2011), aping mankind, acumen. turok, n. (2013), from quantum to cosmos: the universe within, faber & faber. wilber, k. (ed.) (2001), quantum questions: mystical writings of the world’s great physicists, shambhala. wilczek, frank (2008), the lightness of being. penguin. woolfson, a. (2000), life without genes, flamingo. zeilinger, anton (2010), dance of the photons. farrar, straus and giroux. dna decipher journal | july 2022 | volume 12 | issue 1 | pp. 67-84 67 pitkänen, m., horizontal gene transfer by remote replication? exploration horizontal gene transfer by remote replication? matti pitkänen 1 abstract this article was inspired by the discovery that a horizontal gene transfer (hgt) between eukaryotes is possible. the belief has been that hgt is possible only from prokaryotes to prokaryotes or eukaryotes. the basic obstacles are that the host dna is within the cell nucleus and that dna is tightly bound to chromosomes. the transfer should also occur to germ cells in order to have a lasting effect. the case considered is hgt of antifreezing gene (afg) from herring to smelt, which could have occurred during simultaneous spawning of herring and smelt in the same area. the aft of herring associated with a transposon could have somehow attached to the sperm cell of the smelt and carried by it to the egg of the smelt. vector carrying aft to the sperm cell of smelt is needed and there are only guesses about what it might be. that hgt however occurs, justifies a heretical question. could it be only the genetic information, which is transferred and used to construct dna in the host as a kind of remote replication analogous to quantum transportation? the findings of gariaev and montagnier indeed suggest remote replication and tgd provides a new physics model for it. 1 introduction this article was inspired by a quantamagazine article ”dna jumps between animal species. no one knows how often” (https://cutt.ly/7ukasrp), which described the findings of laurie graham and pete davies published in the article ”horizontal gene transfer in vertebrates: a fishy tale” in trends in genetics [4] (https://cutt.ly/sukamqp). 1. marine life around the arctic and antarctica has evolved many defense mechanisms against the lethal cold. one common adaptation is the ability to make anti-freezing proteins (afps) that prevent ice crystals from growing in blood, tissues and cells. this solution has emerged repeatedly and independently, not just in fish but in plants, fungi and bacteria. afps make possible survival at water temperature, which is by 1 degree c colder than the unprotected freezing point of fish blood and this offers an evolutionary advantage. remark: tgd based general mechanisms possibly associated with heat and cold shock, involving zero energy ontology (zeo) [41][25] in an essential manner, have been considered in the model for the effects of various shock proteins in [60]. the key idea is that the macroscopic counterparts of ordinary state function reduction changing the direction of time change the arrow of time at the level of the magnetic body of the system so that, from the point of view of observer with the standard arrow of time, the system seems to extract energy from the environment instead of dissipating it. 2. herrings and smelts are two groups of fish, which have learned to make afp. the story began when graham discovered that smelt had a protein gene very similar to one of the afg genes of herring. the gene’s introns, stretches of non-coding dna involved also with tes, which in general mutate rather fast, are more than 95 % identical. that both have exactly the same gene coding for afp proteins, is surprising since their ancestors diverged more than 250 million years ago and the afp gene is absent from all species relating to them. somehow the afp gene must have found its way to the genome of smelt. 1correspondence: matti pitkänen http://tgdtheory.com/. address: rinnekatu 2-4 a8, 03620, karkkila, finland. email: matpitka6@gamail.com. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://cutt.ly/7ukasrp https://cutt.ly/sukamqp http://tgdtheory.com/ mailto:matpitka6@gmail.com dna decipher journal | july 2022 | volume 12 | issue 1 | pp. 67-84 68 pitkänen, m., horizontal gene transfer by remote replication? 3. cross breeding of herring and smelt is not possible so that direct horizontal gene transfer (hgt) should have occurred. hgt is known to be possible between prokaryotes (mono-cellulars) and also between prokaryotes and eukaryotes (multi-cellulars). herring and smelt are not rare exceptions: recent studies demonstrate that hgt occurs also in other fish, reptiles, birds and mammals. 4. however, the belief has been that hgt is not possible for eukaryotes (multicellulars) and there are several good arguments in favor of this belief. in the case of bacteria, it is enough for the gene to get through the cell membrane since there is no nucleus and hgt occurs quite generally. the dna of eukaryotic cells is however isolated inside the nuclei and most of the time the dna is tightly bound in chromosomes. gene should also find its way to germ cells in order to have a lasting effect. the transferred gene of the donor should also integrate to the genome of the host. 5. in 2019, the full genome of herring was published. it turned out that the genome contains several afp genes with associated transposable elements (tes). the herring genome contains several copies of these tes but they are absent from other fish with a single exception: the genome of smelt contains only a single afp gene and this gene with similar transposable elements occurs also in the genome of herring. therefore there is little doubt that the hgt has taken place. somehow hgt must be possible. 1. 94 % hgts occur between fishes and only 3 per percent between birds and mammals. therefore the water environment must be part of the explanation. 2. what comes first in mind is spawning. in a situation in which one has sperms and eggs in water, germ cells which are effectively monocellulars apart from the presence of cell nuclei. most of the cells degrade and could produce fragments of dna, say te+afp gene. if the spawning of two species occurs at the same time at the same location, hgt might have taken place from the sperm or egg cells of herring or of their degradation products to the sperm cells of smelt. these would have naturally found their way to the eggs of smelt. the amount of spawn in the sea water is so high that it changes the color of water white: this would increase the probability of hgt. 3. maybe the afp gene of herring has somehow attached to the dna of the smelt sperm cells during spawning. sperm mediated gene transfer is indeed a standard technique of genetic engineering. the challenge is to understand how the afp genes were transported from herring cells to the smelt sperm cells. afp gene is not able to make the travel between cells alone. in standard biology, some vector should have transported the gene between the two cells and one can make only guesses about the mechanism. 1.1 the notions of transposon and horizontal gene transfer the notions of transposon or transposable element (te) and horizontal gene transfer (hgt) will be needed in the sequel. 1.1.1 transposons transposable elements or simply transposons (tes) (https://cutt.ly/huziitw) were discovered by barbara mcclintock. tes are jumping genes, which involve introns were once regarded as ”junk”. the basic operation is cut and paste operation. tes are now known to have several important functions: they make the genome dynamic and affect its identity and size, induce mutations or their reversals, and can also lead to a duplication of pieces of the genome. tes are also involved with the control of gene expression and epigenesis (amusingly, they are still regarded as selfish genes!). issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://cutt.ly/huziitw dna decipher journal | july 2022 | volume 12 | issue 1 | pp. 67-84 69 pitkänen, m., horizontal gene transfer by remote replication? tes are abundant in eukaryotic cells. tes make approximately 64 % of the maize genome, 44 % of the human genome, and almost half of the mouse genome. tes serve as a kind of text editing tool. the te (https://cutt.ly/huziitw) consists of inverted repeats (tes in my terminology) at its beginning and end, and the structural genes between them. there are at least two kinds of tes: class i and class ii. in the human genome 98 per cent of tes class i and the rest are of type ii. 1. class i tes or retrotransposons are first transcribed to rna, and reverse transcriptase often encoded by the te itself catalyzes the reverse transcription of rna to dna, which is then pasted to dna sequence. the text processing analog is copy and paste. retrotransposons are classified into 3 types: • retrotransposons with long terminal repeats (ltrs), which encode reverse transcriptase producing dna from the rna transcribed from te, which is then glued to a dna. retrotransposons are similar to retroviruses. • retroposons, long interspersed nuclear elements (lines). also they encode reverse transcriptase but lack ltrs and are transcribed by dna polymerase ii to rna. • short interspersed nuclear elements (sines) do not encode reverse transcriptase and are transcribed by dna polymerase ii. also retroviruses can be regarded as tes. they can transfer genes between eukaryotic target and host cell. the integrated gene in the host cell is called produces and this transfer can be seen as an eukaryotic analog of the transfer of bacterial tes. 2. class ii tes or dna transposons encode for protein transposase, which they require for excision and insertion. no intermediate rna is produced. the text processing analog is cut and paste. the figure https://en.wikipedia.org/wiki/file:dna_transposon.png of the wikipedia article illustrates the situation. the structure of te is : tsd+tir+gene+tir+tsd. two inverted tandem repeats (tir) flank the transposase gene. two tandem site duplications (tsd) are present on both sides of the insert. transposase makes a staggered cut at the target site with sticky ends and the complex tir+gene+tir is transferred to the new site. gene itself is not duplicated as in the copy and paste process for retrotransposons. tsds are left at the target site. dna polymerase fills in the gaps at the target site leading gradually to long repeating sequences. the insertion sites can be identified by short direct repeats followed by inverted tirs. 3. tes can also replicate. tes can be also classified as autonomous and non-autonomous. autonomous tes can move by themselves whereas non-autonomous tes require other tes to move. 1.1.2 horizontal gene transfer horizontal gene transfer (hgt) (https://cutt.ly/zukted5) occurs mostly in prokaryotes but also in some eukaryotes. hgt tends to occur in extreme environments. diatoms and algae have received genes from bacteria. for eukaryotes hgt to germ cells is required, which makes the process difficult to realize. donor and host tend to be closely associated organisms. hgt from bacteria to chordates occurred shortly after this lineage arose. there are several mechanisms of bacterial hgt. 1. transformation involves three steps: introduction, uptake and expression. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://cutt.ly/huziitw https://en.wikipedia.org/wiki/file:dna_transposon.png https://cutt.ly/zukted5 dna decipher journal | july 2022 | volume 12 | issue 1 | pp. 67-84 70 pitkänen, m., horizontal gene transfer by remote replication? 2. transduction: dna is transferred by virus 3. bacterial conjugation. dna is transformed in cell-to-cell contact. 4. gene transfer agents are viruslike elements coded by the host. transposable elements (te) are often involved with hgt. one speaks of the transfer of horizontal te (htt). te transfer occurs also for eukaryotes. this suggests that tes, which distinguish between prokaryotes and eukaryotes, involve a new transfer mechanism. the mechanism of te transportation requiring a vector carrying the te, has not been identified and this allows us to wonder whether only information could be transferred? 1.2 general constraints on the model consider first general constraints on the model. 1. for eukaryotes, cell and nuclear membranes make hgt difficult if not impossible. the transfer should also occur to germ cells. 2. water must be essential since in other species than fish the process is much rarer. 3. sperm cells are analogous to monocellulars, and the hgt occurs for monocellulars. note however that sperm cells and eggs have a nucleus and chromosomes, which are obstacles for hgt. 4. that hgt would occur during spawning looks a highly plausible hypothesis. this increases the probability of hgt, whatever the mechanism is. sperm mediated transfer would allow to overcome the basic obstacles and the basic properties of tes involved would make possible the integration to the host genome. 5. most of the cells and their dna degrades during the spawning and the resulting dna fragments would also contain afg+te, which could be transferred to the smelt sperm cells. how the te involving the afg from the sperm of herring could be transported to the sperm of smelt? this is not known. according to wikipedia: though the actual mechanism for the transportation of tes from donor cells to host cells is unknown, it is established that naked dna and rna can circulate in bodily fluids. many proposed vectors include arthropods, viruses, freshwater snails, endosymbiotic bacteria and intracellular parasitic bacteria. in some cases, even tes facilitate the transport for other tes. this justifies a heretic question. could it be only the genetic information, which is transferred and used to construct dna in the host as a kind of remote replication analogous to quantum transportation? 2 some key ideas of tgd inspired quantum biology in this section basic notions of tgd inspired quantum biology relevant to the recent article are discussed. the ideas discussed the notion of magnetic body (mb) as a controller of ordinary matter; the hierarchy of effective planck constants assigned to the hierarchy of extensions of rationals defining a hierarchy of phases of ordinary matter behaving like dark matter; galois confinement as a universal mechanism for the formation of bound states; dark realizations of genetic code; communications and control in tgd inspired quantum biology. zero energy ontology (zeo) [41] [25] plays a central role in tgd inspired quantum biology but is not discussed in the sequel. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 1 | pp. 67-84 71 pitkänen, m., horizontal gene transfer by remote replication? 2.1 mb carrying dark matter as controller of ordinary biomatter mb contains dark matter identified, as phases of ordinary matter characterized by eq with a dimension n = heff/h0 serving as a measure of the algebraic complexity of a given space-time region [48, 49], and interpreted as a universal iq. the scales of quantum coherence increase with heff . the layers of mb characterized by the value of n naturally form a master-slave hierarchy in which ordinary matter with the smallest planck constant is at the bottom, and controlled by higher levels. the energies of systems increase with heff and since heff tends to be spontaneously reduced, an energy feed is needed to preserve the distribution of heff : the interpretation is as an analog of a metabolic energy feed. mb acts as a ”boss” controlling ordinary matter and induces self-organization [40]. 2.1.1 anatomy of mb mb has, as its body parts, magnetic flux quanta: flux tubes and flux sheets. there are two kinds of flux quanta. flux can be vanishing, which corresponds to a maxwellian regime. flux can also be nonvanishing and quantized corresponding to a monopole flux. in the monopole case, the magnetic field requires no current for its creation. this option is not possible in the maxwellian world. by fractality of the tgd universe, these flux tubes play a key role at all scales [39]. also the earth’s magnetic field with nominal value of be = .5 gauss has two parts. 1. the monopole flux part corresponds to the ”endogenous” magnetic field bend = .2 gauss and explains the strange effects of elf em radiation on the physiology and behavior of vertebrates [15]. the presence of this part explains the stability of the earth’s magnetic field. this field should have decayed long ago in a maxwellian world since it is generated by currents which disappear.the contribution of the molten iron in the earth’s core to be decays but the changes of the orientation of bend regenerate it [33]. also, magnetic fields that penetrate super-conductors as quantized fluxes and even those of permanent magnets (as opposed to electromagnets) may have a monopole part consisting of flux quanta. 2. the interaction of mb with the gravitational field of earth is discussed in [58]. intriguingly, the metabolic energy currency with the nominal value of .5 ev is rather close to the energy for the escape velocity of a proton. could the transfer of ions from the surface of the earth to mb be a standard process? 2.1.2 communications to and control by mb communication from the biological body (bb) to mb and its control by mb would rely on dark photons, which can transform to ordinary photons with a large heff and vice versa. molecular transitions would represent one form of control. 1. cell membranes could act as generalized josephson junctions generating dark josephson radiation with energies given by the sum ej + ∆ec of ordinary josephson energy ej and the difference ∆ec of cyclotron energies for flux tubes at the two sides of the membrane. the variation of the membrane potential modulates the josephson frequency and codes the sensory information at the cell membrane to a dark photon signal sent to mb. 2. the large effects of radiation at elf frequencies observed by blackman and others [15] could be understood in terms of the cyclotron transitions in bend = .2 gauss if ”h in e = hf is replaced with heff . heff should be rather large and possibly assignable to the gravitational flux tubes with ~eff = ~gr = gmm/v0. for the simplest model, m represents the earth’s mass coupling to the small mass m, and v0 is a parameter with dimensions of velocity expected to have discrete spectrum. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 1 | pp. 67-84 72 pitkänen, m., horizontal gene transfer by remote replication? the energies e = hefff of dark photons should be in the biophoton energy range (visible and uv) characterizing molecular transitions [22, 23]. 3. for the value v0/c ' 2−11, suggested by the nottale’s model for planetary orbits [1], the predicted cyclotron energy scale is 3 orders of magnitude higher than the energy scale of visible photons. several solutions of this problem were considered [57]. the most plausible solution [57, 50] is β0 = v0/c = 1/2 for living matter so that gravitational compton length λgr = gm/β0 equals to schwartschild radius at the surface of earth. and brings nothing new to the original nottale hypothesis. by its higher level of ”iq”, mb would naturally be the master controlling bb by cyclotron radiation possibly via a genome accompanied by dark genome at flux tubes parallel to the dna strands. 1. cyclotron bose-einstein condensates (becs) of bosonic ions, cooper pairs of fermionic ions, and cooper pairs of protons and electrons would appear as dark matter in living systems and the heff = hgr hypothesis predicts a universal cyclotron energy spectrum in the range of bio-photon energies. 2. dark photons may transform to bio-photons [29, 28] with energies covering the visible and uv energies associated with the transitions of bio-molecules. this control of biomolecules implies that remote mental interactions are routine in living matter. eeg signals would represent a particular instance of these communications: without the presence of mb it is difficult to understand why the brain would use such large amounts of energy to send signals to outer space. 3. in zeo, the field body (fb) and mb correspond to 4-d rather than 3-d field patterns and quantum states correspond to quantum counterparts of behaviors and biological functions. conscious holograms could be generated as a result of interference of a dark photon reference beam from mb and a dark photon beam carrying the sensory information. this hologram would be read by mb using the conjugate of the reference beam. in zeo time reversals of these processes also take place. this makes it possible to understand memory as a result of communications with memory mental images. 2.2 galois confinement galois confinement is a universal number theoretical mechanism for the formation of all bound states [55, 54]. galois confinement emerged originally in tgd inspired quantum biology but has become a central theme of also the tgd view about condensed matter. galois confinement provides a purely number-theoretic mechanism for the formation of hierarchies of bound states. 1. galois confinement involves m8−h duality and requires heff > nh0 > h. m8 has an interpretation as an analog of momentum space and the points of x4 ⊂m8 assignable to polynomial p with rational coefficients have interpretation as 4-momentum. monic polynomials p are physically especially interesting [56]. p defines an algebraic extension of rationals with dimension n = heff/h0. the physical interpretation is as a hierarchy of phases of ordinary matter with an increasing value of effective planck constant behaving like dark matter. 2. the roots rn of p correspond to 3-d mass shells m2 = rn in fixed m4 ⊂m8 and x4 itself contains these mass shells and is determined as a deformation of m4 which corresponds to an element of local group su(3) ⊂ g2, where g2 is automorphism group of m8 c having interpretation as complexified octonions. the condition that u(2) ⊂ su(3) leaves the point g(x) invariant implies that one has local cp2 element defining the m8 −h duality.su(3) corresponds to color group physically. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 1 | pp. 67-84 73 pitkänen, m., horizontal gene transfer by remote replication? 3. quark states as solutions of algebraic octonionic dirac equation (all equations are algebraic at m8 side of m8−h duality while everything is differential geometric at h side) correspond to points of m8 assume to correspond to algebraic integers in the extensions of rationals defined by p so that the points carrying quark define what i have called cognitive representation playing a key role in adelic physics [35, 36]. for instance, p-adic variants of the cognitive representations make sense. 4. periodic boundary conditions allow only many-quark states assignable to mass shells for which the total m4 momentum is an ordinary integer (in suitable units defined by the size scale of cd considered) are possible [55, 54]. this is the simplest realization of galois singlet property/confinement. the integer valued total momenta emerge also in the twistorial construction of scattering amplitudes [56]. this is the simplest realization of galois singlet property/confinement. 5. this gives rise to an infinite hierarchy of bound states. one can also consider composite polynomials and if they vanish at origin, the roots of composite polynomials contain also the roots of the functional factors of the composite. this is analogous to conservation of genes. all kinds of states: nucleons, nuclei, photons, etc... , can form galois bound states. it is enough that one deforms the states so that they are not galois singlets with the original galois group or to increase the extension so that they are not galois singlets in the larger extension. from these kinds of states one can form galois singlets. 2.3 dark realizations of genetic code the model of bio-harmony [24, 38, 45, 51, 52] is essential for the tgd based understanding of what might be called emotional intelligence (whose reality is accepted) and its relations with ordinary intelligence. the surprising outcomes are the connection with genetic code and the key role of bioharmony in quantum information processing in living matter. 1. the notion of bioharmony relies on icosahedral and tetrahedral geometries. the representation of the 12-note scale as a sequence of quints, reduced by an octave equivalence (notes differing by octave are experienced as equivalent) to the basic octave, defines the harmony for a given hamiltonian cycle: the 20 allowed 3-chords of the icosahedral harmony correspond to the 20 triangular faces. the symmetries of the harmony are defined by some subgroup (z6,z4, or z2) of the icosahedral group. 2. genetic codons correspond to dark photon triplets (3-chords of light) defined by the triangular faces of an icosahedron and tetrahedron. the counterparts of amino-acids are identified as orbits of 3-chords under the symmetries of a given harmony. any combination of 3 icosahedral harmonies with 20 chords with symmetries z6, z4 and z2 and of the tetrahedral harmony with 4 chords gives a particular bioharmony with 20+20+20+4=64 chords assignable to dna codons. dna codons coding for a given amino acid correspond to the chords at the orbit of the symmetry group. rather remarkably, the numbers of dna codons coding for a given amino acid come out correctly. 3. music expresses and creates emotions. musical harmony codes for moods and emotions as holistic aspects of music. bio-harmony with 64 3-chords, would assign the binary, local, aspects of information to the 6 bits of the codon and its holistic, emotional aspects to the bio-harmony. a chemical representation of the genetic code can thus correspond to several moods represented by bioharmony. in contrast with physicalism, emotions would appear already at the molecular level, and would have physical effects that are not reducible to bio-chemistry. this understanding is not possible without using the notion of mb. the model of bio-harmony requires that the values of bend correspond to those associated with the pythagorean scale definable by the quint cycle. these frequencies correspond to energies that a issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 1 | pp. 67-84 74 pitkänen, m., horizontal gene transfer by remote replication? molecule must have in order to serve as a basic biomolecule. this criterion could select dna, rna, trna, and amino-acids. in the second model of genetic code [37, 34, 38], codons are represented as dark proton triplets assignable to flux tubes parallel to dna strands. 1. the numbers of dark proton triplets turn out to correspond to numbers of dna, rna, trna codons, and amino acids. the numbers of dna and rna codons assignable to a given amino-acid in the vertebrate genetic code are correctly predicted. genes would correspond to sequences of dark proton triplets [42]. 2. dark proton triplet dark codon would be analogous to baryon and galois confinement [47] behaving like a single quantum unit. the n dark codons of a dark gene would, in turn, bind to galois confined states of the galois group of an eq associated with the sequence of codons. an entire hierarchy of confinements is possible. 3. galois confinement can be realized also for dark photon triplets and the sequences of n darkphoton triplets representing genes as dark 3n -photon states. genes could serve as addresses for communications based on dark 3n -photon resonances. for communications between levels with the same value of heff there would be both energy and frequency resonance and for levels with different values of heff only the energy resonance. it is an open question whether dark 3n -photons transform to a single ordinary photon or 3n ordinary photons (biophotons) in dark-ordinary communications. 4. the basic hypothesis is that both dna, rna, trna, and amino acids are paired with their dark analogs, and that energy resonance mediates the interaction between the members of pairs. how could the icosahedra and tetrahedra be realized? why must one glue them together? this looks aesthetically unappealing. however, surprisingly, both icosahedrons and tetrahedrons appear in, perhaps the simplest honeycomb of the hyperbolic 3-space h3 (cosmic time = constant hyperboloid). h3 is also central to special relativity and cosmology [52]. dark genetic code can be realized in terms of both dark protons and photons using this particular tessellation and would be universal. this master tessellation would induce sub-tessellations at the space-time surface, in particular representations of genetic code at magnetic flux tubes. also 2-d and even 3-d representations of genetic code can be considered (i.e. cell membrane and microtubules) [53]. 2.4 communication and control in living matter the tgd inspired model for bioharmony suggests a universal communication and control mechanism based on frequency modulation of dark photon radiation and its resonant receival producing a sequence of pulses. the signal sent by the dna sequence would be resonantly received by a similar dna sequence as a temporal sequence of resonance peaks determined by the modulation. an interesting hypothesis is that nerve pulse patterns are basically produced by this mechanism transforming membrane potential oscillations producing josephson radiation sent to mb and producing pulse sequences initiating nerve pulse pattern at the level of cell membrane. u-shaped flux tubes serve as the basic tools of communication. their reconnection replaces u-shaped flux tubes with pairs of flux tubes between two objects and occurs when a resonant dark photon communication between objects is possible. this requires the same cyclotron energy implying identical cyclotron frequencies if the values of heff are the same: this implies the value of magnetic field and by flux quantization the same thickness of flux tubes. galois confinement allows a generalization replacing u-shaped flux tubes with n-flux tubes along which dark n-photons can propagate and to replace dark photon resonance with m-resonance. this issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 1 | pp. 67-84 75 pitkänen, m., horizontal gene transfer by remote replication? communication and control mechanism would be realized at the level of dna and other biomolecules. the generalization of the notion of genetic code allowing higher dimensional realization of dna generalizes this communication mechanism further. 2.4.1 some applications the proposed general model of communications and control has an impressive number of applications to living matter. 1. the model of water memory involves dark dna [19] [27, 30] assignable to the ordinary dna and also the dark variants of other biomolecules can be involved. the mbs of water clusters can vary the thickness of their u-shaped flux tubes and therefore their cyclotron frequencies. this makes possible recognition of bio-active molecules with mb involving flux tubes with cyclotron frequencies shared by living matter. when the u-shaped flux tube meets a similar flux tube of a bio-active molecule, reconnection takes place and if it leads to dark photon resonance, a long-lived flux tube pair is formed. the bioactive molecule is ”caught”. 2. the mb of water clusters can mimic the mbs of invader molecules and this could give justification for the claimed homeopathic effects. resonant reconnection could be behind water memory, immune system, the claim about homeopathic healing [19], and the bio-catalysis involving the mysterious looking ability of reactants to find each other in dense molecular soup. 3. the most general option is that every polar molecule in living matter is accompanied by a dark nucleon sequence or several of them (as in the case of amino-acids) serving as its ”name””. this would also associate a unique dark nucleon sequence with the mb of dna so that dna-dark dna association would be automatic. the same applies to mrna and trna and amino-acids. the model for the communications also leads to a model for the emergence of language [61, 62]. amazingly, only a few point mutations for relatively few genes seem to have led to human languages and transformed biological evolution to cultural evolution? what happened to these genes? in the biochemistry framework it is difficult to imagine an answer to this question. here tgd could come to the rescue. one can assign a value of heff characterizing the evolutionary level also to genes. the genes with larger heff would serve as control genes and the increase of heff would mean an evolutionary step. perhaps a dramatic increase of heff occurred to foxp2 and some other genes as human language emerged. the fundamental language would be defined by genetic code realized in terms of dark 3n -photons and heff as a measure of algebraic complexity and a universal ”iq” would characterize the realizations of this language. 2.4.2 what is the role of introns and tes? interesting questions relate to the role of introns and transposons (tes), which involve introns besides genes. 1. introns do not express themselves as proteins and their fraction is highest in humans so that the interpretation as junk dna does not look realistic. tgd inspired quantum biology motivates the proposal that the dark genes could express themselves electromagnetically and that remote replication (and the remote variants of transcription and even translation) could rely on this. this leads to a general model for communications and control. 2. the simplest assumption is that all dna related structures and also rna proteins and trna, can ”talk” by applying these communication mechanisms. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 1 | pp. 67-84 76 pitkänen, m., horizontal gene transfer by remote replication? the difference between tes and genes not belonging to tes brings to mind the difference between animals and plants. tes can move and actively control their environment. tes are also involved with epigenesis, that is control of gene expression, and modifications of genes. animals and plants differ also in that animals have a nervous system. could also tes and ordinary genes have an analogous difference? animals are thought to represent a level of evolution higher than plants. could this be true also for tes? a higher value of heff for the mbs of tes would concretize this idea. nervous system in tgd inspired quantum biology means communications to mb by josephson radiation. could one think something like this also now? the relation of tes to genes looks like the relation of a programmer to the program modules of a software. this suggests that the mbs of tes represent a higher level in the heff hierarchy than the mbs of genes. the higher value of heff means also a longer scale of quantum coherence so that tes might be involved also between communications of even different organisms of the same species. 3 is remote replication of dna involved with hgt? in remote replication only the information about te would be transferred and one would have a biological analog of teleportation. 3.1 is replication of the magnetic body behind biological replication? the vision [32] about exclusion zone (ez) like regions discovered by gerald pollack [10, 3, 14, 13] as primordial life forms and facts about water memory and homeopathy [19] lead to a vision about how a primitive immune system might have developed and how the recent genetic code might have emerged. magnetic bodies and dark analogs of bio-polymers should still play a key role in living matter. the basic idea is that the time evolution of the mb is the template for the time evolution of the biological body. in [20] [31] various pieces of evidence for the role of the mb as ”morphogenetic field” is discussed. for instance, the replication of dna and cell would reduce basically to that for corresponding magnetic bodies. replication of the mb is analogous to what happens in the 3-vertex of a feynman diagram. this occurs on several scales. this would make possible dark dna (ddna) replication and copying of ddna to ddna+drna as well as copying of drna to drna+dark protein. replication process should start from the higher levels of dark matter hierarchy and proceed to shorter scales. the basic constraint from zeo is that the time evolutions of magnetic bodies at various levels of the hierarchy are highly unique as preferred extremals connecting initial and final 3-surfaces. for the maxima of vacuum functional only preferred pairs of 3-surfaces are possible. this gives rise to what might be called ”standard behaviors”. also the replication would be this kind of behavioral pattern. in the context of the positive energy ontology it is extremely difficult to understand the predictability of cell replication or the development of the organism from a single cell by repeated cell divisions. remote gene replication [26] might be one application: the model described was actually developed before the idea that the replication of the mb could be the fundamental mechanism. its reversal could be a basic mechanism of bio-catalysis and induce the attachment of the bio-molecules together. also ordinary dna replication could be induced by the same electromagnetic signal as remote replication. 3.1.1 tgd based model for ordinary dna replication consider first a tgd based model for the ordinary replication of dna. 1. assume that the portion of dna promoting dna replication is activated by dark radiation at some frequency and that the promoter region emits radiation with the same frequency. this activates further promoter regions -also in other cell nuclei. the replication process is amplified exponentially. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 1 | pp. 67-84 77 pitkänen, m., horizontal gene transfer by remote replication? the negative feedback is necessary in the general case and is provided by attachment of the produced proteins (basically dark proteins) to the genes making them inactive. 2. this might occur during cell division which might involve irradiation by dark analog of white noise exciting all promoter regions. certainly the coherence of this process is essential and here the higher levels of the dark matter hierarchy would be essential. 3.1.2 remote replication in weak sense gariaev has reported a phenomenon suggesting remote replication in the sense that the dna strands exist in b and the irradiation of the dna at a induces the remote replication in b. in the sequel i will speak about the weak form of remote replication (wrr). we have written together with peter gariaev an article discussing a possible tgd based model for the findings [59]. the work of gariaev [6, 5][7, 11] provides the experimental guidelines. 1. the phantom dna [6] identified as dark nucleon sequences in tgd framework and the evidence for remote activation of dna transcription [5] both discovered by gariaev’s group are assumed as the first two key elements of the model. 2. the notion of wave dna introduced suggests that genes express themselves by em radiation and that genetic code is involved. wave dna should provide a mechanism of information transfer. somehow dna should be encoded to spatial or temporal patterns in turn decoded somehow to dna. gariaev has suggested that the modulation of polarization direction for the radiation propagating along the dna strand could encode for the dna to a temporal pattern. the tgd based model for wrr using existing dna in both a and b is discussed in the article [59] written together with peter gariaev. this discussion and also later developments can be found in [26, 20]. wrr would use existing dna strands in b accompanied by dark dna strands realizing the genetic codons as dark proton triplets. the replication would be remotely induced by the dark radiation from dna at a possibly arriving to b via the mb having contacts with both a and b. this would be a general mechanism of remote mental interactions in the tgd universe. 1. wrr becomes possible if the dark radiation exciting promoter region can leak to other cells or even other organisms. large heff might make this possible. 2. also remote transcription is possible by the same mechanism. actually remote variants of very many basic processes seem to be possible. 3. the observations of peter gariaev’s group about effects of laser light on genes [7, 11] could be interpreted as remote replication in this sense. the analog of this mechanism could make remote transcription and even remote translation at the dark level possible. these processes would induce these processes at the level of biochemistry in accordance with the proposal that biochemistry is quite generally shadow dynamics induced from the level of the mb. 3.1.3 tgd based model for the remote replication in strong sense for the strong form of remote replication (srr) only dna codons are available at b, and under some conditions the presence of dna at a induces the remote replication at b. the findings of the group of hiv nobelist montagnier [8, 9] could be interpreted in terms of srr. in this case the information about dna at a must be transferred from a to b. peter gariaev has reported replication in this sense for years after montagnier’ findings [12]. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 1 | pp. 67-84 78 pitkänen, m., horizontal gene transfer by remote replication? 1. montangier’s experiment involves two chambers a and b. a contains water plus genes and b contains water plus dna nucleotides. there were channels between the chambers but so thin that dna could not get through. also an em field with 7 hz frequency was present. same genes as in a appeared also in b. as if remote replication of genes in a had happened in b. in the tgd framework the presence of 7 hz frequency suggests that mb was present: the identification either as schumann frequency or the cyclotron frequency of k ion in the endogenous magnetic field of .2 tesla is suggestive. 2. polymerase chain reaction (pcr) [2] (see http://tinyurl.com/ybv6mn5l) is the technique used in the experiments of montagnier’s group and in somewhat modified experiment by gariaev’s group involving irradiation of the second test tube by laser light. the findings of montagnier et al [8, 9] can be described in terms of srr. the model for srr has developed gradually and the latest version was discussed in 2020 [46]: this discussion is included also in[26, 20]. the following describes the definition and development of the model for srr. 1. consider two positions a and b. a could be a chamber containing dna strands and b a chamber containing dna codons. assume that dna to be remote-replicated is in a and the codons producing the replica are in b. the dark flux tubes parallel to ordinary dna in a and carrying dark codons would be accompanied by dark planar flux tube bundles transverse to them and leading to b. each flux tube would be analogous to a wave guide for dark photons. in gariaev’s model photons polarized orthogonally to dna would propagate along these. 2. the planar flux tube bundles extending from a to b would have heff > h. the associated spacetime surface which could be seen as a many-valued map from cp2 or its lower-d surface to m4 giving rise to a planar bundle of parallel u-shaped flux tubes in m4 as a quantum coherent structure. dna codons floating in water in b would reconnect to the ends of these u-shaped flux tubes by resonance mechanism and the resulting dna strand in b would be the same as in a. 3. the dark photon signal representing dna sequence could catalyze the formation of conjugate dna in chamber b from existing dna sequences in chamber a serving as a template. since the catalytic interaction of dna polymerase takes place with already existing dna sequence, the simplest possibility is that first some conjugate dna sequences are generated by wrr after which dna polymerase utilizes these sequences as templates to amplify them to original dna sequences. whether the product consists of original dna or its conjugate can be tested. i have also commented on montagnier’s findings from the tgd point of view [27, 30]. 4. the crucial assumption, which is in conflict with the standard picture, is that the dark dna nucleotides (dark protons) serving as building bricks of dna strands do not float freely in water but are already loosely bound to form dark codons. the motivation for this assumption is that one cannot assign the frequencies of the 3-chord with different nucleotides of the codon but only to the entire codon. the difference between ordinary codon and dark codon is like that between spoken and written language: in spoken language word is basically a single entity but in written language it decomposes to letters. interestingly, in written chinese the words decompose to syllables but not to letters. the assumption of effective independence of codons makes sense if the magnetic flux tubes connecting the codons have either value of string tension or larger value of heff than in the dark codon accompanying the ordinary codon. galois confinement allows to generalize the model and gives a justification for the formation of units with increasing complexity and size and behaving quantum coherently. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/ybv6mn5l dna decipher journal | july 2022 | volume 12 | issue 1 | pp. 67-84 79 pitkänen, m., horizontal gene transfer by remote replication? 1. triplets of dark codons can bind to a single dynamical unit by galois confinement [55, 54]. dark codons can in turn bind to dark genes and even to dna strands with a larger galois group. strands can in turn bind to double strands and double strands to chromosomes. even larger structures are possible since galois confinement is hierarchical and new levels correspond to the increase of algebraic complexity associated with the polynomials p defing 4-surfaces in m8 and by m8 − h duality in h [43, 44, 55]. biological evolution could be seen as a number theoretical evolution of galois singlets with increasing size as the algebraic extension and the galois group associated with space-time regions defined by polynomials would increase and become more complex. 2. dark codons represented by 3 dark photons would be galois singlets. from these dark photon genes and even larger dark photon structures can be formed as analogs of dark bose-einstein condensates. photons as particles would be replaced by dark 3n photons. also the planar flux tube bundles would be particle-like entities: 3n -flux tubes forming quantum coherent structures. the entire gene would use this 3n -tentacle to build resonant connections to other similar genes or to build similar genes from dark codons to which ordinary codons would be attached. the communications between dark proton genes with n codons would be by using dark photon genes involving 3n -fold cyclotron resonance selecting the receiver. in communications, the simultaneous frequency modulation would yield the message transformed to a sequence of resonance pulses with temporal durations between pulses determined by the modulation. 3.2 could hgt rely on remote replication in strong sense? transposons are abundant in eukaryotic cells unlike in prokaryotic cells. this suggests that tes could make possible srr and thus allow to circumvent the problems posed by the presence of nuclear membrane and chromosome structure. the reason for this could be simply that the value of heff is so large for the tes (or rather, for their mbs) that it makes coherent activities possible in longer length scales and therefore also the control by mb. mb would have a larger size scale and higher ”iq”. perhaps te is one particular structure behaving like a unit expressing itself in terms of codons realized as dark photon triplets. te would be moving gene as an analog of animal. this structure could be essential for srr. if te has mb with large heff , it (or its mb) would be able to behave autonomously: this is what jumping genes are. genes not associated with tes would be like plants coding for structure and tes would be like animals making the structure dynamical. therefore the question in the concrete example considered is the following: could srr take place and yield a copy of a te involving the afg of herring inside the sperm cell or egg of smelt? the te complex could belong to the sperm cell or egg of herring or their degradation products. 3.3 some reckless speculations it is interesting to try to see this proposal in a more general context. 1. introns were for a long time regarded as ”junk dna”. junk interpretation does not resonate with the fact that human genome has the highest portion of introns and humans have also developed culture and language [61, 62], which in tgd framework would correspond to an evolution of collective consciousness. the reasons for the junk interpretation might have been the repetitive nature of introns and the belief that genes can be expressed only as proteins or rna. tes as jumping genes are now known to have many important functions: they make the genome dynamic and affect its identity and size and can lead to a duplication of pieces of the genome. they are involved with the control of gene expression and epigenesis (amusingly they are still regarded as selfish genes!). issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 1 | pp. 67-84 80 pitkänen, m., horizontal gene transfer by remote replication? dna is interpreted as information theoretically and one can wonder whether tes might play an essential role in the communications at molecular level. magnetic body (mb) and the hierarchy heff = nh0 of effective planck constants are a central element in tgd inspired quantum biology. the larger the value of heff , the longer the quantum coherence length and time scales are and genes could be classified using the value of heff for their mb as a criterion, a kind of universal iq. 2. tes dominate also in the genomes of crops (see https://cutt.ly/5uzgvby and https://cutt. ly/quzg8qa) and trees. it has become clear that trees are not isolated entities but know each other and take this into account in their behavior. forest is not a collection of isolated trees, but a highly refined self-organizing social structure. for instance, conifers have a high amount of tes, which suggests that forest is a conscious entity, which has mb controlling the forest at the level of the ordinary biomatter. concerning crops, at least 35 % of the rice genome % of the sorghum genome [3], and nearly 85 % of the maize genome is made up of transposable elements (tes). it is difficult to avoid seeing an analogy between human community and crop field or forest. could tes make possible communications in the scale of the crop field and forest and make it, or rather, its mb, a conscious intelligent creature? 3. i know that i should overcome the temptation of mentioning crop circles although most mainstream biologists certainly regard crop circles as human made. i cannot. it is also better to immediately confess that i have even written two articles about crop circles about a quarter century ago [17, 18]. i of course know that there is no statute of limitations for this kind of science crimes so that this is not intended to be a defense for what i have done. are the crop circles really human made? some biologists have risked their career by studying them and have found that the folded straws of crops of the crop circle have the appearance of being affected by microwave radiation (think of a tomato, which has exploded in a microwave oven). also light balls have been reported around crop circles as well as glass balls resulting from molten quartz. microwave photons are known to induce ”burning” of water, an effect which is poorly understood. if microwave photons are dark with energy e == hefff , say in biophoton range, this might be understood. one can also create in a microwave oven small light balls consisting of plasma. this raises questions: could tes make possible communications between individual plants of the crop field? could tes make it possible for the mb of the crop field to control the field? could mb of the crop field of some other conscious entity use dark microwave photons to induce the formation of crop circles. could the crop circles be interpreted as an expression of an intelligent conscious entity (not necessarily the mb of crop field) and analogs of patterns of neural activity as i proposed years ago [17, 18]? 4. cannabis is one of humanity’s oldest crops and has a high proportion of tes https://cutt.ly/ 8uzw5v1. could this relate to its dramatic effects on human consciousness? usually these effects are interpreted as being due to the biochemistry of cannabis (https://cutt. ly/8uzet6t). in the tgd framework, the idea that the binding of various psychoactive molecules on synaptic contacts activates flux tubes to mbs, even those in outer space, is attractive. the book ”inner paths to outer space” [16] by rick strassman, slawek wojtowicz, luis eduardo luna and ede frecska inspired an model [21] for the possible mechanism of the action of psychedelics. could also the tes in the dna of cannabis play some role? could they have mbs with especially high heff? could it make sense to speak of co-evolution of the human consciousness and cannabisconsciousness (or crop-consciousness in general) based on interactions not directly conscious to us? received january 16, 2022; accepted july 22, 2022 issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://cutt.ly/5uzgvby https://cutt.ly/quzg8qa https://cutt.ly/quzg8qa https://cutt.ly/8uzw5v1 https://cutt.ly/8uzw5v1 https://cutt.ly/8uzet6t https://cutt.ly/8uzet6t dna decipher journal | july 2022 | volume 12 | issue 1 | pp. 67-84 81 pitkänen, m., horizontal gene transfer by remote replication? references [1] nottale l da rocha d. gravitational structure formation in scale relativity, 2003. available at: http://arxiv.org/abs/astro-ph/0310036. 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[35] pitkänen m. philosophy of adelic physics. in trends and mathematical methods in interdisciplinary mathematical sciences, pages 241–319. springer.available at: https://link.springer. com/chapter/10.1007/978-3-319-55612-3_11, 2017. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.fi/pdfpool/homeoc.pdf http://tgdtheory.fi/pdfpool/lianpb.pdf http://tgdtheory.fi/pdfpool/lianprm.pdf http://tgdtheory.fi/pdfpool/lianprm.pdf http://tgdtheory.fi/pdfpool/biophotonslian.pdf http://tgdtheory.fi/pdfpool/persconsc.pdf http://tgdtheory.fi/pdfpool/persconsc.pdf http://tgdtheory.fi/pdfpool/harmonytheory.pdf http://tgdtheory.fi/pdfpool/zeo.pdf http://tgdtheory.fi/pdfpool/zeo.pdf http://tgdtheory.fi/pdfpool/remotereplication.pdf http://tgtheory.fi/public_html/articles/mont.pdf http://tgdtheory.fi/pdfpool/biophotonslian.pdf http://tgdtheory.fi/public_html/articles/persconsc.pdf http://tgdtheory.fi/public_html/articles/dnabobs.pdf http://tgdtheory.fi/public_html/articles/dnabobs.pdf http://tgdtheory.fi/public_html/articles/morpho.pdf http://tgdtheory.fi/public_html/articles/morpho.pdf http://tgdtheory.fi/public_html/articles/pollackyoutube.pdf http://tgdtheory.fi/public_html/articles/pollackyoutube.pdf http://tgdtheory.fi/public_html/articles/bmaintenance.pdf http://tgdtheory.fi/public_html/articles/bmaintenance.pdf http://tgdtheory.fi/public_html/articles/genecodemodels.pdf https://link.springer.com/chapter/10.1007/978-3-319-55612-3_11 https://link.springer.com/chapter/10.1007/978-3-319-55612-3_11 dna decipher journal | july 2022 | volume 12 | issue 1 | pp. 67-84 83 pitkänen, m., horizontal gene transfer by remote replication? [36] pitkänen m. philosophy of adelic physics. available at: http://tgdtheory.fi/public_html/ articles/adelephysics.pdf., 2017. [37] pitkänen m. about the correspondence of dark nuclear genetic code and ordinary genetic code. available at: http://tgdtheory.fi/public_html/articles/codedarkcode.pdf., 2018. [38] pitkänen m. an overall view about models of genetic code and bio-harmony. available at: http: //tgdtheory.fi/public_html/articles/gcharm.pdf., 2019. [39] pitkänen m. cosmic string model for the formation of galaxies and stars. available at: http: //tgdtheory.fi/public_html/articles/galaxystars.pdf., 2019. [40] pitkänen m. quantum self-organization by heff changing phase transitions. available at: http: //tgdtheory.fi/public_html/articles/heffselforg.pdf., 2019. [41] pitkänen m. some comments related to zero energy ontology (zeo). available at: http:// tgdtheory.fi/public_html/articles/zeoquestions.pdf., 2019. [42] pitkänen m. an overall view about models of genetic code & bio-harmony. dna decipher journal, 9(2), 2019. see also http://tgtheory.fi/public_html/articles/gcharm.pdf. [43] pitkänen m. a critical re-examination of m8 −h duality hypothesis: part i. available at: http: //tgdtheory.fi/public_html/articles/m8h1.pdf., 2020. [44] pitkänen m. a critical re-examination of m8 −h duality hypothesis: part ii. available at: http: //tgdtheory.fi/public_html/articles/m8h2.pdf., 2020. [45] pitkänen m. how to compose beautiful music of light in bio-harmony? https://tgdtheory.fi/ public_html/articles/bioharmony2020.pdf., 2020. [46] pitkänen m. new results about dark dna inspired by the model for remote dna replication. available at: http://tgdtheory.fi/public_html/articles/darkdnanew.pdf., 2020. [47] pitkänen m. results about dark dna & remote dna replication. dna decipher journal, 10(1), 2020. see also http://tgtheory.fi/public_html/articles/darkdnanew.pdf. [48] pitkänen m. a critical re-examination of m8h duality: part i. pre-space-time journal, 11(8), 2020. see also http://tgtheory.fi/public_html/articles/m8h1.pdf. [49] pitkänen m. a critical re-examination of m8h duality: part ii. pre-space-time journal, 11(8), 2020. see also http://tgtheory.fi/public_html/articles/m8h2.pdf. [50] pitkänen m. eeg and the structure of magnetosphere. https://tgdtheory.fi/public_html/ articles/mseeg.pdf., 2021. [51] pitkänen m. galois code and genes. https://tgdtheory.fi/public_html/articles/galoiscode. pdf., 2021. [52] pitkänen m. is genetic code part of fundamental physics in tgd framework? available at: https: //tgdtheory.fi/public_html/articles/tih.pdf., 2021. [53] pitkänen m. meshcode theory from tgd point of view. https://tgdtheory.fi/public_html/ articles/talin.pdf., 2021. [54] pitkänen m. tgd and condensed matter. https://tgdtheory.fi/public_html/articles/ tgdcondmatshort.pdf., 2021. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.fi/public_html/articles/adelephysics.pdf http://tgdtheory.fi/public_html/articles/adelephysics.pdf http://tgdtheory.fi/public_html/articles/codedarkcode.pdf http://tgdtheory.fi/public_html/articles/gcharm.pdf http://tgdtheory.fi/public_html/articles/gcharm.pdf http://tgdtheory.fi/public_html/articles/galaxystars.pdf http://tgdtheory.fi/public_html/articles/galaxystars.pdf http://tgdtheory.fi/public_html/articles/heffselforg.pdf http://tgdtheory.fi/public_html/articles/heffselforg.pdf http://tgdtheory.fi/public_html/articles/zeoquestions.pdf http://tgdtheory.fi/public_html/articles/zeoquestions.pdf http://tgtheory.fi/public_html/articles/gcharm.pdf http://tgdtheory.fi/public_html/articles/m8h1.pdf http://tgdtheory.fi/public_html/articles/m8h1.pdf http://tgdtheory.fi/public_html/articles/m8h2.pdf http://tgdtheory.fi/public_html/articles/m8h2.pdf https://tgdtheory.fi/public_html/articles/bioharmony2020.pdf https://tgdtheory.fi/public_html/articles/bioharmony2020.pdf http://tgdtheory.fi/public_html/articles/darkdnanew.pdf http://tgtheory.fi/public_html/articles/darkdnanew.pdf http://tgtheory.fi/public_html/articles/m8h1.pdf http://tgtheory.fi/public_html/articles/m8h2.pdf https://tgdtheory.fi/public_html/articles/mseeg.pdf https://tgdtheory.fi/public_html/articles/mseeg.pdf https://tgdtheory.fi/public_html/articles/galoiscode.pdf https://tgdtheory.fi/public_html/articles/galoiscode.pdf https://tgdtheory.fi/public_html/articles/tih.pdf https://tgdtheory.fi/public_html/articles/tih.pdf https://tgdtheory.fi/public_html/articles/talin.pdf https://tgdtheory.fi/public_html/articles/talin.pdf https://tgdtheory.fi/public_html/articles/tgdcondmatshort.pdf https://tgdtheory.fi/public_html/articles/tgdcondmatshort.pdf dna decipher journal | july 2022 | volume 12 | issue 1 | pp. 67-84 84 pitkänen, m., horizontal gene transfer by remote replication? [55] pitkänen m. tgd as it is towards the end of 2021. https://tgdtheory.fi/public_html/ articles/tgd2021.pdf., 2021. [56] pitkänen m. about tgd counterparts of twistor amplitudes. https://tgdtheory.fi/public_ html/articles/twisttgd.pdf., 2021. [57] pitkänen m. three alternative generalizations of nottale’s hypothesis in tgd framework. https: //tgdtheory.fi/public_html/articles/mdmdistance.pdf., 2021. [58] pitkänen m. time reversal and the anomalies of rotating magnetic systems. available at: https: //tgdtheory.fi/public_html/articles/freereverse.pdf., 2021. [59] pitkänen m and p. gariaev. quantum model for remote replication. dna decipher journal, 1(3), 2011. see also http://tgtheory.fi/pdfpool/remotereplication.pdf. [60] pitkänen m and rastmanesh r. homeostasis as self-organized quantum criticality. available at: http://tgdtheory.fi/public_html/articles/sp.pdf., 2020. [61] pitkänen m and rastmanesh r. new physics view about language: part i. available at: http: //tgdtheory.fi/public_html/articles/languagetgd1.pdf., 2020. [62] pitkänen m and rastmanesh r. new physics view about language: part ii. available at: http: //tgdtheory.fi/public_html/articles/languagetgd2.pdf., 2020. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://tgdtheory.fi/public_html/articles/tgd2021.pdf https://tgdtheory.fi/public_html/articles/tgd2021.pdf https://tgdtheory.fi/public_html/articles/twisttgd.pdf https://tgdtheory.fi/public_html/articles/twisttgd.pdf https://tgdtheory.fi/public_html/articles/mdmdistance.pdf https://tgdtheory.fi/public_html/articles/mdmdistance.pdf https://tgdtheory.fi/public_html/articles/freereverse.pdf https://tgdtheory.fi/public_html/articles/freereverse.pdf http://tgtheory.fi/pdfpool/remotereplication.pdf http://tgdtheory.fi/public_html/articles/sp.pdf http://tgdtheory.fi/public_html/articles/languagetgd1.pdf http://tgdtheory.fi/public_html/articles/languagetgd1.pdf http://tgdtheory.fi/public_html/articles/languagetgd2.pdf http://tgdtheory.fi/public_html/articles/languagetgd2.pdf introduction the notions of transposon and horizontal gene transfer transposons horizontal gene transfer general constraints on the model some key ideas of tgd inspired quantum biology mb carrying dark matter as controller of ordinary biomatter anatomy of mb communications to and control by mb galois confinement dark realizations of genetic code communication and control in living matter some applications what is the role of introns and tes? is remote replication of dna involved with hgt? is replication of the magnetic body behind biological replication? tgd based model for ordinary dna replication remote replication in weak sense tgd based model for the remote replication in strong sense could hgt rely on remote replication in strong sense? some reckless speculations the strange world of wave genetics dna decipher journal | may 2014 | volume 4 | issue 1 | pp. 30-38 gariaev, p. p., the essence of linguistic & wave genetics in theory and practice issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 30 exploration the essence of linguistic & wave genetics in theory and practice peter p.gariaev * abstract a new branch of biology and medicine, linguistics-wave-enetics, is proposed. this new branch will be based on the understanding of the genetic apparatus as quantum biocomputer (qb) with the characteristic elements of consciousness and thought. the main principles of qb are based on holographic and quantum non-locality. the pilot model of the artificial world is created with laser-based technologies. qb will be capable of the following functions of bio-computation: a) reading wave of genetic information from chromosomes and cell tissue; b) scanning for converting (recording information) laser photons modulated wide-spectrum electromagnetic radiation (mshei) keeping received primary photon of genetic information; c) wave broadcasting genetic information at macro distances; d) the introduction of genetic information in mshei form the body of the recipient in its intracellular water; and e) programmable managment and corrections of metabolism, physiology of the recipient, such as a patient or the old man. this new branch is theoretically substantiated and experimentally demonstrated in our research. key words: linguistic, wave genetics, theory, practice, quantum bio-computation. the current understanding of genetic code may be incomplete when it comes to inheritance and regulations of protein synthesis. this is due to the way it treats the role of the second half of the codons. the 1st 32 codons have been long understood. in the second half of the codons, some codons are not unique, i.e., same codons may encode different amino acids and the stop position in the biosynthesis of proteins. this would imply that the ribosome could err in selecting amino acids and stop positions. however, ribosomes are not wrong. this is the dilemma in the current understanding. however, in reality there is uniqueness. why is the ribosome not wrong? the answer is found in the context of mrna. it is the understanding of the mrna a marketing context of the proteinsynthesizing system allows a biological system to select the exact semantics codon-homonyms and, accordingly, an amino acid, and (or) the stop position. if context is understood to mean the genetic apparatus has a quasi (almost) consciousness, it out on others, meaning, the vectors of the protein code and the ability to adapt organisms to changing environmental conditions in the course of evolution and the ability to turn out pools of test proteins. for a long time, contextoriented role codon-homonyms have been ignored, leading to serious consequences in the use of so-called "transgenic engineering." *correspondence: peter gariaev, ph.d., quantum genetics institue, maliy tishinskiy per. 11/12 25, moscow 123056, russia. email: gariaev@mail.ru mailto:gariaev@mail.ru dna decipher journal | may 2014 | volume 4 | issue 1 | pp. 30-38 gariaev, p. p., the essence of linguistic & wave genetics in theory and practice issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 31 with the development of biotechnology for introducing foreign genes (transgenes) into the chromosomal dna, it is possible to very quickly produce genetically modified foods supply. the problem is the creation of dangerous synthetic cells, the so-called "cynthia," the artificial genome. in such a counterproductive genetic real problem homonymy half codons suddenly acquired a formidable character. misunderstanding and even ignoring strategic role of the codonhomonyms has already led to the protein pathogenicity genetically modified food, sometimes leading to cancer, the strongest allergies. now revealed uncontrolled aggression "cynthia" used for the disposal of oil pollution in the gulf of mexico, the aggression against the whole living, including humans (called "blue plague"). there is another strategic issue. do we understand the basic principles of embryo formation in the adult body? no, they are purely descriptive, and, eventually, wrong. mechanisms of differentiation of stem cells are not understood at the present. dynamic space-time structure of the developing embryo is a gradient wavefronts genomic polarization holograms created by liquid crystals of dna cholesteric chromosome continuum in cell-tissue areas. chromosomes which are sources of coherent light (250 -800nm) are required to read genomic holograms. the second strategic organization of the embryo to the adult organism is a quasi-verbal structure of protein texts translated from the body language of the primary dna-rna texts. that is, genome not only thinks but shows a holographic scheme and provides text (protein) comments. the third strategic organization is instant in time and space coordination of all cells and their genomes through quantum non-locality, i.e., teleporting the wave of genetic-metabolic information between hundreds of billions of cells that form the body. are there experimental support of the above? yes, to a certain extent the phd thesis research of jenny jiang kang (khabarovsk), dr. budagovsky (michurinsk), dr. a.b.burlakova (msu) plus our own experiments. further, luc montagnier and his team have also done important work which confirmed our data on the transmission of genetic wave data by the macro range. montagnier’s experiments were much simpler but no less significant. in view of the importance of the work of luc montagnier, give it a reasonable evaluated in comparison with our own, earlier, research in this area. luc montagnier penetrated into the area of linguistics-wave genetics in science which was launched by russian biologists gurvitch and lyubischevym beklemishev in the 20's 40's of last century. why the results of luc montagnier (and our in significantly more advanced version) demonstrating electromagnetic broadcast dna water structure, including the structure of intracellular water in vivo are important? in medicine a critical situation in terms of non-use of information of huge reserves of "junk" dna, respectively, now real opportunities lcg. the reason the long-term and continued misunderstanding of the main strategic principles information center man his genetic apparatus, which is responsible not only inheritance, but carries a key regulation of metabolism and physiological functions, up to the level of thought and consciousness. the main problem – in misunderstanding, ignoring the contradictions of the genetic code in the model (cim). in fact, it is a blunder not realizing or rather, ignoring the importance of ambiguity coding amino acids of dna decipher journal | may 2014 | volume 4 | issue 1 | pp. 30-38 gariaev, p. p., the essence of linguistic & wave genetics in theory and practice issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 32 the protein code. this led, as mentioned, the so-called transgenic engineering, gave the main result, cheap genetically modified foods. it threatens to collapse all life on earth. the second consequence fallibility of cim the inability of medicine to treat major diseases cancer, aids, tuberculosis, failure to extend the active life of the people and up to 200 years. it can and must make a new branch of biology and medicine linguistics-wave genetics. it is based on an understanding of the genetic apparatus as quantum biocomputer (qb), with the characteristic elements of consciousness and thought. the main principles of qb are based on holographic and quantum non-locality the pilot model of the artificial world is created with qb laser-based technologies. qb is capable of the following functions bio-computation a) reading wave of genetic information from chromosomes and cell tissue, b) scanning for converting (recording information) laser photons modulated wideband electromagnetic radiation (mshei) keeping received primary photon of genetic information, and c) wave broadcast genetic information at macro distances, d) the introduction of genetic information in mshei form the body of the recipient in its intracellular water, e) programmable management correction metabolism, physiology of the recipient, such as a patient or the old man. it is theoretically substantiated and experimentally demonstrated in our publications. our research predates the work of the work of luc montagnier’s team. our first publication was in 2003 in tom.8, № 2, pp. 52-60; p.gariaev, 2003, der wellengenetische code. tattva viveka, № 20, pp.68-73. (in german). luc montagnier “dna waves and water” http://arxiv.org/pdf/1012.5166.pdf . it caused a loud echo in the scientific world, because it contains experimental evidence of distant (high) wave transmission structure of dna directly into the water. luc montagnier team confirmed the main results that we have already proven remote transfer of genetic information running through the wave, a new era in biology, genetics and medicine. this offers real opportunities to manage health and prolong the lives of people, using linguistic and quantum attributes chromosomes, what we talked about and published work for the past 26 years. importantly, about 20 years ago physicist and crystallographer, nikolai bulyonkov, proved that the structure of water can create clusters, from which we can build a "water counterparts, copies" of dna and rna [bulenkov n., 1991, biophysics, t.36, no.2, p.181-243. on the possible role of hydration as a leading integrative factor in the organization of biological systems at different levels of hierarchy]. the below is a summary of the importance of our work and that of montagnier’s group: 1. regeneration of teeth, 2. regeneration of the rectum, 3. regeneration of hair 4. restoration of lost vision, 5. gradual healing of the syndrome of charcot-marie 6. simultaneous normalization condition of a large group of people, http://arxiv.org/pdf/1012.5166.pdf dna decipher journal | may 2014 | volume 4 | issue 1 | pp. 30-38 gariaev, p. p., the essence of linguistic & wave genetics in theory and practice issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 33 7. rapid and complete recovery from a brain hemorrhage and then comes paralysis 8. healing of bone cancer and breast cancer, 9. antidiabetnye effects 10. initial signs of inhibition of aging. and other data that collected and systematized. also note that the potential use of locally convex groupuscule much wider. 11. we have just received the results by permissive wave broadcast one of the genes in the stem cells, and data recovery damaged brain after injury. materials are prepared to patenting and subsequent publication. can these technologies be implemented in practice? consider using our technologies on placenta, cord blood, and photos of healthy children, a person can take mp3-avi record mshei beneficial spin-torsion information (tsi) contained in umbilical cord blood, placenta, photograph of child. what kind of information? to understand this, i would suggest to view lecture of russian scientist, the late academician a.e.akimova, with whom i worked for almost 30 years. be especially careful at 86-89 minute recording. there e. anatoly http://via-midgard.info/news/video/5482-akimov-ae-torsionnye-polya.html says tsi photography. initial record tsi held a special laser that can generate photons that change their polarization (spin state), when probing any objects living cells and tissues, bioactive compounds. the spin states of the atoms, members of the sensed object pictures are recorded in photosensitive layer films and photographs. but this is only the first stage of the recording. this notation is common and very extensive information read from the picture, a kind library. the second stage cannot be separated from the first and is to convert probing and spin the information acquired in the broadband laser photons electromagnetic spectrum (mshei), including radio-wave range. it conversion takes place in accordance with the known physics' theory localized light '. this radio wave range, overwriting photon information, we will digitize and translate into audio format to mp3 initial act of listening to the brain when the patient entered all library, or the most part. the same range of radio wave we are simultaneously translate into a format txt, ie again digitized. then a huge digital digital array handles certain computer program to retrieve its point of reference information that is recorded in avi. this format lets take orienting information in a dynamic and harmonious audio-video images. but the question arises: is the information in this mp3 audio version does not are well-known distortion occurring when encoded signal mp3 format? here we have to say about one of the most important properties of spectra obtained by us. this property is fractal, i.e., self-similarity, multi-scale self-identity. this follows from the fact that the initial act of recording photon information of samples are colliding-beam laser when reflected sensed model laser beam back into the laser cavity, and again comes out on the sample. in fact, we get the photon interferogram (hologram) probing the sample (blood, placenta, metabolites, photographs, etc.) then converted into radio frequency and, ultimately, in the mp3-acoustic hologram. it is important to understand that any hologram is fractal (the reverse is not always true). a fundamental characteristic of holograms, fractals is their information redundancy, noise immunity. therefore the loss of some frequencies in the translation we obtained spectra in the mp3 format does not violate the general bioactive information. hologram, as you know, you can scratch, break into pieces – with this distortion write on it not happening. http://via-midgard.info/news/video/5482-akimov-ae-torsionnye-polya.html dna decipher journal | may 2014 | volume 4 | issue 1 | pp. 30-38 gariaev, p. p., the essence of linguistic & wave genetics in theory and practice issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 34 so, we have the first phase of recording (mp3) and the second (avi), several but little to help navigate the library. the human brain is in this sense self-sufficient. listening to the "library" is perceived by man as noise, because such a reading can be compared with the reading at the same time thousands of volumes of books. further, the possibility of our brain is such that it is able to navigate even to the extent of information. it seems to me, is strategic information, based on the laws of beauty and harmony. these laws are primary and initials in our universe and build living organisms, and man, according to the laws of beauty and harmony. undistorted and concentrated form, these laws are implemented in avi file format. their audio-video series works as an additional corrector health, especially when using different bioactive substances. melodies and avi video files provides a number of harmonic images, rigidly connected to the original spin modulation of probing laser photons, removing information from extracts of ginseng ginseng, propolis, etc. pantokrina and also with photographs of children. our computer programs in various ways the original melody voice to avi files musical instruments and even a choral performance. this is logical – extract our musical information to digest and much more effective in treating this polyphonic version. recently, we found that information avi better use, writing it with bioactive substances listed above and others. so we created bilioteku avi files of this kind and give their patients in addition to mp3 software. use mp3 and avi files should be one by one in the morning and at night. often, the feelings. it is important to know that, as a rule, work with our files, programs, accompanied by some worsening condition. it lasts differently to 3 of 4 days, and is associated with dramatic positive body-core tuning. since the total length of the file is quite large and listen to their tedious succession, then, as an option, you can break program for three or four overlapping with, for example, 1,2,3 3,4,5 5,6,7 etc. for many, a natural question. if the photo is removed spinor information in accordance with the provisions of acad. a.e.akimova, and her record is based on that the grains of silver emulsion is fixed spin states photographed man, what if the original photo is scanned, copied, copied over. and, in general, it is digital. does the unknown with the medical and retarding aging information? remains, and evidence of this is the case with cure patients, including from "incurable" diseases, such as cystic fibrosis. then how to explain it, without falling into the magic at african tribe voodoo shaman? i believe that there is magic, but in the spirit of brilliant book by s.i.doronina "quantum magic” http://www.kodges.ru/13646-kvantovaja-magija.html. the idea of quantum communication photographic image of man with man himself derives from the concept of the universe, as the world hologram. this idea put forward by physicist david bohm and development in relation to human well-known physicist simon berkovich http://www.seas.gwu.edu/~berkov/theory.htm, http://www.nderf.org/berkovich.htm . close to those ideas and teachings of vernardskogo’s noosphere. in our practice, we use children's picture healthy relatives of patients children. for example, we have for the treatment of cystic fibrosis in an 8-year-old girl alice baby photos of her healthy sister, read from it in a special way (using laser), quantum information, and introduced her to a sick child. the disease is fully left. this success is unprecedented. earlier, as mentioned, the disease cf is considered incurable. http://www.kodges.ru/13646-kvantovaja-magija.html http://www.seas.gwu.edu/~berkov/theory.htm http://www.nderf.org/berkovich.htm dna decipher journal | may 2014 | volume 4 | issue 1 | pp. 30-38 gariaev, p. p., the essence of linguistic & wave genetics in theory and practice issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 35 this medical-information-rich sound and worked on alice, cured it from cystic fibrosis. another important factor in favor of the technology we use – is possibility of regeneration of human organs and tissues in situ, that is, in the human body. for those who would like to understand in more detail the physics of laser removal of the wave medical information, we can recommend our articles http://dnadecipher.com/index.php/ddj/article/view/4 our other developments: program matrix disk (cd) or on a flash drive in a format mp3 (audio in frequency range of human speech): 1st program correction of the immune system. 2nd program correction of bone metabolism and circulatory systems, and also the brain. third program oncology. 4th program correction of general metabolism. 5th program option 1 inhibition of aging slows the aging of the current the patient's age. recently, it became clear that it also blocks many types cancer processes. 6th programme 2nd version deceleration of aging. it is based on the recording of the spectrum mshei cells (including stem) of the root of the hair bulb patient. slows aging in the current age of the patient. now all programs are made so that they work individually, i.e., on individual patient and cannot be spread to other people, as in this if do not work and may even be harmful. it is very important to understand these programs do not have any, we create artificial wave designs, which are introduced into the body of people. 1st 5th of the program it records mshei-spin equivalents of various biologically active substances, have long known and proven medicinal preparations of natural origin, for example, extracts of ginseng, eleuterakokka, mummy, royal jelly and bee etc. only 6-i program contains information of your own chromosomes (dna) at the current time. that is, the information of your dna is lead, significantly slowing the aging process. rules listening 1. consecutive record listen and listen in the mornings and evenings. if it is difficult listen to everything, arbitrarily divided into parts (see above), each of them listen week. in the future, you can hear all the parts together. 2. determine which records subjectively feels the best perceived by you to continue to listen to mostly these record (s). http://dnadecipher.com/index.php/ddj/article/view/4 dna decipher journal | may 2014 | volume 4 | issue 1 | pp. 30-38 gariaev, p. p., the essence of linguistic & wave genetics in theory and practice issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 36 3. volumes are to be large. better minimally audible. 4. listen preferably before bedtime or during sleep with headphones or without them. 5. before listening tune in to the program, relax completely, no extraneous thoughts, focus on your own feelings, or just about nothing think. but not necessarily. it works in the background and the business as usual, a little less effectively. 6. in the early days of auditions may be some deterioration of health, as your body is rebuilt, gets rid of toxins. (application of the matrix does not mean the rejection of conventional medicine, but complements it) warning. copy for the mass dissemination of universal program matrices (1st 5th) leads to inactivation of both originals and copies. references 1. gariaev pp, 1994, wave genome. m. ed. the public benefit. 279s. 2. gariaev pp, gorelik vs, kozulin ea shcheglov va, 1994, the two-photon excited luminescence in the solid phase dna. quantum electron., n6, s.603-604. 3. gariaev pp, 1994, dna as source of new kind of god "knowledge", act and facts / impact series, n12, pp ,7-11. 4. maslov mu, gariaev pp, 1994, fractal presentation of natural language texts and genetic code. 2nd international conference on quantitative linguistics "qualico-94". september 20-24. (1994). moscow, lomonosov moscow state university, philological faculty, pp.193-194. 5. gariaev pp, vasiliev aa, berezin aa, 1994, holographic associative memory and information transmission by solitary waves in biological systems. spie the international society for optical engineering. cis selected papers. coherent measuring and data processing methods and devices v.1978, pp.249-259. 6. gariaev pp, vnuchkova va, ga shelepin, komissarov gg, 1994, verbal and semantic modulation resonances of fermi-pasta-ulam as a methodology of entering the command and imagery of the genome. russian journal of physical thought. n1-4, p.17-28. 7. gariaev pp, 1994, the crisis of genetics and genetics of the crisis., russian thought., n1-6, p.46-49. izd. "the common good." 8. trubnikov ba gariaev pp, 1995, looks like a "speech" of dna molecules on a computer program? nature, n1, p. 21 32. 9. berezin aa, gariaev pp, 1995, simulation of electro radiation dna as the carrier of bio-information., 2nd international symposium "mechanisms of action of ultra-low doses of radiation," may 23-26, 1995., moscow. , p.122. (thesis) 10. gariaev pp, leonova ea, 1996, the genetic apparatus as wave control system., international scientific and practical conference "system analysis on the threshold of xxi century: theory and practice.", p.69-78. 11. gotovsky yv, komissarov gg, gariaev pp, 1996, a new technique for diagnosing diseases in seven main acupuncture points (chakras) and equipment for sale. ii international conference "theoretical and clinical aspects and multiresonance bioresonance therapy." center for intelligent medical systems "imedis." moscow, 1996. p.164-169. 12. goldfinches va gariaev pp, 1996, laser-laser interactions and phantom effects in genetic structures. materials of scientific conference with international participation "science on the threshold of xxi century the new paradigm." dna decipher journal | may 2014 | volume 4 | issue 1 | pp. 30-38 gariaev, p. p., the essence of linguistic & wave genetics in theory and practice issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 37 13. gariaev pp, 1996, semiotic ranges of wave genes. materials of scientific conference with international participation "science on the threshold of xxi century the new paradigm." 14. blagodatskikh vi gariaev pp, leonova ea, maslov m., kv shaitan, shcheglov va, 1996, on the dynamics of dislocations in the dna molecule. brief reports on physics. physical institute of russian academy of sciences, n3-4, p.9-14 15. gariaev pp maslov, m., sa reshetnyak, shcheglov va, 1996, the interaction of electromagnetic radiation with information biomacromolecules. "antenna" model. brief reports on physics. physical institute of russian academy of sciences, n1-2, p.54-59. 16. gariaev pp maslov, m., sa reshetnyak, shcheglov va, 1996, model of interaction of electromagnetic radiation with information biomacromolecules., bulletin of physics. physical institute of russian academy of sciences, n1-2, p.60-63. 17. gariaev pp, leonova ea, 1996, revision of the model of the genetic code. consciousness and physical reality., vol. "folium", vol.1, n1-2, p.73-84. 18. sareshetnyak, vashcheglov, viblagodatskikh, ppgariaev, and mumaslov, 1996, mechanism of interaction of electromagnetic radiation with a biosystem, laser physics, v.6, n2, p.621-653. 19. berezin aa, gariaev pp, gorelik vs, reshetniak sa, shcheglov va, 1996, is it possible to create laser based on information biomacromolecules? laser physics, v.6, n6, pp.1211-1213. (and preprint pnlebedev physical institute ras, № 49, 12p.) 20. am agaltsov, pp garyaev, vs gorelik, ia rakhmatullayev, va goldfinches, 1996, two-photonexcited luminescence of genetic structures. quantum electronics, v.23, n2, p.181-184. 21. p.p.garyaev, 1996, epigenetic role of extracellular matrix. hypothesis code hierarchy. inter country correspondence scientific workshop "the use of lasers in science and technology", vyp.8. irkutsk. ed. irkutsk branch of the institute of laser physics sb ras, p.85-107. 22. p.p.garyaev, 1996, information and the wave properties of living systems. the holographic aspect. inter country correspondence scientific workshop "the use of lasers in science and technology", vyp.8. irkutsk. ed. irkutsk branch of the institute of laser physics sb ras, p.137-159. 23. p.p.garyaev, 1996, on the nature of reflexology. modern concepts of the primary mechanisms of acupuncture and acupressure. inter country correspondence scientific workshop "the use of lasers in science and technology", vyp.8. irkutsk. ed. irkutsk branch of the institute of laser physics sb ras, p.188-206. 24. gariaev pp, leonova ea, 1996, a new model of the genetic code. collection of scientific works. academy of medical and technical sciences. branch "of bioengineering and education" at mstu. ne bauman. issue 1. pp.25-34. 25. gariaev pp, tertyshniy gg gotovsky y., 1997, the transformation of light into radio. iii international conference "theoretical and clinical aspects of adaptive resonance and multiresonance therapy." "imedis." moscow. april 18-20, 1997. p.303-313. 26. gariaev pp, macedonian, sn, leonova ea, 1997, biocomputer on genetic molecules as reality. information technology, № 5, p.42-46. 27. gariaev pp, 1997, wave genetic code. monograph. ed. "izdattsentr." 108 pages 28. garber mr, gariaev pp, lebedev ll tertyshny gg, january 5, 1999 the international application for the invention № pct/ru99/00007 «method of analysis of physical objects and device for its implementation" . 29. gariaev pp, tertyshniy gg loshchilov vi, va shcheglov, gotovsky y., 1997, the phenomenon of transition of light in relation to radio biosystems. moscow. collection of scientific works mstu. ne bauman. "actual problems of creation of biotechnological systems." academy of medical and technical sciences. issue 2. c.31-42. 30. pp garyaev, mr garber, ea leonov., 1998, virtual prion gene. friedmann reading. scientific conference. perm, 7-12 september 1998. p.140-142. 31. pp garyaev, mr garber, ea leonova g.g.tertyshny, 1999, the question of the central dogma of molecular biology. consciousness and physical reality, ed. "folium" v.4, № 1, p.34-46. dna decipher journal | may 2014 | volume 4 | issue 1 | pp. 30-38 gariaev, p. p., the essence of linguistic & wave genetics in theory and practice issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 38 32. gariaev pp, tertyshniy gg gotovsky yu.v., leonova ea, 1999, holographic and quantum nonlocality of the genome. 5th international conference "theoretical and clinical aspects of bioresonance and mul'tirezonansnoy therapy." part ii. "imedis", moscow. p.256-272. 33. gariaev pp, tertishny gg, kampf u., muchamedjarov f., leonova ea, 1999, fractal structure in dna code and human language: towards a semiotics of biogenic unformation. 7th international congress of the international association for semiotic studies (iass / ais). tu dresden, october 3-6, 1999. p. 161. 34. gariaev p., tertishniy g. the quantum nonlocality of genomes as a main factor of the morphogenesis of biosystems. / / 3th scientific and medical network continental members meeting. potsdam, germany, may 6-9, 1999. p.37-39. 35. i.v.prangishvili, p.p.garyaev, g.g.tertyshny, e.a.leonova, a.v.mologin, m.r.garber, 2000, genetic structure of both the source and destination of the holographic information. sensors and systems, № 2, p.3-8. 36. i.v.prangishvili, p.p.garyaev, g.g.tertyshny, v.v.maksimenko, a.v.mologin, e.a.leonova, e.r.muldashev, 2000, spectroscopy of microwave radiation localized photons: access to non-local quantum bioinformatics processes. sensors and systems, № 9 (18), p.2-13. 37. peter p. gariaev, boris i. birshtein, alexander m. iarochenko, peter j. marcer, george g. tertishny, katherine a. leonova, uwe kaempf., 2001, the dna-wave biocomputer. "casys" international journal of computing anticipatory systems (ed. dmdubois), liege, belgium, v.10, pp.290-310. 38. peter p. gariaev, george g. tertishny, katherine a. leonova., 2002, the wave, probabilistic and linguistic representations of cancer and hiv. journal of non-locality and remote mental interactions vol. i, № .2 39. p.p.gariaev, g.g.tertishny, a.m. iarochenko, vvmaximenko, ealeonova, 2002, the spectroscopy of biophotons in non-local genetic regulation. journal of non-locality and remote mental interactions vol.i nr. 3 40.http :/ / www.geocities.com/nwbotanicals1/oak/newphysics/metaphysics/bioholography_a.htm 41. jiang kandzhen, bioelectromagnetic field -z. 1993, № 3, p.42-54. patent number 1,828,665. how to change the hereditary characteristics of the biological object and device for directional transmission of biological information. request number 3434801. priority of invention 30.12.1981g., registered 13.10.1992g. login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x dna decipher journal | july 2020 | volume 10 | issue 1 | pp. 01-06 1 pitkänen, m., darwinian or neutral theory of evolution or something else? article darwinian or neutral theory of evolution or something else? matti pitkänen 1 abstract darwinian and neutral theories of evolution represent too competing views about evolution darwinian theory seems to be the winner in the competition. tgd view about evolution represents that the third view in which the random changes correspond to quantum jumps according to zero energy ontology (zeo). the number theoretical vision about tgd predicts that state function reductions tend to increase in statistical sense the number theoretical complexity of the system characterized by the dimension n for an extension of rationals coded by the value of effective planck constant heff/h0 = n serving also as a kind of iq. magnetic body (mb) is the carrier of dark matter in tgd sense and the controlling agent master using biological body as slave. in particular, genome has dark analog realized as dark proton sequences dark nuclei. ordinary genome is its secondary representation and its dynamics is induced from that of dark genome: this view is inspired by the tgd based model for pollack effect. in the sequel i will explain briefly these three views about evolution, and propose a concrete model for how evolution at the gene level could be induced from the reconnections of the flux tubes at the level of dark mb. species preserving mutations would correspond to recombinations of maternal and paternal genomes occurring in meiosis, and evolutionary leaps to addition of new portions to genome realized at the level of dark genome as reconnections and inducing corresponding change at the level of ordinary genome. 1 introduction i learned recently that the so called neutral theory of evolution has been challenged by evidence for dna selection (see http://tinyurl.com/ybhyh6rc). i must admit that i had no idea what neutral theory of evolution means. i had thought that darwinian view based on random mutations and selection of the most adaptive ones is the dominating view. the debate has been about whether darwinian or neutral theory of evolution is correct or is some new vision needed. 1.1 darwinian and neutral theories of evolution darwinian and neutral theories of evolution and their variants represent two different views about evolution. 1. adaptive evolution is the darwinian view. random mutations are generated and organisms with the most adaptive genome survive. one can of course argue that also recombination occurring during mitosis creating germ cells creates new genetic combinations and must be important for the evolution. selection can be either negative (purifying) and eliminate the non-adaptive ones or positive favoring the reproduction of the adaptive ones. one can argue that notions like ”fight for survival” and selection do not fit with the idea about organisms as basically inanimate matter having no goals. also second law poses problems: no evolution should take place, just the opposite. metabolic energy feed induces self-organization but by second law all gradients about which metabolic energy feed is an example, disappear. 1correspondence: matti pitkänen http://tgdtheory.com/. address: rinnekatu 2-4 a8, 03620, karkkila, finland. email: matpitka6@gamail.com. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/ybhyh6rc http://tgdtheory.com/ mailto:matpitka6@gmail.com dna decipher journal | july 2020 | volume 10 | issue 1 | pp. 01-06 2 pitkänen, m., darwinian or neutral theory of evolution or something else? 2. neutral evolution theory was proposed by morita 50 years ago and gained a lot of support because of its simplicity. point mutations for the codons of dna would create alleles. already in darwinian evolution one knows that large fraction of mutations are neutral having not positive or negative effect of survival. morita claims that all mutations are of this kind. there would be no ”fight for survival” or selection. the so called genetic drift, which is completely random process is possible in small populations and can lead to counterpart of selection: it can happen that only single allele remains and is counterpart for the winner in selection. this is purely random and combinatorial effect and in physics one would not call it drift. the first objection is that if one has several isolated small populations, the outcomes are completely random so that in this sense there is no genetic drift. furthermore, there is no reason why further mutations would not bring the disappeared alleles back. second objection is that there would not be no genuine evolution how one can speak about theory of evolution? now the feed of experimental and empirical data is huge as compared to what it was 5 decades ago and it is now known that the neutral theory fails: for instance, varying patterns of evolution among species with different population sizes cannot be understood. it is also clear that selection and adaptions really occur so that darwin was right. 3. the shortcomings of the neutral theory led ohta to propose nearly neutral theory of evolution. mutations can be slightly deleterious. for large populations this leads to a purging of slightly deleterious mutations. for small populations deleterious mutations are effectively neutral and lead to the genetic drift. there is however a further problem: why the rate of evolution varies as observed between different lineages of organisms. 4. one reason for fashionability was that the model was very simple and allowed to compute and predict. only the size of the population and rate for the mutations is enough to predict the future in small populations. the predictions have been poor but this has not bothered the proponents of the neutral evolution theory. as an outsider i see this as a typical example of a fashionable idea: these have plagued theoretical particle physics for four decades now and led to a practically complete stagnation of the field via hegemony formation. simple arguments show that the idea cannot be correct but have no effect. article explains several related notions. 1. it has been possible to determine the mutation rates at the level of individual sites of genome since 2005. only subset of mutations of say cancer cells are functionally important to cancer and they can be identified. this leads to a selection intensity as basic notion. this notion is expected to be very valuable for the attempts to find targeted cure of cancer. 2. neutral theory of evolution assumes that only point mutations matter. theory was therefore completely local at the level of genome and certainly simple! innocent outsider knowing a little bit about biology wonders why the recombination of maternal and paternal chromosomes in meiosis creating the chromosomes associated with germ cells are not regarded as important. this mechanism is non-local at the level of genome and would naturally lead to a selection at the level of individuals of the species. it has been indeed learned that the genetic variation and the rate of recombination in meiosis correlate in given region of genome. this sounds almost obvious to the innocent novice but had to be discovered experimentally. one can however still try to keep the neutral theory of evolution by assuming that recombination is completely random process and there is no selection and adaption contrary to the experimental facts and the basic idea behind the notion of evolution. recombination would bring only an additional complication. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2020 | volume 10 | issue 1 | pp. 01-06 3 pitkänen, m., darwinian or neutral theory of evolution or something else? besides the direct purifying selection and neutral drift there would be recombination creating differences in the levels of variation across the genomic landscape. this leads to the notion of genetic hitchiking. when beneficial alleles are closely linked to neighboring neutral mutations, selection acts as a unit on them. one speaks about linked selection. frequencies of neutral alleles are determined by more than genetic drift but one can speak of neutrality still. linkage of hitchiker to allele beneficial or not is however random. does genuine evolution takes place at all? 3. most of the dna is not expressed as proteins. it would not be surprising if this part of dna could have important indirect role in gene expression or perhaps be expressed in some other manner say electromagnetically. how important role this part of dna has in evolution? there are also transposons inducing non-point like mutations of this part of dna: what is their role. there also proposals that viruses, usually though to be a mere nuisance, could play decisive role in evolution by modifying the dna of host cells. 4. it is now known that up to 80-85 per cent of human genome is probably affected by background selection. moreover, height, skin color blood pressure are polygenic properties in the sense that hundreds or thousands of genes are acting in concert to determine these properties. this strongly suggests that point-like mutations cannot be responsible for evolution and not even recombinations are enough if random. a control of evolution in longer scales seems to be required. this of course relates to the basic problem of molecular biology: what gives rise to the coherence of living matter. mere bio-chemistry cannot explain this. something else perhaps controlling the bio-chemistry is needed. 1.2 criticism of the standard view one can start by criticizing the standard view. 1. is the standard view (to the existent that such exists) about evolution consistent with second law? one can even ask whether standard view about thermodynamics assuming a fixed arrow of time is correct. 2. if mutations and more general changes of genome occur by pure change, can they really lead to a genuine evolution. the notions of selection and survival of fittest are notion, which do not conform with the view about evolution as mere standard physics. a probable motivation for neutral evolution theory has been the attempt to get rid of these notions: physicalism taken to extreme. 3. the reduction of life to bio-chemistry does not allow to understand the coherence of organisms. 4. one can also criticize the reduction of life to mere genetics. (a) genetic dogma does not tell much about morphogenesis. (b) is genetic determinism a realistic assumption? clones of bacterium are know know to have personalities behaving differently under given conditions (see http://tinyurl.com/us7fxlh). (c) most of the genome of the higher organisms consists of dna not transcribed to rna still interpreted as junk by some biologists. what about introns? could there exists other forms of gene expression say electromagnetic. tgd view about evolution represents that the third view in which the random changes correspond to quantum jumps according to zero energy ontology (zeo). the number theoretical vision about tgd predicts that state function reductions tend to increase in statistical sense the number theoretical complexity of the system characterized by the dimension n for an extension of rationals coded by the value of effective planck constant heff/h0 = n serving also as a kind of iq. magnetic body (mb) is the carrier of dark matter in tgd sense and the controlling agent master using biological body as slave. in issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/us7fxlh dna decipher journal | july 2020 | volume 10 | issue 1 | pp. 01-06 4 pitkänen, m., darwinian or neutral theory of evolution or something else? particular, genome has dark analog realized as dark proton sequences dark nuclei. ordinary genome is its secondary representation and its dynamics is induced from that of dark genome: this view is inspired by the tgd based model for pollack effect. in the sequel i will explain briefly the three views about evolution, and propose a concrete model for how evolution at the gene level could be induced from the reconnections of the flux tubes at the level of dark mb. species preserving mutations would correspond to recombinations of maternal and paternal genomes occurring in meiosis, and evolutionary leaps to addition of new portions to genome realized at the level of dark genome as reconnections and inducing corresponding change at the level of ordinary genome. 2 tgd inspired vision about evolution tgd based view about evolution can be seen as a response to these criticisms but actually developed from a proposal for a unification for fundamental interactions and from the generalization of quantum measurement theory leading to a theory of consciousness and generalization of quantum theory itself. 2.1 basic conceptual building bricks the basic assumptions of tgd based view about evolution are following. 1. tgd leads to a new view about space-time and classical fields. in particular, many-sheeted spacetime and magnetic body bring in new element changing dramatically the views about biology. the notion of maxwellian fields is modified. unlike in maxwellian theory any system has field identity, field body, in particular magnetic body (mb) carrying dark matter n tgd sense and in well-define sense at higher evolutionary level as compared to ordinary bio-matter. this expands the standard pairing organism-environment to a triple mb-organism-environment. mb can be seen as the controlling intentional agent and its evolution would induce also the evolution of the ordinary bio-matter. mb carries dark matter as heff/h0 = n phases giving rise to macroscopic quantum coherence at level of mb. mb forces the ordinary bio-matter to behave coherently (not quantum coherently). tgd leads also to a realization of genetic code at the level of dark analog of dna represented as dark proton sequences [4] dark nuclei, which are now essential element of tgd based view about nuclear physics [5]. dark photons are essential for the communications between mb and ordinary bio-matter. also dark photons would realize genetic code with codon represented as 3chord consisting of 3 dark photons. genetic modification would take place at the level of magnetic flux tubes containing dark analog of dna and induce changes of the ordinary genome, which would do its best to mimic dark genome. in particular, the recombination occurring during the meiosis would be induced by the reconnection of the flux tubes of dark genome. 2. number theoretical vision about evolution deriving from the proposal that p-adic physics for various primes combining to what i call adelic physics is second needed element [3]. any system can be characterized by a extension of rationals defining its algebraic complexity. the dimension of extension identifiable in terms of the effective planck constant heff/h0 = n defines evolutionary level as a kind of iq. what is remarkable that n increases in statistical sense since the number extensions with n larger than that for given extension is infinitely larger than that of lower-dimensional extensions. intelligent ones have larger scale of quantum coherence and thus coherence of bio-matter and survive. evolution is directed process forced by number theory alone. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2020 | volume 10 | issue 1 | pp. 01-06 5 pitkänen, m., darwinian or neutral theory of evolution or something else? quantum jumps in the sense of zeo tending to increase n occurring naturally in mitosis generating germ cells lead also to a more intelligent genomes. point mutations could be seen something occurring at the level of ordinary matter rather than being induced by dark matter. 3. zero energy ontology (zeo) is behind the generalization of quantum measurement theory solving the basic problem of standard quantum measurement theory. there are two kinds of state function reductions. ”small” state function reductions (ssfrs) as analogs of weak measurements give rise to the the life cycle of conscious entity self having so called causal diamond (cd) as a correlate. under ssfrs the passive boundary of cd is unaffected as also members of state pairs at it: this gives rise to the ”soul” as unchanging part of self. ”big” state function reductions (bsfrs) correspond to ordinary state function reductions. they change the arrow of time and one can say that self dies and re-incarnates with a reversed arrow of time. this applies in all scales since consciousness and cognition predicted to be universal. in bsfrs the value of heff increases in statistical sense and this gives rise to evolution also at the level of genome. the reversal of the arrow of time allows to see self-organization and metabolism as dissipation in non-standard time direction so that generalization of thermodynamics to allow both arrows of time allows to understand both self-organization and evolution. 2.2 evolution at dna level a possible application would be tgd based model for meiosis and fertilization. the starting point is that recombinations occurring in meiosis represent a fundamental step in evolution preserving the species and point mutations are mostly noise having also negative effects. there are also modification which produce a new species. consider first recombinations. 1. in meiosis bsfr for the dark proton sequences defining dark dna could induce reconnections of parallel maternal and paternal dark proton flux tubes inducing recombination at the level of the ordinary genome. 2. the resulting germ chromosomes or rather their dark variants realized in terms of dark proton sequences would have arrow of time opposite that of chromosomes. they would be in a dormant state analogous to sleep. 3. fertilization involves the pairing of paternal and maternal germ chromosomes and looks almost like time reversal of meiosis. in the proposed picture it would indeed change the arrow of time for the germ chromosomes wake up them. the sequence meiosis replication-meiosisi-division meiosisii would correspond to 4 bsfrs leading to germ cells having dark genome as as time reversal of ordinary genome. remark: one can ask whether also the passive strand of ordinary dna has arrow of time opposite to that of the active strand. recombinations do not change the genome dramatically and can be said to be species preserving. big leaps in evolution change genome more drastically say by adding new genes to yield what might be regarded as a new species. they represent a challenge also for the tgd based view. the big changes should occur at the level of the magnetic body inducing in turn modifications at the level of ordinary genome. the addition of a portion of dna double strand of same length to the end of dna double strand could be a species changing modification. this would not change the earlier genome and could add a new gene for instance. how this change could occur? 1. in tgd dark genome acts as master controlling the ordinary genome playing the role of slave. dark genes correspond to dark proton sequences with possibly subset of protons behaving like neutrons due to the presence of negatively charged bonds between two neighboring protons of the sequence. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2020 | volume 10 | issue 1 | pp. 01-06 6 pitkänen, m., darwinian or neutral theory of evolution or something else? large modification would add to this sequence new dark protons: dark counterpart of nuclear fusion would take place. in water pollack effect [1] [2] would correspond to this process this process and would give rise to charge separation creating negatively charged regions called exclusion zones (ezs) by pollack. there is no reason why this process could not occur also inside cells containing pairs maternal and paternal chromosomes. 2. at the level of dark magnetic body the modification of dark double strand could be realized if it corresponds to a closed monopole flux loop having double helical structure: the conjugate strand would carry the return flux. the addition of a piece of dna would be induced by a reconnection gluing shorter helical flux loop to the end of the helical loop. the chemical counterpart of dark dna would be formed by the pairing of dark codons with the ordinary codons kind of transcription process. 3. the modifications of paternal and maternal dark genomes are expected to occur independently and typically lead to different lengths of paternal and maternal dnas. hence the condition that the paternal and maternal modifications of germ cells are identical (same length) is too strong. can the maternal and paternal dna double strands have different lengths? this seems to be possible. the reconnection process in meiosis does not require same lengths for maternal and paternal genomes. in fertilization the chromosomes of paternal and maternal gametes form pairs and also this allows different lengths. therefore the big leaps in the evolution could correspond to additions of new pieces to maternal an/or paternal dark genome. this picture is of course over-simplified. also addition of dna portions in the middle of genome say adding a new gene or par of gene should be possible at the level of dark matter. also this process should occur by reconnection process at the level of dark matter. also now it seems that the process can occur independently for maternal and paternal chromosomes. references [1] the fourth phase of water : dr. gerald pollack at tedxguelphu. available at: https://www. youtube.com/watch?v=i-t7tcmudxu, 2014. [2] pitkänen m. pollack’s findings about fourth phase of water : tgd view. available at: http: //tgdtheory.fi/public_html/articles/pollackyoutube.pdf, 2014. [3] pitkänen m. philosophy of adelic physics. available at: http://tgdtheory.fi/public_html/ articles/adelephysics.pdf, 2017. [4] pitkänen m. an overall view about models of genetic code and bio-harmony. available at: http: //tgdtheory.fi/public_html/articles/gcharm.pdf, 2019. [5] pitkänen m. solar metallicity problem from tgd perspective. available at: http://tgdtheory. fi/public_html/articles/darkcore.pdf, 2019. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://www.youtube.com/watch?v=i-t7tcmudxu https://www.youtube.com/watch?v=i-t7tcmudxu http://tgdtheory.fi/public_html/articles/pollackyoutube.pdf http://tgdtheory.fi/public_html/articles/pollackyoutube.pdf http://tgdtheory.fi/public_html/articles/adelephysics.pdf http://tgdtheory.fi/public_html/articles/adelephysics.pdf http://tgdtheory.fi/public_html/articles/gcharm.pdf http://tgdtheory.fi/public_html/articles/gcharm.pdf http://tgdtheory.fi/public_html/articles/darkcore.pdf http://tgdtheory.fi/public_html/articles/darkcore.pdf introduction darwinian and neutral theories of evolution criticism of the standard view tgd inspired vision about evolution basic conceptual building bricks evolution at dna level mattipitkanen_v4n3.pdf dna decipher journal | december 2014 | volume 4 | issue 3 | pp. 161-198 161 pitkänen, m. music, biology and natural geometry article music, biology, and natural geometry matti pitkänen 1 abstract in an earlier article i introduced the notion of hamiltonian cycle as a mathematical model for musical harmony and also proposed a connection with biology: motivations came from two observations. the number of icosahedral vertices is 12 and corresponds to the number of notes in 12-note system and the number of triangular faces of icosahedron is 20, the number of aminoacids. this led to a group theoretical model of genetic code and replacement of icosahedron with tetraicosahedron to explain also the 21st and 22nd amino-acid and solve the problem of simplest model due to the fact that the required hamilton’s cycle does not exist. this led also to the notion of bioharmony. this article was meant to be a continuation to the mentioned article providing a proposal for a theory of harmony and detailed calculations. it however turned out that the proposed notion of bioharmony was too restricted: all isosahedral hamilton cycles with symmetries turned out to be possible rather than only the 3 cycles forced by the assumption that the polarity characteristics of the amino-acids correlate with the properties of the hamiltonian cycle. in particular, it turned out that the symmetries of the hamiltonian cycles are the icosahedral symmetries needed to predict the basic numbers of the genetic code and its extension to include also 12st and 22nd aminoacids. one also ends up with a proposal for what harmony is leading to non-trivial predictions both at dna and amino-acid level. 1 introduction for some time ago i introduced the notion of hamiltonian cycle as a mathematical model for musical harmony and also proposed a connection with biology: motivations came from two observations [13],[9, 10]. the number of icosahedral vertices is 12 and corresponds to the number of notes in 12-note system and the number of triangular faces of icosahedron is 20, the number of amino-acids and the number of basic chords for the proposed notion of harmony. this led to a group theoretical model of genetic code and replacement of icosahedron with tetra-icosahedron to explain also the 21st and 22nd amino-acid and solve the problem of simplest model due to the fact that the required hamilton’s cycle does not exist. this article was meant to be a continuation to the mentioned article providing a proposal for a theory of harmony and detailed calculations. it however turned out that the proposed notion of bio-harmony was too restricted: all isosahedral hamilton cycles with symmetries turned out to be possible rather than only the 3 cycles forced by the assumption that the polarity characteristics of the amino-acids correlate with the properties of the hamiltonian cycle. this working hypothesis had to be given up. the fuel of the minirevolution was the observation the symmetries of the hamiltonian cycles (z6, z4, z2) are nothing but the icosahedral symmetries needed to predict the basic numbers of the genetic code and its extension to include also 12st and 22nd amino-acids. thus icosahedral hamiltonian cycles predict genetic code without further assumptions. one also ends up with a proposal for what harmony is leading to non-trivial predictions both at dna and amino-acid level. 1. 3-adicity and also 2-adicity are essential concepts allowing to understand the basic facts about harmony. the notion of harmony at the level of chords is suggested to reduce to the notion of closeness in the 3-adic metric using as distance the distance between notes measures as the minimal 1correspondence: matti pitkänen http://tgdtheory.com/. address: köydenpunojankatu 2 d 11, 10940, hanko, finland. email: matpitka@luukku.com. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2014 | volume 4 | issue 3 | pp. 161-198 162 pitkänen, m. music, biology and natural geometry number of quints allowing to connect them along the hamilton’s cycle. in ideal case, harmonic progressions correspond to paths connecting vertex or edge neighbors of the triangular faces of icosahedron. 2. an extension of icosahedral harmony to tetra-icosahedral harmony was proposed as an extension of harmony allowing to solve some issues of icosahedral harmony relying on quint identified as rational frequency scaling by factor 3/2. this extension is kept also now. one must however give up the idea about correlation between polarity characteristics of proteins and properties of hamilton cycles. one must allow all 11 icosahedral harmonies with symmetries as bio-harmonies: their symmetry groups z6, z4, z2 can be identified as the symmetry groups defined the decomposition of 60 dna codons to 20+20+20 codons in the model of the genetic code. the 4 remaining dnas and amino-acids can be assigned to both tetra-icosahedron and tetrahedron and icosahedron regarded as defining separate genetic codes. this explains why stopping codons can code for the 21st and 22nd amino-acid under some circumstances. tetrahedral code is second member in the hierarchy of genetic codes [?] inspired by the notion of combinatorial hierarchy m(n + 1) = mm(n) = 2m(n) − 1 giving the numbers 2, 4, 7, 64, 2126, ... as numbers of dna codons. the fourth member would correspond to what i called “memetic code”allowing representation of codons as sequences of 21 dnas. it is not known whether the combinatorial hierarchy of mersenne primes continues as hilbert conjectured. 3. the notion of bio-harmony is partially characterized by the triplet n = (n0, n1, n2), characterizing the numbers of 0-, 1-, and 2-quint chords which in turn correspond to dna codons in consistency with the observation that codons indeed correspond to triplets of nucleotides. n-quint chord corresponds to a triangle (face of icosahedron) containing n edges of the hamiltonian. particular bio-harmony requires a selection of a specific hamiltonian cycle from each class of cycles (1 z6 symmetric cycle having n = (2, 12, 6), 2 z4 symmetric cycles n ∈ {(0, 16, 4), (4, 8, 8)}, 3 z2 = zrot 2 with n ∈ {(0, 16, 4), 1(2, 12, 6), (4, 8, 8))} and 5 z2 = zrefl 2 symmetric cycles with (n ∈ {(2, 12, 6), (4, 8, 8)}. note that the are only three different triplets n. 4. the original idea was that the rules of bio-harmony could be applied to amino-acid sequences interpreted as sequences of basic 3-chords. dna would have represented the notes of the music. for given choice of harmony as hamiltonian cycle meaning selection of of 4, 5 or 10 amino-acids coded by the 20 dnas in question, the hypothesis had to be modified by replacing amino-acid sequences with dna sequences. these dna sequences however define also amino-acid sequences identifiable as specific triangle at the orbit of zn defining the dna codons assigned to that amino-acid (there is a singular fiber space structure). together the three 20-plets of dnas define an amino-acid harmony with (4+5+10 =19 chords with tetrahedral extension defining a harmony with 22 chords/amino-acids). hence both dna sequences and amino-acid sequences define “bio-music”. 5. the assumption that harmonic transitions between chords (dna codons) minimize the distance between chords defined by quint-metric leads to highly non-trivial and testable predictions about both dna sequences and amino-acid sequences. negentropy maximization principle (nmp) [8] suggests that evolution favors the generation of harmony which should thus increase in the proposed sense for dna sequences defining particular genes or other functional units of dna during evolution. large quint-distances between subsequent codons/chords would tend to polished out under evolutionary pressures. 6. could icosahedron, tetrahedron, and tetra-icosahedron have direct physical counterparts in living matter? for instance, water molecules form icosahedral clusters and the chlathrates associated with isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2014 | volume 4 | issue 3 | pp. 161-198 163 pitkänen, m. music, biology and natural geometry synaptic contacts have icosahedral symmetries. tetra-icosahedron has 13 vertices with the added vertex representing one notesay ein c-key as note with slightly different frequency to resolve the basic problem of rational number based 12-note scale (12 quints give slightly more that 7 octaves). intriguingly, microtubules consist of basic structures consisting of 13 tubulins with 2 states defining bit: could these bit sequences define representation for the 3-chords and thus representation of sequence of dna codons and realization of genetic code. 7. music is language of emotions and peptides are molecules of emotion as candace pert [j3] expressed it. could bio-harmonies serve as direct correlates for emotions? what is bio-music? a natural tgd inspired guess is that sounds can be replaced with heff = n×h dark photons with low frequencies and having energies in the range of bio-photons (visible and uv range maximally effective biologically) as proposed on basis of some physical facts and theoretical ideas [9]. the frequency spectrum of dark cyclotron photons along magnetic flux tubes would define bio-music as “music of dark light”and bio-harmonies would correlate with emotions and moods. if one can find various icosahedral hamilton’s cycles one can immediately deduce corresponding harmonies. this would require computer program and a considerable amount of analysis. my luck was that the all this has been done. one can find material about icosahedral hamilton’s cycles in web, in particular the list of all 1024 hamilton’s cycles with one edge fixed[1, 2] (this has no relevance since only shape matters). if one identifies cycles with opposite internal orientations, there are only 512 cycles. if the cycle is identified as a representation of quint cycle giving representation of 12 note scale, one cannot make this identification since quint is mapped to fourth when orientation is reversed. the earlier article about icosahedral hamiltonian cycles as representations of different notions of harmony is helpful [13]. the tables listing the 20 3-chords of associated with a given hamilton’s cycle make it possible for anyone with needed computer facilities and music generator to test whether the proposed rules produce aesthetically appealing harmonies for the icosahedral hamiltonian cycles. biologist with access to dna sequences could experiment with dna codons to see whether their are harmonious in the sense that the distance between subsequent chords assignable to dna codons tend to be small in quint metric. note that dna decomposes to pieces corresponding to different hamiltonian cycles (harmonies) so that the comparison is not quite straightforward. 2 what could be the basic principles of harmony? it indeed seems that the idea about definition of notion of harmony in terms of hamiltonian cycles makes sense. 1. chords (major and minor) are labeled by their basic tones and comes either as major or minor. harmony in classical sense requires that the transitions from key to another take place by a small number of quints and that the piece does not wander too far from the major key, say c. if quint corresponds to a step along the edge of the cycle in the direction of its orientation, the notion of tonal closeness corresponds to the closeness in the metric of icosahedron. for instance c,f, and g are commonly used keys in same piece and correspond to 3 subsequent points along hamiltonian cycle. note that the number of ♯s of the key increases by one unit in standard direction and the number of ♭s by one unit in opposite direction. 2. it turns out that major and minor 3-chords and are mapped to each other in the orientation reversal for icosahedral path so that basic moods “happy”and “sad”in music have this orientation as a geometric correlate. the effect of orientation reversal does not actually depend on the icosahedral representation but is implied by quint cycle representation alone. c and half-octave f♯ defining the tritonus interval are the fixed points of the orientation reversal. orientation reversal induces pairings (c ↔ c, f♯ ↔ f♯, g ↔ f , d ↔ b♭, a ↔ d♯, e ↔ g♯, h ↔ c♯. quints of cycle isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2014 | volume 4 | issue 3 | pp. 161-198 164 pitkänen, m. music, biology and natural geometry correspond to the fourths of oppositely oriented cycle so that majors and minors are mapped to each other and one can say that the moods “happy”and “sad”have geometric correlates in the sense that majors and minors are transformed to each other in the reversal of orientation of the cycle. the notion of harmony can be characterized in terms of numbers of basic 3-chords identified as faces of the icosahedron and their neighborhood relationship telling when corresponding chords are near to each other or vertex or face neighbours. the wall neighbours assignable to given edge are expected to be in very special relationship harmonically since they possess a common quint. the basic classification is according to the number n = 0, 1, 2 of edges of cycle contained by them and the triplet n = (n0, n1, n2) for the numbers of faces of various kinds gives the first rough classification. 2-quint chords have common edge and thus two common notes with two 1-quint chords and are therefore natural intermediates in transitions between them. 0-quint chords are tonal loners having no edge neighbours turns out that they involve dissonances since they consists of three notes spanning length of 1 or 3/2 steps (say efg, ef♯g or d♯ef ). maximally symmetric harmony is an exception: 0-quint chords correspond to augmented chords of type ceg♯ with two major thirds. the numbers of three different kinds of face neighbor pairs for the 12 edges of the path serve as an additional classification criterion in terms of the p = (p1,1, p1,2, p2,2) for the numbers pi,j of different kind of edges. note that the neighbor faces of an edge correspond to 3-chords, which possess two common notes and are in this sense close to each other. these numbers characterize the most natural transitions between the chords of the harmony. a further criterion is the distribution of these neighbor pairs along the cycle. 2.1 icosahedral harmonies 1. chords (major and minor) are labeled by their basic tones and comes either as major or minor. harmony in classical sense requires that the transitions from key to another take place by a small number of quints and that the piece does not wander too far from the major key, say c. if quint corresponds to a step along the edge of the cycle in the direction of its orientation, the notion of tonal closeness corresponds to the closeness in the metric of icosahedron. for instance c,f, and g are commonly used keys in same piece and correspond to 3 subsequent points along hamiltonian cycle. note that the number of ♯s of the key increases by one unit in standard direction and the number of ♭s by one unit in opposite direction. 2. it turns out that major and minor 3-chords and are mapped to each other in the orientation reversal for icosahedral path so that basic moods “happy”and “sad”in music have this orientation as a geometric correlate. the effect of orientation reversal does not actually depend on the icosahedral representation but is implied by quint cycle representation alone. c and half-octave f♯ defining the tritonus interval are the fixed points of the orientation reversal. orientation reversal induces pairings (c ↔ c, f♯ ↔ f♯, g ↔ f , d ↔ b♭, a ↔ d♯, e ↔ g♯, h ↔ c♯. quints of cycle correspond to the fourths of oppositely oriented cycle so that majors and minors are mapped to each other and one can say that the moods “happy”and “sad”have geometric correlates in the sense that majors and minors are transformed to each other in the reversal of orientation of the cycle. the notion of harmony can be characterized in terms of numbers of basic 3-chords identified as faces of the icosahedron and their neighborhood relationship telling when corresponding chords are near to each other or vertex or face neighbours. the wall neighbours assignable to given edge are expected to be in very special relationship harmonically since they possess a common quint. the basic classification is according to the number n = 0, 1, 2 of edges of cycle contained by them and the triplet n = (n0, n1, n2) for the numbers of faces of various kinds gives the first rough classification. 2-quint chords have common edge and thus two common notes with two 1-quint chords and are therefore natural intermediates in transitions between them. 0-quint chords are tonal loners having no edge neighbours turns out that they involve dissonances since they consists of three notes spanning length of 1 or isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2014 | volume 4 | issue 3 | pp. 161-198 165 pitkänen, m. music, biology and natural geometry 3/2 steps (say efg, ef♯g or d♯ef ). maximally symmetric harmony is an exception: 0-quint chords correspond to augmented chords of type ceg♯ with two major thirds. the numbers of three different kinds of face neighbor pairs for the 12 edges of the path serve as an additional classification criterion in terms of the p = (p1,1, p1,2, p2,2) for the numbers pi,j of different kind of edges. note that the neighbor faces of an edge correspond to 3-chords, which possess two common notes and are in this sense close to each other. these numbers characterize the most natural transitions between the chords of the harmony. a further criterion is the distribution of these neighbor pairs along the cycle. 2.2 why quints are near to each other harmonically? the naive expectation would be that frequencies near to each other (using half-note as unit) are close to each other. this is not true. their simultaneous presence is experienced as dissonance. this probably has a neurophysiological correlate: in ear the hair cell groups detecting notes which are near to each other in frequency space are overlapping. this explanation does not however tell why the conscious experience is dissonance. the distance measure for notes could be formulated in terms of distance defined as the number of quints connecting them. for quint the distance would be minimal. this measure applies also to chords and allows to understand the basic rule of classical harmony stating that harmonic transitions take place the chords related by quint shift of the basic note (adding either one ♯ or one ♭ to the scale). also the key changes can be understood using the same rule: consider the changes c→ g and c→f as examples. note that in this case the chords have common note. one could of course question the assumption that it is possible to choose the shortest route. the notes obtained by quint scaling are not quite same in the two directions and means that ♯ is the inverse of ♭ in well tempered scale only. could it be that people with absolute ear are able to distinguish between the two slightly differing scales and experience notes of quint c-g as harmonically close when 1 quint connects them but as harmonically distant 11 quints in opposite direction connects them? if cognition is p-adic, one can ask whether the notion of harmony can be formulated in terms of p-adic distance concept. 1. by octave equivalence the scaling by power of two means nothing so that the scalings by 3/2 are equivalent with scalings by 3 and the distance defined by 3-adic norm having values 3k, where k is the number of quints makes sense. the distance defined as quints could be identified the absolute value of k along the quint cycle in the direction in which the distance is shorter. if so, the maximal distance is 6 units. 2. 3-adic measure of distance seems to be rather realistic. quint corresponds to 1 unit distance. half step corresponds to a distance of 5 units and 6 units defines the largest distance and corresponds to the tritonus interval which was forbidden by catholic church. fourth (c-f) corresponds to 1step in opposite direction and 11 steps in standard direction. 3. there is also a problem. second (c-d) corresponds to 3 quints but third (c-e) corresponds to 4 quints and small third to 3 quints in opposite direction. major third would thus correspond to a longer harmonic distance than second. this is a genuine problem, whose solution might be provided by the extension of icosahedral scale to icosatetrahedral one bringing in one additional note which is very near to one of the icosahedral notes and is major or minor third of icosahedral note. 4. could one use the number of icosahedral edges as distance between notes but not as a minimal distance along the hamiltonian cycle but along a minimal edge path along icosahedron? the icosahedral measure of distance would be analogous to a distance between points of object along shortest route in space that it inhabits and depends on harmony characterized by the shape of icosahedral cycle. c and e (and also c and f♯!) could be close to each other in some harmony isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2014 | volume 4 | issue 3 | pp. 161-198 166 pitkänen, m. music, biology and natural geometry and distant from each other in some other harmony. icosahedral geometry would become an active determinant of the harmony. to sum up, music seems to have both 2-adic (octave equivalence) and 3-adic (12-note scale by quint scalings) characters. the principle of tonal unity for classical music stating that modulations of key should not lead too many quints away from the basic chord would have 3-adic interpretation. 2.3 what could be the rules for building a harmony? what guarantees good harmony when one has fixed the key/harmony/representation of particular hamilton cycle? 1. one should pose conditions on the allowed transitions between chords. are there principles would imply harmonic smoothness in geometric sense? could the transitions occur only between chords with a common note? or can one require a common pair of notes? or can one require even a common quint. if so, 0-quint chords would become tonal hermits and could not be used at all. in practice their dissonant character has eliminated them in popular music and much of classical music too. the standard quint and fourth transitions (say c to g and c to f ) are basic examples in which there is only one common note between chords, and it seems that one cannot require more than this in the general case. playing with the chords of bio-harmony however suggests that smooth bossa nova/jazz emotionally ambivalent mood is created if common pair of notes or even quint connects the neighboring chords. the rule is that only transitions between chords with same basic note are allowed. obviously this is too stringent a condition. 2. could 2-quint chords act as bridges between two 1-quint chords? for instance, for the maximally symmetric harmony consisting of disjoint groups of chords related by half-octave scaling the augmented chords (f aug = fac♯ and gaug mapped to each other both by half-octave scaling and reversal of orientation could serve as mediating bridges. 3. could harmonic transitions take place only between neighboring faces of icosahedron (see http: //en.wikipedia.org/wiki/icosahedron) or should it only tend to minimize the quint distance between subsequent chords (this distance vanishes if they have a common note)? for the 0-quint distance harmony, the harmonic movement could be seen as a path in dodecahedron which is dual of icosahedron. in the most general case the transition can take place to both wall and vertex neighbors, whose total number is 3+3=6. in this geometric picture harmony and melody could be seen as duals of each other. dodecahedron is dual of icosahedron and one can ask whether the harmonic motion could correspond to a path at dodecahedron. the vertex of dodecaehdron is pentagon and has 3 neighbours (see http://en.wikipedia.org/wiki/dodecahedron). the above argument gives 3 + 3 > 3 neighbors for the triangle of icosahedron. are the wall neighbors of icosahedral triangle mapped to nearest neighbor vertices? if so then transitions between vertex neighbor triangles should correspond to longer steps at dodecahedron. by the duality triangles of icosahedron correspond to three pentagons associated with the vertex of dodecahedron. the rule that comes in mind is that steps can occur between vertices for which the 3-pentagons have one or 2 common pentagons. note that if the dodecahedral path is hamiltonian cycle, it is unique apart from isometries of dodecahedron and would define a unique chord progression. one can and of course must allow self-intersecting harmonic paths. the condition that there exists a basic chord from which everything begins and to which everything ends implies that closed but in general self-intersecting path is in question. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2014 | volume 4 | issue 3 | pp. 161-198 167 pitkänen, m. music, biology and natural geometry 4. an interesting test for the idea would a computerized generation of random chord sequences satisfying at least one common vertex rule and finding whether they are aesthetically appealing. incidence matrix (see appendix) for the icosahedral (and tetra-icosahedral) triangles wholes element tells how many common vertices two chords have have allows computational construction of the allowed chord sequences as random sequences. 5. for most harmonies 0-quint chords involve dissonances induced by three nearby notes (such as cc♯d) and spanning large number of quints (maximally symmetric harmony has 2 0-quint chords, which do not have dissonances and second harmony with 2 reflection symmetries has no 0-quint chords). also maj7 − , sus4+, and 6 − 1-quint chords have half-note dissonances. dissonances as such are however not un-sesthetical. for instance, bach used them to create a deeply melacholic feeling. 2.4 more general notion of harmony the notion of harmony discussed in previous section is rather conservative and certainly too stringent. 1. 0-quint rule is too restrictive already in chord based music. for instance, the downwards progression am,g,f,e appearing in spanish music and music forms like passacaglia would have chords with 1-quint distance. hence one must consider also a weaker notion of harmonic chord progression according to which this distance is minimized and below some maximum value kmax. one quint would define the smallest non-vanishing maximal distance. one can define incidence matrices for chords with n-quint distance. the incidence matrices with different values of kmax have disjoint sets of non-vanishing elements and the total incidence matrix is their sum. 2. even this is not enough. the direction of step matters for scales (major-minor difference) and it seems to matter also for chord harmonies. the inverse e,f,g,am of the above mentioned progression does not sound harmonic in the same am key. the impression of achieving the goal/ending down to something dictated by fate is lost. instead of efga one often has ef♯g♯a as a melodic progression and with e,b7, e7, am as a chord progression having only 0-quint steps. the rule seems to be that 1-quint steps are possible only downwards in minor harmony, whereas upwards steps are 0-quint steps. climbing slowly upwards by 0-quint steps and falling down by 1-quint steps! could this “gravitational analogy”serve as a metaphor? also the number of n-quint steps between chords matters. the larger this number, the closer the chords are. two 0-quint steps means that chords have two common notes, 1 0-quint stet that they have single common note. the two 1-quint steps for downwards step am−g are between 3rd and 1st (c → g) and 5th and 3rd (e → h). for upwards 0-quint steps e − h7 1-quint steps are between 5th and 5th (h → f♯) and 1st and 1st (e → h). for h7 → e the reversals of these steps occur. for e7 → am one has 3 1-quint steps: (the reversals 1-quint steps e → a and h → e steps and 1 quint step d → a. the laste step seems to be the smallest one in a well-defined sense. for g-f step the number of 1-quint steps is one (c → c): same is true for f-e step (a and e). using geometry language, for chords connected by 1-quint step(s) the mutual orientation of corresponding triangles with shape defined by the intervals involved matters since the number of 1-quint steps depends on the orientation. the notion of chord harmony does not apply as such to polyphonic music with several simultaneous melodies unless on can say that it involves definite chord sequence. one could try to apply the concept of harmony for melody also in this case. the challenge is to guess what harmony for melodies could mean. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2014 | volume 4 | issue 3 | pp. 161-198 168 pitkänen, m. music, biology and natural geometry 1. a conjecture inspired by the genetic code is that the codons defining the allowed melody notes associated with a given chord are in one-one correspondence with the triangles at the orbit of the triangle associated with the chord under the group z6, z4, or z2 characterizing the chord as a counterpart of amino-acid. in table 4.3 the z6 orbits are represented as groups of 6 similar chords (2 for 1-quint chords and 1 for 2-quint chords). in table 4.3 for z4 chords the groups consist of 4 similar chords and in the tables 4.3 and4.3 for z2 harmony the chord groups consist of 2 similar chords. 2. the first guess is that the union of the notes of these chords could define the chords, whose notes are compatible with chord in the time scale shorter than the duration of the chord. note that same triangle can appear at orbits of several chords since the orbits of each group span entire icosahedron. if the note lasts for a duration of several chords, the notes must be consistent with all the chords involved. the rule would explain why fast chromatic sequences (in the scale of chord duration) sound harmonic but slow chromatic sequences do not. for melodies inam key efga is rare and does sound harmonic being often replaced with e,f♯,g♯,a. as far as intervals are considered, this is the inversion d♯, f,g,g♯ of agfe shifted upwards by 5 quints. could one regard progressions (say am,g,f,e) breaking the strongest rule for chord harmony as polyphonic progressions satisfying the rules for polyphonic progressions. to conclude whether the dna inspired notion of harmonic is realistic, one should understand how the sub-groups zn, n = 6, 4, 2 of the isometries of the icosahedron and defining the genetic code act on the hamiltonian cycles. 1. the simplest guess is that these groups are represented as subgroups of z12 (also a subgroup of icosahedral group) representing quint cycle. zn generator would shift the basic note of the chord by 12/n that is 2, 3, 6 quints. 2. zn maps chords of same type to chords of same type only if it is a rotational symmetry of the harmony. for instance, the action of z6 (see fig. 1) on icosahedron allows doublet orbit consisting of xaug type chords, since z3 maps 2 0-quint triangles in the middle of the figure to themselves and reflection group z2 permutes them. 6-element orbits consist of either minor or major chords. more generally, the inspection of the cycles shows that the cyclic orbits of triangle under zn correspond to the orbits of corresponding subgroups of icosahedral group. 3. z2refl maps the shape of the chord to its mirror images and so that the character of the chord can vary along z4 orbits. the rules are (m ↔ m),(6 ↔ 7)). for other chords the character is unaffected. 4. any subgroup of icosahedral isometry group a5 × zrefl 2 having 120 elements must map chords to chords (faces to faces). in particular any zn) even if it is not a symmetry of a particular harmony. the character of the chord is not preserved and the number of quints can change. whether these maps have interpretation in terms of music remains unclear. these considerations forced me to finally realize that the 3 groups z6, z4,and z2 that i had assigned to 20+20+20 dna codons in the model of the genetic code are nothing but z6-, z4-,and z2-symmetric hamilton cycles! the numbers of amino-acids associated with various types would be 3+1=4,5, and 10 (with empty amino-acid included). tetrahedral extension based on gluing of tetrahedron at triangle corresponding to x6 type chord possessed by all zrefl 2 type harmonies would give 3 additional real amino-acids giving altogether real 22 amino-acids as required. this has implications. 1. all 11 hamilton cycles are realized separately as dna level harmonies. amino-acid level harmonies would correspond to selection of three hamiltonian cycles, one for each zn. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2014 | volume 4 | issue 3 | pp. 161-198 169 pitkänen, m. music, biology and natural geometry 2. to get something one must give something away. now one must give up the idea that (4, 8, 8) is special via the corresponding of n-quint property with polarity properties. this is a pity, since just taking this correspondence seriously led to the extension of the icosahedral cycles to tetra-icosahedral ones. fortunately, the extension itself makes sense for all hamiltonian cycles. to understand the action of symmetries one must look how the groups zn act on c major chord. 1. z2 would induce half-octave shift and map c = (c,e,g) to f♯m = f♯,b♭,d♯). the assignment of f♯ -tritonus with c note sounds strange in the ears of harmonic conservatives. 2. z4 would map c = (c,e,g) to a = (a,c♯,e), f♯ = (f♯,b♭, c♯) and d♯ = d♯ = (d♯,g,b♭). these would span 8 notes since e,g,b♭, c♯, appear twice. note that c,e,g,a are the notes assignable to the tetrahedron in the extension of the scale and pentatonic scale corresponds to c,d,e,g,a. z4 orbit does not contain the notes dfg♯h but the orbit of g chord does so. the orbit of c chord plus g7 chord alone define the notes of c major key. 3. z6 would map c and e to the same “impressionistic”6-note scale consisting of 6 whole notes. together with the z6 image of g one obtains all 12 notes of the scale. 3 harmony and biology 3.1 could harmonic principles be realized in biology? the basic idea behind icosahedral harmony is the connection with biology suggested by the fact that the number of icosahedral basic chords is 20 which is also the number of amino-acids. actually there are two additional amino-acids and one ends up to an extension of genetic code by attaching to icosahedron a tetrahedron and thus adding one vertex more. the number of dna codons increases from 60 for icosahedral code to 64 for the real code. the triangle along which icosahedral and tetrahedral aminoacids are attached together corresponds to punct coded by stopping codons. could the application of harmonic principles to biology make sense? the triangles of the icosatetrahedron correspond to amino-acids or dna codons for the amino-acids coded by 20 codons in question. 1. the strictest rule stating that there must be common edge of hamiltonian cycle between the aminoacids/dnas cannot be satisfied since 0-quint amino-acids/dna codons would be total loners and effectively eliminated from biology. 2. the weaker “common edge or vertex” rule could however make sense. a given codon in the group of 20 codons/amino-acid could be followed only by 3+3 different nearest neighbor similar codons/amino-acids. if the first amino-acid is fixed there would be only 6n n-amino-acid sequences instead of 20n sequences. this kind of symmetry would have been probably observed if exact but one can ask whether harmonic pairs could more probable than completely random pairs. 3. a more plausible formulation is obtained by restricting the rule to the level of dna sequences and generalizing it so that it applies also to transitions between harmonies with different symmetries so that a transition between corresponding amino-acids is induces. 4. an even weaker formulations states that the transitions occur with highest probabilities between codons/amino-acids having shortest quint distance. a natural conjecture is that evolution favors the generation of harmony even in the very concrete sense that proteins defined by harmonious chord sequences for bio-harmony are emerge as what darwinist would call the fittest ones. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2014 | volume 4 | issue 3 | pp. 161-198 170 pitkänen, m. music, biology and natural geometry 3.1.1 icosahedral water clusters made from tetrahedra the obvious questions concern the concrete realization of the icosahedron or more generally icosahedral symmetries. one should also understood what the attachment of tetrahedron to icosahedron means (note that tetra-icosahedron is not the the same thing as icosi-tetrahedron, which is archimedean (not platonic) solid (http://en.wikipedia.org/wiki/pentagonal_icositetrahedron)). what comes in mind is attachment of an information molecule to the receptor of cell membrane. water molecules form icosahedral structures and what is amazing to me plato regarded icosahedron as a symbol of water (http://www.interferencetheory.com/blog/files/4a3378c13bcad793a52213a325db7db0-30. html)! the page “water structure and science” of martin chaplin gives illustrations about the rather complex icosahedral structures. icosahedral structures of size 3 nm can be formed from 20 14-molecule tetrahedral water molecule clusters containing 280 water molecules altogether. they can also consists of cyclic pentamers and tricyclo-decamers and also from bi-cyclo-octomers. the 20 tetrahedrons correspond to the faces of the icosahedron and tetra-icosahedron would be formed as tetrahedron is glued to the the icosahedron along one of the faces. the bioharmonies could manifest themselves already in the structure of water molecules. second more plausible option is that they differ only at the level of the magnetic body of the biomolecule. bioharmony suggests that 3 radial magnetic flux tubes or flux tube pairs emerge from each water tetrahedron. hamilton’s cycle could be realized as a flux tube connecting the vertices of the icosahedron and assigning the quint cycle to the cyclotron frequencies (magnetic field strengths). this scenario raises several questions related to the pairings between ordinary dna/amino-acids, their icosahedral representations, and their representations as dark proton sequences. suppose that one takes seriously the idea that genetic code is represented as dark proton sequences with the states of dark protons formed from 3 quarks representing dna and rna codons, amino-acids, and even trna. 1. how dark proton sequences are realized? could one regard them as icosahedral bound states of 20 dark protons? or with a hamiltonian cycle consisting of penta-quarks and representing dark nuclear string? could the icosahedral representation as dark nucleus consisting of 20 dark protons and dodecahedral representation as dark nucleus consisting of 12 dark 5-proton states be dual manners to interpret the state or are they different states related duality. equivalence of the two pictures would require that dark protons are color excited and in an entangled state. 2. could dark proton sequences correspond to sequences of icosahedrons connected by flux tubes connecting the dark protons assignable to the dark proton states assignable to the faces of the icosahedrons? these dark nuclei would be definitely different from those possibly associated with the hamiltonian cycle. 3. what about the tetrahedral part of the genetic code in relation to dark protons sequences? what dark proton states could tetrahedral codons and amino-acids correspond? are they associated with water tetrahedrons representing the faces of the water icosahedron? note the amusing numerological co-incidence that the vertices of tetrahedron have 3 quarks associated with them and those of icosahedron 5 and that the quint for icosahedral edge is replaced with third for tetrahedral edge. 4. could the chords correspond to triplets of cyclotron frequencies for quarks associated with the three flux tubes emanating from the each face of the icosahedron? could the breaking of the rotational symmetry from so(3) to so(2) now actually z3 ⊂ so(2) assumed to occur for dark proton states correspond to the reduction forced by the triangular geometry? 5. how dna -amino-acid correspondence is represented at the level of dark dna? the correspondence should be realized in terms of magnetic flux tube triplets connecting dark dna and dark aminoacid and resonance condition would be essential. when the chords at the orbits of zn are of same type, different dnas correspond to the same chord but with different key. when zrefl 2 is involved, isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2014 | volume 4 | issue 3 | pp. 161-198 171 pitkänen, m. music, biology and natural geometry the two chords at the orbit are not of same type (note the analogy with left and right-handed biomolecules). the only manner to circumvent the problem is to assume that the chord associated with amino-acids magnetic body is that of dna. information is not actually lost in translation, it is only transformed to different kind of information perhaps representing correlates of emotions. 6. could the non-representability of one of the z6 codons as amino-acid have an analog? the fiber space having icosahedron as a base and 3 copies of icosahedron assigned with 3 regions of icosahedron corresponding to zn, n = 6, 4, 2, defines a formal geometric representation of genetic code. could this space represented in terms of water icosahedra? 1. perhaps one should first try to identify the function of water icosahedrons. the first guess is that they serve as local bridges between dark dna/amino-acid sequences and ordinary dna/aminoacid sequences. this would suggest that dark proton of dark dna forms a flux tube connection with the face of water icosahedron dictated by the state of the dark proton : this would take place by flux tube reconnection and cyclotron resonance. water icosahedron in turn couples with the dna/amino-acid like dna conjugate codon with codon so that kind of double helix is formed. 2. what about the pairing of ordinary dna/amino-acids and water icosahedrons? water icosahedron has size of about 3 nm. the size of single dna codon is about 1 nm. single codon corresponds to a twist of 3π/5=36 degrees, an angle closely related to golden mean. if the radius of the helix consisting of water icosahedrons is above some minimal radius which is easy to estimate from an equation for the helix. there are 10 dnas per l(151) = 10 nm and they correspond to a total twist of 3 × 2π. therefore the twist angle is ∆φ = π/5 = 36 degrees for single codon and corresponds to a distance of l(151)/10 = 1 nm). from this one has equation for dna and icosahedron helices as z = kφ, k = h/(6π), h = l(151) = 10 nm (radii are constant). single codon corresponds to a distance s = √ dz2 +r2dφ2∆φ along the water icosahedron helix of radius r accompanying dna helix. one must have s ≥ l = 3 nm defining the size of water icosahedron in order to avoid overlap. deltas ≥ l = 3 nm gives the condition r ≥ 10× √ 2/(3π) nm ≃ 1.5 nm. 3. if the representation of genetic code is possible, do the fiber icosahedrons correspond to subsets of faces of the icosahedron itself? or do they correspond to faces the of icosahedrons in some manner associated with the amino-acid icosahedron. direct attachment is not possible but association could be achieved by connecting the icosahedrons by flux tubes with the tetrahedron at the ends of flux tubes identified as representation of the same amino-acid. this kind of structure with three icosahedra emanating from a given icosahedron could be iterated and one would obtain a fractal structure representing a binary tree. could the water icosahedrons organize in this manner to form larger clusters? what could be the physical correlates of hamilton cycles representing harmonies? 1. could z6, z4 and z2 orbits associated with the hamiltonian cycles be realized even in the structure of water icosahedrons? could they be realized as structures formed by the water tetrahedra and correspond to three separate regions of these icosahedral structures? could one assign to each of the three regions of icosahedron icosahedron such that the attached icosahedron decomposes to the orbits associated with that particular region? could the hierarchy of the icosahedral symmetry breakings have a direct counterpart at the level of the icosahedral structures formed by water molecules? my intuitive feeling is that the answer to these questions is negative. 2. could hamiltonian cycles be realized only at the level of dark photons as quint cycles defined by closed flux tube giving rise to dark nucleus, that is in terms of 3-chords formed by dark photons propagating along flux tubes emanating from the icosahedron? if cyclotron frequencies of dark quarks are in question then the magnetic fields associated with the flux tubes would define the notes. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2014 | volume 4 | issue 3 | pp. 161-198 172 pitkänen, m. music, biology and natural geometry 3. the breaking of zrefl 2 symmetry is of special interest since it could serve as a prebiotic analog of chiral selection and could relate to dark variant of weak physics with effectively massless weak bosons in nano-scales. this would require dark magnetic body. half-octave scaling is second broken symmetry and would have also an analog in zrefl 2 variant of icosahedron. note that 256 variants of the bio-harmony are predicted and could be realized for magnetic body naturally. the presence of electric fields at flux tubes is possible and if the electric and magnetic fields are non-orthogonal, u(1) instanton density is non-vanishing and induces parity breaking. is this breaking associated with zrefl 2 only? 3.1.2 clathrin molecules as icosahedral structures clathrin (http://en.wikipedia.org/wiki/clathrin is a structure appearing at the ends of microtubules and necessary for the transmission of signals between the presynaptic and post-synaptic neurons. clathrin consists of triskelions kind of triangular structures with three spiral like legs and having as symmetries the rotational symmetry group z3 of equilateral triangle. clathrins can form hexagonal planar lattices and pentagonal icosahedral lattices consisting of 12 pentagonal faces the number of vertices of icosahedron . one can associate 3 triskelions with each pentagonal face: this makes 12 × 3 = 36 triskelions altogether. one can regard the centers of the 12 faces as vertices of icosahedron and assign to this structure 20 faces, which are triangles formed by 3 pentagons. if proteins and other molecules attach to the faces of clathrin, one can ask whether each icosahedral triangle of this kind has an address formed by the three notes associated with it and serving as a password: only those molecules, which “know”this password can attach to the face. the realization would be in terms of three u-shaped magnetic flux tubes emerging from the 3 pentagonal faces representing the three notes as frequencies of dark heff = n × h cyclotron photons with elf frequencies but energies of biophotons (in visible and uv range). the binding of the molecule to the face triangle would be preceded by reconnection of u-shaped flux tubes of the clathrin and molecule, by a resonant interaction by dark cyclotron photons, and by an heff reducing phase transition bringing the molecule to the face. 3.1.3 microtubules as music instruments? it has become clear that microtubules have a central role in biology, neuroscience and perhaps also in consciousness theory and the evidence that they are quantum coherent systems is accumulating. could music metaphor could help to understand microtubules? 1. tetra-icosahedron has 13 vertices with the added vertex representing one notesay ein c-key as note with slightly different frequency to resolve the basic problem of rational number based 12-note scale (12 quints give slightly more that 7 octaves). intriguingly, microtubules consist of basic structures consisting of 13 tubulins with 2 states defining bit: could these bit sequences define representation for the 3-chords and thus representation of sequence of dna codons and realization of genetic code. 2. the recent tgd inspired model of microtubules [12],[11] was inspired by the findings of the group of bandyopadhyay (https://www.youtube.com/watch?v=vqngptkpye8) [3],[4] relies on the general vision about bio-communications and control as being based on dark cyclotron photon radiation travelling along magnetic flux tubes. these dark photons have a universal energy spectrum in the range of bio-photons (visible and uv) to which they transform as the value of heff = n × h reduces to its standard value. frequencies would span a wide energy range but eeg frequencies would be of special importance since they would also couple to acoustic vibrations. the precise value of the energy scale of cyclotron photons would be determined by the strength of the magnetic field at flux tube. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2014 | volume 4 | issue 3 | pp. 161-198 173 pitkänen, m. music, biology and natural geometry 3. frequency modulation would be the general manner to code information in living matter: “whale’s song”would be a good metaphor for it. this is assumed in the model for cell membrane as generalized josephson junction: the modulation would be now induced by the variations of generalized josephson frequency by variations of the membrane potential. also microtubules have been proposed to base their communications on frequency modulation. 4. the first possibility coming in mind is that the continually varying microtubule length codes for the frequency [12]. the change of the frequency by say octave would however require quite fast and large variations of microtubule length. neither does this realization conform with the idea that the state of single tubulin corresponds to frequency. microtubule length could also code for the length of the music piece represented by the microtubule serving as a music instrument or musician at the bio-molecular level. it would also the number of microtubular units and thus the size of the orchestra consisting of 13-units. 5. another possibility inspired by the proposal is that magnetic flux tubes form an analog of 3-d grid ideal for communication purposes using 12-note (or actually 13-note) system as a code equivalent with genetic code. also microtubules would involve three kinds of flux tubes [12] defining coordinate grid of cylindrical coordinates: longitudinal, radial and those which rotate along the microtubule. radial flux tubes would be ideal for communication using 13-note system as a realization of genetic code. 6. 13-note system as cyclotron frequency spectrum for given value of heff would be determined by the spectrum of the magnetic field strengths going transversally through the microtubule and each tubulin would correspond to one particular note represented as magnetic field strength. the system would be highly analogous to the system formed by hair cells in cochlear. note would indeed characterize single tubulin molecule rather than entire microtubule as required if one wants to code chords using the two tubulin conformations as a bit. tubulin conformation would determine whether the tubulin serves as a sending/receiving antenna or not. 7. melody in 12-note system can be interpreted as a discretized version of frequency modulation with frequency being piece-wise constant in time. obviously the 13 bit sequences defined by tubulin conformations code for the chords of rational 12-note scale involving a representation of one particular note (the third note of the pythagorean scale) with two slightly different frequencies in order to avoid problems caused by the rational number ratios of frequencies. 13th bit could also serve as a kind of period. also chords could be coded up to a chord with 13 notes so that microtubules would have quite a high representative power. the is an objection against the model. 1. one could argue that a unit consisting of 13 tubulins allows only one octave to be represented. one can of course assume that the magnetic field strengths for subsequent units differ by octave. what makes this interesting is that microtubules allow two variants, called a and b. b type microtubules appear as 13-units since microtubular surface has a gap so that the helical symmetry is broken. for variant a, which is not found in vivo or in vitro, 13-units integrate to form longer helical units. this is assumed in penrose-hameroff model and the experimental absence of a type microtubules is one of the basic objections against penrose-hameroff hypothesis. 2. the tgd inspired proposal is that a type microtubules corresponds to a critical state having therefore an enhanced symmetry and long range correlations: criticality would explain their experimental absence. the experiments of the group of bandyopadhyay support that the critical state is induced by a resonant excitation at specific ac frequencies [12]. long range correlations would mean enchance helical symmetry that is fusion of several 13-units to form a longer helical structure. this structure would allow an interpretation as a structure with frequency spectrum of several octaves isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2014 | volume 4 | issue 3 | pp. 161-198 174 pitkänen, m. music, biology and natural geometry represented coherently in terms of magnetic field strength: the 10 octave span for hearing would mean the integration of 10 microtubule units meaning length scale of order micrometer assuming that tubulin size is of order 10 nm. 3. if the field strength for subsequent units differ by octave, one can argue that for variant b various octaves play their own music without knowing of each other and thus without coherence. in state a they would play together forming something analogous to orchestra or choir. if the octave is same for all 13-units, the phase transition would involve octave scaling of the magnetic field strength at the flux tubes. the flux tube radius should suffer p-adic scaling by an integer number of half-octaves, which makes sense if one accepts p-adic length scale hypothesis. this kind of phase transition have been proposed as candidate for a basic step of energy metabolism since they can store or liberate cyclotron energy as metabolic energy. 4. microtubules could directly couple with both dna and clathrin molecules if they represent 12 note system as a resonant system able to receive the radiation with corresponding frequencies. 12note system and the 3-chord system associated with it could define universal communication code allowing communications between dna, proteins, and microtubules. to sum up, 13-note extension of 12-note system could be seen as a realization of the genetic code in terms of frequencies. the existence of kind of realization was obvious from the beginning and i proposed it in the model of microtubules as quantum antennas during the first years of tgd inspired theory of consciousness [?]. discovering the precise realization of the proposal has however required time. 3.2 could biology help in the understanding of musical harmony? one can also ask whether biology could provide ideas about the notion of harmony. could icosatetrahedral harmony possessing additional 13th note very near to the fourth of basic major chord provide a better view about harmony? 1. the extension of the ideas about harmony to the case of isosatetrahedron is a non-trivial task. if one assumes that the extended hamiltonian cycle is obtained by deforming tetrahedral hamiltonian cycle according to the proposal made earlier, one ends up with a problem since the cycle makes a wedge while making a side track of two steps via the new vertex. the two steps must give one quint so that the new vertex must correspond to either minor or major third of note where it started from (and ended to). this would add to the scale a chord of type cgd a chord of type ceg or ce♭g (plus two other chords containing major or minor third. depending on the orientation of the cycle one would obtain major or minor key. the remarkable feature of icosahedral harmonies is that they often lack a unique basic chord. could it be that the addition of tetrahedron breaks the symmetry and fixes the key? 2. the added third could be slightly different from the icosahedral third and this could allow to resolve the problems due to the fact that quint cycle does not quite close ((3/2)12 = 27 does not hold true exactly. the problems can be of course solved by introducing well-tempered scale defined in terms of powers of 21/12: for this choices the topologically induced by these scalings is same as that induced by real topology in frequency space. algebraically this means introduction of an algebraic extension of rationals. the problem is that persons with absolute ear prefer rational number based scale and experience tempered scale as unaesthetic. the problem with 3-adic distance of notes was already described: the distance is 4 quints for major third (c-e) and 3 quints for minor third (c − e♭). a smaller distance is suggestive for major third. 1. the proposed extension of the scale would break symmetry by bringing a third which is indeed nearest neighbor of the basic note plus two other notes, which are in corners of a 1-quint triangle isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2014 | volume 4 | issue 3 | pp. 161-198 175 pitkänen, m. music, biology and natural geometry in the biological realization. thus chord ceg and and chord containing eg and third note would be introduced. 2. using the general results one can readily find the possible extensions of harmony if one assumes that both major and parallel minor with same number of ♯s or ♭s are obtained. the chord chosen for extension must be cga, which an be seen as part of c6 or am7. if the added vertex corresponds to e one obtains c = ceg, am = cea, and the gea which is part of c6/am7 as also the lost chord. in amino-acid analog cga would become “empty” amino-acid, punct, and would be replaced with gea contained also in c6. one can perform this kind of realization for all 11 harmonies and/or their mirror images. the modification induces symmetry breaking and defines a key which is otherwise not obvious for the icosahedral harmonies. also half-octave symmetry is broken. 3. one can perform the modification also for the inverted harmony. the transformation to reverted harmony x → y corresponds to x7 ↔ y 6 and vice versa so that the presence of x7 type chords in harmony guarantees the existence of the required type extension in the reverted harmony. one can of course define extension also using x7 type chords. this would generate besides ceg two dissonant chords of type gee♭ and cee♭. 4. in maximally symmetric harmony (2,12,6) with 6-fold rotation symmetry, there are as many as 6 manners to perform this modification so that any note of the 6-note scale spanning “impressionistic”octave can define the key. the key is either f,g,a or dm,e, f♯m. the harmony contains however no x7 type chords and since the transition to the reverted harmony acts as x6 ↔ y 7, it does not allow a modification generating both major and parallel minor. there are also other harmonies possessing no x6 type chords such as (2, 12, 6) and bio-harmony (4, 8, 8) with 2-fold rotational symmetry so that the extension in the simplest form can be performed only for their reversals. 5. for the two harmonies with 4-fold reflection symmetry there are 2 manners to perform the modification and modified chords are related by half-octave shift. with the conventions of table ?? the modification introduces key which is either a (f♯m) or d♯ (cm) for both harmonies (second one is bio-harmony (4, 8, 8)). 3.3 about the interpretation of bioharmonies 3.3.1 how ideas about harmony evolved? a brief summary about the evolution of the notion of bio-harmony is in order. 1. the first guess [13] was that amino-acids could be understood as chords of icosahedral bio-harmony characterized by 3-tuples (3,10,7), where the integers tell the numbers of icosahedral triangles with 0,1, or 2 edges of the hamiltonian cycle and identifiable as 3-chords with 0,1,or 2 quints. the interpretation was that 3 0-quint chords correspond to 3 basic polar amino-acids, 10 1-quint chords to the 10 non-polar amino-acids, and 7 2-quint triangles to the 7 polar and acidic polar amino-acids. it turned out however that (3,10,7) does not appear as hamiltonian cycle although it satisfies the necessary conditions. 2. i introduced also a model of genetic code motivated by the properties of the code table suggesting that 60 dna codons are grouped into 3 groups of 20 codons. the idea that dna codons coding for a given amino-acid form an orbit of a subgroup of icosahedral group with order which is not smaller than the number of these dnas and has the aminocid at it. three subgroups z6, z4, and z2 would predict 3 amino-acids coded by 6 codons and two amino-acids coded by 1 codon, 5 amino-acids coded by 4 codons, and 10 amino-acids coded by 2 codons. the total number of codons would be 3× 6+ 2+4× 5+ 10× 2 = 20+ 20+ 20 = 60 rather than 64. the number of doublets is 10 instead isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2014 | volume 4 | issue 3 | pp. 161-198 176 pitkänen, m. music, biology and natural geometry of 9. could one z2 orbit corresponds to punct coded by two stopping codons? but what about the codon triplet associated with ile? something is clearly missing. there is also second problem: a really realistic model of genetic code should include also 21st and 22nd amino-acids (pyl and sec). pyl or pyrrolysine is modification of lys and is basic polar amino-acid so that the number 3 of basic polar amino-acids increases to 4. contrary to the original naive extrapolation sec (selenocystein) is acidic polar rather than non-polar so that the number 2quint triangles increases from 7 to 8. for the properties of amino-acids see http://en.wikipedia. org/wiki/amino_aci{d\sharp}physicochemical_properties_of_amino_acids. the notion of hydrophobicity is discussed at http://en.wikipedia.org/wiki/hydrophobicity_scales). 3. the solution of the problems came from the extension of icosahedral code with tetrahedral code bringing 4 additional codons and 3 amino-acids assigned with the external faces of the tetrahedron (ile, pyl, and some standard non-polar amino-acid), and increasing the number of stopping codons from 2 to 3. this gives 60+3+1=64 codons but one should code also pyl and sec. the solution of the problem would be that stopping codons code also these under some conditions. are dna codons or their mrna counterparts pairing with trnas perhaps their magnetic body modified somehow? for instance, pyl and sec could correspond to icosahedral codons before fusion. after fusion they cease to be coded most naturally because the group orbits containing punct are replaced with those associated with tetrahedron. the 3 ordinary amino-acids represented by tetrahedron are ile, 1-quint amino-acid and 2-quint amino-acid. as fusion is broken temporarily pyl and sec are coded. 4. the geometric correlate for the fusion of the codes is gluing of tetrahedron to icosahedron along one face which corresponds to “empty” face identifiable as punct coded by stopping codons. the icosahedral hamiltonian cycle (4,8,8), which exists as two variants, is extended to (4,10,8) with two new amino-acids. 5. the music analogy for the fusion of tetrahedron is symmetry breaking bringing in a definite key by introducing the major and minor chords as 1-quint chord (but with 2-edges since tetrahedral edges correspond to major and minor thirds). 3.3.2 understanding the misunderstanding this was the picture as i started to work again with the notion of bio-harmony. just when i thought that i understand the notion, i realized that something very essential is missing and even wrong. 1. one could argue that the assumption about the correlation of forms of amino-acid polarity with character of hamiltonian cycle leading to (4,4,8) identification is ad-hoc: why not allow all harmonies? one can also wonder whether the group structure behind the genetic code leading to the identification of sets of dna codons coding for a given amino-acid as orbit of the corresponding triangle can be totally dependent on the group structure emerging from the construction of the hamiltonian cycles. 2. the question whether the group structures associated with genetic code and with the hamiltonian cycles might have something to do with each other leads to the realization of the obvious: the groups involved are the same: z6, z4, and z2! the symmetries of dna are the symmetries of cycles. dna code would be inherent to the hamiltonian cycles, and the triangles of the icosahedron representing the harmony would correspond to dna codons! 20+20+20 icosahedral triangles to 60 genetic codons and 4 icosahedral triangles the remaining 4! the three 20-plets corresponds to 3+1 amino-acids coded by 6 (resp 2) codons, to 5 amino-acids coded by 4 codons, and to 10 amino-acids coded by two codons. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2014 | volume 4 | issue 3 | pp. 161-198 177 pitkänen, m. music, biology and natural geometry by direct inspection of the illustrations of the appendix one can indeed convince oneself that the groups in question map chords to chords of same type and one obtains appropriate number of orbits. this of course follows from group theory alone. 3. one must give up the assumption that the integers n = (n0, n1, n2) correspond to the numbers of the basic polar, non-polar, and polar and acidic polar implying that only n = (4, 4, 8) would define bio-harmony. all hamiltonian cycles with symmetries define bio-harmonies and both zrot 2 and zrefl 2 define z2 type bio-harmonies assignable to 10 amino-acids coded by 2 codons. this is somewhat frustrating outcome, since just this correspondence served as guideline leading to the extension of the icosahedral code. the extension as such is however independent of this identification and needed in order to get the 4 missing dna codons and to understand the coding of 21st and 22nd amino-acids pyl and sec. what do the hamiltonian triplets n then correspond? harmonies correlate with moods in music: maybe the serve as mathematical correlates for emotions and moods. 4. harmonies are not for amino-acids but for dnas coding them. one can however identify aminoacids as specific triangles the orbits and the chords associated with the amino-acids define much more restricted notion of harmony involving one representative of each basic type of chord. perhaps the additional chords correspond to modulations of the harmony. 5. the rules of harmony generalize as such to transitions between dna codons regarded as chords. if chords are near to each other with respect to the distance measured as quints, the transition between the chords respects harmony. one must think that dna codons form a singular fiber space such that the union of fibers for type n gives the space of 20 amino-acids. the “gauge group” zn acting in the fiber is different in the 3 regions of the amino-acid space and the the number of elements in the fiber is factor of n actually equal to n for n 6= 6 and having values 6 and 2 for n = 6. each choice for the 3 hamilton cycles of type zn, n = 6, 4, 2 defines a variant of this fiber space. the distance along the fiber isomorphic to the space of amino-acids is measured as minimal quint distance. note that the dna codons for two different variants of the fiber space need not define same kind of chord so that also given amino-acid can correspond to several different chords. it is enough that the notes of the chords are specified as they indeed are. the zn, n = 6, 4, 2 in turn can correspond to any hamilton cycle with symmetry zn so that for n = 1, 4, 2 one can have 1, 2, 3 + 5 = 8 different fiber spaces. the hierarchy of fibonacci numbers is involved. a hierarchy of symmetry breakings is highly suggestive and leads to increasingly richer harmonies. z6 has maximal symmetry but z4 is not a subgroup of z6 so that only the symmetry breakings z4 → zrot 2 and z4 → zrefl 2 can be said to occur. note that transition between different realizations of the covering space has interpretation as a phase transition and that it could occur at rna rather than dna level. these phase transitions need not relate to the biochemistry but to serve as correlates for emotions and moods. also the degeneracy due to the existence of several dnas coding given amino-acid could have similar interpretation. one can of course play with more stringent scenarios for the transitions between dnas or rnas). for instance, the assumption that transitions can occur between chords of same type, leads to contradiction since the xaug chords of z6 harmony do not appear in any other harmony. in any case, the quint-rule in its various forms is readily testable for dna sequences. 6. an open question concerns the change of the key. the convention of the illustrations is that 1-2 edge corresponds to c-g quint. should one allow the dnas at various sheets of covering space to be in different keys? change of the key could be identified as a rotation by some number of quints. it would change the graph representing icosahedron and change the chords. z12 would allow to realize isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2014 | volume 4 | issue 3 | pp. 161-198 178 pitkänen, m. music, biology and natural geometry all keys. z12 is not however a subgroup of the icosahedral isometries (whereas z6 = z3×zrot 2 is) so that the transformation should be interpreted as a translation in quint space acting as coordinate transformation. the active transformations induced by isometries of icosahedron do not change the graph and would map chords to new ones. the action of z6 is well-defined also for other harmonies than z6 symmetric ones. could the modulations of the basic key correspond to z6 transformations. if so, one would have 6 keys. unfortunately, the most common modulation by quint (g → g) would be missing. the change of key could correspond also the change of the chords defined by the extension to tetraicosahedral harmony. one can choose the chord for extension in several manners for zrot 2 and zrefl 2 and these choices could define the allowed modulations of the key. 7. what would be the correlates of different keys the level of dna? an attractive assumption is that notes are realized in terms of dark photons, which could also transform to ordinary sound since living matter is piezo-electric system. the general hypothesis is that dark photons have universal energy spectrum, which is that of bio-photons. change of key corresponds to a change of frequency scale and would correspond the change of either planck constant or of magnetic field strength the flux tubes of the magnetic body associated with dna codon (or amino-acid perhaps). this would mean that 12-note scale would correspond to 12-note scale for the magnetic fields strength to which cyclotron frequency is proportional or equivalently for the thickness of the flux tube since magnetic flux is quantized if monopole fluxes are in question. 12-note scale could mean in biology a standardization of frequencies used. one must modify the extension of the icosahedral hamiltonian cycles to tetra-icosahedral ones appropriately. 1. the z6 symmetric 20-plet contains 3 6-plets and 1 doublet and the z2 symmetric code contains 10 doublets so that here is one 11 dna doublets in the icosahedral code. “ordinary” amino-acids have only 9 doublets. the interpretation is that the z6 doublet corresponds to ile and the additional ile is coded by tetrahedral codon. the second surplus doublet can be identified as 2 codons coding for punct , “punct”. this gives 4+5+ 10 =19 amino-acid if “punct”is counted. 2. what is lacking is one ile, met, trp, plus pyl and sec. also 4 dna codons are needed. one of them must code ile, one met, one for punct, and one for trp. the tetrahedral codons would thus correspond to orbits of z1. this is actually the only possible subgroup since for the choices zn = 2, 3, 4 the numbers of codons and amino-acids are not correct. this exhausts all dna codons. 3. the only manner to proceed is to assume that icosahedral and tetrahedral codes can appear also as unfused versions. this would naturally occur for zref 2 for which all cycles contain x6 type chord but can occur also for zrot 2 if the completion is done for the inverse harmony and then mapped to the harmony back. the icosahedral code would be as already described. the “free”tetrahedral codes would correspond to z1 and the faces coding punct in the two codes would code for pyl and sec. the fusion of the tetrahedral and icosahedral codes codes gives just the ordinary genetic code so that the proposal is consistent with the proposal that dark proton sequences realize genetic code [7]. 4. note that geometrically this extension means only that the amino-acid sheet of the fiber space is extended by tetrahedral sheet. the challenge is to construct the covering space of the icosahedron representing amino-acids. 1. the has as a local fiber the orbit under zn associated with the amino-acid defining base point. the space of amino-acids decomposes to disjoint regions corresponding to the 20+20-20 dna codons. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2014 | volume 4 | issue 3 | pp. 161-198 179 pitkänen, m. music, biology and natural geometry zn is the analog of gauge group and by symmetry breaking is different from three different regions of amino-acid space. there are 1 × 2 × 8 = 16 variants of this space due to existence of several harmonies for given symmetries. there are actually only three different options for n given by n = (0, 16, 4), (2, 12, 6, and (4, 8, 8). 2. the zn orbits of the three disjoint amino-acid regions (containing 3+1=4, 5, resp. 10 amino-acids) intersect each other. the challenge is to choose the representative amino-acids from the orbits of zn in such a manner that the chosen amino-acids belong to the three disjoint regions. it remains to be proven that this is possible. one must also understand how uniquely this can be done. 3. one could think of choosing a set p2 of 10 representatives from the 10 orbits of z2 related by 6-quint scaling along hamiltonian cycle. the 3+1+5=9 amino-acids associated with z6 and z4 would belong to the mirror images p (s) of this 10-element set. p (s) decomposes into set p6 of 3+1 triangles and set p4 of 5 triangles and there are 2-element, 4-element and 6-element orbits connecting the elements of the sets p2, p4, and p6. the following observations lead to a rather detailed and surprisingly simple picture. 1. the key observation is that the construction of the covering space that is identifications of aminoacids at the orbits of the groups involved depends only on whether the choice of z2 as zrot 2 or zrefl 2 ! thus the two codes (ordinary one and code with pyl and sec coded by stop codons) are distinguished by different dna-amino-acid covering spaces. the details of the hamiltonian cycle do not matter. only the structures and mutual relationships of the groups z6 = z3 × zrefl 2 , z4 = zrot 2 ×zrefl z and zrot 2 and zrefl 2 matter. furthermore, the actions of the groups zrot 2 , z3 and zrefl 2 determine also the actions of z6 and z4. only zrot 2 and z3 are non-commuting actions. 2. one can decompose amino-acids to 10 pairs of zref 2 orbits and visualize the 20 codons involved as two layers on top of each other such that two on top of each other correspond to the same 2-orbit 2 boxes on top of each other. the choice of the two layers is not unique since one can permute the members of any vertical box pair. 3. by a suitable choice of the members of vertical box pairs one can arrange that z3 and zrot 2 act along the two layers horizontally. zrot 2 orbits divide each layer to 5 pairs of horizontal boxes. one can also permute the vertical pairs horizontally in such a manner that the 5+5 zrot 2 orbits correspond to neighboring horizontal boxes along upper and lower layer giving 2+2+2+2+2 decomposition. this still leaves the possibility to permute these 5+5 horizontal pairs defining 4-orbits of z4 horizontally with each other. simply by drawing one find that z3 orbits divide each layer to 3 triplets and 1 singlet and by a suitable choice z3 singlets correspond to the 10th box on the right for both layer. the z3 orbits and zrot 2 orbits overlap in such a manner that the middle z3 orbit contains entire zrot 2 orbit. 4. it is clear how to choose amino-acids from the orbits. (a) consider first the z2 = zrefl 2 case. the lower layer corresponds to the 10 zrefl 2 amino-acids (punct included) coded by 2 codons. one must choose from each z4 orbit consisting of a square of 4 boxes one upper box to represent z4 amino-acid (ala,val, gly, pro, thr). each 4unit contains one free upper box to which one can assign 1 z6 amino-acid. one cannot however put two amino-acids on 3-orbit. there are 3+1 z6 amino-acids and 5 boxes so that one box remains unused. this must be the case. the used box must belong to either second or third horizontal zrot 2 2-box: if it were filled, the middle z3 3-orbit would contain 2 z6 amino-acids and the fiber space-structure would fail. contrary to the original intuition, the unfilled box is not at the 2-orbit of z6 containing as ile but at the middle upper 3-orbit, which would contain 2 amino-acids if filled. it is associated isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2014 | volume 4 | issue 3 | pp. 161-198 180 pitkänen, m. music, biology and natural geometry with one of the 10 amino-acids coded by two codons and is same for both zrot 2 and zrefl 2 . one expects that this amino-acid is somehow special: maybe it is punct. also the corresponding 6-amino-acid (ser, arg, or leu) might be somehow special. (b) z2 = zrot 2 can be treated similarly. the upper row of boxes is filled in the same manner as in the previous case. the horizontal box pairs in the lower row contain one z2rot box and one z4 box. the difference to the previous case is that z2 boxes are now shared by the both rows: in the previous case they belonged to the lower row. 5. the assignment of amino-acids to the orbits is not unique: for n similar orbits there are n! different assignments. inside orbit there is also some non-uniqueness. the following table represent the two situations graphically. 4 6 4 6 4 4 6 4 6(2) 2 2 2 2 2 2 2 2 2 2 2 6 2 6 2 2 6 2 6(2) 4 2 4 2 4 2 4 2 4 2 table1: the representations of the associations of amino-acids to the orbits of of zn, n = 6, 4, 2 for z2 = zrefl 2 (upper two rows) and z2 = zrot 2 (lower two rows). the integer n in box tells that the amino-acid associated with that box corresponds to zn type amino-acid. “(2)” tells that the z6 orbit in question consists of 2 codons. 3.3.3 music and physical correlates of emotions peptides are regarded as molecules of emotion and also information and positive/negative coloring of emotions would naturally correlate with the increase/reduction of negentropic resources of the system as negentropy is transferred to or from it away or increases as a whole. music induces and expresses emotions. therefore the idea that music in generalized form say represented by dark photons with elf frequencies and having energy spectrum in visible and uv energy range of bio-photonscould be the fundamental correlate of emotions and whether tetra-icosahedral music could be in special role (note that one can associated hamilton’s cycles and “music”with any graph). there are 11 candidates for the icosahedral harmony and its extensions. the candidates have either z6 (fig. 1, z4 reflection symmetry (figs. 2, 3), or z2 rotation symmetry (figs. 4, 5,6), and z2 reflection symmetry (figs. 7, 8, 9, 10, 11). for the first case z2 reflection symmetry and for the second case z2 rotation symmetry are represented as as half-octave shift. second reflection symmetry corresponds geometrically to reflection in horizontal direction. the extension assigns to them definite key and adds to 1-quint chords minor and major chords absent for the icosahedral bio-harmonies. the question is whether one of these harmonies is selected in biology or whether all three can appear and are perhaps realized at the level of magnetic bodies of amino-acids. the reversal of the harmony differs from the original one and major-minor transformation takes place. could it be that both “moods” are realized at the level of magnetic body and even serve as the physical correlates of moods and emotions? could emotions be realized at the level of amino-acid magnetic bodies as phase transitions affecting parts of organism or even entire organisms and in this manner changing the mood. peptides are regarded as molecules of emotion: could these phase transitions occur only for peptides and other information molecules involving proteins? could peptides also serve as seeds of these phase transitions? could even the hamiltonian cycle be changed for the magnetic body of the entire organism and correspond to some importance two-valued characteristic of emotional profile? could orientation reversal relate to time reversal, which in zero energy ontology (zeo) corresponds to state function at opposite boundary of causal diamond (cd)? this reversal would occur in volitional acts: isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2014 | volume 4 | issue 3 | pp. 161-198 181 pitkänen, m. music, biology and natural geometry the subsequent reduction would not affect the quantum state in positive energy but in tgd framework they affect the state at opposite boundary cd and in this manner give rise to the experience flow of time. the simplest extension of the harmony in the proposed form requires that harmony possesses x6 chord. it does not exist for for the candidate with zrot 2 symmetry but for its reversal 4 of them are present as images of d7, e7 and g♯7, b♭7 which are chords of type x6. one can however map the harmony to its reversal, perform the completion for it, and perform the reversal back to the original harmony. the reversal depends on what note remains invariant in the reversal. one can require that it is the basic note of the chord to itself: with this condition one would obtain dm,em,g♯m,b♭m and major keys c♯, f,a,h. 4 different harmonies would result. without the restriction the number of harmonies is different and each has different emotional characteristics. 3.3.4 religious myths, music, and biology these symmetries define a hierarchy of symmetry breakings. this hierarchy has amazing connections with the myths, which i believe to reflect deep facts about consciousness and biology at fundamental level. the story of genesis is a good representative in this respect. 1. the hierarchy of symmetry breakings proceeding from z6 down to zrefl 2 brings strongly in mind evolution as loss of innocence. for z6 one as 4 orbits. one orbit contains 2 triangles (chords, dna codons assignable to ile). the other orbits correspond to six codons assignable to amino-acids ser, arg, and leu. the chords at the orbits are major chords and 7-chords, and minor chords and 6-chords for the inverse of the harmony. there are no dissonant chords in 0-quint sector: dissonances appear only for the remaining groups as 0-quint chords. this is musical representation of paradize. this harmony is based on 6-note scale for the basic notes of the chords and used by impressionistic composers. amino-acids correspond to selections of preferred chord from each orbit and there are only four different chords: this subharmony is very simple. life in paradize is simple! 2. next comes an intriguing observation. the number of amino-acids obtained as projections of the icosahedral dna orbits is 19, not 20. could it be impossible to have 20 amino-acids as projections of the orbits and that 19 is the maximum number? the reason for 19 is that the number of aminoacid of type z6 is 3 + 1 = 4 rather than 5. therefore there is one ”non-playable” chord -perhaps located at some ”paradize orbit” -, which does not correspond to any amino-acid. the first guess for the non-playable chord is as one of the aug type chords (say ceg♯, which is the last breath in many finnish tangos telling about unhappy love end it is something between happy cm and sad am, ”raueta” is finnish word for this manner to come to an end: ”expire” might be the nearest english counterpart). this chord is located at the 2-chord orbit related to the other chord of the orbit by half-octave shift (chords could be ceg♯ and f♯b♭d), the tritonus denied by church. unfortunately, this identification is not consistent with the argument identifying the amino-acid chords at zn orbits (see table 3.3.2) the non-playable chord must belong to an intersection of 6orbit and 4-orbit and is not completely unique without further assumptions. it belongs to a 2-orbit of zrefl 2 : if it is somehow special, it could belong to the 2-orbit assignable to punct. if the chords at the 2-orbit have basic notes differing by tritonus, the inspection of the table 4.3 shows that it is possible to find a unique chord pair having this property for all 5 zrefl 2 cycles. one cannot avoid the associations between non-playable chord and the denied fruit hanging in the tree of good and bad knowledge in the story of adam and eve, and its analog in many fairy tales. the non-playable chord also brings in mind the hilarious story of gödel-escher-bach about non-playable record (a truth unprovable in given axiom system). isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2014 | volume 4 | issue 3 | pp. 161-198 182 pitkänen, m. music, biology and natural geometry 3. the hierarchy of symmetry breakings leading from z6 to zrefl 2 encourages one to continue with the biblical analogies. z6, z4 and zrot 2 cycles have half-octave shift as a symmetry: good and evil do not exist in paradise, but dissonances are already there for z4 and z2 harmonies the evil snake! these states correspond to the consciousness of animals, children, and saints. note that bio-harmony corresponds to the presence of one sub-harmony of type zn, n = 6, 4, 2. 4. the banishing from the paradize takes place as zrefl 2 symmetric harmony replaces zrot 2 harmony: half-octave shift is not a symmetry anymore, and one can tell between good and evil, and eventually church decides to deny tritonus as a symbol of evil! paradise is left as icosahedral and tetrahedral code are fused to form the tetra-icosahedral code the ordinary genetic code leading to the breaking of zrefl 2 symmetry. 5. in banishment punct (”empty” amino-acid) as a counterpart of chord shared by tetrahedron and icosahedron emerges and means stopping of the music piece altogether. death of the sinner! for unfused codes this chord is playable as sec/pyl and the music piece is never-ending: life is eternal in paradise! no notion of time, no sin, no death! amusingly, impressionist music with 6-note scale is music of ”now”, attempt to catch this moment. 6. also the holy trinity finds an analog as z6−z4−z2 trinity of the bio-harmony. holy spirit, father, son: perhaps in this order. even more, zrot 2 can be associated with son in heaven and z2refl with son at earth as ordinary mortal! 3.3.5 what do dnas/amino-acids sound like? if dna/amino-acid sequences correspond to chord sequences of tetra-icosahedral harmony, one can ask what they sound like. the best manner to study this question is to build concrete simulations of the dna/amino-acid sequences. 1. this requires specification of harmony by selecting one hamiltonian cycle from the cycles belonging to the groups of cycles with zn, n = 6, 4, 2 symmetry and decomposing amino-acids to 3 groups correspondingly (those coded by 6, 4, and 2 codons). one must include tetrahedral codons and amino-acids. 2. the basic rule of harmony would be the minimization of quint distance between initial and final chords of the transition. one can consider probabilistic versions of this rule or pose strict form of the rules stating in the most stringent form that only transitions with vanishing quint distance (between neighboring triangles) are possible. 3. the transitions between different amino-acid regions would be governed by this rule. aso the transitions between different variants of the dna-amino-acid space defined by different choices of the hamilton cycles would be governed by the same rule 4. the most plausible looking model considers only transitions between dna codons since dna sequences induce amino-acid sequences. appendix represents an example about randomly generated chord sequence assignable to bio-harmony defined as a composite of 3 harmonies one from each symmetry type and z2 = zrefl 2 involving tetraicosahedral extension. anyone having garage band skills in guitar playing can check what these chord sequences sound like and maybe try to build a melody on the background. one could also test the proposal that codons at the orbit of amino-acid define the melody by finding a concrete representation for the orbits and building random melodies defined by dna sequences coding for the chord sequence. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2014 | volume 4 | issue 3 | pp. 161-198 183 pitkänen, m. music, biology and natural geometry 4 icosahedral harmonies in the following the icosahedral harmonies are discussed in detail. this includes overall summary and tables giving the 20 3-chords of the harmonies and illustrations of the hamiltonian cycles. 4.1 about symmetries of the icosahedral harmonies some words about the symmetries associated with the icosahedral harmonies and genetic code are in order. there are 3 different kind of bio-harmonies characterized partially by the symmetry group which can be z6, z4 or z2 which acts either as rotations or reflections. 1. the first variant as zrot 3 × zrefl 2 subgroup of icosahedral group as symmetries and its orbits correspond to 3 6-plets and 1 2-plets for which z3 leaves the triangle invariant. the counterparts for the orbits are 3 dna 6-plets and one 2-plet. 2. the second variant has z4 symmetry generated by two commuting reflection as symmetries as is obvious from figures 3,??: the reflections act on vertical and horizontal coordinates. the orbits are five 4-plets of chords. vertical reflection induces half-octave shift and horizontal one permutes the note sequences b♭cdg♯f♯e and d♯c♯hfga. 3. zrot 2 or zrefl 2 acts as symmetries of the remaining 3+5 cycles. the covering space of 10 amino-acids involved defined by 20 dna codons decomposes to 10 2-plets. the 2-fold rotation symmetry of the hamiltonian cycles is obvious from the illustration ??: it corresponds to 6-quint rotation and the chord sets must be invariant under this rotation. this rotation corresponds to the 1/2 octave shift realized as rotation. these symmetries are realized as “coordinate transformations”for the cycle a curve in the “imbedding space”defined by icosahedron but induced from the “imbedding space symmetries”acting as isometries of icosahedron. dna codons have also almost exact z2 symmetry discussed in [?, 5, 6]. 1. for the last codon the reflection a-t, c-g is an almost symmetry broken only for special cases. this approximate symmetry could be understood as following from the fact that the number of dnas coding given amino-adic is even in most cases. the exceptions are ile, met, trp coded by odd number of dna codons. by mapping dnas to binary sequences one can order the situation so that the 6:th binary digit is the almost-symmetry digit. 2. what is trivial is that rna has chosen the third bi-digit to be the almost symmetry digit with the ordering ucag of the nucleotides so that a genuine physical symmetry is in question. an interesting question is how this symmetry relates to the model of genetic code based on tetra-icosahedral orbits. the restriction of dnas to 60 icosahedral dnas demonstrates that this symmetry originates from the icosahedral z2. the tetrahedral extension of the code breaks this symmetry by extending ile and punct multiples by one codon and introducing also 4 singlets met, trp, pyl, and sec. the detailed correspondence between chords of the harmony and dna codons is also a problem to be solved. 1. the correspondence matters in the proposed scenario since the chords at at the orbits are different and the gluing of tetrahedron breaks the symmetry in z2 sectors so that quint rule determining harmonic dna sequences is different. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2014 | volume 4 | issue 3 | pp. 161-198 184 pitkänen, m. music, biology and natural geometry 2. the common face of tetrahedron and icosahedron corresponds to punct so that the quint rule for different representations says something about the pairs of form codon-stop codon that is about the codon preceding the last codon of gene! this codon could allow to recognize what hamiltonian cycle is in question. if c-major is one of the added chords, stop codons correspond to what was c6 = cga chord and its z2 image, which is x7 type chord. by the strongest form of the quint rule only the chords having common notes with these chords would correspond to dna codons of z6 and z4 cycles which can precede stopping codon. 3. there are some restrictions on the correspondence. zrefl 2 symmetry would correspond to the flipping of the 6th bit for the bit representation defined by nucleotides representing 2-bits in the case of z3 = z3 × zrefl 2 . z4 = zrot 2 × zrefl 2 . for z2 = zrot 2 the role of zrefl 2 must be taken by zrot 2 . one can of course ask whether zrot 2 cycles are realized at all. for z4 cycles zrot 2 would correspond to symmetry permuting the at, cg doublets for the first nucleotide. for z6 subgroup z3 would cyclically permute the 3 doublets with respect to third nucleotide. these constraints do not fix the correspondence completely. to sum up, there is a connection between genetic code and the groups acting along the hamiltonian cycle. the simplest option fixes the orbits of the triangles and therefore also the representation of genetic code. 4.2 summary of the basic results one can find the list of hamiltonian cycles at http://cs.smith.edu/~orourke/mathoverflow/hpaths. html. the edge {1, 2} is fixed and cycles are oriented so that there are 1024 of them. all of them are relevant from the point of music interpretation and the change of orientation corresponds to major-minor duality, albeit not in the simplest sense. note that this duality does not affect the characteristics listed above. the general following general results hold true as one can learn at http://mathoverflow.net/ questions/37788/why-are-there-1024-hamiltonian-cycles-on-an-icosahedron. one can classify the cycles using their symmetries which can correspond to isometries of icosahedron leaving them fixed or to a reflection taking the vertex n at the cycle to vertex 12− n. this symmetry is not same as change of orientation which is purely internal operation and cannot change the cycle. one can even find images of the cycles possessing symmetries at https://www.flickr.com/photos/ edwynn/sets/72157625709580605/ and deduce the triplets n and p characterizing them by visual inspection. also one can write explicitly the 3-chords defined by the three kinds of faces. i have deduced the triplets n and the 3-chords defining the harmony by the inspection of the images. “bio-harmony” (4,8,8) forced by the model of extended genetic code involving also the 21st and 22nd amino-acids is of special interest.the classes of cycles with symmetries 6-fold rotational symmetry and two distinct reflection symmetries realize it. before continuing some terminology and notation is in order. take c as the major key. submediant or relative minor corresponds to am, subdominant (sharp or flat) to f major (f ) or fminor (fm), dominant to g. the notation for chords is such that quints correspond to subsequent notes in the chord. for 1-quint chords this means that first two notes define the quint. the following table summarizes notation inspired by the popular music notation. the basic different is that the third is in most cases excluded so that the emotional character of the chord is not fixed. ceg ≡ c , cd♯g ≡ cm , cd♯f♯ ≡ co , ceg♯ ≡ caug , cfg ≡ c4 , cf♯g ≡ c4+ , cgg♯ ≡ c6 − , cga ≡ c6 , cgb♭ ≡ c7 , cgb ≡ cmaj7 , cgc♯ ≡ c9 − , cgd ≡ c9 . (4.1) besides these notions it is convenient to introduce additional notations for various dissonant chords appearing as 0-quint chords. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2014 | volume 4 | issue 3 | pp. 161-198 185 pitkänen, m. music, biology and natural geometry cc♯d ≡ cex1 , cc♯d♯ ≡ cex2 , cdd♯ ≡ cex3 , cde ≡ cex4 , cd♯e ≡ cex5 , cc♯e ≡ cex6 , cdf♯ ≡ cex7 , cdg♯ ≡ cex8 . (4.2) clearly, the sets {ex1}, {ex2,ex3}, {ex4,ex5,ex6}, {ex7}, {ex8}, corresponds to the span of 2,3,4,6,8 half notes for the chord. the following summarizes the results. note that cex7 can be seen as part of d7 chord. 1. there are 6 collections of cycles without any symmetries containing 48 cycles each: these 48 cycle are mutually isometric so that one can say that there 6 different harmonies. 2. there is a collection with 6-fold rotational symmetry, 48/6=8 examples. n = (2, 12, 6). the chords of this scale define 6-note scale involving only total steps. cdf and and its 6 translates by integer number of steps define 6 1-quint chords. ce♭g (cm) and its 6 translates (they obviously correspond to the 6-fold rotational symmetry) define also 6 1-quint chords. the reflection transforms these series to those defined by gb♭g and its translate and byfac (f major) and its translates. impressionists like debussy used 6-note scale of this kind. half-octave shift is an exact symmetry. 1-chords lack the third so that one cannot assign to 3-chords any emotional quality. the extension to 4-chord can however bring either “happy”or “sad”quality. clearly, these harmonies have “jazzy”character. 0-quint chords are faug ≡ fac♯ and gaug ≡ ghd♯ are transformed to each other by both half-octave shift and inversion. 3. there are 2 collections with 2 distinct reflectional symmetries with 12=48/4 representatives in each. half-octave scaling is a symmetry of both these scales as one might guess. the first cycle (see fig. 2) has n = (0, 16, 4) so that there are no 0-quint chords which in general are dissonant. second cycle (see fig. 3) realizes n = (4, 8, 8) bio-harmony and deserves some comments. it will be discussed in detail later. (a) the 8 2-quint chords consist of b♭fg ≡ b♭9, c9, f9, g9 and their half-octave scalings. clearly, the simple four-note scale appears here. (b) using the popular notion introduced earlier 1-quint chords consist of two 4-plets dmaj7, e9 − , a7, a6 and g♯maj7, b♭9 − , d♯7, d♯6 related by half-octave shift. the harmony contains no “simple”major or minor chord and only the extension to tetrahedral harmony can provide them. the same is true for the second bio-harmony. (c) the 4 0-quint chords are cex3 ≡ cdd♯ and eex2 ≡ efg and their half-octave scalings f♯ex3 ≡ f♯g♯a and b♭ex2 ≡ b♭bc♯g. 4. there are 3 collections with z2 rotational symmetry with 48/2 = 24 representatives in each. the triplets n are (0, 16, 4) (see fig. 4), (2, 12, 6) (see fig. 5), and (4, 8, 8) (see fig. 6). all these harmonies are symmetric with respect to half-octave shift (tritonus), which obviously corresponds to the z2 rotation. tritonus would not have been tolerated by catholic church! this symmetry characterizes all 3 harmonies. basic 3-chords do not contain pure minor and major chords. the reflection of the scale does not leave the collection of chords invariant but it is not clear whether this corresponds only to a change of scale, probably not. consider the (4,8,8) case (see fig. 6). (a) the 8 2-quint chords appear as four-plet h9, c♯9, d♯9, f9 and its half octave shift (tritonus interval) acting as a symmetry of the harmony. 2-quint chords are always of type x9 (note that the third is missing) but also 1-quint chord can be of form x9 as explicit construction of chords demonstrates: i have denoted these 1-quint chords by symbol x4 (cdg is obviously equivalent with cdg). isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2014 | volume 4 | issue 3 | pp. 161-198 186 pitkänen, m. music, biology and natural geometry (b) using the popular music notation introduced earlier, the 8 1-quint chords ared7, amaj7, a4+, e7 and their half-octave shifts g♯7, d♯7, d♯4+, b♭7. no major and minor chords are included and only the extension to tetra-icosahedral harmony can provide them and also break the symmetry giving rise to well-defined key. 5. the four 0-quint chords appear in two types. d♯ex2 ≡ d♯ef♯ and its half-octave shift aex2 ≡ ab♭c plus hex3 ≡ hc♯g and its half-octave shift fex3 ≡ fgc♯. according to usual thinking these chords involve dissonances. this dissonance character is a rather general phenomenon for the harmonic loners and classical views about harmony would exclude them as asocial cases! in the case of maximally symmetric harmony the loners are diminished chords and thus not so dissonant. in some cases there are no 0-quint chords. there are 5 collections with z2 reflection symmetry having 24 representatives in each (see figs. 7, 8,9,10,11). the integer triplets n are (2, 12, 6), (2, 12, 6), (4, 10, 6), (2, 12, 6), (2, 12, 6). bio-harmony has representative also in this class (see fig. 9). the half-octave scaling symmetry is broken for these harmonies. i have not found simple characterization for the symmetry which corresponds to reflection in the direction of x-axis since it changes the interval structure of the chords. some comments (4, 8, 8) case are in order (see fig. 9). 1. 2-quint chords appear as reflection related multiplets c9, d9, h♯9, d♯9 and c♯9, h9, f9, b♭9. 2. 1-quint chords appear as symmetry related mutiplets g,d7, amaj7, e7 and c♯m,f♯6, h6 − , e6. key g major and c♯ minor would be natural looking keys even without tetrahedral extension. for the mirror image b♭ minor and e major would be the natural looking keys. for extension e major would be the key. to sum up, half octave shift is a symmetry of all harmonies expected those having only z2 reflection symmetry, and fails thus also for the corresponding bio-harmonies. 4.3 tables of basic 3-chords for the icosahedral harmonies with symmetries the tables below give list for the three types of 3-chords for the 11 harmonies possessing symmetries. one must remember that the reversal of the orientation for the cycle induces the transformation c ↔ c, f♯ ↔ f♯, h ↔ c♯, f ↔ g,d ↔ b♭, e ↔ g♯, a ↔ d♯ and produces a new scale with minor type chords mapped to major type chords and vice versa. also one must remember that all 3-chords except those which are simple majors or minors lack the third so that their emotional tone remains uncharacterized. for instance, c6 does could be replaced with cm6 and g7 with gm7. the reader can check the chords by direct inspection of the figures. the convention used is that vertex number one corresponds to c note. (n0,n1,n2) 0-chords 1-chords 2-chords (2,12,6) (faug,gaug) (cm,dm,em,f♯m,g♯m,b♭m), (c9, d9, e9, f ♯9, g♯9, b♭9). (f6, g6, a6, b6, c♯6, d♯6). table 2. the table gives various types of 3-chords for harmonies with z6 rotational symmetry. note that half-octave shift is an exat symmetry. note that gaug = ceg♯, f aug act as bridges between the groups related by half octave shift. the chords have been arranged so that they form orbits of z6. “ amino-acid chords”correspond to preferred chords at the orbits. (n0,n1,n2) 0-chords 1-chords 2-chords (0,16,4) (d7, d6, g♯7, g♯6) , (b♭9, b9, e9, f9). (g4+, a9−, c♯4+, d♯9−), (emaj7, gmaj7, b♭maj7, c♯maj7), (c9−, a9−, f ♯9−, d♯9−). (4,8,8) (cex3, eex2, f ♯ex3, b♭ex2). (dmaj7, e9−, a7, a6), (b♭9, f9, c9, g9). (g♯maj7, b♭9−, d♯7, d♯6). (e9, b9, f ♯9, c♯9). isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2014 | volume 4 | issue 3 | pp. 161-198 187 pitkänen, m. music, biology and natural geometry table 3. the table gives various types of 3-chords for the two harmonies with z4 = zrot 2 × zrefl 2 symmetry. 4-plets represent the orbits. first cycle has no harmonic loners. second cycle gives rise to bioharmony (4,8,8) for which 0-quint chords are dissonant. both cycles have z2 rotation symmetry acting as a vertical reflection symmetry in figures and realized also as half-octave shift so that 4-plets contains chords and their half-octave shifts. the genuine reflection symmetry acts as a horizontal reflection symmetry in figures. the cycles correspond to figures 2, 3. (n0,n1,n2) 0-chords 1-chords 2-chords (0,16,4) (em,b♭m), (cm,f♯m), (d9, g♯9), (g6, c♯6), (a6, d♯6), (e9, b♭9). (d4+, g♯4+), (b4+, f4+), (cmaj7, f ♯maj7), (g6−, c♯6−). (2,12,6) (aex4, d♯ex2). (am,d♯m), (g9−, c♯9−), (c9, f ♯9), (c4, f ♯4), (e4+, b♭4+), (a9, d♯9), (dmaj7, g♯maj7), (d9, g♯9). (bmaj7, fmaj7). (4,8,8) (aex2, hex8, d♯ex2, f ex8). (d7, g♯7), (amaj7, d♯maj7), (g9, c♯9), (a9, d♯9), (a4+, d♯4+), (e7, b♭7). (b9, f9), (e9, b♭9). table 4. the table gives various types of 3-chords for harmonies with z2 rotation symmetry acting as half-octave shift. the doublets represent 2-chord orbits. the cycles correspond to figures 4, 5, and 6. (n0,n1,n2) 0-chords 1-chords 2-chords (2,12,6) (f♯ex3, hex4), (am,d♯), (a6, d♯7), (c9, f9), (b9, f ♯9), (d7, b♭6), (g6−, fmaj7), (e9, c♯9). (d4+, b♭9−), (e9, g♯4+), (2,12,6) (dex4, hex4). (f, fm), (c6−, b♭maj7), (c9, d♯9), (d7, g♯6), (gmaj7, d♯6−). (d♯9, c♯9), (c♯4−, a4+), (e4+, f ♯6). (e9, b9). (4,8,8) (fex1, d♯ex3, g♯ex1, aex2). (e7, e6), (amaj7, b9−), (d9, b9), (c9, c♯9), (g,c♯m), (d7, f ♯6). (f9, g♯9), (d♯9, b♭9). (2,12,6) (hex3, eex7). (d7, g♯6), (g,d♯m), (c9, d♯9), (f, fm), (c6−, b♭maj7), (d9, c♯9), (a9−, c♯4+), (e7, f ♯6). (e9, b9). (2,12,6) (f♯ex2, f ex3). (f,b♭m), (c7, g♯6), (b♭9, d♯9), (amaj7, b9−), (e6, e7), (c9, c♯9), (g,c♯m), (d7, b6). (d9, h9). table 5. the table gives various types of 3-chords for harmonies with single reflection symmetry. the cycles correspond to figures 7, 8, 9,10, 11. references mathematics icosahedral graph. wolfram mathworld. http://mathworld.wolfram.com/icosahedralgraph.html. why are there 1024 hamiltonian cycles on an icosahedron? http://mathoverflow.net/questions/ 37788/why-are-there-1024-hamiltonian-cycles-on-an-icosahedron. neuroscience a. bandyopadhyay. experimental studies on a single microtubule (google workshop on quantum biology), 2011. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2014 | volume 4 | issue 3 | pp. 161-198 188 pitkänen, m. music, biology and natural geometry a. bandyopadhyay g. ghosh, s. sahu. evidence of massive global synchronization and the consciousness: comment on ”consciousness in the universe: a review of the ’orch or’ theory” by hameroff and penrose. biosens bioelectron, 2013. c. b. pert. molecules of emotion. simon & schuster inc., 1997. books related to tgd m. pitkänen. dna as topological quantum computer. in genes and memes. onlinebook. http: //tgdtheory.fi/public_html/genememe/genememe.html#dnatqc, 2006. m. pitkänen. evolution in many-sheeted space-time. in genes and memes. onlinebook. http:// tgdtheory.fi/public_html/genememe/genememe.html#prebio, 2006. m. pitkänen. homeopathy in many-sheeted space-time. in bio-systems as conscious holograms. onlinebook. http://tgdtheory.fi/public_html/hologram/hologram.html#homeoc, 2006. m. pitkänen. negentropy maximization principle. in tgd inspired theory of consciousness. onlinebook. http://tgdtheory.fi/public_html/tgdconsc/tgdconsc.html#nmpc, 2006. m. pitkänen. quantum model for hearing. in tgd and eeg. onlinebook. http://tgdtheory.fi/ public_html//tgdeeg/tgdeeg/tgdeeg.html#hearing, 2006. m. pitkänen. three new physics realizations of the genetic code and the role of dark matter in biosystems. in genes and memes. onlinebook. http://tgdtheory.fi/public_html/genememe/genememe. html#dnatqccodes, 2006. m. pitkänen. quantum mind, magnetic body, and biological body. in tgd based view about living matter and remote mental interactions. onlinebook. http://tgdtheory.fi/public_html/pdfpool/ lianpb.pdf, 2012. articles related to tgd m. pitkänen. new results about microtubules as quantum systems. http://tgdtheory.fi/public_ html/articles/microtubule.pdf, 2014. m. pitkänen. pythagoras, music, sacred geometry, and genetic code. http://tgdtheory.fi/public_ html/articles/pythagoras.pdf, 2014. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. original-review-letter-invited article dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 218-244 miller, i., mill, r. a. & webb, b., quantum bioholography issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 218 article quantum bioholography iona miller*, richard a. miller & burt webb abstract complex information can be encoded in em fields, as we all know from coding and decoding of television and radio signals. even more complex information can be encoded in holographic images. dna acts as a holographic projector of acoustic and em information which contains the informational quintessence of the biohologram. only 3% of human dna encodes the physical body. the remaining 97% of the 3 billion base pair genome contains over a million genetic structures called transposons, that have the capacity to jump from one chromosomal location to another (kelleher, 1999). we are 99.9% alike in our genetic legacy. our individuality is expressed in three million small variations in our cells, called single nucleotide polymorphisms. gene-expression is the mechanism by which new patterns are called into being (rossi, 2000). there is also a strong correlation between modulation of the brain‟s em field and consciousness (persinger, 1987; mcfadden, 2002). the gariaev group has discovered a wave-based genome and dna phantom effect which strongly supports the holographic concept of reality (miller, webb, dickson, 1975). this main information channel of dna is the same for both photons and radio waves. superposed coherent waves of different types in the cells interact to form diffraction patterns, firstly in the acoustic domain, secondly in the electromagnetic domain -a quantum hologram -a translation process between acoustical and optical holograms. creative, novel and enriching psychotherapeutic experiences can lead to neurogenesis, gene expression, and healing which facilitate mindbody communication and can have a long-term transformative effect on the whole person (rossi, 2002). thus, bioholography has relevant applications for optimizing health, well-being and even self-realization. it is relevant in biophysics, medicine, psychobiology, psychotherapy and the holistic healing arts. it provides us with a more genetically integrated model of the complex dynamics of the mindbody -one arising in the domain underlying the standard genetic code triplet model. keywords: dna, dna phantom, wave biocomputer, genome, wave-based genome, quantum holography, bioholography, organismic evolution, vacuum substructure, biophysics, psychobiology, gene expression, psychotherapeutic applications. introduction hypothesis: the organization of any biological system is established by a complex electrodynamic field which is, in part, determined by its atomic physiochemical components. this field, in turn, determines the behavior and orientation of these components. this dynamic is *correspondence author: iona miller, http://ionamiller.weebly.com email: iona_m@yahoo.com note: this work was completed in 2002. http://ionamiller.weebly.com/ mailto:iona_m@yahoo.com dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 218-244 miller, i., mill, r. a. & webb, b., quantum bioholography issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 219 mediated through wave-based genomes wherein dna functions as the holographic projector of the psychophysical system a quantum biohologram. a model of the mind-body relationship is developed in which novel biophysical principles in genome function generate a dynamic possessing attributes consistent with both our psychophysical nature and consciousness. the model invokes a fractal link between neurodynamical chaos and quantum uncertainty. transactional wave collapse allows this link to be utilized predictably by the excitable cell, in a way which bypasses and complements formal computation. the formal unpredictability of the model allows mind to interact upon the brain, the predictability of consciousness in survival strategies being selected as a trait by organismic evolution (king, 2001). this quantum evolution is orchestrated by the information transduction of dna. the gariaev group (1994) has proposed a theory of the wave-based genome where the dnawave functions as a biocomputer. they suggest (1) that there are genetic "texts", similar to natural context-dependent texts in human language; (2) that the chromosome apparatus acts simultaneously both as a source and receiver of these genetic texts, respectively decoding and encoding them; (3) that the chromosome continuum acts like a dynamical holographic grating, which displays or transduces weak laser light and solitonic electro-acoustic fields. the distribution of the character frequency in genetic texts is fractal, so the nucleotides of dna molecules are able to form holographic pre-images of biostructures. this process of "reading and writing" the very matter of our being manifests from the genome's associative holographic memory in conjunction with its quantum nonlocality. rapid transmission of genetic information and gene-expression unite the organism as holistic entity embedded in the larger whole. the system works as a biocomputer -a wave biocomputer. the quantum nonlocality of the genetic information is fundamental. experimental work of the gariaev group shows how quantum nonlocality is directly related to laser radiation from chromosomes (coherent light), which jitterbugs its polarization plane to radiate or occlude photons. dna and the genome have now been identified as active "laser-like" environments. roughly speaking, dna can be considered as a liquid crystal gel-like state that acts on the incoming light in the manner of a solitonic lattice. a soliton is an ultra stable wave train that arises in the context of non-linear wave oscillation. the dna reading process can be modeled as a complex mechanical oscillator capable of producing solitonic wave transmissions. dna, modeled as a kind of rotary pendulum can be simulated as a chain of non-linear oscillators. complex dynamic patterns arise when taking into account the non-linear covalent connections between nucleotides. the same researchers suspect the ability of chromosomes to transform their own genetic-sign laser radiations into broadband genetic-sign radio waves. the polarizations of chromosome laser photons are connected nonlocally and coherently to polarizations of radio waves. (thus, we seem to have an explicit physical analogue for the traditional mystical apprehension of "inner light" and the "audible life stream"). this is the main information channel of dna, the same for both photons and radio waves. superposed coherent waves of different types in the cells interact to dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 218-244 miller, i., mill, r. a. & webb, b., quantum bioholography issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 220 form diffraction patterns, firstly in the acoustic domain, secondly in the electromagnetic domain -a quantum hologram -a translation process between acoustical and optical holograms. i. quantum bioholography in languages of the brain (1971), pribram postulated a neural hologram made by the interaction of waves in the cortex, which in turn is based on a hologram of much shorter wavelengths formed by the wave interactions on the sub-atomic level. thus, we have a hologram within a hologram, and the interrelatedness of the two somehow gives rise to our sensory images. bohm (1980), in wholeness and the implicate order went further, declaring the brain is a hologram interpreting a holographic universe. in a holographic model this inseparable interconnectedness begins at the even more fundamental level of human existence, rooted in our existential blueprint, dna. the brain is a hologram, enfolded within our holographic mind-body, enfolded within a holographic universe. recent discoveries by russian scientists peter gariaev & al. and later speculations by vladimir poponin shed tremendous light on our proposal that the human being is a transducer of universal energy and consciousness -essentially a biocomputer. the new feature of this research is the ability to physically demonstrate subtle fields emerging from the quantum foam or vacuum potential. this makes the effect quantifiable and measurable -objective. this takes the phenomenon and subjectivity of consciousness out of the realm of quantum metaphysics and plants it firmly under the rubric of hard science. it heralds the unification of quantum mechanical and chaotic dynamics in human consciousness. we can now model the human bio-computer. poponin (1995) boldly suggests that this deeper understanding of the mechanisms underlying subtle energy phenomena include many of the observed alternative healing phenomena and includes a physical theory of consciousness. this hypothesis is based on a precise quantitative background and combines both quantum mechanics and complexity or chaos dynamics in a startling and compelling new way. it posits that some new field structure is being excited from the physical vacuum by an intrinsic ability that emerges through dna. gariaev discovered the dna phantom effect in 1985, when he worked in correlation spectroscopy of dna, ribosomes and collagen in the institute of physics, in the academy of science of the ussr. he was first able to publish his results in 1991, leading to a book in 1994, wave based genome. his dna phantom effect demonstrates a dynamic new field in the vacuum substructure by bombarding it with coherent laser light and coupling it to conventional electromagnetic fields. the experimental protocols for this procedure are rigorous, and have been reproduced in moscow and at stanford. r. a. miller, i. miller, and b. webb (2001) are now consulting on the project to suggest the next research directions and applications. miller and webb have a long-standing background in this field. long before david bohm published his wholeness and the implicate order (1980), miller and webb published "a holographic concept of reality" in the journal psychoenergetic dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 218-244 miller, i., mill, r. a. & webb, b., quantum bioholography issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 221 systems, ed. stanley krippner, vol. 1, 1975. 55-62. gordon & breach science publishers ltd., great britain. "holographic concept" was later reprinted in the book psychoenergetic systems, s. krippner, editor. 1979. 231-237. gordon & breach, new york, london, paris. it was reprinted again in the journal psychedelic monographs and essays, vol. 5, 1992. 93-111. boynton beach, fl, tom lyttle, editor. this foundational paper was followed shortly by "embryonic holography: an application of the holographic concept of reality", also in 1973. presented at the omniversal symposium, california state college at sonoma, saturday, september 29, 1973. reprinted in lyttle's journal psychedelic monographs and essays, vol. 6, 1993. 137-156. miller followed this project with a proposal prepared for the government through mankind research unlimited, described in a formerly unpublished, proprietary paper called "bioluminescence, kirlian photography and medical diagnostics" (1974), which is only now seeing the light of day. it was an application of his paper on "the physical mechanisms of kirlian photography." in 1993, iona miller published "the holographic paradigm and the consciousness restructuring process," another application to psychotherapeutic mindbody healing. subsequently she has published extensively on the role of complex dynamics in relationship to consciousness and process-oriented psychotherapy, through asklepia foundation. a deep interest in the nature of synergetics (fuller, 1975), zero-point field, the vacuum potential, and quantum foam has led her to develop innovative applications of chaos theory in consciousness studies. she has dovetailed many of those discoveries with the reports of mystics of their intuitive inner-plane experiences of light and sound (shabd) throughout history (singh, 1979; blavatsky, 1987; puri, 1964; miller and miller, 1983). could it be that these mystics somehow perceive holographic processes when they look inside themselves? endogenous dmt (n,n-dimethyltryptamine) is described as the source of visionary light in transpersonal experiences. its primary source, the pineal, has traditionally been referred to as the third eye. dmt production is particularly stimulated, according to strassman (2001), in the extraordinary conditions of birth, sexual ecstasy, childbirth, extreme physical stress, neardeath, and death, as well as meditation. pineal dmt also plays a significant role in dream consciousness. how might meditation evoke the pineal dmt experience? "meditative techniques using sound, sight, or the mind may generate particular wave patterns whose fields induce resonance in the brain. millennia of human trial and error have determined that certain "sacred" words, visual images, and mental exercises exert uniquely desired effects. such effects may occur because of the specific fields they generate within the brain. these fields cause multiple systems to vibrate and pulse at certain frequencies. we can feel our minds and bodies resonate with these spiritual exercises. of course, the pineal gland also is buzzing at these same frequencies. the pineal begins to "vibrate" at frequencies that weaken its multiple barriers to dmt formation: the pineal cellular shield, enzyme levels, and quantities of antidmt. the end result is a psychedelic surge of the pineal spirit molecule, resulting in the subjective states of mystical consciousness." (strassman, 2001). but these philosophical aspects are best addressed further elsewhere. dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 218-244 miller, i., mill, r. a. & webb, b., quantum bioholography issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 222 here, in this presentation, the joint work of decades by miller, miller and webb comes to fruition and perhaps finds a physical proof. the organization of any biological system is established by a complex electrodynamic field. this em field is, in part, determined by its atomic physicochemical components and, in turn, determines the behavior and orientation of these components. the holographic model of reality emerging from this principle provides a scientific explanation of psychoenergetic phenomena, (miller, webb, dickson, 1973). in 1973, miller and webb suggested bioholograms as the projectors of our material reality: in the nuclei of each cell in the human body, the dna (deoxyribonucleic acid) carries the structure of our whole body. not just our physical form, but also the processes that that form undergoes in terms of survival. if all of these things are in truth locked in the dna, how does that turn into a functioning being? the dna could possibly be the holographic projectors. the dna could be projecting a field that would be experienced by other dna in the body. the dna molecules, in a sense, could be linked together. the dna molecules are also linked to their own cell, which they are controlling via mechanisms of rna transfer and enzymatic action in the cell. we believe that it is likely that the dna and the rna are in non-local communication. it is known from the epr phenomenon that entangled photons retain a mutual informational bond even at a distance, through polarization, and allow a kind of quantum teleportation, which has finally been experimentally verified. dna molecules, included in chromosomes, possess a substance--wave duality which is similar to the dualism of elementary particles. in accordance with it, dna codes an organism in two ways, both with the assistance of dna matter and by dna sign wave functions, including coding at its own laser radiation level [28]. the genetic apparatus can be non-local at the molecular level (holographic memory of a chromosome continuum) and at the same time quantum mechanically non-local in compliance with the einstein-podolsky-rosen effect [4]. the latter means that the genome genetic and other regulatory wave information is recorded at the polarization level of its photons and is nonlocally (everywhere and in no time) transferred (plays out) throughout the entire space of a biosystem by the polarization code parameter. this helps to set a quick-response information contact among the billions of cells constituting an organism. the genome on the whole and the individual nucleus of cells can generate and recognize textassociative regulatory structures with the application of a background principle, holography and quantum non-locality. (gariaev, et al, 2000). we believe that the dna is the projector of the biohologram, both at the cellular level and at the whole-organismic level. this means that the dna creates a situation of a complex pattern of three-dimensional electromagnetic standing and moving wave fronts in the space that the organism occupies. dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 218-244 miller, i., mill, r. a. & webb, b., quantum bioholography issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 223 other researchers soon obtained similar results, and not only based on photons. multi-frequency physical fields are now teleported. based on this data, it‟s possible to suppose that photon fields, emitted by chromosomes as sign fields, can be teleported within or even outside the organism‟s space. the same is true for wave photon fronts, which were read from the chromosome continuum similar to reading from a multiplex hologram. if photons are transformed into radio waves (the situation we found ref. to [8, 33,37]) through the epr-mechanism, then this phenomenon is vital. in fact, the importance of quantum non-locality existence for a genome is hard to overestimate. (gariaev, et al, 2001). we think that these wave fronts interact with, interpenetrate with, and interdetermine the physical substance that makes up the physical creature. according to the holographic model of reality, all the objects we can observe are three-dimensional images formed of standing and moving waves by electromagnetic and nuclear processes. all the objects of our world are threedimensional images formed electromagnetically, i.e. holograms. just like a hologram encodes a 3-d image, the biohologram encodes and projects the blueprint of the human being, as well as other biological systems. we also believe that the nervous system constitutes a coordination mechanism that integrates dna projections of the rest of the cells in the system, that it is first and foremost a coordination mechanism which aligns these cellular holograms. imagine the information pleroma, beyond energy and matter, as the source of all infinitely coherent light, “shining” itself into its own entropic womb where our temporo-spatial universe is given its life-potential as a single laser beam. the dna in a particular cell is not totally active. it has been determined that there may be as little as 1% of the dna present in the nucleus of the cell acting as the determinant for the structure of that cell. the nervous system, interestingly enough, has the highest percentage of operating dna of any cell system in the body, of up to at least 10% of the dna in the brain cells. the neuron nuclei are most active. we suggest that the nervous system projects a global biohologram which interacts with the cellular bioholograms. if the membrane structure of the neuron nuclei is examined closely, it will be seen that the different cavity systems that enter the outer membrane also enter the inner membranes, therefore topologically, these are one and the same. hence the nucleus is lacking a membrane, or the neurons are lacking a membrane in the sense that two of their membranes are topologically one. we suggest that the neurons are not actually brain cells as such. we believe that the brain is the cell, and the neurons are like a distributed nucleus for that cell. that makes the glial cells organelles in the giant brain-cell. but they are also cells in their own right, much more so than neurons are. we believe the glial cells are infinitely involved with the biohologram, in its projections, and its coordination. to go further, the biohologram, projected by the brain, creates standing and moving electromagnetic wave patterns at different frequencies of the spectrum in order to effect different dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 218-244 miller, i., mill, r. a. & webb, b., quantum bioholography issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 224 biochemical transformations. there may be specific electrostatic fields, or there may be electrodynamic fields varying at various frequencies, from low (radio waves) all the way up the spectrum into visible light and beyond. another process of holography is called "acoustical holography". acoustical holography employs sound waves to create a movement on a surface that is used as the basis for creation of an optical hologram. so we essentially convert between a pattern of sound waves reflected off an object in space into a pattern of light waves that can reconstruct the shape of that object. we have a transformation between two levels of vibration, two media as it were, preserving a pattern in space. (miller and webb, 1973). we suggest that this happens to a much greater degree in the dna control of our bodies. the liver, for example, contains special function cells. the special function of the liver cells is created by the influence of the projection of the liver pattern on the dna in the cells in the area where the liver is created. we are suggesting an important feedback mechanism between the activation of the dna in a particular cellular tissue type that causes it to be that tissue type, and the biohologram being projected by the nervous system. this is bioholography. returning to the recent russian discoveries (gariaev, and reporter poponin), which seem to confirm the seminal discovery of miller and webb: both quantitative and qualitative data are crucial for the development of a new unified nonlinear quantum field theory which includes the physical theory of consciousness. the dna phantom field effect may be interpreted as a manifestation of a new physical vacuum structure which has been previously overlooked. it is perhaps a specific example of a more general category of electromagnetic phantom effects. results of the experiments as described by poponin showed that when dna was placed in a scattering chamber and bombarded with laser light a "phantom" was revealed, even when the dna itself had been removed. the dna was bombarded with weak coherent laser radiation in two frequencies; the intensity of the scattered light was measured, as well as non-linear localized excitations. the experimental team found a surprising effect while measuring the vibrational modes of dna in solution using a sophisticated “malvern” laser photon correlation spectrometer (lpcs), which tests the fluctuation dynamics of dna solutions. “in each set of experimental measurements with dna samples, several double control measurements are performed. these measurements are performed prior to the dna being placed in the scattering chamber. when the scattering chamber of the lpcs is void of physical dna, and neither are there any phantom dna fields present, the autocorrelation function of scattered light looks like the one shown in figure 2a. this typical control plot represents only background random noise counts of the photomultiplier. note that the intensity of the background noise counts is very small and the distribution of the number of counters per channel is close to random. figure 2b demonstrates a typical time autocorrelation functions when a physical dna sample is placed in the scattering chamber, and typically has the shape of an oscillatory and slowly exponentially decaying function. when the dna is removed from the scattering chamber, one anticipates that the autocorrelation function will be the same as before the dna was placed dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 218-244 miller, i., mill, r. a. & webb, b., quantum bioholography issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 225 in the scattering chamber. surprisingly and counter-intuitively it turns out that the autocorrelation function measured just after the removal of the dna from the scattering chamber looks distinctly different from the one obtained before the dna was placed in the chamber. . . two conditions are necessary in order to observe dna phantoms. the first is the presence of the dna molecules and the second is the exposure of the dna to weak coherent laser radiation.” (poponin). researchers hypothesize that some new field structure is being excited from the physical vacuum substructure. as long as the chamber is not disturbed, it is measurable for long periods of time. what is measured is light scattering from the dna phantom fields. what is attained is qualitative and quantitative information about the nonlinear dynamical properties of the phantom dna fields. its origin is related to physical dna. as yet, they have found no other substance which recreates or emulates the effect of the dna molecule. it is this model which suggests a more general nonlinear quantum theory which may explain many of the observed subtle energy phenomena and might lead to a physical theory of consciousness. this suggests that the electromagnetic phantom effect is a more fundamental phenomenon which can be used to explain other observed phantom effects, though not to be confused with the often misinterpreted secondary emission of electrons seen in kirlian photography and dubbed "phantoms." [ref. r.a. miller on "the physical mechanisms of kirlian photography," psychoenergetic systems, stanley krippner, ed., 1974]. evidence suggests a relationship to the phenomena of [endogenous] bioluminescence, liquid crystals, and superconductivity, which we intend to pursue, elsewhere. bioluminescence can be considered an indicator of life activity. it is the emission of photons of light produced when certain energized electrons drop into a lower or ground state. a common example is the visible light (or electromagnetic radiation) generated by the firefly. the importance of this phenomenon is seen by taking the broad view of the life process as we know it: photons from the sun excite electrons here on earth; this high energy state is transformed into high energy phosphate bonds by the process of photosynthesis; the release of the energy stored in these bonds is the fuel of life; electrons are transferred between molecules in a downward cascade fashion to lower energy states; this action produces the electric current that produces the motion that we call life. (miller, 1974). entities can also luminesce at higher frequencies than the normal visible spectrum, such as in the uv or microwave region. it has been shown that the human being is an emitter of various electromagnetic radiations. different emissions correspond to different body structures across the emission spectrum. these electromagnetic radiations are of course indicative of the energy state of the organism, and can be indicative of the state of health. other research (childre, 1992; paddison, 1992; king, 2001) suggests that consciousness is nonlocalized in the bodymind. joseph chilton peace in his latest, the biology of transcendence: a blueprint of the human spirit, (2001) points out that we have five neural centers or brains--and dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 218-244 miller, i., mill, r. a. & webb, b., quantum bioholography issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 226 establishes that our fourth and most recently developed brain is located in the head while the fifth is located in the heart. it is the dynamic interaction of this head brain (intellect) and heart brain (intelligence), of biology and spirit, which allows transcendence from one evolutionary place to the next. pearce declares we are quite literally, made to transcend. he says, "transcendence is our biological imperative, a state we have been moving toward for millennia." in less scientific and more mystical terms, we emerge through self-organization from the void and to the void we can return for renewal and sustenance. it is, in fact the heart sutra that informs us that "form is not other than void; void is not other than form." our human form is not other than this void, and biophysics now demonstrates this quantitatively and qualitatively. we are more fundamentally electromagnetic, rather than chemical beings. the void state, "cosmic zero," is the primal matrix and proportionately our most fundamental reality. in essence, we emerge from pre-geometrically structured nothingness, and dna is the projector of that field which sets up the stress gradients in the vacuum or quantum foam to initiate that process of embryonic holography, (miller and webb, 1973-93). the holographic paradigm is one of reciprocal enfolding and unfolding of patterns of information. all of the potential information about the universe is holographically encoded in the spectrum of frequency patterns that constantly bombard us. we can imagine that the self-organizing emergent function of the “rippling” effects of immense numbers of criss-crossing interference waves must be one way of making mutually interactive, or reciprocal, holographic projections of holographic projections. our dna projects our psychophysical self, and likewise “our brains mathematically construct objective reality by interpreting frequencies that are ultimately projections from another dimension, a deeper order of existence that is beyond both space and time: the brain is a hologram enfolded in a holographic universe,” (talbot, 1991, p. 55). researchers have found that at the moment of ovulation there is a definite shift in the electrical fields of the body of the woman. the membrane in the follicle bursts and the egg passes down the fallopian tube. the sperm is negative with respect to the egg. when the sperm and egg unite, the membrane around the egg becomes hyperpolarized, shutting out other sperm. it is at this moment that the electromagnetic entity is formed. the fertilized egg cell contains all the information necessary to create a complete operational human being. the biohologram begins to function at conception and ceases only at death. our contention is that the dna at the center of each cell creates the multi-cellular creature hologram by expressing the dna in the center of the cells. the biohologram projected by the embryonic nervous system forms a three-dimensional pattern of resonant structures. these include points, lines, and planes that electromagnetically behave as the acoustic waves the material waves of the drumhead, acting as field guides to flowing matter and energy. the gariaev group has proposed a theory of the dna-wave biocomputer. they suggest (1) that there are genetic "texts", similar to natural context-dependent texts in human language; (2) that dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 218-244 miller, i., mill, r. a. & webb, b., quantum bioholography issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 227 the chromosome apparatus acts simultaneously both as a source and receiver of these genetic texts, respectively decoding and encoding them; (3) the chromosome continuum acts like a dynamical holographic grating, which displays or transduces weak laser light and solitonic electro-acoustic fields. the distribution of the character frequency in genetic texts is fractal, so the nucleotides of dna molecules are able to form holographic pre-images of biostructures. in other words, the basic assumptions of the gariaev team include the following: 1. the genome has a capacity for quasi-consciousness so that dna “words” produce and help in the recognition of “semantically meaningful phrases”; 2. the dna of chromosomes control fundamental programs of life in a dual way: as chemical matrixes and as a source of wave function and holographic memory; 3. processes in the substance-wave structures of the genome can be observed and registered through the dispersion and absorption of a bipolar laser beam. this process of "reading and writing" the very matter of our being manifests from the genome's associative holographic memory in conjunction with its quantum nonlocality. rapid transmission of genetic information and gene-expression unite the organism as holistic entity embedded in the larger whole. the system works as a biocomputer -a wave biocomputer. the quantum nonlocality of the genetic information is fundamental. experimental work of the gariaev group shows how quantum nonlocality is directly related to laser radiation from chromosomes (light), which jitterbugs its polarization plane to radiate or occlude photons. the same researchers suspect the ability of chromosomes to transform their own genetic-sign laser radiations into broadband genetic-sign radio waves. curiously, mystics have always called the pervasive creative sacred sound, logos or word, the audible life stream (blavatsky, 1987; hines, 1996). they declare the light and the sound are one, and holographic concept is another name for unity. the polarizations of chromosome laser photons are connected nonlocally and coherently to polarizations of radio waves. the signal can be "read out" without any loss of the essential information in the form of polarized radio waves. the liquid crystal phases of the chromosome apparatus (laser mirror analogues) can be considered a fractal environment which stores the localized photons. this creates a coherent continuum of quantum-nonlocally distributed polarized radio wave genomic information. the genetic wave information from dna, recorded within the polarizations of connected photons, being quantum nonlocal, constitutes a broadband radio wave spectrum. this spectrum is correlated by means of polarizations with the photons. this is the main information channel of dna, the same for both photons and radio waves. this biocomputer memory and retrieval program features photon-laser-radiowave polarization spectroscopy. complex dynamics are expressed as fractal patterns at all levels of organization in nature. and this is no exception. the fundamental notion is, that the photon-laser-radiowave dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 218-244 miller, i., mill, r. a. & webb, b., quantum bioholography issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 228 features of different objects (the fourier-spectra of the radiowaves of crystals, water, metals, dna, etc.) are stored for definite but varying times by means of laser mirrors, such that the "mirror spectra" concern chaotic attractors with a complex fractal dynamics, recurring in time. this research is the first example of a novel static storage/recording environment (laser mirrors) capable of directly recording the space-time atomic/molecular rotary dynamical behavior of objects. it also demonstrates an essentially new type of radio signal, where the information is encoded by polarizations of electromagnetic vectors. this could even be the basis of a new type of still or video recording, leading to a new form of cinema. this newly detected phenomenon of quantized optical activity can be considered as the means by which an organism obtains unlimited information on its own metabolism. such information is read by endogenous laser radiations of chromosomes. the chromosome, in turn, produces the regulative ("semantic") radio emission of the genome biocomputer. semantic resonances in the biosystem's space are realized at both the wavelength level, and level of frequencies and angles of twist of the polarization modes. a gene has a holographic memory, (which is typically distributed, associative, and nonlocal), where the holograms "are read" by electromagnetic or acoustic fields. these carry the gene-wave information out beyond the limits of the chromosome structure. at this and subsequent levels, the nonlocality takes on its dualistic material-wave nature, as may also be true for the holographic memory of the cerebral cortex (pribram, 1991). pribram posits a neural holographic process, wherein images are reconstructed when representations in the form of distributed information systems are appropriately engaged. these representations operate as filters or screens. the temporary organization of cortical columns and the arrival of impulses at neuronal junctions converge from at least two sources, forming interference patterns. these patterns are made up of classical postsynaptic potentials, coordinated with awareness. this microstructure of slow potentials is accurately described by the equations that describe the holographic process which is also composed of interference patterns. from this it follows that in the brain information representing input is distributed over the entire extent of the neural pattern. in the bodymind information is also holographically distributed, each "part" having more or less information about the whole organism. information is fractally distributed and present in greater or lesser resolution. a neural holographic or similar process does not mean that input information is distributed willynilly over the entire depth and surface of the brain. it is confined primarily to those limited regions where reasonably stable junctional designs are initiated by the input participating in the distribution. holographic memory processing does away with the need for keeping track of where information is stored. the "filter," "sieve," or "screen" of holographic patterns is composed not only of the lattice of membrane macromolecules making up the synapto-dedritic net, but also of a facilitation of all tendencies toward image formation and the initiation of certain departure patterns of nerve impulses (pribram, 1971). dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 218-244 miller, i., mill, r. a. & webb, b., quantum bioholography issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 229 at the junctional patterns of neural activity, image forming capacity is enhanced. superposition, i.e. spatial interactions among phase relationships of neighboring junctional patterns occurs, with properties akin to those of optical information processing systems -the properties of holograms. chaotic dynamics are part of this image-forming process. there is order even in disorder. there is order, manageable chaos (fractals) and unmanageable chaos. the fractal dimension expresses the complexity of a particular fractal form. “fractal” comes from the latin fractus, which mean broken or fragmented. fractals delineate a whole new way of thinking about structure and form even the forms of dis-ease, which take root organically in the body and psyche. like holograms, magnify a fractal again and again and more detail emerges from its infinitely embedded structure. the same self-similar patterns repeat, over and over, no matter what level you care to examine. you look closer and closer and still see the same form. a single image is infinitely reiterated. thus, a wealth of structure emerges from simplicity. so, too, the dis-ease process can be seen at the physical, emotional, mental, and spiritual levels. yet, the form remains the same. "at the most fundamental level of our individual being, we too, our bodies and our psyches are part of the interference patterns caused by the interaction of consciousness and wave fronts arising from fields of infinite possibility. we then must also operate by holographic principles, thus our internal perception of this reality is itself a hologram in our brain. it is the means of perception that gives the universe its apparent forms and solidity. it is also this holographic perception that influences the dynamics of our brain's and our body's chemistry, our selfhologram. in this perceptual hologram resides the fundamental basis of our structure and our sense of self and external environment, including our health and illness in both our physiological and psychological being. our disease structures are incorporated within it. it is here, at this level of our being where fundamental healing and physical-psychic restructuring occur. this hologram is what i have termed the primal existential sensory self-image or existential hologram. . .our sense of self is a holographic, existential, multi-sensory image." (swinney, 1999). the key to this process lies in our dna, in our genes and gene-expression. our understanding of the human biocomputer must be based on a new understanding of the higher forms of the dna memory, and the chromosome apparatus, as the recording, storing, transducing, and transmitting system for genetic information, to be considered simultaneously at the level of matter and physical fields. the wave-biocomputer model helps explain the apparatus of protein biosynthesis of living organisms, providing an important interpretation of the initial stages within the hierarchic chain of material and field, sign, holographic, semiotic-semantic and, and figurative encoding and deciphering of chromosome functions. at the gene-sign continuum of any biosystem, dna forms pre-images of biostructures and the organism as a whole as a registry of dynamical "wave copies" or "matrices", succeeding each other. this continuum is the measuring, calibrating field for constructing or creating any biosystem, (gariaev). dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 218-244 miller, i., mill, r. a. & webb, b., quantum bioholography issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 230 ii. mechanisms: quantum mechanics and complex dynamics a quick review of the holographic concept refreshes us on the basics of biophysics. particles found in biological processes include photons, electrons, protons, elementary ions, inorganic radicals, organic radicals, molecules, and molecular aggregates. photons act upon electrons by raising their energy state. this process is called excitation. excited electrons can drop back to more stable energy levels and emit photons. electron excitation can lead to the formation of an electronic bond between molecules. this is the traditional bond of classical chemistry. the breaking of such bonds can, by reverse process, lead to the excitation of electrons. in living systems the excitation of electrons by photons and the subsequent conversion of that excitation into the bond energy is called photosynthesis and is the basic builder of biological structures. the reversal of this process is called bioluminescence. this phenomenon is the transfer of energy from a bond to an excited electron, resulting in the emission of a photon. it has been suggested by szent-gyorgyi (1957: 8) that the energetics of living creatures can be understood in terms of photosynthesis and its reversal, bioluminescence. all cellular processes are driven by energy derived from the breaking of chemical bonds and the excitation of electrons. depending upon the particular environment and circumstances, the excitation of the electron can be converted in one of three ways: (1) conversion into heat and dissipation (2) translation of molecules or ions through the cell, or (3) transformation of the molecules' shapes which profoundly influences their biological reactivity. the formation of a certain type of chemical bond known as the resonance bond (which is most easily seen in the case of the benzene molecule) leads to a peculiar situation in which certain electrons are freed from a local or particular location in the molecule. these are then free to travel around the entire molecule. this means that the electrons occupy an energy shell of the whole molecule as opposed to any particular atom in the molecule. the existence of molecular systems with mobile electrons has been found to be of profound significance in the phenomena of life. hydrogen, carbon, nitrogen, and oxygen, which compose 99 percent of all living systems, are among the atoms in the periodic table which form the multiple bonds most easily leading to mobile electrons. sulphur and phosphorus, which are extremely important for life processes, also form such multiple bonds quite easily. all the essential biochemical substances, which perform the fundamental functions of living matter, are composed completely or partially of such mobile electrons. molecules which contain these electrons are known as conjugated systems (pullman and pullman, 1963, chapter 18). the essential fluidity of life may correspond with the fluidity of the electronic cloud in conjugated molecules. such systems may best be considered as both the cradle and the main backbone of life. conjugate bonded molecules may interact in a variety of ways. among these types of interaction can be found the interpenetration of electron orbitals which permit an electromagnetic coupling. this coupling can permit activated electron energy to pass from one molecule to another in the dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 218-244 miller, i., mill, r. a. & webb, b., quantum bioholography issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 231 same way a radio can transmit a message to a radio receiver. there is also the possibility of the transfer of an entire electron which is known as charge transfer. it is possible for a molecular complex to contain several radicals at different positions on the main molecule, each of which are conjugated. if these are in close enough proximity, or can be brought into proximity by changes in the structural configuration of the molecule, a charge can pass between these two groups. this is the case of the transfer of electron charges on or around a single molecular complex. it has been suggested by szent-gyorgyi (1968) that the sugars and phosphates that make up the side of the alpha helix of dna can permit the passage of electrons, functioning as a conductor. the biological conduction systems operate primarily on an amorphous semiconductor mode as opposed to resembling metallic conductors. these do not have sharply defined energy bands in which electrons may flow, as opposed to other bands in which they are bound rigidly. there is a spread or bell-curve in which the points or tails are bound more closely to a particular molecule. the hump indicates a conducting band that permits electrons to flow across the surface of a particular molecule or between molecules (mcginness, 1972). this means, in essence, that protein molecules which are composed of amino acid sequences, may act as organic circuits. the amino acids each have a donor group and an acceptor group on opposing ends. this means that a string or series of amino acids could pass a charge along as if it were being passed along a series of spines sticking up from the main body of the molecule. different pathways could be defined across the surface of a protein molecule by the amino acid radicals projecting out from the surface of the protein. the shape of the protein molecules is a function of the charges and the conjugate systems on the radicals that make up the protein. when a protein is manufactured and peels off the ribosome, it immediately assumes a threedimensional spatial pattern that is directly related to the charges on its surface and the ways in which they interact. the biological activity or specificity of action of various molecules is intimately related to their structure or their exact three-dimensional spatial configuration. electronic energy and electrons can move through a protein molecule between its different parts and can pass among different molecules. we now come to understand a possible mechanism for biological regulation involving flows of electrons and transfer of electronic energy between molecules. these can change their shape and thereby change their specific action and activity. the fusion of electron clouds can exist within a conjugated system and among conjugated systems. this can account for cohesion or the adherence of such molecules to each other. such fusion is a very important determinate of the structure of larger aggregates of molecules and portions of living cells, such as membranes. iii. biohologram field theory a liquid crystal in a cell through its own structure becomes a proto-organ for mechanical and electrical activity, and when associated in specialized cells in higher animals gives rise to true dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 218-244 miller, i., mill, r. a. & webb, b., quantum bioholography issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 232 organs such as muscles and nerves. the oriented molecules in liquid crystals furnish an ideal medium for catalytic action, particularly of the complex type needed to account for growth and reproduction. a liquid crystal has the possibility of its own structure through singular lines, rods and cones, etc. such structures belong to the liquid crystal as a unit and not to its molecules which may be replaced by others without destroying them, and they persist in spite of the complete fluidity of the substance (needham, 1936). bernal's statement (1933) would seem to support burr and northrop's macro-atomic theory (1935), which postulates that there are two aspects to reality, the field and the particle. they associate the field with what they term the macroscopic aspect and the electron with the particle. they associate the field with what they term the macroscopic aspect and the electron with the particle. the particle is associated with movement. the structure of biological material seems to be associated with the field aspect. the electric field causes polarization of the macromolecules in the solution due to the fact that molecules possess a dipole moment, and changes the position of protons in the molecule. such action can affect the relative stability of different possible configurations of the macromolecules. the field affects the degree of structure present in the solution. a constant magnetic field can, in principle, affect the various processes in biological objects. three possible mechanisms for this biomagnetic affect are (1) the orientation of diamagnetic or paramagnetic molecules by the magnetic field (2) distortions of the angles in the molecules and (3) orientation of the spins of molecules in a magnetic field (fowler and bernal, 1933; freedericks and zolina, 1933; van iterson, 1933; osborne, ambrose and stuart, 1970). presman (1970) has postulated that such electromagnetic fields normally serve as conveyors of information, from the environment to the organism, within the organism, and among organisms. he suggests that organisms employ these fields in conjunction with the well known sensory, nervous, and endocrine systems, in effecting coordination and integration. muses (1970) has proposed the possibility of unit impulse functions evolving from the gaussian. his work traces the relation of that mathematical concept to quantum biological indeterminacy in terms of a process of the modulation of random fluctuations by target-seeking perturbations which points the way to the understanding and computing of the parameters of volitional experience in quantum biological terms. he maintains that we are dealing with gaussian wave packets, put to use in terms of a close-range reaction in turn resulting in the resonant microbiological specificity (arising from the relatively large number of specific molecular parameters) necessary to the essential life and evolutional processes of chromosome synapses, replication, and mutagenesis. muses holds that inherently indeterminate processes may be biologically used in achieving determinate ones such as our repeatable and commonly accepted volitional experiences of effort and direction. the range of quantum indeterminate fluctuation of biological efficacy is in the far ultraviolet, and it is in this spectral region that we should expect to look for any modulation effects on gaussian wave packets by volitional energies manifesting as ultramicrobiological field perturbations. dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 218-244 miller, i., mill, r. a. & webb, b., quantum bioholography issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 233 biologically, there is a threshold of non-randomicity below which peaks tend to emerge that are sharp enough to possess biodirectiveness in an enzyme-guiding sense. random biological quantum energies which are physiologically unassigned are the clue to psychosomatic directing, which can be beneficial or deleterious to the organism. muses (1970) describes the mechanism of this effect as a microbiolaser type process. heisenberg explored the possible relevance of the quantum indeterminacy of elementary particles for biological systems, especially human systems (discussed in koestler, 1972). he stated that there are two places in the human system where the quantum indeterminacy of a single particle can have a profound influence. the first important effect is that of mutation in the genetic code. the second important influence is the alteration of the behavior of neurons during human thought processes. tien (1969) has conceptualized mind as mass in relative motion and brain as energy at relative electrical charges in motion, like electrons bombarding a television screen, and personality is seen as a time series of scintillating frames of consciousness. personality becomes a reverbating input-output pattern of self-creation, seeking information or patterns of energy from the environment as well as from its own memories. the stability of any given personality of its identity is maintained by feedback upon the principle of most similarity. the personality never recreates itself, but creates only a close approximation which is accepted due to the principle of constancy as being the same. the phenomena of unique individuality and personal continuity depend on memory, of which consciousness is the most recent and, thereby, the most subject to erasure and loosening. personality transformation becomes energy pattern modification of not only scintillating consciousness but also of recent circulating memories and older stored memories of childhood. according to the holographic model of reality, all the objects we can observe are threedimensional images formed of standing and moving waves by electromagnetic and nuclear processes. all the objects of our world are three-dimensional images formed electromagnetically, i.e., holograms. this concept and the models of human information processing based on the hologram, throw interesting light on the philosophical tradition which holds that the world of objects is an illusion. with the triumph of relativity and quantum physics, the interpenetration of the philosophical and the scientific is possible. leshan (1969) has observed, in discussing some individuals who purportedly experience psycho-energetic phenomena, that their view of the universe as a great thought of which they are a part is quite similar to many physicists' view that they see reality only in their own mental image. we propose that the "reality hologram" which appears as a stable world of material objects is the elementary particle which has a long-term existence and fairly simple rules of interaction. we also propose the existence of a "biohologram" which appears as mobile and evolving, through dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 218-244 miller, i., mill, r. a. & webb, b., quantum bioholography issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 234 the dna molecule. this "biohologram" projects a dynamic three-dimensional image that serves as a guiding matrix for the manipulation and organization of the "reality hologram." (miller, webb, dickson, 1973). thus we have mobile self-organizing holograms moving through a relatively static simpler hologram. the possibility exists that such "bioholograms" could achieve sufficient coherence to continue existence as a pattern of radiant energy apart from a material substrate. we feel that such an occurrence could form the scientific basis of such psychoenergetic phenomena as psycho-kinesis, clairvoyance, telepathy, and precognition. quantum holography asserts that dna satisfies the principle of computer construction as defined by von neumann (1966). it carries a copy of itself and is its own blueprint written in the genetic texts where the mechanism engineering the dna replication is the biophotonic electromagnetic field, while the "letters" of the genetic texts, a, g, c, u are held invariant. in replication of the organism, the blueprint creates the "acoustic field" which mechanically constructs/engineers the organisms out of the available matter, in accordance with the information held in the electromagnetic field holograms. both quantum entanglement and therefore quantum teleportation can be related to quantum holography, through solitons, resonance effects, and superconductivity. experimental evidence confirms that the mutual recognition of one dna antiparallel half chain (+) by the other (-) concerns special super persistent/resonant acoustic-electromagnetic waves or solitons. dna solitons express two types of memory which concern the capability of non-linear systems to remember initial modes of energisation and to periodically repeat them [dubois, 1992]. the dna liquid crystals within the chromosome structure form such a non-linear system. the dna-continuum is quasi-holographic/fractal and relates, as is the case for any hologram or fractal, to the fundamental property of biosystems, i.e. their ability to restore the whole out of the part. dna solitary waves (solitons), and in particular, the nucleotide waves of oscillatory rotation, "read" the genome's sign patterns, so that such sign vibratory dynamics may be considered as one of many genomic, non-linear dynamic semiotic processes. the key parameter of such patterns is fractality. it can therefore be hypothesized that the grammar of genetic texts is a special case of the general grammar of all human languages. we can realize the wave-coding capabilities of the matter-wave sign functions of dna as true wave control capabilities facilitates in an aqueous solution acting as a liquid-crystal condition. the living cell is a computer based on dna. the genome has been identified as an active "laser-like" environment. yet this approach to dna-wave biocomputation means entering into new semiotic areas of the human genome and the biosphere in general. these are the areas which are used by nature to create humankind. the quasi-speech of chromosomes of all organisms concerns semantic exobiological influences wherein dna acts as a kind of aerial open to the reception of internal influences and changes within the organism as well as those outside it. this extends beyond it to the extent of the entire universe through complex fractal embedding and non-locality. dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 218-244 miller, i., mill, r. a. & webb, b., quantum bioholography issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 235 creation of biocomputers can be based on these totally new principles of dna-wave biocomputation, which use quantum teleportation [sudbury, 1997], (see also sciamer on quantum teleportation). experiments show that dna considered as a liquid-crystal gel-like state, reveals a periodically reoccurring pattern which acts on the incoming light in the manner of a solitonic lattice. what could such an action achieve? a soliton is an ultra stable wave train often with a seemingly simple closed shape, which can arise in the context of non-linear wave oscillations. really it consists of a rather complexly interrelated assembly of sub wave structures, which keep the whole solotonic process in a stationary state over a comparatively long time. the soliton is neither a particle nor wave in much the same as a quantum is characterized by wave-particle duality. it is a means to carry information. it probably reads the codons, as a travelling "window" that opens in the double helix structure as the reading takes place. in this model the reading process is a complex mechanical oscillator (gariaev, 1994), capable of producing solitonic wave transmissions, which take the form of a system of rotary pendulums. dna forms such pendulums in this model which are simulated as a chain of non-linear oscillators. the window as it travels is highly context dependent on the actual layout of the elements as specified by the actual genetic code sequence involved. complex dynamic patterns arise in the non-linear covalent connections between nucleotides. oscillatory activities are located somewhere together in the "acoustic" wave domain. as a liquid crystal, dna probably influences the polarization of the weak light emission known to exist in cells, as so-called biophotons. such biophotonic, mitogenic radiation or mitogenic light, while being ultraweak, is yet highly coherent. it has an inherent laser-like quality. endogenous intracellular coherent light is emitted by the dna molecule itself. the superposed coherent waves of different types in the cells are interacting to form diffraction patterns, first in the "acoustic" domain and then in the electromagnetic domain. this is a kind of quantum hologram. interactions of solitonic oscillations in the liquid crystal structure of dna and the polarization vector of the ultraweak biophotonic highly coherent light, could be understood as a mechanism of translation between holograms in the "acoustic" frequency domain of short range effects and those in the electromagnetic domain, and vice versa. quantum holography has been used to predict the workings of mri (schempp, 1992,1998). the dna-wave biocomputer model is also in agreement with the qubit model explanation of dna. in the quantum holographic dna-wave biocomputer theory, dna is a self-calibrating antenna working by phase conjugate adaptive resonance capable of both receiving and transmitting quantum holographic information stored in the form of diffraction patterns -quantum holograms. the model describes how during the development of an embryo of the dna's organism, these holographic patterns carry the essential holographic information necessary for that development. the quantum holographic theory requires that the dna consists of two antiparallel (phase conjugate) helices, between which are located hologram planes/holographic gratings, where the dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 218-244 miller, i., mill, r. a. & webb, b., quantum bioholography issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 236 necessary 3 spatial dimensional holographic image data of the organism is stored. endogenous laser illumination can be expected to turn the dna into a series of active adaptive phase conjugate mirrors/holographic transducers. a beam of radiation resonantly emerges on which is carried the holographic information as encoded in the dna. this confirms the quantum holographic prediction that dna functions as an antenna capable of both encoding and decoding holographic information. we can also model the quantum holography of the neuron. this model is in good accord with the biological neuron's information processing morphology and signal dynamics. this is the quantum holographic model of the brain as a conscious system. we can incorporate signal theory into quantum physics through the concept of the pilot wave or radar. quantum holography predicts polarized or orthogonally rotated holograms encoded on a "paged" associative holographic memory. sharp frequency adaptive coupling conditions specify very narrow spectral windows, i.e. the "pages." "magic windows" are a naturally tuned frequency of a good hyperchannel between orthogonal frames where scalar wave anenergies crosstalk readily. they are frequency dependent interdimensional nodal points. some magic windows are 38-40 hz; 150-160 khz; 1.1-1.3 mhz; 1.057 (lambshift) and the near ultraviolet (life energy frequency), (beardon, 1988). described in terms of tensor multiplication, the orthgonality condition can be seen as specifying a set of diagonal elements, which traces in a unit matrix in the frequency domain. the planes on which the base pairing takes place concerns two quantum holograms. the tensor operation, in quantum holography, describes a quantum entanglement. murray gell-mann describes quantum entanglement in the quark and the jaguar (1994). he first points out that coarse graining can wash out interference terms. the interference terms between two coarse-grained histories is the sum of all the interference terms between pairs of fine-grained histories belonging to those two coarse-grained ones. the underlying explanation for decoherence is the mechanism that makes interference terms sum to zero and permits the assignment of probabilities. it is the entanglement of what is followed in the coarse-grained histories with what is ignored and summed over. iv. biological effects of scalar energy there are only a few known forces in nature and unfortunately we are at a loss to explain what their actual sources are. the best physics has been able to do is ascribe them to some fundamental characteristics of the universe, a charge of some kind. that's why we can more abstractly view a force as the variation of a certain potential and therefore practically every influence field can be thought of as a force field. this potential can be a scalar as in the case of coulomb's law; a vector as in the case of the electromagnetic vector potential which neatly streamlines the mathematics of maxwell's equations; or a tensor, which is the case of the metric tensor of the riemann space in einstein's gtr equations. dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 218-244 miller, i., mill, r. a. & webb, b., quantum bioholography issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 237 there is a predominance of non-linear processes in biological systems. several types of quasiparticles, each with their own characteristic resonant frequencies have been proposed to mediate these non-linear phenomena, including solitons, excitons, and plasmons. the right frequencies of non-linear energies might have profound healing properties, according to stanford researcher dr. glen rein. due to the non-linear nature of biological systems it is proposed that scalar waves should be more biologically active than their linear electromagnetic counterparts. in the simplest cases, scalar resonance can be imagined as two ordinary single-frequency em standing waves in a resonant cavity, with the two waves coupled exactly 180 degrees out of phase so that --externally--their e fields sum to zero and the capacity is said to be in scalar resonance. the cavity walls must act as phase conjugate mirrors (pcm). mass itself is simply a standing scalar resonance, with the standing walls tapped by particle spin. the atomic nucleus continually bombarded by virtual photon flux from the vacuum is a pumped pcm. since the nucleus is positively charged, it produces phase conjugate replicators (pcrs), having negative energy and negative time. it thus produces negentropy, which prevents the entropic decay of the atom. essentially all frequencies can be and are present at once, but certain nuclear resonance frequencies are thought to predominate. by increasing the amplitude of the standing scalar wave that is the nuclear pseudopotential, inertia and mass of the nucleus are increased. zeroing the amplitude dematerializes the nucleus. (beardon, 1980). so, scalar energy is transduced into linear electromagnetic energy in the body by liquid crystals in the cell membrane and solid crystals found in the blood and in several biological tissues. clinical studies of the effects of scalar energy on the mind-body and brainwaves have been conducted since the 1980s. if they can be believed, research from stanford university medical center produced some tantalizing results. electrochemical oscillation between membrane-bound lipids near phase-transition temperature have been analyzed with and described by nonlinear quantum mechanical equations. they also analyzed the coupling between harmonic oscillators represented by action potentials generated from active neuronal networks in the central nervous system, finding evidence of chaos. the extraction of scalar components from maxwell's original electromagnetic equations and from schrodinger's equation using imaginary numbers has been reported, and their unusual non-linear waves described by many experimenters. a crystalline transduction theory has been put forth to explain the interactive mechanism of scalar waves with biological systems. another possibility is transduction in microtubules dispersed throughout the whole organism. tissue culture studies imply that the action of scalars on biological systems is more than a placebo effect mediated by the brain/mind, such as stress, moods or beliefs. stray em energy in the ambient atmosphere makes it difficult to study the healing properties of scalar energies in a clinical setting. clinical healing sometimes occurred several months after initial exposure to the scalar waves. it is known that the brain and body, each the immune system, communicate bidirectionally. thus, a direct action of scalar energy on the body could cause a subsequent change in brain state. therefore eeg studies do not indicate whether scalar energy also effects the body directly or whether the brain and the body are both affected. even if scalar energy directly affects individual dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 218-244 miller, i., mill, r. a. & webb, b., quantum bioholography issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 238 cells, it may also affect the mind resulting in an altered psychological outlook which results in clinical improvement. dr. michael persinger (1987) was the first person to test the effects of scalar energy using isolated cells. the scalar waves were generated by partially canceling two vortex-type magnetic fields (0.shz, 10pt) by intersecting them in the air. the biological endpoint, degranulation of mast cells, was increased by the scalar fields. dr. puharich, in another study, grew tissue samples of e. coli, and detected an increased activity of ubiquitone, a protein involved in dna repair. these results indicate that scalar energy can have a direct effect at the subcellular level as well as a direct effect on the immune system. another project detected an effect of scalar energy on neurotransmitter function, which mimicked the effect of antidepressant medication. scalars appear to modulate the basic biochemical communication between nerve cells mediated by neurotransmitters. cultured nerve cells called pc 12 cells were isolated from rats, and the functional properties of noradrenaline release from pc 12 cells was shown to be increased by a 500hz monopolar square wave, and noradrenaline uptake was inhibited by a 15hz biopolar square wave, (rein). noradrenaline uptake was chosen because it is directly mediated by the plasma membrane via an intramembrane protein carrier. the plasma membrane, with its liquid-crystal structure, is the critical cellular barrier which interfaces with the chemical and electromagnetic environment. since other intramembrane proteins show non-linear properties, the plasma membrane is a likely target for scalar energy. the physiological function of carrier mediated neurotransmitter uptake is to remove excess neurotransmitter from the synaptic cleft after its release from presynaptic nerves. thus, inhibiting uptake results in the accumulation of the neurotransmitter in the synaptic cleft. this is the mechanism of action of tricyclic antidepressants, since they inhibit noradrenaline uptake. depression is associated with decreased noradrenaline levels. rein exposed confluent monolayer culture of pc12 cells to noradrenaline in the presence or absence of scalar energy. after 30 minutes, the cells were washed and centrifuged and noradrenaline uptake measured. overall, uptake was inhibited by 19.5% in the presence of the scalar field as compared with the control value obtained in its absence. this is a significant statistical difference of p 0.01. researchers think a wide variety of physiological changes could be created resulting in improvement of a variety of clinical diseases, only one of which could be depression. scalar energy can have a direct effect on the cell membrane. researchers want to test whether diseased cells are preferentially sensitive to scalar energy; and what characterizes its mechanisms of action. v. rossi’s dream-protein hypothesis on healing ernest rossi (1999; 2002) has developed a pertinent creativity hypothesis: “enriching life experiences that evoke psychobiological arousal with positive fascination and focused attention dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 218-244 miller, i., mill, r. a. & webb, b., quantum bioholography issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 239 during creative moments of art, music, dance, drama, humor, spirituality, numinosity, awe, joy, expectation, and social rituals can evoke immediate early gene protein cascades to optimize brain growth, mindbody communication, and healing.” “[the] psychotherapeutic approach can contribute to psychobiological arousal, enrichment and relaxation; it may be possible to help people find optimal levels of mental stimulation to facilitate actual growth in the hippocampus of their brain to encode new memory, learning and behavior...optimizing psychobiological growth and healing.” rossi (1999) describes a mind/body communication channel that is pertinent in that it may describe another way neural plasticity and healing manifests from rem. he describes how immediate-early genes (also called “primary response genes” or third messengers) play a central role in the dynamics of waking, sleeping, dreaming, and mind-body healing at the cellular level. there is evidence that immediate-early genes (iegs) function as mediators of information transduction between psychological experience, behavioral states, and gene expression. a wide range of behavioral state-related gene expression (from relaxation, hypnosis and sleep to high arousal, performance, stress and trauma) culminate in the production of new proteins or homeostasis, physical and psychosocial adaptation.” behavioral states modulate certain patterns of gene expression. interaction between the genetic and behavioral levels is a two way street. genes and behavior are related in cybernetic loops of mind-body communication. how does this relate, for example, to manic depression? a look at the systems related to iegs, shows that they affect all the systems disrupted in bipolar disorder. they are expressed continually in response to hormone messenger molecules mediating processes of adaptation to extracellular signals and stimuli. extracellular stimuli come from the outside environment, including temperature, food, sexual cues, psychosocial stress, physical trauma, and toxins. iegs are fundamental in the sleep-wake cycle, appetite regulation, sexual response, and reactions to stress, trauma, and toxins (rossi, 1986; 1999; 2002). there are persistent alterations in ieg expression in the process of adaptive behavior on all levels from the sexual and emotional to the cognitive. they can transduce relatively brief signals from the environment into enduring changes in the physical structure of the developing nervous system as well as its plasticity in the form of memory and learning throughout life. if external cues can modulate cell function through regulation of gene expression, this could also be true for internal cues. iegs are also fundamental in the regulation of rem-on, rem-off neurons, neuronal networks that are associated with rem sleep and dreaming. that makes them significant as molecules which can modulate mind, emotions, learning and behavior. they influence the rhythm of the natural healing process and circadian and ultradian rhythms of the body, in general. ultradian rhythms are those shorter than the 24-hour circadian rhythms (rossi; cheek, 1988). dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 218-244 miller, i., mill, r. a. & webb, b., quantum bioholography issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 240 milton erickson discovered that his therapy sessions usually took from one and a half to two hours to come to natural closure. later it was discovered that this delineates the natural work cycle that is harmonious with our own internal rhythms. iegs modulate this process. this ultradian time frame is related to the activation or deactivation of the expression of specific genes and can occur in a matter of hours or even minutes. “most arousing environmental stimuli that have been studied can induce immediate-early genes within minutes, their concentrations typically peak within fifteen to twenty minutes and their effects are usually over within an hour or two. these time parameter ieg expressions and their ultimate translation into the formation of new proteins correspond to the parameters of a complete work cycle of mind-body communication and healing. the changes in gene transcription and new protein formation initiated in this time frame, however, can lead to lasting changes in the central nervous system by converting short term memory to long lasting learning by the process of long term potentiation. . .the activation or deactivation of the expression of specific genes can occur in a matter of hours or even minutes." (rossi, 1999). this mechanism assesses the duration and intensity of prior waking and/or the homeostatic or executive mechanisms that bring about sleep. sleep deprivation leads to a wide variety of psychotic and non-psychotic symptoms. this system is also associated with the neuronal network associated with the dynamics of rem sleep. deprivation of rem and dreaming creates its own phenomenology. “the study of iegs indicates that sleep and wake, as well as synchronized and desynchronized sleep, are characterized by different genomic expressions, the level of iegs being high during wake and low during sleep. such fluctuation of gene expression is not ubiquitous but occurs in certain cell populations in the brain. thus...ieg induction may reveal the activation of neural networks in different behavioral states. do the areas in which iegs oscillate during sleep and wake subserve specific roles in the regulation of these physiological states and a general „resetting‟ of behavioral state? is gene induction a clue to understanding the alternation of sleep and wake, and of rem and non-rem sleep?” (rossi, 1999). in rossi‟s dream-protein hypothesis, “new experience is encoded by means of protein synthesis in brain tissue...dreaming is a process of psychophysiological growth that involves the synthesis or modification of protein structures in the brain that serve as the organic basis for new developments in the personality...new proteins are synthesized in some brain structures associated with rem dream sleep.” rossi generalizes the dream-protein hypothesis, “to include all states of creativity associated with the peak periods of arousal and insight generation in psychobiologically oriented psychotherapy.” enriched internal and external environments leads to the growth and development of new cells. ieg cascades lead to the formation of new proteins and neurons along with increased synapses and dendrites that encode memory and learning. on the other hand, excessive trauma and psychosocial stress can lead to suppression of growth processes in the brain. when dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 218-244 miller, i., mill, r. a. & webb, b., quantum bioholography issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 241 psychotherapy contributes to arousal, enrichment, and relaxation it facilitates actual growth in the brain to encode new memory, learning and behavior, optimizing growth and healing. “communication within the neuronal networks of the brain is modulated by changes in the strengths of synaptic connections...meaning is to be found in the complex dynamic field of messenger molecules that continually bathe and contextualize the information of the neuronal networks in ever changing patterns. most of the sexual and stress hormones...have state dependent effects on our mental and emotional states as well as memory and learning, a constantly changing dynamical field of meaning.” (rossi, 1991). novel and enriching psychotherapeutic experiences can lead to neurogenesis and gene expression which facilitate mindbody communication and can have a long-term transformative effect on the whole person (rossi, 2002). rossi points out that many of the essential dynamics of gene expression involved in the formation of the brain and body in embryology are now recognized as a continuing creative development through an individual's lifetime. he also asserts that a lack of optimal gene expression and neurogenesis is associated with psychological depression and stress. thus, bioholography has relevant applications for optimizing health and well-being across disciplines, such as biophysics, medicine, psychobiology, psychotherapy and the holistic healing arts. vi. conclusion sidorov (2002) has summarized the thrust of the gariaev group: since the early '90s, gariaev's team has been developing a new theoretical and experimental approach to the study of genetic material encoding and expression. in a pioneering paper (gariaev 2001; jnlrmi i(2)), he and his colleagues challenge the limits of the genetic code triplet model and propose instead a dual, substance/wave basis for the encoding and expression of genetic material. the wave-like, non-local aspect of genetic regulation is recorded at the polarization level of dna-associated photons, and the genome is seen as a quasi-hologram of light and radio waves which create the background necessary for the appropriate expression of genetic material. the authors argue that the genome emits light and radio-waves whose delocalized interference patterns create calibration fields (blueprints) for a system's space-time organization. this holographic-type information is being constantly and simultaneously read in billions of cells, accounting for the quick coordinated response typical of living systems. we can use the observations of the gariaev group to further summarize the essence of the human biocomputer: "thus, nonlocality can be postulated to be the key factor explaining the astonishing evolutionary achievement of multicellular biosystems. this factor says that bioinformatic events, can be instantaneously coordinated, taking place "here and there simultaneously", and that in such situations the concept of "cause and effect" loses any sense. this is of a great importance! the dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 218-244 miller, i., mill, r. a. & webb, b., quantum bioholography issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 242 intercellular diffusion of signal substances and of the nervous process is far too inertial for this purpose. even if it is conceded that intercellular transmissions take place electro-magnetically at light speeds, this would still be insufficient to explain how highly evolved, highly complex biosystems work in real time." [5] gariaev asserts that quantum nonlocality and holography is indispensable to a proper explanation of such real time working. "[t]he genes can act as quantum objects, and that, it is the phenomenon of quantum nonlocality/teleportation, that ensures the organism's super coherency, information super redundancy, super knowledge, cohesion, and, as a totality or whole, the organism's integrity (viability)." [5] quantum holography defines an admitter/absorber quantum vacuum model of quantum mechanics in terms of annihilation/creation operators [schempp, 1993]. this implies that dna does indeed behave like a single quantum, which induces a "hole" temporarily in the vacuum by its removal. this new understanding of biocomputers, constitutes a further step in a development of computer technology in general. an understanding that brings about a total change of the constituent basis of that technology to the figurative semantic (nonlocal) wave computer or biocomputer, based on dna memory, and the chromosome apparatus. quantum bioholography argues that dna satisfies the principle of computer construction, since it carries a copy of itself, its own blueprint, with the mechanism engineering the dna replication being the biophotonic electromagnetic field, while the "letters" of the genetic texts a, g, c, u are held invariant. the existence of the genetic text constitutes the classical signal process of quantum teleportation, and facilitates the quantum mechanical signal processes of both the copying of the dna as its own blueprint, and of the construction of the organism in a massively parallel way by means of quantum teleportation. references 1. beardon, thomas (1980, 1988, 2002), excalibur briefing, strawberry hill press, san francisco. 2. berezin, a.a., gariaev, p.p., et al (1996), "is it possible to create laser based on information biomacromolecules?", laser physics, v.6, n6, pp. 1211-1213. 3. blavatsky, h.p. 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(1969), pattern recognition and psychosynthesis. american journal of psychotherapy, 23, 53-66. 58. von neumann, j. (1966), theory of a self-reproducing automaton, university of illinois press, urbana and london. login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x dna decipher journal | october 2015 | volume 5 | issue 2 | pp. 78-93 king, c., evolution, sexual reproduction & the future of human society (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 78 article evolution, sexual reproduction & the future of human society (part i) chris king * abstract in this two-part article, the author argues that we urgently need to invest in ethical, social and political processes that respect the passage of the generations, and the genetic and fertility principles upon which conscious life depends. we need to invest in forms of government and decision-making which contain cumulative principles which will both generate a capacity to value long-term investment for the future of life and enable social change and cultural evolution to have a truly genetic character, as effective for long-term stability and survival as molecular genetics are. all people need to respect that fertility is a sacred process through which we all become conscious beings, that childbirth is an essential component of the passage of the generations. central to this is protecting the rights of women to reproductive, social and educational choice and providing adequate social, financial and contractual employment provisions to enable women to have children without compromising their professional or entrepreneurial careers. this is the ultimate test and end point of the scientific revolution, and is the fulfillment of the sense of living purpose religious traditions try to lay exclusive claim to, in which an ethic of living diversity and its protection must needs emerge and assert a natural morality for justice to prevail. science has provided us with the knowledge to understand, in confounding detail, overthrowing all our preconceived assumptions, how the natural processes in the universe actually work and come together to enable the continuity of life. it is now up to us to engender a moral and ethical movement that can function to cherish and replenish the earth throughout our generations to come. part i of this article includes: 1. introduction; 2. human emergence and the evolutionary paradigm; and 3. founding civilizations, religion and the patriarchal reproductive imperative. keywords: evolution, sexual reproduction, tree of life, genetic pathway, biological diversity. 1. introduction virtually all of the serious global problems facing the planet, from climate change, through habitat destruction to use of energy and natural resources, the ability to feed and care for a rising future population and our future viability, are long-term issues with time spans varying from decades to centuries, millennia and even millions of years. while addressing world poverty and resource equitability could take decades to achieve, even with the best of will, climate change will cause rising ocean levels and desertification that are likely to continue to reduce viable land areas for a thousand years to come. loss of species diversity will bring a detriment to our * correspondence: chris king http://www.dhushara.com e-mail: chris@sakina.org http://www.dhushara.com/ mailto:chris@sakina.org dna decipher journal | october 2015 | volume 5 | issue 2 | pp. 78-93 king, c., evolution, sexual reproduction & the future of human society (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 79 planetary genetic resources on a time scale since the last mass extinction of around 65 million years. many of these losses will never be recovered. fig 1: four global scenarios requiring urgent long-term solutions, clockwise from top left: (1) predicted world average july temperatures, indicating loss of crop production due to temperature and rainfall changes (nasa). (2) biodiversity zones surviving four different global warming scenarios (groombridge 1992 global biodiveristy). (3) world gross national income per capita shows spread of world poverty and affluence. (4) loss of land area in a 6m sea level rise (wikipedia). because of the long response time, it has been estimated that we are already committed to a sea-level rise of around 2.3m for each degree of temperature rise within the next 2,000 years. a temperature rise of 3 degrees would lead to a 6.9m rise, but up to 50m if antarctic ice sheets melted from below. dna decipher journal | october 2015 | volume 5 | issue 2 | pp. 78-93 king, c., evolution, sexual reproduction & the future of human society (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 80 these issues require collective action on a planetary scale and a sense of future consciousness which can weigh up needs for major and potentially costly action in the present, whose effects will only slowly be felt, because they are cumulative over much longer time scales and the capacity to balance immediate priorities against much longer term goals. yet all the evidence is that as the pace of change accelerates, our future time horizons are shrinking towards rapid reaction on ever shortening time scales as technology and communication provide more rapid ways of reacting to accelerating changes and instabilities, which dominate our crisis management and tantalize our investment opportunities. . fig 2: top left: increasing instability in forex trading over two decades due to accelerated computer trading. top: right the flash crash. explanations included order flow toxicity, market order depth and net aggressive buy volume, but eventually navinder singh sarao, the "hound of hounslow" was charged with wire and commodities fraud, and market manipulation using an automated trading programme, "spoofing" financial markets using commercially available software to place $200m of false trades. lower charts: the extent to which global wealth has become corralled by a virtual handful of the so-called 'global elite' (2014 oxfam). the richest 85 people on the globe control $1 trillion, as much wealth as the poorest half of the 7 billion global population put together. the wealth of the one percent of richest people in the world amounts to $110 trillion, 65 times as much as the poorest half of the world and the situation has clearly been getting more inequitable between 1980 and 2012, as the right hand chart shows. this is not progress. far right super-exponential l-shaped curve of extreme affluence displayed in a logarithmic plot of us income. . we have entered an age where it has become demonstrably obvious that the time scale of major decision-making has shortened to the detriment of our long-term planetary futures. we are depleting non-renewable resources that have taken hundreds of millions of years to accumulate in a matter of decades, precipitating climate change whose effects will exacerbate for a thousand dna decipher journal | october 2015 | volume 5 | issue 2 | pp. 78-93 king, c., evolution, sexual reproduction & the future of human society (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 81 years and a mass extinction of the diversity of life that will deplete the living resources of future generations for millions of years to come. at the same time our investment horizons are ever shortening, both in terms of national and global economic management and in terms of the dynamics of commodity trading and investment to the point where future horizons look forward no more than six months and lightspeed commodities trading using computer algorithms on a time scale of milliseconds has become a norm, causing instabilities like the 'flash crash' in which over a thousand points were abruptly wiped off the us stock exchange in a matter of seconds due to predatory computer trading algorithms, only to recover minutes later. winner take all venture capital investment and its tendency to cause a tragedy of the commons through the struggle to capture resources before a competitor can do the same, and with it intellectual property rights which extend to the natural gene system of the planet hold sway over international diplomacy and the foundation of major trade agreements such as the prospective trans pacific partnership (tpp). in such a climate, short term investments realizable in the immediate term take precedence over long term investments, which may themselves be unwound by short term gains of competitors, so that in a so called informed era, long-term precautionary actions essential for our long-term viability and survival are given scant attention or put in the 'too hard' basket. the inability of even the most educated and highly-developed democratic countries to some to terms with effective long-term strategies, which can balance short-term economic growth against our long-term future survival has become a pathological feature of an electoral system where competing parties vie with one another to promote often highly emotive conflicts of agenda which will serve their short-term goals, targeted to each upcoming election cycle, to the abandonment, or even outright denial, of serious long term issues that could harm the future welfare of generations to come. how has this situation come about? is it a function of the failure of human intelligence to deal with completely understandable issues in the mass, or is it a product of something deeper to do with how cultures have emerged out of an evolutionary paradigm, which until recently maintained long-term stability through generation-by-generation conservation of social patterns modulated only by gradual changes at the genetic level through mutation and natural selection over many generations. dna decipher journal | october 2015 | volume 5 | issue 2 | pp. 78-93 king, c., evolution, sexual reproduction & the future of human society (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 82 fig 3: latest high accuracy predictions show no sign of population growth peak by 2100. left: world population trends in the latest 2014 study show high confidence estimates of world population growing from the current 7 billion to 11 billion by 2100 with no sign of reduction (10% and 5% variations in darkening colours). right: growth by continent with africa failing to curb population growth (gerland p et al. 2014 world population stabilization unlikely this century doi:10.1126/science.1257469). this shows that the unrestrained population growth is largely confined to africa, with other continents stabilizing and some countries experiencing a population decline due to falling fertility rates. inset left: current fertility rates in children per woman. at the same time that the world human population is reaching potentially unsustainable levels in terms of food and energy supplies, precipitating the destruction of the natural wilderness for large scale agricultural production, human reproduction rates have become highly unstable. the advent of hormonal contraception has led to a divorce between sexuality and reproduction which has resulted in educated secular populations and particularly educated intelligent women choosing not to reproduce in favor of their work and careers. at the other extreme, conservative religious followers, driven by patriarchal doctrines, try to ensure their womenfolk get pregnant at every opportunity to "go forth and multiply", expanding the utopian power of their religious hegemony and underprivileged and maladjusted individuals who fail to manage contraception continue to reproduce unabated in an age where medical science has vastly reduced the natural limits of infant mortality in all but the most deprived economies. the end result is a series of evolutionary paradoxes where the most capable people are tending to breed themselves out of existence, while the least advantaged and most religiously traditional sectors of society are reproducing in a relatively unrestrained trajectory. many developed countries, from germany to japan are failing to replace their existing populations and are likely to be gradually overtaken by migrant subcultures, while overcrowded countries such as egypt and india are becoming even more overcrowded. this picture raises fundamental questions both about how human society got itself into this situation and how we can learn from these events to develop a sustainable culture which both respects individual freedoms and freedom of reproductive choices on the part of both sexes in a way which is also consistent with our future evolution as a species and our planetary survival as a species and a culture. dna decipher journal | october 2015 | volume 5 | issue 2 | pp. 78-93 king, c., evolution, sexual reproduction & the future of human society (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 83 2. human emergence and the evolutionary paradigm if we look back to our human origins and the societies of our sister species, we can see that stability in evolutionary epochs is maintained through the genetic process. a lion a gazelle and a shark have the form and behavior that they do because, over countless generations, small changes to their genes have been fixed through mutation and selective advantage in a paradigm which otherwise conserves the genetic pattern and with it their social behavior from generation to generation. the evolutionary process is thus cumulative on a comparable time scale to geological, and natural climatic change. a shark does not transform into a sea gull in the next generation nor a gazelle into a lion. the greatest changes we see from generation to generation are differential a small increase in flipper size for a mud dwelling fish as it moves out of the sea onto land over many generations, or a greater facility with talking and understanding speech. animal societies share many features with human societies. for example chimpanzees like humans are female exogamous, with the females moving to join patrilineal troupes consisting of related male individuals, dominated by an alpha male. unlike humans, chimp females are openly promiscuous and mate in estrus with all and sundry from their home troupe so as to avoid infanticide. however, like humans, females will also mate on the side with partners of their choice 'on safari' when they are out discretely foraging in the forest. ape societies thus maintain a genealogical paradigm not unlike a human gather-hunter band of related individuals. they learn forms of tool use for catching termites with sticks and cooperative group hunting for smaller prey. they form both hierarchies of power and cooperative coalitions and express both support for trusted comrades and retribution for individuals who have threatened their security or attacked their offspring. but the form of the society is rooted in the reproductive paradigm and in well-established ecological niches of the species in its foraging and hunting and protection from larger predators. the relative dominance of males in chimpanzee society can be contrasted with that of bonobo societies, where a dominant female holds sway over a coalition of females who keep male aggression in check, with a young male gaining status through his mother and both femalefemale and male-female sexual engagement being a universal mediator of tension in which female-female sexual intimacy can occur up to seven times more frequently than heterosexual coitus. . http://dhushara.com/paradoxhtm/homo.htm#anchor-pan-58521 http://dhushara.com/paradoxhtm/homo.htm#anchor-pan-13458 dna decipher journal | october 2015 | volume 5 | issue 2 | pp. 78-93 king, c., evolution, sexual reproduction & the future of human society (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 84 fig 4: the evidence from human sexual evolution implies that female reproductive choice has been pivotal in the emergence of human culture and super-intelligence. lower center: the human female makes one of the greatest parenting investments of all mammal species in a pregnancy which comes at great risk because of the large human baby's head. she is also highly vulnerable. it is thus essential for her to be selective about who she gets pregnant with to ensure enough support and protection. female sexual characteristics include voluptuous breasts, not shared by the apes, and an hour-glass physique emphasizing her fecundity. unlike the overt ape estrus, human females are permanently sexually receptive, except perhaps during menstruation, have clandestine ovulation and display lunar-coupled menstrual synchrony (lower left). it has been suggested this was linked to granting of sexual favours for meat. it was noted in 19 th century south africa that bushmen were driven to steal cattle to satisfy their women's demands for meat for sex. the related sandawe have a fertility rite called phek'umo resembling the san eland dance of menarche, fig 5, in which the women twerk their buttocks at the men in the full moon. all these factors imply that in early human societies, female coalitions, who provided 85% of the diet through gathering, were astute in their sexual choices of men who were skilled hunters who provided meat for pregnancy, while also being resourceful and entertaining partners. top-left: the human vagina and clitoris is ecstatically orgasmic, providing human females with an ultra-sensitive measure of how intimate they feel with a sexual partner. top right: the human penis, by contrast with the muscular bony ones of the chimp and bonobo (illustrated) are larger and entirely tumescent, requiring both virility and good communication a genuine evolutionary indicator of fitness evolved through sexual selection by the female. lower-right female bonobos have an enlarged clitoris and mediate tensions by frequent orgasmic sex with both sexes. . the evidence from our own sexual evolution suggests that the large tumescent human penis, which differs from the more voluntary muscular boned penises of apes has been selected as a genuine indicator of fitness by human female reproductive choice, and that the ecstatically orgasmic clitoris, perpetual sexual receptiveness, expanded fatty breasts and hour-glass torso indicating nubile fecundity, concealed estrus making it hard for a male to know when a female is ovulating, and lunar phased menstrual synchrony are human features of sexual selection demonstrating the key role of female reproductive choice and female coalitions in the emergence of homo sapiens as a super-intelligent culture-forming species. http://dhushara.com/paradoxhtm/homo.htm#anchor-chris-23240 dna decipher journal | october 2015 | volume 5 | issue 2 | pp. 78-93 king, c., evolution, sexual reproduction & the future of human society (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 85 . with the advent of human culture, cumulative genetic change has given way to much more rapid changes. while we share 98% of our dna with chimps although splitting from their line around five million years ago. about 1.5-2 million years ago homo erectus emerged and by 500,000 years ago we find the divergence of homo sapiens andneanderthal and denisovan lines. we can also see back 150,000 years to founding forms of human culture with the mitochondrial division of the san bushmen into two lines separated by the arid kalahari between 150,000 years ago and about 70,000 years. the discovery of shell ornaments and ochre dating back a similar period, along with evidence of ceremonial cave use, shows humans of the time valued their beauty and fecundity and had already entered the cultural era. however, like chimpanzee and bonobo societies, these early forms of human culture remained highly attuned to the ecological niches of their natural environment, in which the females contributed 85% of the diet through astute gathering, while the males hunted game as meat in return for sexual favours, displaying their targeting prowess, complementing their musical and story-telling skills around the campfire. fig 5: top left: scored ochre block. blombos (c 77,000). peasized nassarius kraussianus shells pierced and showing wear from leather thongs (blombos cave c 75,000). second row: hundreds of small scale-like carvings on a snake-shaped rock along with 70,000-year-old spearheads nearby from a cave in the tsodilo hills of botswana, sacred to the local san people, who call it the mountain of the gods, has dramatically pushed back the earliest evidence for 'religious' ritual behavior. center: genographic project study of mitochondrial origins shows a deep split separating khoisan mitochondrial inheritance from other groups, including those migrating out of africa, and a deep division between two khoisan types l0k (*) and l0d (#) going back 140,000 years, suggesting a separation of some 100,000 years possibly caused by long term drought in africa (behar et al. 2008 the dawn of human matrilineal diversitydoi:10.1016/j.ajhg.2008.04.002). right: fulton cave drawing 1000 bc celebrating the first menstrual rite, drakensberg mountains, natal (van der post). the central figure is a young robed woman undergoing her first menstruation ceremony in a special shelter. circling her are clapping women, female dancers and (in the outer ring) men with their hunting equipment. two figures hold sticks; the women bend over and display 'tails' as they imitate the mating behaviour of elands. among living san, such rituals are intimately connected with success in hunting. each male figure has a bar across his penis, suggesting abstinence associated with menstruation valued for hunting luck. the surrounding figures, are all bending over, their buttocks playfully thrust in the direction of the menstruating girl. left lower row: these details match those still practiced by san and related groups in the eland dance of menarche. http://dhushara.com/paradoxhtm/homo.htm#anchor-erectus-35882 http://dhushara.com/paradoxhtm/homo.htm#anchor-the-49575 http://dhushara.com/paradoxhtm/homo.htm#anchor-more-47857 http://dhushara.com/paradoxhtm/culture.htm#anchor-11481 http://dhushara.com/paradoxhtm/culture.htm#anchor-24819 http://dhushara.com/paradoxhtm/culture.htm#anchor-35882 http://dhushara.com/paradoxhtm/culture.htm#anchor-11481 dna decipher journal | october 2015 | volume 5 | issue 2 | pp. 78-93 king, c., evolution, sexual reproduction & the future of human society (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 86 the san have preserved their gatherer-hunter culture throughout this long period partly because their reproduction rates have maintained parity with existing population sizes, through measures such as prolonged breast-feeding, which tends to suppress ovulation, and through forms of gathering and hunting which depend on taking from the natural environment, through ones knowledge of plant diversity and hunting skills, only those resources required to keep the existing population fed. while the san currently live on arid land in the semi-desert, which takes great skill and effort to eke out a surviving diet, eight thousand years ago they occupied more fertile lands across the southern half of africa, yet the deep trenches in their mitochondrial diversity attest to an almost static population living off gatherer-hunting in a stable ecological paradigm over periods of a hundred thousand years. moreover san peoples show many archetypes of features we might often associate with modern emancipated culture, individual autonomy and even spiritual attainment. they are loath to censure their children because they need to be able to grow up resourceful in an environment where individual prowess and good social judgment is essential. while they are nominally patriarchal and have male elders, it is traditional for a young woman delivering her first child to do so with the maternal family. they celebrate menarche as a sacred rite of power and significance to the whole group in a manner also depicted in cave paintings lasting back thousands of years. while they are skilled hunters with potentpoisons that can kill a man or large beast even using a small dart, they mitigate personal violence through living in small partially related bands in which emotional or physical violence is quickly reacted to. although men will mistreat women, women are able to make choices about whom they care to be with in a manner not unlike the hard-won gains of women in modern culture. they share a mystic experience in the trance dance and have religious notions of a creator deity and a deity of misfortune, along with shadowy sexual consorts, whom they regard in philosophical terms, without slavishly worshipping them, and share a concept of the afterlife not unlike those of the theological notions of major world religions. it is thus clear that human culture emerged as an extension of ecologically attuned animal sociobiology and that well into the cultural era, and the development of language, this attunement continued through the ethos of gatherer-hunter culture which sought to survive in the natural environment by consuming only what it could sustain to feed a small human population, without straining it to the point of depleting the natural supply. 3. founding civilizations, religion & the patriarchal reproductive imperative however with the advent of agriculture, triggered by discoveries by the female gatherers and animal husbandry as an extension of hunting, the emphasis shifted to intervening in the environment and ecology on a massive scale. we then enter a period of rapid change, in which the time scales of evolutionary and geological change become disrupted by vastly more rapid cultural changes. spoken languages diversify rapidly and written languages emerge on a time scale of transformation vastly faster than evolutionary change. cultures and civilizations rise and fall even more rapidly due to conflict between populations as new resources are exploited. http://dhushara.com/paradoxhtm/culture.htm#anchor-24819 dna decipher journal | october 2015 | volume 5 | issue 2 | pp. 78-93 king, c., evolution, sexual reproduction & the future of human society (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 87 agriculture and animal husbandry resulted in a sudden ballooning of human populations, expanding tribal bands to become our early civilizations, although the evidence of deficiency diseases points to a qualitative reduction in human dietary health, and denser populations became subject to the emergence of epidemic diseases. this also had major repercussions for social stability. as populations grew, so did the conflicts between burgeoning societies, leading to increasing militarization and the formation of male armies, which could protect a large population against invasion, but also served to repress social unrest internally in favour of dominant male leaders. the biological basis of morality is a reduction of intra-social strife through foregoing individual advantages over one another so that a society can maintain internal vitality and dominance in the event of inter-social conflicts. as urban societies grew, the cycle and pace of inter-social conflict increased, setting the process into overdrive, with large empires from assyria and rome, to the later conquests of leaders such as genghis khan. such leaders almost without exception used their power to enhance their own reproductive dissemination. currently around one in 200 people worldwide share the y-chromosome of genghis khan, and up to 8% in wide areas of central asia, due to he and his next two generations of male heirs siring a hugely disproportionate number of offspring. likewise tamerlane was said to have held 10,000 virgins behind flaming walls and solomon had seven hundred wives of royal birth and three hundred concubines (1 kings 11:3). in this sense, monarchy is and has always been a reproductive paradigm intended to be dynastic and pass on sovereignty to the royal line. the same hierarchical reproductive paradigm applies to rule by a clan strongman and to feudal rule by a local military land-holder. recent genetic evidence points to a massive change in the reproductive paradigm across all cultures and continents, from the establishment of agriculture 10,000 years ago. only 3% of mammals are socially monogamous due to the females delivering live young and having a principal reproductive investment in parenting, while males have a principal investment in fertilization. the variance in male reproductive success is thus always much greater than that of females, due to male competition for reproductive success among the available females, all of whom can get pregnant unless they are physically infertile. and social monogamy means just that, not reproductive or genetic monogamy. in socially monogamous species, from the albatross to the prairie vole, where circumstances favour a parenting resource from both sexes, females exert reproductive choice through clandestine sex with other males of superior genetic fitness as the opportunity arises, because, given the much greater parental investment of the female, it is counterproductive in evolutionary terms for females to literally put all their eggs in one resourcing partner's basket. humans share with such species a pattern where between 10 and 20% of offspring, allegedly of the resource-bearing partner, are sired by another male. although humans do show traits of strong pair bonding, and mutual partner choice as a function of the need of human infants for full-time care up to the age of about four, when they become socially and physically competent enough to fend for themselves as active members of an extended family, female reproductive choice is essential for the long-term viability of the human germ line because astute female choice of which male to entrust their huge parenting investment to is key to maintaining the mammalian xy based sexual selection, where the male has a single x and thus manifests the x-linked genes, many of which are involved in brain function in a unique pattern unmasked by the paired alleles of female double x. astute female reproductive choice thus plays a pivotal role in evolutionary selection. http://dhushara.com/paradoxhtm/fall.htm#anchor-emergence-23240 http://dhushara.com/paradoxhtm/prisoners.htm#anchor-only-44591 http://dhushara.com/paradoxhtm/prisoners.htm#anchor-only-44591 dna decipher journal | october 2015 | volume 5 | issue 2 | pp. 78-93 king, c., evolution, sexual reproduction & the future of human society (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 88 . humans and most traditional human cultures still share mammalian features ofpolygyny if a male has the prowess and resources to support (or even seduce) more than one female to reproduce with him, he will do so. thus in such societies around one in eight men have two wives. in western culture serial monogamy also serves as a clandestine form of polygyny, with men seeking new younger nubile partners to sire a second family with on divorcing their original wives whom they will generally have already had children with. fig 6: reproductive bottleneck in y-chromosome diversity began about 10,000 years ago and continued for several millennia (karmin m et al. 2015 a recent bottleneck of y chromosome diversity coincides with a global change in culture(doi:10.1101/gr.186684.114). because of these factors, over all time in human genetic emergence, from our last common human ancestors, the mitochondrial eve dating back 176,000 years and y-chromosome adam dating back some 73,000 years (wilder et al. doi:10.1093/molbev/msh214), one can verify a sexual reproduction ratio of around one reproducing male to every two females, with half of the males failing to find reproductive partners. this leads to manifest differences between the evolutionary trees of the y-chromosome carried only down the male line, and the mitochondrial dna carried only through the ovum of the mother to her children. however, with the emergence of agriculture and animal husbandry, the reproductive sex ratios became wildly skewed to a dna decipher journal | october 2015 | volume 5 | issue 2 | pp. 78-93 king, c., evolution, sexual reproduction & the future of human society (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 89 value of 17:1 over the entire period from 10,000 years ago to around 4,000, so that powerful agricultural landlords had their pick of an average of 17 female reproducing partners, while the other men effectively had no offspring, existing only as slaves, serfs, or soldiers maintaining the military domination of the mighty lords. the result was a precipitous decline in y-chromosome diversity unparalleled in mitochondrial evolution that became apparent only when extensive genetic studies of many populations were completed in 2015. neither is the effect confined to one historical culture, but extends to very degrees of severity across all the populated continents of the planet, confirming this has been a species-wide phenomenon, as shown in fig 6 (karmin et al. doi:10.1101/gr.186684.114). human cultures have been predominantly of patriarchal 'chimpanzee-like' patrilinial pattern, in which a woman moves to her husbands locale, and joins his patrilineal line, however there have also been significant matriarchal cultures, following a more 'bonobo-like' paradigm, in which women remain with the maternal family, sometimes having only transient encounters with their partners as lovers, in a so-called 'walking marriage', while maternal uncles act as surrogate fathers. the root reason this became an issue of violent conflict, as we shall see, is not just that men like to live with their wives in conjugal intimacy, but the uncertainty that comes from men never being sure who their offspring really are, while a woman is absolutely certain that each natural born child that comes out of her womb is hers. thus while jealousy in a woman is primarily about losing her relationship resourcing, jealousy in a man evokes potentially homicidal emotions because he fears his partner has been 'polluted' by another man's sperm and may give borth to a child who is not his. paternity certainty is the probability that you are your children's father. at the critical figure of 1/3 the following two calculations for patriarchal and matriarchal societies are equal: 1. you are therefore related to your own children by (1/2)(1/3) = (1/6), since if you were certain you were the father and half your child's genes come from the mother, the value is 1/2. 2. your relatedness to your "full" sister is at least 1/4 (representing your common mother) plus 1/4 (your putative common father) times the paternity certainty of 1/3, totaling 1/4 + (1/4)(1/3) = 1/3. since you thus share 1/3 of your genes with your sister and she provides 1/2 the genes of her children, you are related to her children by (1/2)(1/3) = 1/6. thus patriarchal societies enforce marriage to a husband to try to ensure paternity certainty is as close as possible to 1 even though this comes at the expense of curtailing female reproductive choice. there is clear evidence for early violent conflict between these two traditions in the founding civilizations of the fertile crescent. the book of genesis notes that polygynous jacob had to tarry for seven years for each wife with laban's maternal family before being ordained by god to depart with rachel and leah and his cattle to found the twelve patriarchal tribes of israel. rachel steals the maternal teraphim (house gods) and hides them under her menstrual skirt when laban comes to search for them, confirming the women have made the transition to religious patriarchy. . this is followed by a homicidal warning in judges 19, that matrilineal patterns were to be violently overthrown by a zealous patriliny. the concubine of bethlehem-judah is accused of dna decipher journal | october 2015 | volume 5 | issue 2 | pp. 78-93 king, c., evolution, sexual reproduction & the future of human society (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 90 'whoring' by going back to live with her father-in-law for four months. when the levite returns to claim her, the father-in-law keeps saying to stay a little longer for six days, nigh on a week. when the couple leave and turn in at gibeath of the benjaminites, men of belial ask to 'know the man within'. in an attempt to avoid sodomy, the host offers his daughter, to which they refuse. the levite then offers his concubine. she is raped and abused all night and dies on the doorstep, while her master sleeps peacefully. the story is a glaring affront to those matriarchal traditions, which expected the son-in-law to stay with the wife's family as jacob did. he then cuts her in twelve pieces and sends them to all the coasts of israel setting off the benjaminite wars. these are finally resolved in moving four hundred virgins of jabesh-gilead to their husbands homes, capped by the abduction of the daughters of shiloh dancing at a festival, to satisfy the remaining benjaminite men. religions in successive cultures have acted to reinforce the patriarchal reproductive paradigm, to ensure male control of female reproductive choice and the hyper-fertility of the religious community. while the code of hammurabi ordains drowning for adultery, but allows for forgiveness, deuteronomic law invokes the cruel and unusual punishment of stoning: . 22:20 but if this thing be true, and the tokens of virginity be not found for the damsel: then they shall bring out the damsel to the door of her father's house, and the men of her city shall stone her with stones that she die. . 22:23 if a damsel that is a virgin be betrothed unto an husband, and a man find her in the city, and lie with her; then ye shall bring them both out unto the gate of that city, and ye shall stone them with stones that they die; the damsel, because she cried not, being in the city. . islam has taken this homicidal tradition, which had centuries before been discontinued by the jews, and applied it to muslims as well: . narrated 'abdullah bin umar: the jews brought to the prophet a man and a woman from among them who had committed adultery. the prophet said to them, "how do you usually punish the one amongst you?" they replied, "we blacken their faces and beat them," he said, "you have told a lie! bring here the torah and recite it if you are truthful." so the prophet ordered the two adulterers to be stoned to death, and they were stoned to death near the place where biers used to be placed near the mosque. i saw her companion bowing over her so as to protect her from the stones. . to this day women suffer this diabolical form of torture and homicide at the hands of muslim men, buried to their waists and slowly knocked to pieces. these crimes against women and against the sanctity of all humanity occur both in sunni countries such as saudi arabia and in shiite iran. they are an unforgivable stain on the muslim tradition, which has an endless river of blood of women on its hands throughout history. it is compounded by patriarchal tribal customs enshrined in the quran and more restrictively in dubious hadith, that a woman is only half the value of a man in law and that women have to be veiled because their bodies are almost entirely sexual pudenda seductive enough to corrupt all men, to be confined to the home and sequestered dna decipher journal | october 2015 | volume 5 | issue 2 | pp. 78-93 king, c., evolution, sexual reproduction & the future of human society (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 91 by their male relatives to avoid any chance of them being impregnated. honour killings abound if a woman so much as touches a man of her own choice. . fig 7: islam is unique among world religions for invoking violent and homicidal penalties for non-lethal and sometimes harmless offences to society, completely inconsistent with its claim to be a religion of peace. left: genocide and sexual slavery (fitna) seven hundred jews were beheaded in the souk of medina, despite not actually betraying the muslims to the meccan quraysh, and their womenfolk taken into sexual slavery, after muhammad appointed a mortally wounded fighter as judge over their fates. right: both shiite iran and sunni afghanistan are among several muslim countries that stone women to death for alleged adultery (internet news) it difficult or impossible for a muslim to 'switch out'. center: muslim women are required to cover themselves, sometimes including their eyes and entire face, because muslim culture fears unveiled women are too sexually attractive (eid news). they are sequestered and in many countries not allowed to associate socially without a male member of their family chaperoning them. the world needs to consider whether such homicidal crimes against humanity can be allowed to continue as an institutional manifestation of 'freedom of religion'. . this severity of repression of women and reproductive female choice has to be understood historically in glaring contrast to the fact that mecca and its surrounding centers such as taif were places of worship of the goddesses, al-lat, manat and al uzza. meccan culture before islam respected both religious diversity and women's status. this shows claims that islam improved the lives of women to be a strategic deception. in fact women were killed or maimed for opposing the muslim take over, as nawal elsadaawi in "the naked face of eve" attests: "sarah was a famous slave singer who aimed her barbed words against the moslems. she was among those whom mahomet ordered to be executed on the day of his victorious entry into mecca. in the region of el nagir, it was recounted that some women had rejoiced when the prophet died and abu bake, the first of the caliphs, ordered their hands and feet to be cut off. thus women who dared to give voice to their protest or opposition could be exposed to cruel punishment. their hands might be cut off, or their teeth pulled out, or their tongues torn from their mouths. this last form of punishment was usually reserved for those who were singers. it was said of these women that they used to dye their hands with henna, brazenly display the seductions of their beauty, and beat time with their fingers on tambourines and drums in defiance of god, and in derision towards the rights of god and his prophet. it was therefore necessary to cut off their hands and tear out their tongues". dna decipher journal | october 2015 | volume 5 | issue 2 | pp. 78-93 king, c., evolution, sexual reproduction & the future of human society (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 92 according to al-tabari muhammad had already murdered om kerfa (mother of kerfa), one of the most revered meccan matriarchs who was torn in half by camels at the age of 90 for writing poetry ridiculing him: "mother of kerfa married a prince of the tribe of hathifa and bore for him 13 children the first of whom was kerfa by whom she is surnamed. all her children became leaders of their tribes. she was the dearest of all arabs, and an example of honor and pride to them. it was said if two tribes fought and mother of kerfa sent her scholl on a spear that was displayed to both parties, then they would reconcile out of respect for her. she used to annoy the prophet with her poetry so in the sixth year of the hijra (638 ad) he sent zaid son of haritha on a military expedition to kill her in the most heinous of ways. for he tied her legs with ropes and tied each of the ropes to a camel so that she was split in two. she was an old woman when this happened and her head was severed as proof to all that she had died. " although judaism still adheres to the biological reality that a person is a jew by birthright only if their mother is jewish, jewish culture nevertheless has subjected women to severe ritual confinement. the second chapter of genesis, although beginning in the edenic garden of gatherer-hunter integration with nature, casts a shadow of sexual guilt over the entire female sex, because eve the mother of all living enticed adam to eat the forbidden fruit of the knowledge of good and evil, when assured by the serpent that it would make one wise, so that they both became conscious of carnal knowledge and covered themselves with fig leaves. yahweh then withdraws the tree of life and shuts them out of primal paradise with a flaming sword, to sweat in agricultural struggle "thorns also and thistles shall it bring forth to thee; and thou shalt eat the herb of the field" with woman to be ruled over by her husband and to go travail in the pain of childbirth. nevertheless, the central command of god is "go forth and multiply". a woman thus takes an intermediate position in the commandments between a man's house and cattle: thou shalt not covet thy neighbour's house, thou shalt not covet thy neighbour's wife, nor his manservant, nor his maidservant, nor his ox, nor his ass, nor any thing that is thy neighbour's." note however that the commandment to honour one's parents is not simply a dictate for obedience to authority, but an insightful statement about how inter-generational consciousness engenders an enduring life process through the passage of the generations, central to this article's thesis: honour thy father and thy mother: that thy days may be long upon the land which the lord thy god giveth thee. christianity has taken up on the theme of the fall from eden, to accuse women of being 'the devil's gateway', placing all humanity in the shadow of 'original sin', with women to be seen but not heard in the church, and priests of the catholic tradition being required to be celibate men. it regards sex as purely to reproduce and that pleasure outside fertilization is sinful, and treats contraception as a crime against god. it has enforced monogamous marriage and outlawed dna decipher journal | october 2015 | volume 5 | issue 2 | pp. 78-93 king, c., evolution, sexual reproduction & the future of human society (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 93 divorce in the shadow of jesus' statement: "have ye not read, that he which made them at the beginning made them male and female for this cause shall a man leave father and mother, and shall cleave to his wife: and they twain shall be one flesh? what therefore god hath joined together, let no man put asunder." however this does not imply monogamy. jewish midrash claims that eve of genesis 2 was adam's second wife, while the woman made female with him in genesis 1 was lilith, who took flight when he insisted she take the 'missionary' position in subservience to him. these biased reproductive traditions extend to many other patriarchal cultures, from hindu india, where wives were expected to throw themselves on their husband's funeral pyre in the rite of suttee, and brides are regularly burned to death over the dowry, through china where women's feet were bound and a wife's principal task was to be subservient and produce a son for the family line, to the warrior cultures of the americas, where, among some tribes, such as the yanomamo, up to 20% of women are forcibly abducted and have to bear the burden of hard physical work, and to countries from egypt to sierra leone, where girls are genitally mutilated to cut off the source their their ability to enjoy sex to ensure they will remain faithful. an estimated 130 million women, averaging 6000 a day have undergone sexual mutilation. . fig 8: left: female genital mutilation in muslim egypt where 75% of women are mutilated (cnn) right: bride burning in india. contrast between ages of female burning victims in the uk and india, where there is a huge peak at marriageable age, shows the cumulative effect of bride burning, which involves around 25,000 deaths a year , a three times higher per-capita rate then th uk. between 1994 and 2001 the proportion of burned women in postmortems rose from 12% to 30%. . how sad it is to be a woman!! nothing on earth is held so cheap... no one is glad when a girl is born: by her the family sets no store... she bows and kneels countless times. she must humble herself even to the servants. fu xuan (217-278) (continued on part ii) http://dhushara.com/paradoxhtm/girlchild.htm#anchor-till-49575 http://dhushara.com/paradoxhtm/warrior.htm#anchor-yanomamo-54980 http://dhushara.com/paradoxhtm/circ.htm#ole_link1 http://dhushara.com/paradoxhtm/circ.htm#ole_link1 dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 540-541 smetham, g. p., brief biography of graham p. smetham 540 brief biography graham smetham, b.a., studied mathematics at essex university, england and philosophy of religion at sussex university. during his time at sussex he taught a subsidiary course for scientists on the interconnections between western science and eastern philosophical perspectives and it was through the investigations undertaken during the preparations for this course that he began to have the insights which later developed into wide ranging and detailed explorations contained in his first book quantum buddhism: dancing in emptiness. at sussex he was also part of the religious studies society and at one of its meetings he met the inspirational western theravadin monk ajahn sumedho, then the abbot of chithurst monastry, sussex. ajahn sumedho electrified the audience with his joyful effervescent presence and wisdom. at the time graham was becoming increasingly disillusioned with the western academic practice of endless conceptual juggling with no transformational practice and the contact with the community of chithurst monks and nuns convinced him of the need for both intellectual understanding and transformative meditation practice. although at that time graham had a publisher eager to publish his ph.d. work, illness and increasing disillusionment with western-style academic life led him to abandon an academic career and he gave up working on the ph.d., subsequently he began to lose contact with his intellectual and spiritual roots as he pursued other aspects, ultimately less fulfilling, of life’s pathways. during this time, however, buddhism and the philosophy of science always played a part in the background as he was always drawn to these subjects and somehow ‘knew’ that they were significant for him. he always had a strange feeling that something which had been left behind for the moment was still lingering in the wings. then, some twenty years after leaving sussex university, at a time of extreme personal crisis, graham returned to a serious meditation practice, something that had fallen by the wayside. during one meditation session he was astonished to have a profound meditation vision, like having a cinema screen inside his head, during which he was surrounded by an assembly of manjushris whilst a bowl of orange nectar at his heart radiated channels of orange nectar to the hearts of the surrounding manjushris. graham was further astonished to come across a book a week or two later in which the vision was described as being one of a set used by buddhist practitioner-philosophers prior to writing dharma texts. graham subsequently joined a buddhist community and resumed the researches that he had abandoned twenty years earlier. the result is quantum buddhism: dancing in emptiness–reality revealed at the interface of quantum physics and buddhist philosophy. graham has written three more books: the grand designer: discovering the quantum mind matrix of the universe, quantum buddhist wonders of the universe and quantum buddhism and the higgs discovery: the power of emptiness. further details of these can be found at www.shunyatapress.com. further details of the first book, and some free articles, can be found at www.quantumbuddhism.com. graham is currently working on his fifth book evolution: the greatest illusion on earth, the articles in the current issue are draft chapters from this work. http://www.shunyatapress.com/ http://www.quantumbuddhism.com/ dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 540-541 smetham, g. p., brief biography of graham p. smetham 541 quantum karma: bohm’s implicate order and the mind-only buddhist ground consciousness (alayavijnana) dna decipher journal | november 2011 | vol. 1 | issue 3 | pp. 351-382 smetham, g. p., quantum evo-devo universe ii: materialists’ metaphoric phantoms of matter in mind issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 351 article quantum evo-devo universe ii: materialists’ metaphoric phantoms of matter in mind graham p. smetham * abstract in this exploration of ramachandran’s account of metaphor and language, taking account of the actual evidence provided by evolutionary development biology and quantum physics, we find that his naïve materialist perspective of how brain functioning creates the world of meaning is nothing more than a phantom in his brain. yet again it will be shown that the primary process of evolution is not that which takes place over time on the material plane but, rather, it is that process of development which cascades from a deep quantum level of intentionality through a sequence of immaterial and subtle “implicate orders” of “unfoldment”, to use the terminology of david bohm. keywords: ramachandran, sean b. carroll, dawkins, dennett, stapp, hawking, wheeler, bohm, materialism, evolution, evo-devo, language, synesthesia, metaphor, consciousness, intelligent design, creationism. early on in his recent work the tell-tale brain v. s. ramachandran recounts a conversation that he once had with a member of a ‘creation science institute’, a vocation which ramachandran indicates must be oxymoronic. having established the mental defectiveness of his interlocutor by association with the notion of creationism ramachandran proceeds to tells us about the account given by the ‘distinguished looking man’ of the process of vision: there is an optical image of the chair in my eye – on my retina. the image is transmitted is transmitted along a nerve to the visual area of the brain and you see it. of course, the image is upside down, so it has to be made upright again before you see it. 1 this account, ramachandran tells us, ‘embodies a logical fallacy called the homunculus fallacy’, which is the mistaken view that there must be a ‘little man – a homunculus – inside you head looking at the image and interpreting or understanding it for you.’ 2 now, although one might accept that the creationist’s account of the mechanism of vision is somewhat vague, imprecise and perhaps inept, given that he is addressing someone he might know to be a researcher into neurological mechanisms, it does not explicitly require the adoption of the notion of a homunculus inside the skull. our unfortunate target for ramachandran’s implicit ridicule might just as likely, if pressed, in fact more likely if you think about it for a moment, to have suggested that there must be some kind of brain mechanism doing the job of reverting the image, rather than an interpretative inhabitant inside the skull. however, i guess that creation scientists are oxymoronic enough to warrant the odd lampoon. * correspondence: graham smetham, http://www.quantumbuddhism.com e-mail:graham@quantumbuddhsim.com http://www.quantumbuddhism.com/ mailto:qb@delysid.bltc.net dna decipher journal | november 2011 | vol. 1 | issue 3 | pp. 351-382 smetham, g. p., quantum evo-devo universe ii: materialists’ metaphoric phantoms of matter in mind issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 352 an interesting side effect of this unkind treatment on the part of ramachandran is the standard that it sets for the evaluation of ramachandran’s own somewhat cavalier accounts of the mechanisms which he thinks are responsible for the remarkable phenomena he describes in his book. consider this account from an earlier part of the book of why a patients’ phantom limb was exorcised along with the associated pain by the patient using a mirror in order to make his mind and brain ‘think’ that his remaining arm, reflected in the mirror, was the missing limb, a technique or trick ramachandran calls ‘mirror visual feedback’: when faced with such a welter of conflicting sensory inputs-no joint or muscle feedback, impotent copies of motor-command signals, and now discrepant visual feedback thrown in via the mirror box-the brain just gives up and says, in effect, “to hell with it, there is no arm.” the brain resorts to denial. 3 sounds like the kind of explanation a neuroscientist might come up with at a dinner party to entertain non specialists. ramachandran is quite exuberant with his metaphoric and anthropomorphic treatment of the brain and elements of the brain such as neurons. does the fact that when the region of the brain called the angular gyrus is damaged a patient can no longer do simple arithmetic indicate that the ability to 'know number' and perform arithmetic is 'neatly packaged in the small tidy confines of the angular gyrus'? 4 damage to this area also leads to a loss of ability to use metaphor, so we know that ramachandran’s angular gyrus is in good working order. does the fact that certain ‘mirror neurons' in the brain of a monkey ‘fire’ in response to the observation of another member of the species performing some task actually mean that the mirror neurons are: adopting the other animal's point of view. these neurons … were for all intents and purposes reading the other monkey’s mind, figuring out what it was up to. 5 admittedly ramachandran, in places, indicates that his brain is operating with the neurons responsible for employing metaphors firing vigorously: it is as if higher brain functions are reading the output from [mirror neurons] and saying (in effect), "the same neuron is now firing in my brain as would be firing if i were reaching out for a banana; so the other monkey must be intending to reach for that banana now'. it is as if your mirror neurons are nature's own virtualreality simulations of the intentions of other beings. 6 but the relentless use of this kind of personification of various areas of the brain and 'neural circuits' leads to the image of various bits and pieces of the brain behaving like little homunculi interpreting or understanding inputs, messages and so on. and on some occasions he invokes the metaphorical empathizing power of the mirroring capacity of some neurons quite literally: imagine the head surgeon's astonishment when he found that the sensory pain neuron he was monitoring responded equally vigorously when a patient watched another patient being poked! it was although the neuron was empathizing with someone else. ... i like calling these cells "gandhi neurons" because they blur the boundary between self and others not just metaphorically, but quite literally, since the neuron can't tell the difference. 7 dna decipher journal | november 2011 | vol. 1 | issue 3 | pp. 351-382 smetham, g. p., quantum evo-devo universe ii: materialists’ metaphoric phantoms of matter in mind issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 353 but a few paragraph on ramachandran' metaphor neurons (probably in his inferior parietal lobule) are firing at full capacity when he offers an possible explanation as to why the empathetic firing of sensory mirror neurons don't cause us to ‘feel everything we witness’: …perhaps the null signal ("i am not being touched") from skin and joint receptors in your own hand block the signals from your mirror neurons from reaching conscious awareness. the overlapping presence of the null signals and the mirror neuron activity is interpreted by the higher brain centers to mean "empathize, by all means, but don't literally feel that other guy's sensations. 8 according to ramachandran the phenomenon of metaphor is crucial to the evolution of language. so important is the function of ‘cross-sensory association’ that he speculates that the necessity to develop such a capacity may be responsible for the evolution of the angular gyrus: this leads me to wonder whether the angular gyrus may have originally evolved for mediating cross-sensory associations and abstractions but then, in humans, was coopted for making all kinds of associations, including metaphorical ones. 9 and, as he views and presents his vision against the background of a deeply entrenched belief in a hardcore materialist version of evolution the evolutionary paradigm associated with richard dawkins and daniel dennett it is useful to examine the naïve evolutionary perspective that he adopts. at the outset of his discussion of the evolution of language ramachandran remarks that: with so many interlocking parts working in such a coordinated manner, it’s hard to figure out, or even imagine, how language could have evolved by the essentially blind process of natural selection. (by “natural selection,” i mean the progressive accumulation of chance variations that enhance the organism ability to pass on its genes to the next generation). it’s not difficult to imagine a single trait, such as a giraffe’s long neck, being a product of this relatively simple adaptive process. giraffe ancestors that had mutant genes conferring slightly longer necks had better access to tree leaves, causing them to survive longer or breed more, which caused the beneficial genes to increase in number down through the generations. the result was a progressive increase in neck length. 10 as we can see ramachandran’s presentation of the process of evolution is indeed ‘relatively simple’ and certainly glosses over the fact that in recent years the original simplistic version of materialist darwinism has had to be radically overhauled in ways which undermine the materialist basis of the usual view of ‘natural selection’. most significantly the assumption that the genes in each species must be essentially different has been shown to be mistaken. for instance the molecular biologist sean b. carroll writes in his excellent account of the evolutionary-development revolution endless forms most beautiful that the notion that the same solution to the development of various types of eye structure, the same solution being found in widely differing species, was due to different evolutionary paths has clearly been shown to be radically incorrect. the evolutionary biologist ernst mayr wrote in the 1960’s that: much that has been learned about gene physiology makes it evident that the search for homologous genes is quite futile except in very close relatives. if there is only one efficient solution for a certain functional demand, very different gene dna decipher journal | november 2011 | vol. 1 | issue 3 | pp. 351-382 smetham, g. p., quantum evo-devo universe ii: materialists’ metaphoric phantoms of matter in mind issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 354 complexes will come up with the same solution, no matter how different the pathway by which it is achieved. the saying “many roads lead to rome” is as true in evolution as in daily affairs. 11 however, this assumption, which mayr so confidently asserted was ‘evident’, has now been shown by the evolutionary-development revolution in biology to be completely false, there was absolutely nothing ‘evident’ about it at all! as carroll writes: the first shots in the evo devo revolution revealed that despite their great differences in appearance and physiology, all complex animals flies and flycatchers, dinosaurs and trilobites, butterflies and zebras and humans share a common “tool kit” of “master” genes that govern the formation and patterning of their bodies and body parts. … the important point to appreciate from the outset is that this discovery shattered our previous notions of animal relationships and of what made animals different, and opened up a whole new way of looking at evolution. 12 in other words, all animals, of whatever species whatsoever, share a fundamental genetic structure which underpins a hierarchical development of differentiation: because parts of the genetic tool kit are shared among most branches of the animal kingdom, they must date back, at least, to some common ancestor of those branches. that would place their origin far back in time, before the cambrian explosion that marked the emergence of large, complex animal bodies, more than 500 million years ago. 13 this clearly means that the fundamental gene template structure underlying all forms of animal life was in place at the very beginning of evolutionary diversification. as carroll’s explanation of the operation makes clear, the evolution through ‘random mutation’ producing the long neck of giraffes or the long truck of elephants and so on applies to the manner in which the basic template becomes modified, apparently through interaction with the environment, although, as we shall see, the notion that this is a mechanism mediated purely on the gene level, or that the entire process is essentially ‘random’, is now beginning to look suspect, there is evidence that intentional-like quantum processes, or ‘quantum epiontic’ processes, may be involved. an example of the fact that the various species are the result of variations based upon the theme of a fundamental animal template is provided by hox genes: a large body of work—on birds, frogs, mammals, and snakes, as well as insects, shrimp, and spiders—has proved that shifts in where hox genes are expressed in embryos are responsible for the major differences among both vertebrates and arthropods. those shifts account, for instance, for the way a snake forms its unique long body, with hundreds of rib-bearing vertebrae and essentially no neck, in contrast to other vertebrates [see photograph (below – fig 1)]. the shifts explain why insects have just six legs and other arthropods have eight or more. the new imagery of evo-devo can pinpoint when and how the development of these animals diverges. the study of hox genes has shown how, at an entirely new and fundamental level, these animals are the products of variations on ancient body plans—not wholly independent inventions. 14 dna decipher journal | november 2011 | vol. 1 | issue 3 | pp. 351-382 smetham, g. p., quantum evo-devo universe ii: materialists’ metaphoric phantoms of matter in mind issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 355 fig 1 hox genes determine the form, number, and evolution of repeating parts, such as the number and type of vertebrae in animals with backbones. in the developing chick (left), the hoxc-6 gene controls the pattern of the seven thoracic vertebrae (highlighted in purple), all of which develop ribs. in the garter snake (right), the region controlled by the hoxc-6 gene (purple) is expanded dramatically forward to the head and rearward to the cloaca. 15 the point is that both the chick and the garter snake body morphology develop from the same fundamental template through the alteration of the way that the hoxc-6 gene is expressed, and the expression is in turn determined by the activity of previously expressed genes, down through a hierarchical development of gene expression which takes place upon the basis of a fundamental animal ‘template’, a basic blueprint for sentient existence which carroll refers to as ‘ancient body plans’. as carroll says: …it is now clear that most body-building genes were in place long before most kinds of animal body plans and complex organs emerged. 16 the question which immediately arises, of course, is that of the origin of the ‘ancient body plans’. now a hardened believer in materialist evolution would probably want to say that the primordial template for animal existence itself must have evolved. however, this will not do because the evidence of the evo-devo paradigm clearly indicates, as carroll points out, that evolution requires somewhere back in the distance mists of the primeval swamp there is a ‘common ancestor’ which provides the basic gene template, so somewhere back in the chain there must be some prototypical ultimate common ancestor. the crucial issue, however, is whether or not we are to believe that there were at some point in the mists of the distant evolutionary past some kind of primal animal, swimming, roaming, slithering or, to employ an idiom instigated by susan blackmore, blobbing 17 around a primeval landscape. a good example to consider is the case of the distal-less gene complex which has a remarkable range of applications. simon conway morris describes the situation as follows: dna decipher journal | november 2011 | vol. 1 | issue 3 | pp. 351-382 smetham, g. p., quantum evo-devo universe ii: materialists’ metaphoric phantoms of matter in mind issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 356 as with pax-6 the original function of this gene is not certain, but some evidence suggests that its primary role was linked with the development in the embryo of the nervous system, and especially the sensory organs. now it so happens that in arthropods many of the sensory organs are located on the appendages, and accordingly when there was need for improved sensory perception so parts of the body protruded to extend the sensory range of the sensory cells. only later were such outgrowths on occasion employed for such purposes as locomotion. the widespread expression of the gene distal-less is, therefore, effectively a reflection of the recurrent and independent evolution of such limbs: in a sense distal-less hitchhikes as a sensory protrusion and is subsequently transformed to allow an additional function such as a leg or an antenna. 18 so it appears that the same gene complex responsible for organizing protrusions for extending the range of sensory apparatus were ‘only later’ ‘employed for such purposes as locomotion.’ the impression which is easily gleaned from such presentations is that there must be a sequence of animals across which a sense protrusion is, due to chance random mutation, gradually transformed into walking apparatus. but the notion that there could have been an intermediate animal which used the same protrusion to see and walk, or smell and walk, or hear and walk etc. is clearly difficult to contemplate seriously. this sense of dissonance is even more pronounced with the transformation which is supposed to have taken place, via ‘natural selection’, from gills to wings. carroll tells us that: the gill-to-wing theory always had evidence in its favor (just not enough weight to settle the matter). but, if indeed insect wings came from crustacean gill branches, does this mean that some kind of crayfish or shrimp just crawled onto land and started flying? no, not at all. there were many evolutionary steps between animals that carried a set of respiratory appendages and the origin of powered insect flight on two pairs of wings as we know it today. 19 but such a dogmatic belief in the power of gradualist ‘natural selection’ cannot mask the fact that, if this account were to be correct, there must be a point in the evolution from gill to wing when the final creature in the evolutionary sequence abandoned the gill function completely and threw in its lot with a life on the wing so to speak, and also, just as a few mutations back, there must have been an animal using its wings for extracting the odd fix of oxygen from water. does this sound plausible? for carroll, however, the fact that the same gene complex is responsible for limbs, gills and wings indicates that the one must have somehow transformed into the other through a fully materialized process of animal transformation through intermediate stages, which clearly means that there must have been an animal around at some walking and flying with the same appendage (the bat, of course does cling with its wings, but that is hardly walking!): in addition to showing how evolution can change the number and kind of repeated body structures, evo-devo is shedding light on how novel structures and new patterns evolve. bird feathers, for instance, are prominent examples of novelties that have emerged from changes in the ways tool-kit genes are expressed. so are the hands and feet of four-legged vertebrates, the insect wing, and the geometric color patterns on the wings of butterflies. it is easy to imagine that insects invented “wing” genes, or birds “feather” genes, or vertebrates “hand” and “finger” genes. but there is no evidence that such genes ever arose. dna decipher journal | november 2011 | vol. 1 | issue 3 | pp. 351-382 smetham, g. p., quantum evo-devo universe ii: materialists’ metaphoric phantoms of matter in mind issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 357 on the contrary, innovation seems to be more a matter of teaching old genes new tricks. 20 the notion here is that there was a first in the lineage of appendages, the original appendage whose ‘genes’ subsequently learnt ‘new tricks.’ if we accept the view then there ought to be a straight forward progression, and there are many suggestive snippets of clearly connected sequences such as the development of insect wings, supposedly from the ‘gill-like appendages’ of now extinct aquatic nymph forms, shown in fig 2 which is reproduced from endless forms most beautiful 21 . fig 2 however, the view proposed by carroll and other who wish to defend a thorough going materialist darwinism is that it is the direct material interaction between the activity of the aquatic nymph form and its putative descendents and the environment which drives the purely material functioning of material gene structure underlying the entire process. thus the sequence in fig 2 is considered to be an evolution over time which is taking place purely on a fully materialized level, somehow directly affecting the way in which a fundamental gene structure underlying all animal forms is expressed. however, this one dimensional interpretation is not necessarily correct because it is clearly mediated by the desire to fit a mainstream darwinian interpretation onto the evidence, ruling out other, more plausible, viewpoints. in fact we can detect here exactly the same determination to remain within the materialist darwinian paradigm that led mayr to confidently proclaim the ‘many roads to rome’ view of genetic development which later turned out to be completely wrong. as carroll says the evo-devo revolution ‘vaporized many previous ideas about how animals differ from one another.’ 22 as we shall see it is far more likely that the morphogenetic template which underlies both the expression of wings or gills lies on a deeper intentional structure of reality perhaps residing at the quantum level as quantum ‘probability structures’ or ‘implicate’ organizational structures. the term ‘implicate’ was employed by the quantum physicist david bohm who indicated that the evidence of quantum theory suggests a deep, hidden quantum level of reality from which dna decipher journal | november 2011 | vol. 1 | issue 3 | pp. 351-382 smetham, g. p., quantum evo-devo universe ii: materialists’ metaphoric phantoms of matter in mind issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 358 the life forms within the material world emerge. the quantum ‘implicate’ levels which contains traces of previous events and activities which occurs at the manifested ‘explicate’ level. in this case, rather than having to believe in a fantastic sequence of transformational animals each having a mixed appendage doing two jobs, the percentage devoted to one increasing whilst the percentage allocated to the other decreases, we consider that there may be a feature of the deeper organizational template, probably located within quantum ‘implicate’ orders, within which a protrusion appendage may be employed for various purposes, such as having an eye at the end or, on the other hand so to speak, walking. this multipurpose template is then ‘expressed’ in the appropriate form depending upon the animal and the particular part of the animal being expressed. such a viewpoint does not rule out evolution across time but it does not dogmatically assert this aspect to be the only or even primary cause. the evo-devo evidence fits this scenario far more closely (see my article quantum evo-devo universe: quantum evolution and the evidence of evolutionarydevelopmental biology in dna decipher journal, vol 1, no 2 (2011)); however there seems to be an in built desire, perhaps a product of evolution itself, within the practitioners of the biological sciences to keep the evolutionary perspective fully materialistic and mechanistic in demeanor. this tendency is nicely illustrated by carroll’s discussion of the transition from ‘many gills to a pair of wings’. the origin of insect wings, carroll tells us, had for a long time been a ‘contentious mystery,’ there were a couple of proposals but no consensus and no clinching evidence. but then, apparently, evo-devo came to the rescue with the discovery of the proteins involved in producing wings: apterous and nubbin: in order to test the theory that wings might be derived from the gill branches of crustaceans, michalis averof and stephen cohen traced how the apterous and nubbin proteins were expressed in the appendage of other arthropods, especially crustaceans. they found, quite strikingly, that apterous and nubbin were selectively expressed in the respiratory lobe of the outer branch of crustacean limbs. the best explanation for this observation is that the respiratory lobe and insect wing are homologous-that is, the same body part in different forms in the two animals. … the most probably scenario is that apterous and nubbin were used in making respiratory lobes in an aquatic crustacean ancestor of insects and have stayed on the job ever since… 23 but the fact that the respiratory lobe of the crustacean and the insect wing are homologous as carroll describes does not necessarily prove that crustaceans are ancestors of insects, it more plausibly suggests that there is an ‘implicate’, or quantum level (or somewhere between the deepest quantum level and full materiality), animal template which can vary according various factors including environment, the particular animal forms which end up in various environments over vast tracks of time will obviously depend upon environment. so over long time periods it would appear as if a purely linear materialist type of evolution were taking place where in reality a lot happens to be going on at deeper, hidden, perhaps quantum implicate levels. it is intriguing to note the way in which current evo-devo enthusiasts are desperately trying to fit the new evo-devo evidence, evidence which by carroll’s own admission contradicts the hardcore or ‘ultra-darwinian’ perspective (although it does not contradict darwin’s dna decipher journal | november 2011 | vol. 1 | issue 3 | pp. 351-382 smetham, g. p., quantum evo-devo universe ii: materialists’ metaphoric phantoms of matter in mind issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 359 fundamental insights, only the hardcore interpretation of these), into the darwinian paradigm. thus carroll tells us that: advances in the new science of evolutionary developmental biology—dubbed “evo-devo” for short—have enabled biologists to see beyond the external beauty of organic forms into the mechanisms that shape their diversity. much of what has been learned, about animal forms in particular, has been so stunning and unexpected that it has profoundly expanded and reshaped the picture of how evolution works. in the same stroke, evo-devo delivers some crushing blows against the outdated rhetoric of those who doubt that complex structures and organisms arise through natural selection. 24 in other words the dogmatic beliefs that were foisted onto the simple darwinian insight into the appearance of a purely materialist type evolution of species apparently driven by (selfish!) genes as ultimate units of existence (although such a view was never very plausible, despite its popular appeal) have clearly been shown to be what they always were, mistaken assumptions based on the prior acceptance of a materialist-mechanist worldview. but, carroll is quick to point out that the new insight, having demolished the mistakes of the old style darwinism, still, he thinks, delivers a ‘crushing blow’ to those who disbelieve ‘natural selection.’ the question he fails to address, however, is how different the evo-devo ‘natural selection’ is from the old, dawkins style, perspective. in particular do the new insights allow room, or even suggest, that the operation of some kind of intelligence at work in the process of evolution. the most plausible and coherent explanation of the evo-devo phenomenon is that the primordial template was never a fully materialized animal but, rather, resided as what rupert sheldrake calls quantum ‘virtual’ morphogenetic field within what quantum physicist david bohm called a quantum implicate order. sheldrake describes the process of embryonic development as follows: the development of multicellular organisms takes place through a series of stages controlled by a succession of morphogenetic fields. at first the embryonic tissues develop under the control of primary embryonic fields. then … different regions come under the influence of secondary fields, in animals those of limbs, eyes, ears etc. … generally speaking, the morphogenesis brought about by the primary fields is not spectacular, because it establishes the characteristic differences between cells in different regions that enable them to act as the morphogenetic germs of the organ fields. then in the tissues developing under their influence, germs of subsidiary fields, fields which control the morphogenesis of structures within the organ as a whole… 25 thus the development of the embryo is controlled by a nested hierarchy of morphogenetic fields, which are, according to sheldrake, ‘quantum probability fields’ 26 akin to bohm’s implicate orders. this is exactly what we should expect in a quantum evo-devo universe; the development of the embryo cascades through hierarchical levels of quantum morphogenetic fields in the same way that evolution also took place through a sequence of quantum implicate orders. dna decipher journal | november 2011 | vol. 1 | issue 3 | pp. 351-382 smetham, g. p., quantum evo-devo universe ii: materialists’ metaphoric phantoms of matter in mind issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 360 a crucial implication of this viewpoint is that we should expect to find that aspects of animal morphology should anticipate what is to ‘evolve’ later, a situation which throws the entire materialist evolutionary paradigm into a questionable light. according to conway morris this is exactly what we can find when we look without the blinkers of a presupposed materialistevolutionary perspective: to give one example: the central nervous system of amphioxus is really rather simple. it consists of an elongate nerve chord stretching back along the body, above the precursor of the vertebral column (our backbone, consisting of a row of vertebrae) and a so called brain. the brain can only be described as a disappointment. it is little more than an anterior swelling … and has no obvious sign in terms of its morphology of even the characteristic threefold division seen in the vertebrate brain of hind-, mid-, and fore-sections. yet the molecular evidence, which is also backed up by some exquisitely fine studies of microanatomy, suggests that, cryptically, the brain of amphioxus has regions equivalent to the tripartite division seen in the vertebrates. the clear implication of this is that folded within the simple brain of amphioxus is what can almost be described as a template for the equivalent organ of the vertebrates: in some sense amphioxus carries the inherent potential for intelligence. 27 this insight, that it is ‘molecular evidence’ that indicates a tripartite division within the brain of the amphioxus is precisely what one would expect on the basis of bohm’s implicate order hypothesis, which is the notion that seeds of future development would be ‘enfolded’, which is the term bohm used, into the quantum level, which resides, as it were, just beneath the molecular. so, here, as conway morris suggests, we can see ‘the foundations of the molecular architecture which underpins our brains and sentience’ 28 intriguingly the amphioxus-like animals were extant during the cambrian period so may perhaps be considered to be one of the earliest fully materialized manifestations of a pre-cambrian virtual ‘common ancestor’. indeed, in the same way that aquatic crustaceans are suggested as beings ‘ancestors’, or ‘predecessors’ of insects, amphioxus is assumed to be the beginning of a line of evolution leading to the vertebrates. 29 however, as we have see, the notion that such a development is purely and simply a matter of a materialist-mechanistic accidental random continuous rearrangement of essentially lifeless material stuff is wearing thin, there is significant evidence that there are deeper levels of life-giving dimensions. dna decipher journal | november 2011 | vol. 1 | issue 3 | pp. 351-382 smetham, g. p., quantum evo-devo universe ii: materialists’ metaphoric phantoms of matter in mind issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 361 fig 3 – the amphioxus animal at this point it is worth considering the issue of what kind of ‘stuff’ the evolutionary process is made of so to speak. daniel dennett, possibly the monarch of materialist thought, tells us that: the prevailing wisdom, variously expressed and argued for, is materialism: there is only one sort of stuff, namely matter – the physical stuff of physics, chemistry and physiology – and the mind is somehow nothing but a physical phenomenon. in short the mind is the brain. 30 the notion that ‘the mind is the brain’ will find a willing believer in ramachandran, but if dennett really believes that the stuff of physics is ‘matter’, as the term is generally conceived of is incorrect. in his recent book quantum reality: theory and philosophy jonathan allday, in a section he entitles ‘substance abuse’, tells us that within quantum field theory, at the lowest level so to speak, there is no substance, the quantum field is actually ‘empty’ of substance. he writes: now, from a philosophical point of view, this is rather big stuff. our whole manner of speech … rather naturally makes us think that there is some stuff or substance on which properties can, in a sense, be glued. it encourages us to imagine taking a particle and removing its properties one by one until we are left with a featureless ‘thing’ devoid of properties, made from the essential material that had the properties in the first place. philosophers have been debating the correctness of such arguments for a long time. now, it seems, experimental science has come along and shown that, at least at the quantum level, the objects we study have no substance to them independent of their properties. 31 because there is no substantiality (and here allday is using the term ‘substance’ to indicate ‘matter’ as physicists and philosophers have generally understood the term) within quantum field theory the term ‘particle’ is dropped and the term ‘quanta’ is used, and these are ‘objects which have properties but not substances’. 32 another fundamental feature of quantum field theory is that fields are said to capable of creating and destroying quantum states; mathematically this is represented by creation and dna decipher journal | november 2011 | vol. 1 | issue 3 | pp. 351-382 smetham, g. p., quantum evo-devo universe ii: materialists’ metaphoric phantoms of matter in mind issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 362 destruction operators. but can we give some indication of what is really going on? what is actually doing the creating or destroying? according to the recent ‘quantum darwinism’ perspective: …quantum states, by their very nature share an epistemological and ontological role – are simultaneously a description of the state, and the ‘dream stuff is made of.’ one might say that they are epiontic. these two aspects may seem contradictory, but at least in the quantum setting, there is a union of these two functions. 33 in other words the quantum ‘dream stuff’ of reality, which is the non-substantial quantum field, is capable of producing the seeming solidity of the material world and the processes within it from out of ‘epiontic’ (epistemology creates ontology) acts of quantum perception. according to the quantum darwinism perspective: …focuses on the fact that proliferation of certain information throughout the environment makes its further proliferation more likely. 34 according to this interpretation the more often a quantum event becomes manifest the more likely it is to proliferate throughout the environment. this new quantum perspective indicates that: … the appearance of the classical reality can be viewed as the result of the emergence of the preferred states from within the quantum substrate through the darwinian paradigm, once the survival of the fittest quantum states and selective proliferation of the information about them throughout the universe are properly taken into account. 35 the ‘classical reality’ is the appearance of the everyday ‘material’ world and its apparent processes, including evolution; it therefore would seem to be the case that the appearance of classical level darwinian evolution is ‘the result of the emergence of the preferred states from within the quantum substrate through’ the quantum darwinian paradigm, a paradigm which requires the recognition of a minimalist intentionality capable of driving the epiontic process which creates the emergence of the classical realm from out of the quantum field of potentiality. this is a dramatic conclusion because it means that the confident assertions of materialist philosophers such as dennett are shown to be false. thus dennett’s strange glorification of mindlessness: an impersonal, unreflective, robotic, mindless little scrap of molecular machinery is the ultimate basis of all the agency, and hence meaning, and hence consciousness, in the universe. 36 cannot be taken seriously, physics clearly shows us that there is at least a minimalist epiontic intentionality driving the process of evolution. the influential physicist john wheeler anticipated the quantum darwinian epiontic paradigm when he wrote that he could only conclude from the evidence of quantum theory that: directly opposite to the concept of universe as machine built on law is the vision of a world self-synthesized. on this view, the notes struck out on a piano by the observer participants of all times and all places, bits though they are in and by themselves, constitute the great wide world of space and time and things. 37 dna decipher journal | november 2011 | vol. 1 | issue 3 | pp. 351-382 smetham, g. p., quantum evo-devo universe ii: materialists’ metaphoric phantoms of matter in mind issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 363 so for wheeler: … the universe is fundamentally an information-processing system from which the appearance of matter emerges at a higher level of reality. 38 and the ubiquity with which significant physicists support this kind of view is impressive. here’s martin rees, cambridge university professor and astronomer royal: in the beginning there were only probabilities. the universe could only come into existence if someone observed it. … the universe exists because we are aware of it. 39 and henry stapp, who in his early career worked and discussed these ideas with werner heisenberg: we live in an idealike world, not a matterlike world.’ the material aspects are exhausted in certain mathematical properties, and these mathematical features can be understood just as well (and in fact better) as characteristics of an evolving idealike structure. there is, in fact, in the quantum universe no natural place for matter. this conclusion, curiously, is the exact reverse of the circum-stances that in the classical physical universe there was no natural place for mind. 40 at the beginning of his scientific career planck thought that ‘matter’ was the solid, continuous and independent material ‘stuff’ of reality, whereas at the end of his quantum investigation of the matter of the stuff of reality he came to the conclusion that: i regard consciousness as fundamental. i regard matter as derivative from consciousness. 41 he also said: all matter originates and exists only by virtue of a force... we must assume behind this force the existence of a conscious and intelligent mind. this mind is the matrix of all matter. 42 and schrödinger can to a similar conclusion: mind has erected the objective outside world … out of its own stuff. 43 more recently the physicists bruce rosenblum and fred kuttner, in their important book quantum enigma: physics encounters consciousness, are clearly making a parallel claim regarding the far reaching implications of quantum theory: the physical reality of an object depends on how you choose to look at it. physics had encountered consciousness but did not yet realize it. 44 and: consciousness and the quantum enigma are not just two mysteries; they are the two mysteries; … … quantum mechanics seems to connect the two. 45 in their recent book the grand design stephen hawking and leonard mlodinow also indicate the necessary entanglement of consciousness at the quantum level. they present their conclusion is as follows: dna decipher journal | november 2011 | vol. 1 | issue 3 | pp. 351-382 smetham, g. p., quantum evo-devo universe ii: materialists’ metaphoric phantoms of matter in mind issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 364 quantum physics tells us that no matter how thorough our observation of the present, the (unobserved) past, like the future, is indefinite and exists only as a spectrum of possibilities. the universe, according to quantum physics, has no single past, or history. the fact that the past takes no definite form means that observations you make on a system in the present affect its past. [p82] and they press the point home with a description of the wheeler cosmic delayed choice experiment which shows the reality of determination of the past on the quantum level and conclude: …the universe doesn’t have just a single history, but every possible history, each with its own probability; and our observations of its current state affect its past and determine the different histories of the universe, just as the observations of the particles in the double-slit experiment affect the particles’ past. in the light of all this, one can only wonder how anyone can possibly still maintain a naïve version of materialism as ramachandran certainly appears to do. indeed henry stapp displays a modicum of exasperation with the situation when he observes that: the only objections i know to applying the basic orthodox principles of physics to brain dynamics are, first, the forcefully expressed opinions of some non-physicists that the classical approximation provides an entirely adequate foundation for understanding brain dynamics, in spite of the physics calculations that indicate the opposite; and, second, the opinions of some physicists that the hugely successful orthodox quantum theory … should, for philosophical reasons, be replaced by some theory that re-converts human consciousness into a causally inert witness to the mindless dance of atoms. neither of these opinions has any rational scientific basis. 46 this is not to say that understanding brain structure and functioning at the classical level has no validity or use, such a claim would be ridiculous. ramachandran’s research and work, for instance, clearly has a great deal of use and has helped many people. however, at several points in his recent book the tell-tale brain he indicates that he thinks that his classical level (as opposed to quantum level) investigations, together with anthropomorphic (‘the brain just gives up…’) and metaphoric explanations or descriptions of brain functioning, will solve the deepest mysteries of the universe: i recount my investigations of various aspects of our inner mental life that we are naturally curious about. how do we perceive the world? what is the so-called mind-body connection? … what is consciousness? how can we account for all those mysterious faculties that are so quintessentially human, such as art, language, metaphor, creativity, self-awareness, and even religious sensibilities? 47 but most of ramachandran’s questions, such as ‘what is consciousness?’, require ultimate answers, and if we assume, as has generally been assumed in our academic culture, that ultimate scientific answers as to the ultimate nature of reality is the realm of physics, then ramachandran, who investigates the structure and functioning of the brain, seemingly assuming with dennett that the brain somehow is, or at least generates, consciousness, is surely starting out down an evolutionary dead-end, for from an ultimate quantum point of view, as stapp points out: dna decipher journal | november 2011 | vol. 1 | issue 3 | pp. 351-382 smetham, g. p., quantum evo-devo universe ii: materialists’ metaphoric phantoms of matter in mind issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 365 …no such brain exists; no brain, body, or anything else in the real world is composed of those tiny bits of matter that newton imagined the universe to be made of. 48 furthermore, one would have expected ramachandran to be aware of these issues because in his introduction he writes that: the past two hundred years saw breathtaking progress in many areas of science. in physics, just when the late nineteenth-century intelligentsia were declaring that physical theory was all but complete, einstein showed that space and time were infinitely stranger than anything dreamed of in our philosophy, and heisenberg that at the sub atomic level even our most basic notions of cause and effect break down. as soon as we moved past our dismay, we were rewarded by the revelations of black holes, quantum entanglement and a hundred mysteries that will keep stoking our sense of wonder for centuries to come. who would have thought the universe is made up of strings vibrating in tune with “god’s music”? 49 and in his epilogue he writes in a similar vein: many of the greatest physicists of this century-werner heisenberg, erwin schrodinger, wolfgang pauli, arthur eddington, and james jeans-have pointed out that the basic constituents of matter, such as quanta, are themselves deeply mysterious if not downright spooky, with properties bordering on the metaphysical. so we need not fear that the self might be any less wonderful or awe inspiring for being made of atoms. you can call this sense of awe and perpetual astonishment god, if you like. 50 but, although ramachandran is prepared to allow the use of the term ‘god’ to merely indicate a sense of awe in the face of what he mistakenly describes as a ‘self’ which ‘made of atoms’ (quantum physics tells us that ultimately atoms are not independent of mind – they are, as he himself says, ‘downright spooky’), he is keen to try and debunk the debunkers who propound ‘intelligent design’: many complex, interwoven systems in biology have been held up by would be debunkers of evolutionary theory to argue for intelligent design – the idea that the complexities of life could only occur through divine intervention or the hand of god. 51 but it is clear that he identifies ‘intelligent design’ with ‘creationism’, which means that he seems to operate within the confines of two dogmatic extreme views when considering issue of the ultimate nature of reality: either an independent creator ‘god’ or a naïve materialism, and, remarkably, this naïve materialism seems to be maintained despite an awareness of the remarkably subtle insights into the ultimate nature of reality offered us by modern physics. according to ramachandran, in line with the outmoded views of all materialist minded proponents of the orthodox darwinian perspective, the evolutionary process is totally blind a dark, mindless, random churning of molecular machinery which in essence is antithetical to life but by some mindless mystery creates mind and life. with regard to the development of the eye for instance ramachandran asks: dna decipher journal | november 2011 | vol. 1 | issue 3 | pp. 351-382 smetham, g. p., quantum evo-devo universe ii: materialists’ metaphoric phantoms of matter in mind issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 366 …how could a vertebrate eye evolve via natural selection? a lens and retina are mutually necessary, so each would be useless without the other. yet by definition the mechanism of natural selection has no foresight so it couldn’t have created one in preparation for the other. 52 the answer, we are told, is supplied by richard dawkins who has, apparently, shown that there is a ‘logical evolutionary sequence that leads from the simplest possible light-sensing mechanism-a patch of light-sensitive cells on the outer skin-to the exquisite optical organ we enjoy today.’ 53 but the existence of a logical progression of steps is beside the point, it would be truly, truly amazing if there were not such a progression, the issue is why on earth ‘mindless’ matter, which by definition should have absolutely no desire to see, feel, walk around, eat, reproduce, produce consciousness and language, or survive in any form whatsoever, should suddenly become desperate to survive in various formations. the materialist paradigm offered us by ramachandran, dawkins and dennett and others requires us to conceive of the ultimate bits of reality to consist of ‘mindless little scraps of molecular machinery’ which when accidentally and randomly happen to conglomerate into certain formations suddenly and magically become desperate to survive. not only is such a view incoherent, it is also contrary to the evidence of quantum physics which indicates that there is at least a minimalist ‘epiontic’ intentionality operating within the quantum field of reality. in his book life without genes adrian woolfson presents us with a poetic vision of the sort of field of potentiality that he imagines must have ‘existed’ before the dawn of life within the universe: in the beginning there was mathematical possibility. at the very inception of the universe fifteen billion years ago, a deep infinite-dimensional sea emerged from nothingness. its colourless waters, green and turquoise blue, glistened in the nonexistent light of the non-existent sun … a strange sea though, this information sea. strange because it was devoid of location … 54 woolfson’s, strangely haunting, suggestion is that there must have been some kind of field of potentiality at the inception of the universe. this field can only be the quantum field of potentiality that contains: …all possible histories … through which the universe could have evolved to its present state… 55 in the beginning, of course, the quantum field of the universe would contain the templates for all the future evolutionary possibilities: the information sea is thus a quantum mechanical sea, composed from infinite repertoires of entangled quantum descriptions. 56 within this all encompassing wavefunction all possibilities for evolutionary manifestation are encoded. from out of the vast entangled web of infinite possibilities for manifestation only certain privileged members will actually make it into reality, so to speak: an information space of this sort would furnish a complete description of all potentially living and unrealizable creatures… 57 it therefore follows that there must be a sort of design woven into the potentialities for evolution; it is a vast complex design of all possible manifestations written into the quantum wavefunction of the universe standing on the very edge of time. dna decipher journal | november 2011 | vol. 1 | issue 3 | pp. 351-382 smetham, g. p., quantum evo-devo universe ii: materialists’ metaphoric phantoms of matter in mind issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 367 but such a field of potentiality is not sufficient to explain the origin of life; in addition there must be the internal ‘epiontic’ intentionality to unfold the potentialities into actualities. in buddhist dzogchen (great perfection) thought this is referred to an innate ‘excitatory intelligence’ or ‘pristine cognitiveness’ which operates to unfold fields of meaning and apparent materiality. the following is from herbert v. guenther’s translation and explanations, in his brilliant although metaphysically challenging book the matrix of mystery: scientific and humanistic aspects of rdzogs-chen thought, of the dzogchen writings of the remarkable tibetan philosopher-meditator longchenpa: the root of our material-mental universe is this self-existent pristine cognitiveness, a point instant virtual singularity; since its facticity is open-dimensioned and not discernable as any concrete thing, it is a meaning-saturated field as pristine cognitiveness. the radiation field of this open dimension is the intrinsic photic character of pristine cognitiveness. 58 here we find a description of the metaphysically early virtual energetic manifestations of ‘dynamically pulsating’ ‘pristine cognition fields’ which radiate out from the ‘point-instant virtual singularity’ due to its innate ‘excitatory intelligence (rigpa) whose high energy is termed sheer lucency’. and it is this kind of account of the origins of the astonishing variety of life, which includes a field of quantum potentiality together with an epiontic ‘excitatory cognitive intelligence’, which accords with both evidence of quantum physics and the discoveries of evo-devo. the following is conway morris’ brilliant parody of the kind of image that is regularly resorted to by television programmes devoted to expounding the origin of life: …images of warm ponds, seething volcanic springs, and massive thunderstorms rumbling across a deserted yet pregnant landscape are used to feed the imagination. at this stage, life has yet to exercise its peculiarly specific grip, its spinning of the genetic code, its weaving of biochemical complexities; but no matter: despite the vast pot-pourri of resultant chemicals, the nascent processes of darwinian selection are already winnowing and reaping, the inappropriate is steadily devoured in chemical competition with the winners. metaphorically the molecules slug it out by tooth and claw. cycles develop, life emerges, and four billion years later one species invokes the marvels of autocatalysis and emergent properties to cap the argument. these ideas are the bread and butter, so to speak, of a substantial part of the origin-of-1ife industry. 59 and ‘feeding the imagination’ is precisely correct, the materialist paradigm relies heavily on the technique of lacing their descriptions and explanations with words and phrases indicating intentionality where there should be nothing but blank mechanism, and because materialism is still, despite the weight of contrary evidence, the dominant cultural and academic paradigm, often very weak arguments and analogies pass muster for want of clear philosophical analysis. we shall find examples of such during the course of ramachandran’s account of his theory of the evolution of ‘language competence’: this competence is controlled by genes that were selected for by the evolutionary process. our questions in the rest of this chapter are, why were these genes selected, and how did this highly sophisticated competence evolve? is it modular? dna decipher journal | november 2011 | vol. 1 | issue 3 | pp. 351-382 smetham, g. p., quantum evo-devo universe ii: materialists’ metaphoric phantoms of matter in mind issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 368 how did it get started? and how did we make the evolutionary transition from the grunts and growls of our apelike ancestors to the transcendent lyricism of shakespeare? 60 the usual materialist assumption that evolution is a process of the accidental transformation of absolute meaninglessness into a world of ‘transcendent’ meaning, and this is the paradigm which ramachandran operates within. however, it must be pointed out that in this introductory snippet the picture offered is one of a transition from a ‘lower’ level and much reduced field of meaning-awareness to a much ‘higher’ one. admittedly the difference is dramatic; the ability to use the abstractions inherent within language competence apparently confers a remarkably heightened degree of self-awareness and awareness of the complexity of reality, but that does not mitigate the fact that the majority of the grunts and growls of our apelike ancestors are not ‘meaningless’. we are dealing, rather, with a more immediate nonabstract realm of meaning. ramachandran, however, is able to rely upon the fact that he has been ‘feeding the imaginations’ of his readers a rich diet of materialist metaphors on his way to his current point three-quarters of the way through the book so the implication that some way back in the evolutionary process there was absolutely no meaning of any kind around in the universe. a universe which has no intelligence within its design can hardly have any kind of in-built meaningfulness. as a point of contrast consider the conclusion drawn from quantum theory by david bohm who is adamant that ‘meaning is fundamental to what life actually is’, and, furthermore, this insight can be extended: …to the cosmos as a whole. we can say that human meanings make a contribution to the cosmos, but we can also say that the cosmos may be ordered according to a kind of “objective” meaning. new meanings may emerge in this over-all order. that is, we may say that meaning penetrates the cosmos, or even what is beyond the cosmos. for example, there are current theories in physics and cosmology that imply that the universe emerged from the “big bang.” in the earliest phase there were no electrons, protons, neutrons, or other basic structures. none of the laws that we know would have had any meaning. even space and time in their present welldefined forms would have had no meaning. all of this emerged from a very different state of affairs. the proposal is that, as happens with human beings, this emergence included a creative unfoldment of generalized meaning. later, with the evolution of new forms of life, fundamentally new steps may have evolved in the creative unfoldment of further meanings. that is, we may say that some evolutionary processes occur which could be traced physically, but we cannot really understand them without looking at some deeper meaning which was responsible for the changes. the present view of the changes is that they are random, with selection of those traits that were suited for survival, but that does not explain the complex, subtle structures that actually occurred. 61 thus we see that the conclusion that bohm draws from the quantum evidence is that the ‘big bang’ was not a meaningless explosion so to speak, rather it could only have been accompanied by an ‘unfoldment of generalized meaning’. furthermore, it can only follow that the ‘evolution of new forms of life’ was in essence also a ‘creative unfoldment of further meanings. therefore we see that, in the same way that the quantum evidence clearly undermines the notion that mind somehow emerges from mindlessness, it also clearly shows dna decipher journal | november 2011 | vol. 1 | issue 3 | pp. 351-382 smetham, g. p., quantum evo-devo universe ii: materialists’ metaphoric phantoms of matter in mind issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 369 that meaning does not magically emerge from meaninglessness, the universe itself emerges from a quantum ground of pure undiluted meaningfulness which explodes into the infinite play of the meanings of the experiential world. this view is also suggested by john wheeler’s assertion concerning the evolution of the universe: law without law. it is difficult to see what else than that can be the plan of physics. it is preposterous to think of the laws of physics as installed by swiss watchmaker to endure from everlasting to everlasting when we know that the universe began with a big bang. the laws must have come into being. therefore they could not have been always a hundred percent accurate. that means that they are derivative, not primary … events beyond law. events so numerous and so uncoordinated that, flaunting their freedom from formula, they yet formulate firm form … the universe is a self excited circuit. as it expands, cools and develops, it gives rise to observer-participancy. observer-participancy in turn gives what we call tangible reality to the universe … of all the strange features of the universe, none are stranger than these: time is transcended, laws are mutable, and observer participancy matters. 62 laws do not emerge from meaninglessness, but they can emerge from potentiality through the development of ‘epiontic’ ‘observer participancy’. the term ‘epiontic’ indicates, as does ‘observer participancy’, that epistemological acts, which are acts of knowing, acts of intentionality, which are also acts of meaning, give rise to ontology. bohm, therefore, concludes that ‘meaning’ can be considered to be the ultimate constituent of the process of the universe because it ‘enfolds’ the other primary aspects of ‘matter’ and ‘energy’ (fig 4 – reproduced from bohm’s essay soma significance and the activity of meaning): fig 4 however, in some sense the enfoldment by meaning seems to be more fundamental … meaning refers to itself directly, and this is in fact the basis of the possibility of that intelligence which can comprehend the whole, including itself. dna decipher journal | november 2011 | vol. 1 | issue 3 | pp. 351-382 smetham, g. p., quantum evo-devo universe ii: materialists’ metaphoric phantoms of matter in mind issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 370 … if there is a generalized kind of meaning intrinsic to the universe, including our own bodies and minds, then the way may be opened to understanding the whole as self-referential through its “meaning for itself” … 63 for both bohm and wheeler, then, the universe can be considered to be a self-referential, thereby self-creating process within which infinite meaningful acts of internal cognition create a multitudinous field of dualistic experience within an overall field of pure undifferentiated meaning, which we may identify with the quantum ground. it is truly remarkable how this quantum perspective maps precisely onto the buddhist dzogchen view that the ultimate source of the process of reality is a ‘meaning-saturated field as pristine cognitiveness’ (see above). the materialist view on the matter, however, starts with a meaning-unsaturated field; in fact it is difficult to figure out what kind of field can possibly form the basis for any kind of materialism because the quantum field, as we have seen, is devoid of substantiality. however, in order to pursue the matter let us grant ramachandran’s apparent and mistaken belief in ultimately existent, spooky yet devoid of meaning, atoms of the material kind which manage to club together to produce brains housed in various sentient creatures. we now await the generation of meaning from the meaningless. ramachandran’s ‘framework for thinking about language evolution’ is called ‘synesthetic bootstrapping theory’ 64 . this framework, we are told: …provides a valuable clue to understanding the origins of not only language, but also a host of other uniquely human traits such as metaphorical thinking and abstraction. in particular, i’ll argue that language and many aspects of abstract thought evolved through exaptations whose fortuitous combination yielded novel solutions. 65 the notion that language evolved through the process of ‘exaptations’ is an extraordinary, and as we shall see, ridiculous, claim. an exaptation is ‘a feature that performs a function that was not produced by natural selection for its current use.’ 66 the idea here is that some feature of an organism which, according to current mainstream evolution theory, has developed for some particular purpose, a purpose so necessary for survival that evolution, supposedly utilizing fortuitous random gene mutations, quickly gets on the job of supplying it, is later ‘coopted’ to do something completely different. this wildly counter intuitive notion, that evolution is to a large degree ‘happenstantial’ – seeing if it’s got anything already evolved that it can press into service in a new niche as it were, gets a rave review from ramachandran: you will see me arguing that many of our unique mental traits seem to have evolved through the novel deployment of brain structures that originally evolved for other reasons. this happens all the time in evolution. feathers evolved from scales whose original role was insulation rather than flight. the wings of bats and pterodactyls are modifications of forelimbs originally designed for walking. our lungs developed from swim bladders of fish which evolved for buoyancy control. … i argue that the same principle applies with even greater force to the evolution of the human brain. evolution found ways to radically repurpose many functions of the ape brain to create entirely new functions. some of them – language comes to mind – are so powerful that i would go so far as to argue they have produced a dna decipher journal | november 2011 | vol. 1 | issue 3 | pp. 351-382 smetham, g. p., quantum evo-devo universe ii: materialists’ metaphoric phantoms of matter in mind issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 371 species that transcends apehood to the same degree by which life transcends mundane chemistry and physics. 67 the notions that feathers directly evolved from scales or human lungs from fish bladders with intermediate stages, and others like them, must be some of the most bizarre, if not absurd, notions within the dismal story of the appropriation of darwin’s original insights by the mechanistic-materialist academic cadre still operating to mislead the public as to the nature of reality (i hasten to add i am not a creationist). when darwin started on his musings as to the manner in which the diversity of life took the various courses that they did the notion that there might be a deep level of reality completely at variance with the apparently material structures and processes of the ‘classical’ realm was roughly a hundred years in the future. the idea that the edifice of the material world would dissolve into quantum emptiness (which is not nothingness but ‘empty’ potentiality) would have been incomprehensible to the scientists of his day. indeed many scientists of the early twentieth century had great difficulty understanding it. given the evidence darwin had access to, and the state of science at his time, his work was indeed brilliant and darwin is deservedly considered to have been a genius. the situation today, however, is very different and scientists and philosophers should know better. stapp has pointed out that: philosophers of mind appear to have arrived, today, at less-than-satisfactory solutions to the mind-brain and free will problems, and the difficulties seem, at least prima facie, very closely connected with their acceptance of a known-to-befalse understanding of the nature of the physical world, and of the causal role of our conscious thoughts within it. 68 the crucial phrase here is, of course, ‘known-to-be-false’. the astonishing fact is that, for some incomprehensible reason, the academic community has decided to allow some of its members, some of them neuroscientists, to flagrantly misrepresent the truth of contemporary physics in order to defend obviously incorrect, ‘classical’ positions which are redolent of the worldview of the late nineteenth century. as stapp points out: …the re-bonding [between mind and matter] achieved by physicists during the first half of the twentieth century must be seen as a momentous development: a lifting of the veil. ignoring this huge and enormously pertinent development in basic science, and proclaiming the validity of materialism on the basis of an inapplicablein-this-context nineteenth century science is an irrational act. 69 stapp refers to a re-bonding between mind and matter which occurs precisely because within quantum theory ‘matter’ becomes an aspect of mind. we can also quantumly re-bond ‘life’ and ‘mundane chemistry and physics’ so that we come to see the truth of the fact that these two are not dramatically at variance, as ramachandran seems to think, a variance which requires that life ‘transcends’ the ‘mundane’ machinations of the ‘mindless molecules’ of chemistry and physics. the ‘lifting of the veil’ reveals to us that the processes described by chemistry and physics are the processes through which the deep, up until the twentieth century hidden, field of fecund, life-producing, epiontic quantum intentionality or teleology, acting upon an infinite pool of potentiality for the production of sentient beings of manifold varieties, activates the evo-devo ‘implicate’ templates of life which must lie within the field of potentiality. dna decipher journal | november 2011 | vol. 1 | issue 3 | pp. 351-382 smetham, g. p., quantum evo-devo universe ii: materialists’ metaphoric phantoms of matter in mind issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 372 the american cognitive scientist and philosopher jerry fodor, professor of philosophy at rutgers university, in a recent essay why pigs don’t fly, has questioned the neo-darwinian assumption of random ‘adaptationism’ and has indicated that there are perhaps more viable alternatives: everybody thinks evo-devo must be at least part of the truth, since nobody thinks that phenotypes are shaped directly by environmental variables. even the hardest core darwinists agree that environmental effects on a creature’s phenotype are mediated by their effects on the creature’s genes: its ‘genome’. indeed, in the typical case, the environment selects a phenotype by selecting a genome that the phenotype expresses. once in place, this sort of reasoning spreads to other endogenous factors. phenotypic structure carries information about genetic structure. and genotypic structure carries information about the biochemistry of genes. and the biochemical structure of genes carries information about their physical structure. and so on down to quantum mechanics for all i know. 70 and it is now to the quantum level that we must turn for the secrets of life. it has been discovered, for instance, that photosynthesis employs a quantum ‘look-ahead’ technique for choosing the most efficient possible pathway for energy exchange 71 . it seems that many biological processes which involve the conversion of energy into forms that are usable for chemical transformations are quantum mechanical in nature; it would be remarkable if evolution ignored quantum efficiency enhancing techniques and decided (so to speak) to stick to nuts and bolts ‘classical’ mechanisms. in particular a quantum understanding of the evodevo phenomenon indicates that the connection between feathers and scales lies at a deep, implicate quantum ‘template’ level, not a fully materialized transformation with intermediate animal types between dinosaurs and birds. the notion of ‘exaptation’ will be shown to be as mythological as the notion that genes in differing species must be wildly different, a mistaken notion that mayr confidently asserted, on the basis of a materialist preconception rather than any evidence, in his ‘many roads to rome’ fiasco. it is now time to turn our attention to the details of ramachandran’s ‘synesthetic bootstrapping theory’ of the evolution of language competence. synesthesia is a condition in which perceptual or sensation modes become in some way mixed. examples are specific colors being clearly seen when certain tones are heard or when specific numbers or letters are perceived. according to ramachandran the most common form of synesthesia is letter or number to color form (grapheme-color). ramachandran, with his associate e. m. hubbard have proposed that this phenomenon can be explained by the fact that the brain areas responsible for processing graphemes and colors are adjacent: the key insight comes from anatomical, physiological and imaging studies in both humans and monkeys, which show that colour areas in the brain … are in the fusiform gyrus. we were struck by the fact that, remarkably, the visual grapheme area is also in the fusiform … can it be a coincidence that the most common form of synaesthesia involves graphemes and colours and the brain areas corresponding to these are right next to each other? we propose, therefore, that synaesthesia is caused by cross-wiring between these two areas, in a manner analogous to the cross-activation of the hand area by the face in amputees with phantom limbs… 72 this is the ‘hyperconnectivity’ theory of synesthesia, although a few pages on in their paper, synaesthesia – perception, thought and language, ramachandran and hubbard say that they dna decipher journal | november 2011 | vol. 1 | issue 3 | pp. 351-382 smetham, g. p., quantum evo-devo universe ii: materialists’ metaphoric phantoms of matter in mind issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 373 are using the term ‘cross-wiring’ ‘somewhat loosely’ and that the term ‘cross-activation’ might be more appropriate. such ‘cross-activation’ may come about through several mechanisms; (1) cross-wiring, (2) disinhibition, (3) increased feedback, (4) excess activity. the actual nature of the cross-activation is not directly relevant to our discussion. ramachandran’s musings on this phenomenon led him to consider a possible link between synesthesia and ‘some of the high-level thought processes that humans alone are capable of.’ 73 his own thought process of this issue centrally involves the ‘bouba-kiki effect’. when people at large are asked to look at the two shapes shown in fig. 5 (without the ‘bouba’ and ‘kiki’ labels of course) and asked to say which one is ‘bouba’ and which ‘kiki’ it turns out that about 98 percent match up the shapes and labels as shown. this phenomenon occurs whether the experiment is carried out even in ‘non-english-speaking people in india and china’. as ramachandran indicates this matching is due to the fact that: fig. 5 …the gentle curves and undulations of contour on the amoeba-like figure metaphorically (one might say) mimic the gentle undulations of the sound bouba, as represented in the hearing centers in the brain and the smooth rounding and relaxing of the lips for producing the booo-baaa sound. on the other hand, the sharp wave forms of the sound kee-kee and the sharp inflection of the tongue on the palate mimic the sudden changes in the visual shape. 74 this phenomenon, ramachandran suggests indicates that ‘there is a sense in which at some level we are all “synesthetes,” and, furthermore, he considers that this fact ‘might hold the key to understanding many of the most mysterious aspects of our minds, such as the evolution of metaphor, language and abstract thought.’ dna decipher journal | november 2011 | vol. 1 | issue 3 | pp. 351-382 smetham, g. p., quantum evo-devo universe ii: materialists’ metaphoric phantoms of matter in mind issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 374 so, with a deft sleight of mind, somewhat analogous to the tricks with mirrors that he performs in order to relieve the pains in phantom limbs, ramachandran thinks he has reduced the ‘mysterious aspects’ of the evolution of metaphor, language and abstract thought to nothing more than the material resonance generated cross-wiring or cross-activations within adjacent regions of the brain. by ignoring the quantum realm beneath the appearance of the material world ramachandran is able to adopt a thoroughly materialist idiom which gives the impression that the brain is the ultimate and final source of the mysterious aspects of mind. but, of course, this is not true. in order to get a clearer understanding of the situation it is useful to have an understanding of the central buddhist mahayana-madhyamaka presentation of the ontological/metaphysical structure of reality as being comprised of the ‘two truths’. according to this doctrine the appearance of the ‘conventional,’ or ‘seeming’ realm of the everyday world is an ‘illusion,’ an illusion which conceals the true ‘ultimate’ nature of reality. buddhist scholar jeffrey hopkins, refers to a samvrti satya, a ‘conventional truth’, as a ‘concealer of suchness,’ 75 a misleading mode of ‘reality’ which covers the true ‘ultimate’ reality, which is tathata or ‘suchness,’ the direct and pure nondual experiential essence of reality. thus the metaphysical structure of the buddhist worldview asserts two interpenetrating but radically different perspectives within reality, the ‘seeming’ and the ‘ultimate.’ this viewpoint indicates a metaphysical structure of reality within which the dualistic world is a deceptive veil hiding the ultimate nondual nature of reality. the physicist and buddhist practitioner victor mansfield has clearly indicated that modern quantum physics constitutes an ‘experimental metaphysics 76 ’ precisely because quantum physics has penetrated the veil of the material world to what lies beyond. in fact quantum physics has clearly shown the significance of the notion of ‘the two truths,’ precisely because it turns out that the ‘material’ world, as it was conceived of in the era of ‘classical’ physics, is an illusion because it is generated from the quantum level by the internal epiontic operation of a deep non-individual level of consciousness. the notion of ‘metaphysics’ as a philosophical endeavor within the western tradition had as its central concern the determination of the ‘ultimate’ nature of the seemingly external world of materiality; at its most basic the core issue was that of the ultimate nature of the world: ‘matter’, ‘mind’ or both? in the time when this question was central for western philosophical thought physics was what is now called ‘classical’ physics, the investigation and description of the newtonian edifice of reality. so when quantum mechanics first discovered a mode of existence radically at variance with the ‘billiard ball’ newtonian façade of materiality physics had penetrated through the surface of the material world to see a more ‘ultimate’ nature which lies ‘beyond’. thus victor mansfield tells us: we can now demonstrate that ‘quantum moons’ do not exist when unobserved. such ‘experimental metaphysics’ has an extraordinary resonance with the middle way buddhist principle of emptiness… 77 mansfield uses the term ‘quantum moons’ here in reference to a question that einstein once posed to the a colleague as to whether the moon existed when no one was looking at it. the point is that it has been shown quite clearly that quantum ‘entities’ do not ‘exist’ when not being observed in some fashion. furthermore quantum physics has now shown that consciousness is an essential factor in ‘creating’ existence out of an indeterminate realm of dna decipher journal | november 2011 | vol. 1 | issue 3 | pp. 351-382 smetham, g. p., quantum evo-devo universe ii: materialists’ metaphoric phantoms of matter in mind issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 375 quantum potentiality, a realm which can be shown to be equivalent in ontological nature to the buddhist concept of ‘emptiness’ (shunyata). fig 6. the ‘two truths’ according to john wheeler the photo shows professor john wheeler in mid flow of explaining the ‘two truths’ as discovered by quantum theory: the ‘classical’ realm and the ‘quantum’ realm. on the left of the photo the blackboard drawing shows a ‘classical’ size object moving between two points. at every point in time it has a definite position and it therefore seems to follow a definite trajectory between the points. in other words it behaves like an everyday object. the section of the blackboard drawing behind wheeler’s head indicates the situation at the quantum level; quantum ‘entities’ behave in a completely different and counter-intuitive manner; they spread out or ‘smear out’ over increasingly large areas and fade into a ghostly semi-existence of potentiality. such ‘entities’ only recover their full entity-ness when they are observed. when unobserved quantum entities really are not ‘entities,’ they are a ‘smeared out’ potentiality fields of possible entity experience. henry stapp, who is one of the few physicists still around who discussed such ‘experimental metaphysical’ issues with some of the ‘founding fathers’ of quantum theory, says that the central distinguishing feature between these two physical ‘truths’ is that on the ‘classical’ level motions are ‘apparently independent of our human observations of them.’ 78 the important word in this observation is ‘apparently’, a word we could equally replace with ‘seemingly’, so the ‘classical’ level, or ‘truth’, has been clearly established by physics as a ‘seeming’ reality. it is a ‘seeming’ appearance of an independent material world of newtonian objects, an appearance which, when analyzed from the perspective of quantum theory, is found to emerge from a deeper, more ‘ultimate’, quantum level through the operation of consciousness, although not necessarily individual consciousness. it follows from this discussion that to ascribe ultimate validity to the brain as ultimate cause of mental phenomena is clearly false and, as we shall see, adopting such a ‘known-to-be-false’ perspective, to quote stapp again, leads to bizarre, if not absurd, proposals. in his explanation of the way in which the magical ‘mirror neurons’, neurons whose primary job is to internally mirror other members of the species actions but which also apparently get utilized for more abstract tasks through ‘exaptation’, underpin the bouba-kiki effect he tells us that: dna decipher journal | november 2011 | vol. 1 | issue 3 | pp. 351-382 smetham, g. p., quantum evo-devo universe ii: materialists’ metaphoric phantoms of matter in mind issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 376 the main computation done by mirror neurons is to transform a map in one dimension, such as the visual appearance of someone else’s movement, into another dimension, such as the motor maps in the observer’s brain, which contain programs for muscle movements (including tongue and lip movements). your brain is performing an impressive feat of abstraction in linking your visual and auditory maps. the two inputs are entirely dissimilar in every way except one – the abstract properties of jaggedness or curviness – and your brain homes in on this common denominator very swiftly when you are asked to pair them up. i call this process “cross-model abstraction.” this ability to compute similarities despite surface differences may have paved the way for more complex types of abstraction that our species takes great delight in. mirror neurons may be the evolutionary conduit that allowed this to happen. 79 and he then proceeds to make the following outlandish proposal of why the ability of ‘crossmodal abstraction’, a capacity which ramachandran considers fundamental for the use and appreciation of metaphor, evolved ‘in the first place’: …it may have emerged in ancestral arboreal primates to allow them to negotiate and grasp tree branches. the vertical visual inputs of tree limbs and branches reaching the eye had to be matched with totally dissimilar inputs from joints and muscles and the body’s felt sense of where it is in space – an ability that would have favoured the development of both canonical neurons and mirror neurons. the readjustments that were required in order to establish a congruence between sensory and motor may have initially been based on feedback, both at the genetic level of the species and at the experiential level of the individual. 80 thus the ability to form and understand metaphors reduces to the contingent requirement that animals which for some evolutionary reason took to the trees needed to develop (presumably very quickly) brain mechanisms for swinging form branch to branch: one also wonders about the evolutionary origin of metaphors. once the crossmodal abstraction mechanism was set up between vision and touch … (originally for grasping branches), this mechanism could have paved the way for cross sensory metaphors (‘stinging rebuke,’ ‘loud shirt’) and eventually for metaphors in general. 81 the notion that the presumed evolutionary necessity for our ‘ancestral arboreal primates’ to somehow match and co-ordinate together the ‘totally dissimilar inputs’ from ‘vertical visual inputs of tree limbs and branches reaching the eye’ and ‘inputs from joints and muscles and the body’s felt sense of where it is in space’ is the origin of metaphor is dramatically counter intuitive, and must certainly must be included within the class of what ramachandran himself describes as his ‘wild intuitive hunches’ with which he attempts to ‘navigate the gaps’ of his account of how the evolution of brain neuron circuitry accounts for ‘mysterious faculties that are so quintessentially human, such as art, language, metaphor, creativity, self-awareness, and even religious sensibilities.’ 82 the fundamental capacity of the metaphorical function of consciousness is clearly that of apprehending a significant similarity within two aspects of reality which are in all other respects different. ramachandran, in an apparently ingenious employment of the very function of metaphorical cognition itself, tries to account for the phenomenon itself. this strategy, however, turns out to be disingenuous. consider his account of the way in which the dna decipher journal | november 2011 | vol. 1 | issue 3 | pp. 351-382 smetham, g. p., quantum evo-devo universe ii: materialists’ metaphoric phantoms of matter in mind issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 377 necessary ‘congruence between sensory and motor’ is supposed to be established by ‘readjustments’ which, we are told, are initially ‘ based on feedback, both at the genetic level of the species and at the experiential level of the individual’. the image which we are offered is one in which at some point in evolutionary history our ‘ancestral arboreal primates’ must have been making a bad job of co-ordinating their motor circuits with their visual circuits and, presumably, thereby constantly and frustratingly missing the branches they were aiming to swing from and therefore painfully falling onto the forest floor beneath them. some ‘readjustments’ are called for; but how exactly do these readjustments come about? ramachandran tells us that that some kind of feedback mechanism is involved, elsewhere we are told that mirror neurons are possibly involved in a ‘self-amplifying feedback loop’, but the question posed by such a proposal is that as to upon what basis the feedback loop gets started. and the only significant answer can be that at some point there is some kind of protometaphoric recognition of similarity within dissimilarity which then gets amplified over time. in other words there must be some kind of glimmer of metaphoric capacity internal to brain functioning in order for any kind of amplification of metaphoric functioning to get off the ground, thereby enabling our ‘ancestral arboreal primates’ to also effectively get off the ground without risking skull fractures. so the account clearly fails to account for the metaphorical capacity of the human brain, unless perhaps, we accept it was just a fortuitous random mutation which just happened to connect up two regions of the brain which, fortunately for our ‘ancestral arboreal primates’ patiently awaiting a life amongst the branches, just happened (by random mutation?) to be adjacent. however such an account, leaving aside its massive improbability, simply makes no sense from the perspective of evodevo which suggests that there would have been a kind of primordial gene ‘template’ underlying the evolution; ramachandran’s account relies on brain structure being a matter of random organization. the molecular investigation of the brain amphioxus seems to suggest otherwise, brain organization does seem to be there in potential. in their paper synaesthesia – perception, thought and language, ramachandran and hubbard say that: the bouba/kiki effect example provides our first vital clue to understanding the origins of proto-language, for it suggests there might be natural constraints on the ways in which sounds map on to objects. this, together with ‘the existence of a kind of sensory-to-motor synaesthesia, which may have played a pivotal role in the evolution of language’, leads to the: … conjecture that the representation of certain lip and tongue movements in motor brain maps may be mapped in non-arbitrary ways onto certain sound inflections and phonemic representations in auditory regions and the latter in turn may have non-arbitrary links to the external object’s visual appearance (as in bouba and kiki). the stage has been set for a sort of ‘resonance’ or bootstrapping in the co-evolution of these factors, thereby making the origin of proto-language seem much less mysterious than people have assumed. 83 in order to press the point home various examples are provided, such as: …words referring to something small often involve making a synaesthetic small /i/ with the lips and a narrowing of the vocal tract (e.g. words such as ‘little’, dna decipher journal | november 2011 | vol. 1 | issue 3 | pp. 351-382 smetham, g. p., quantum evo-devo universe ii: materialists’ metaphoric phantoms of matter in mind issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 378 ‘petite, ‘teeny’ and ‘diminutive’) whereas the opposite is true for word denoting large or enormous. 84 and it all does seem to ‘resonate’ magnificently, until, that is, one considers that in this account the organization of the brain which allows such a wonderful cross-modal interactive material resonance came into existence for other purposes (swinging from branch to branch being one of them). in other words for ramachandran there is absolutely no glimmer of inner teleology to produce the most effective means of communication appropriate for any particular level of conscious awareness within the process of evolution itself, and therefore language is considered a remarkably fortuitous unintentional, and random-exaptational result of the mindless machinations, which are supposed to be completely disinterested as to survival (why would inert ‘matter’ ‘think’ that survival matters), little lumps of ‘matter’. but such a view, besides its cartoon like preposterousness in places, ignores both the crucial evidence of evo-devo and quantum theory which, taken together, suggest that organic structure, ‘meaning’ and at least a minimalist intentionality or teleology are an inherent aspect of the universe. fig 7 a ‘quantum epiontic evo-devo mindnature’ understanding of the process of evolution, however, indicates that individuated structures of embodied consciousnesses emerge from a deeper realm of quantum information processes, a view which clearly means that the ‘stuff’ of quantum reality must be some form of non-individuated consciousness or awareness. and this perspective also suggests that brains are intermediate level material constructions, constructed from the deeper level of quantum informational awareness-consciousness precisely in order to individuate consciousness. this process takes place through a sequence of what the physicist dna decipher journal | november 2011 | vol. 1 | issue 3 | pp. 351-382 smetham, g. p., quantum evo-devo universe ii: materialists’ metaphoric phantoms of matter in mind issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 379 david bohm called ‘implicate orders’ which emerge from the fundamental ground quantum ‘implicate’ source and thereby manifest the ‘explicate’ dualistic world of experience (fig 7). as the founding father of quantum physics erwin schrödinger said: mind has erected the objective outside world … out of its own stuff. 85 and it also seems that the fundamental quantum mindnature creates individuated consciousness by organizing its own ‘stuff’ into the apparently ‘material’ stuff of the brain. in his important work wholeness and the implicate order bohm indicates that reality encompasses both the objective aspects and the subjective aspects of what is essentially an interconnected and undivided ‘wholeness’; bohm calls this totality the ‘holomovement’: …what carries the implicate order is the holomovement, which is unbroken and undivided totality. in certain cases we can abstract particular aspects of the holomovement …, but more generally, all forms of the holomovement merge and are inseparable. 86 in an interview for omni magazine bohm explained: i propose something like this: imagine an infinite sea of energy filling empty space, with waves moving around in there, occasionally coming together and producing an intense pulse. let’s say one particular pulse comes together and expands, creating our universe of space-time and matter. but there could well be other such pulses. to us, that pulse looks like a big bang; in a greater context, it’s a little ripple. everything emerges by unfoldment from the holomovement, then enfolds back into the implicate order. i call the enfolding process “implicating,” and the unfolding “explicating.” the implicate and explicate together are a flowing, undivided wholeness. every part of the universe is related to every other part but in different degrees. 87 the assertion that the ultimate source of individuated consciousness is a deeper level of nonindividuated consciousness-awareness does not mean that ramachandran’s account of brain anatomy has no value. it quite clearly does have significance; it indicates the structure that the quantum level of awareness has produced in order for individuated consciousness to function as it does. a problem arises, however, because ramachandran suggests, sometimes directly but on many occasions by more insidious methods, that the matter which makes up the brain is the ultimate source of consciousness and the mental realm. and on the basis of this mistaken conception he aligns himself with a modern movement which seemingly seeks to deny any spiritual dimension do the universe by embracing a ‘known-to-be-false’ materialism: as a scientist, i am one with darwin, gould, pinker, and dawkins. i have no patience with those who champion intelligent design, at least not in the sense that most people would use that phrase. no one who has watched a woman in labor or a dying child in a leukemia ward could possibly believe that the world was custom crafted for our benefit. yet as human beings we have to accept with humility that the question of ultimate origins, will always remain with us, no matter how deeply we understand the brain and the cosmos that it creates. 88 it is clear that the notion of ‘intelligent design’ that ramachandran has in mind is an unintelligent one, a fundamentalist view of an anthropomorphized loving independent creator, dna decipher journal | november 2011 | vol. 1 | issue 3 | pp. 351-382 smetham, g. p., quantum evo-devo universe ii: materialists’ metaphoric phantoms of matter in mind issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 380 which it must be admitted more than a few people embrace. however, to counter such a dogmatic fundamentalist theistic view with an equally unintelligent, and clearly incorrect, view that the process of the universe is nothing other than mindless matter mutely mattering to itself and consciousness has no ultimate significance is counter-productive. to counter one dogmatic false view with an equally false dogmatic view (does the brain create the cosmos?!) simply produces animosity and conflict. the evidence of quantum theory and evo-devo, however, now clearly suggests that the source of the realms of ‘matter’ and ‘mind’ must derive from a unified quantum mindnature which may be considered as a ‘transcendent’ source which is of the nature of awarenessconsciousness. this ultimate source produces the multifarious dualistic realms of individualized experience within the continuums of all sentient beings in order to explore and discover its own possibilities. as rupert sheldrake indicates one possible interpretation of this view: if this transcendent conscious being were the source of the universe and everything within it, all created things would in some sense participate in its nature. the more or less limited ‘wholeness’ of organisations at all levels of complexity could then be seen as a reflection of the transcendent unity on which they depended, and from which they are ultimately derived. 89 and henry stapp has remarked concerning the spiritual implications of quantum theory as follows: this situation is concordant with the idea of a powerful god that creates the universe and its laws to get things started, but then bequeaths part of this power to beings created in his own image, at least with regard to their power to make physically efficacious decisions on the basis of reasons and evaluations. 90 such views are concordant with the ‘quantum epiontic mindnature’ metaphysical perspective which embraces the evo-devo evidence within a quantum context. this viewpoint will be further elucidated in a future article which will be made available shortly: the quantum epiontic metaphysics of symbolic forms, which will deal primarily with the philosophy of ernst cassirer (the philosophy of symbolic forms) in the context of the quantum epiontic mindnature paradigm. 1 ramachandran – the tell-tale brain p46 2 ramachandran – the tell-tale brain p47 3 ramachandran – the tell-tale brain p34 4 ramachandran – the tell-tale brain p104 5 ramachandran – the tell-tale brain p121 6 ibid 7 ramachandran – the tell-tale brain p124 8 ramachandran – the tell-tale brain p125 9 ramachandran – the tell-tale brain p106 10 ramachandran – the tell-tale brain p164 11 carroll, sean b. (2006) p72 12 carroll, sean b. (2006) p9 dna decipher journal | november 2011 | vol. 1 | issue 3 | pp. 351-382 smetham, g. p., quantum evo-devo universe ii: materialists’ metaphoric phantoms of matter in mind issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 381 13 carroll, sean b. the origins of form 14 carroll, sean b. the origins of form 15 http://www.naturalhistorymag.com/features/061488/the-origins-of-form 16 ibid 17 in a talk given at a conference blackmore suggests that we might call the original primal creature a ‘blobbie’. 18 conway morris, simon (2003) p242 19 carroll, sean b. (2006) p176 20 carroll, sean b. the origins of form 21 carroll, sean b. (2006) p177 22 carroll, sean b. the origins of form 23 carroll, sean b. (2006) p175-176 24 carroll, sean b. the origins of form 25 sheldrake, rupert (2009) p136 26 sheldrake, rupert (2009) p104 27 life’s solution p6 28 life’s solution p7 29 life’s solution p180 30 dennett, daniel (1991) p33 31 allday, jonathan (2009) p493 32 allday, jonathan (2009) p496 33 barrow, john d., davies, paul c. w., harper, charles l. (eds) (2004) p136 – wojciech h. zurek: ‘quantum darwinism and envariance.’ 34 barrow, john d., davies, paul c. w., harper, charles l. (eds) (2004) p129 – wojciech h. zurek: ‘quantum darwinism and envariance.’ 35 barrow, john d., davies, paul c. w., harper, charles l. (eds) (2004) p121 – wojciech h. zurek: ‘quantum darwinism and envariance.’ 36 dennett, daniel (1996) p27 37 barrow, john d., davies, paul c. w., harper, charles l. (eds) (2004) p577 – wheeler, j a (1999) ‘information, physics, quantum: the search for links.’ in feynman and computation: exploring the limits of computers, ed a. j. g. hey, p309 (314). cambridge, ma: perseus books. 38 barrow, john d., davies, paul c. w., harper, charles l. (eds) (2004) p10 – paul c. w. davies: ‘john archibald wheeler and the clash of ideas.’ 39 rosenblum, bruce and kuttner, fred (2006) p 40 stapp, henry (2004) p223 41 the observer (january 25th, 1931) 42 das wesen der materie” (the nature of matter), speech at florence, italy, 1944 (from archiv zur geschichte der max-planck-gesellschaft, abt. va, rep. 11 planck, nr. 1797) 43 schrödinger, e. (1944) p121. 44 rosenblum, bruce and kuttner, fred (2006) p67 45 rosenblum, bruce and kuttner, fred (2006) p179 46 stapp, henry: ‘quantum interactive dualism: an alternative to dualism’ p18 47 ramachandran – the tell-tale brain introduction 48 stapp, henry (2007) p139 49 ramachandran – the tell-tale brain – introduction x 50 ramachandran – the tell-tale brain p292 51 ramachandran – the tell-tale brain p164 52 ramachandran – the tell-tale brain p164 53 ramachandran – the tell-tale brain p165 54 woolfson, adrian (2000) p74 dna decipher journal | november 2011 | vol. 1 | issue 3 | pp. 351-382 smetham, g. p., quantum evo-devo universe ii: materialists’ metaphoric phantoms of matter in mind issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 382 55 barrow, d. john & tipler, frank j. (1986) p105 56 woolfson, adrian (2000) p83 57 woolfson, adrian (2000) p76 58 guenther, herbert v. (1984). p52 59 life’s solution p46 60 ramachandran – the tell-tale brain p171 61 bohm, david (2003)p180 62 wheeler quoted in barrow, john d., davies, paul c. w., harper, charles l. (eds) (2004) p73 – freeman j. dyson: ‘thought-experiments in honor of john archibald wheeler.’ 63 bohm, david (2003)p175-176 64 ramachandran – the tell-tale brain p168 65 ibid 66 http://evolution.berkekey.edu/evosite/evo10/iiie5cexaptations.shtml 67 ramachandran – the tell-tale brain pxii-xiii 68 stapp, henry: ‘philosophy of mind and the problem of free will in the light of quantum mechanics’ p19 69 stapp, henry: ‘quantum interactive dualism’ p18 70 fodor, jerry – ‘why pigs don’t fly’, new york review of books 71 http://www.scientificamerican.com/article.cfm?id=when-it-comes-to-photosynthesis-plantsperform-quantum-computation 72 sythaesthesia – perception, thought and language, v. s. ramachandran and hubbard, p9 73 ramachandran – the tell-tale brain p109 74 ibid 75 hopkins, jeffrey (1996) p405 76 www.namgyal.org 77 www.namgyal.org 78 mmqm p233 79 ramachandran – the tell-tale brain p129 80 ramachandran – the tell-tale brain p129-130 81 ramachandran – the tell-tale brain p131 82 ramachandran – the tell-tale brain introduction 83 sythaesthesia – perception, thought and language, v. s. ramachandran and hubbard, p20 84 ibid 85 schrödinger, e. (1944). 86 bohm, david (2003) p131 87 interview with david bohm, conducted by f. david peat and john briggs, was originally published in omni, january 1987 88 ramachandran – the tell-tale brain p293 89 sheldrake, rupert (2009) p244 90 stapp, h. p. (2010). ‘minds and values in the quantum universe’ in information and the nature of reality, davies, paul & gregersen, niels henrik (eds), cambridge university press, p117. login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x why us dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 12-43 smetham, g. p., why us: trespassing on an anthropic lawn (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 12 article why s? trespassing on an anthropic lawn (part i) graham p. smetham * abstract mindful reflections upon a metaphysically misguided materialist advertising campaign: trespassing on einstein’s lawn: a father, a daughter, the meaning of nothing, and the beginning of everything by amanda gefter. gefter, new scientist book reviews editor, presents a philosophically confused account of current quantum metaphysics because she adheres to an out of date materialist metaphysics and claims that, whilst observers in some way create reality, the process does not involve consciousness. her claims are shown to invalid, the various quantum metaphysical perspectives she covers are shown to require consciousness as fundamental. keywords: grand design, observers, consciousness, anthropic principle, darwinism, evolutionary developmental biology, cambrian explosion, quantum morphogenetic archetypes, buddhanature, nothingness, emptiness, primordial consciousness, timeless awareness, substrate of consciousness. the question is what is the question? is it all a magic show? is reality an illusion? what is the framework of the machine? darwin’s puzzle: natural selection? where does space-time come from? is there any answer except that it comes from consciousness? 1 john wheeler wheeler thinks that consciousness could be the criterion for an observer, but that’s obviously bullshit. i mean, consciousness is just a physical process in the brain. it’s not magic. 2 amanda gefter * correspondence: graham smetham http://www.quantumbuddhism.com e-mail:graham@quantumbuddhsim.com http://www.quantumbuddhism.com/ mailto:qb@delysid.bltc.net dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 12-43 smetham, g. p., why us: trespassing on an anthropic lawn (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 13 ..the essence of consciousness can be interpreted as a special type of perception of quantum reality by living beings. 3 michael mensky i regard consciousness as fundamental. i regard matter as derivative from consciousness. 4 max planck the recent book trespassing on einstein’s lawn: a father, a daughter, the meaning of nothing, and the beginning of everything (tel) by amanda gefter, a science journalist who writes for new scientist, scientific american and other science journals, has been greeted with some enthusiastic reviews. one reviewer describes it: beautifully written and hugely entertaining, this book is a heartfelt introduction to the many mind-bending theories in contemporary physics. 5 gefter’s descriptions and explanations of some of the metaphysical conclusions drawn from modern physical theory, derived from her conversations with the physicists she persuaded to grant her interviews, are well written, intriguing and entertaining. the physicist peter woit compares tel to another recent work why does the world exist, wherein the author jim holt interviews various philosophers and scientists on their views on the origin of, and reason for, the existence of the universe. woit writes that the authors of both books are: …lively, entertaining writers with wonderful material about deep questions, and i greatly enjoyed both books. gefter is the funnier of the two, and i had trouble putting the book down after it arrived in my mail a couple of days ago. 6 however, woit also has some severe reservations: while i liked the book, at the same time i found the whole project deeply problematic, and would have reservations about recommending it to many people, especially to the impressionable young. the part of physics that fascinates gefter is the part that has gone way beyond anything bound by the conventional understanding of science. ... the questions being discussed and answers proposed are woolly in the extreme, … not recognizing that this post-modern way of doing science is deeply problematic and leading the field into serious trouble isn’t so much gefter’s fault as that of the experts she speaks to .... those taking the field down this path are dominating public coverage of the subject, and often finding themselves richly rewarded for engaging not in sober science but in outrageous hype of dubious and poorly-understood ideas. only the future will tell whether the significance of this book will end up being that of an entertaining tale of some excesses from a period when fundamental physics temporarily lost its way, or a sad document of how a great science came to an end. 7 in this criticism woit implicitly indicates that the central problem that he finds with approaches to current interpretations within physics lies in the relationship between what he considers to be ‘true’ physical theory, which he considers to be “sober science,” and the metaphysical dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 12-43 smetham, g. p., why us: trespassing on an anthropic lawn (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 14 conclusions that are derived from such “sober science.” in this indication woit has inadvertently put his finger on a crucial issue that rarely gets clearly examined or articulated. however, one significant science writer who has taken on this investigation, in his book farewell to reality: how fairy tale physics betrays the search for scientific truth, is jim baggott, who writes: ...i’m going to accuse a bunch of theoretical physicists of abandoning the scientific method and so betraying the search for scientific truth about the nature of physical reality … i will seek to reject fairy-tale physics as metaphysics. 8 the proposals that baggott identifies as “fairy-tale physics” are the stuff of popular science writing: string theory, supersymmetry, m-theory, many worlds and the multiverse, the holographic principle and so on. some of the perspectives that baggott seeks to chastise are also amongst those enthusiastically and breathlessly expounded by gefter. the term ‘metaphysics’ is, according to many, notoriously difficult to define. originally the term was used simply to indicate the works of aristotle which he wrote after his works which purported to deal with purely ‘physical’ phenomena. the philosopher peter van inwagen describes the aristotelian notion of metaphysics: metaphysics is about things that do not change. in one place, aristotle identifies the subject matter of first philosophy as “being as such,” and, in another, as “first causes.” it is a nice—and vexed—question what the connection between these two definitions is. perhaps this is the answer: the unchanging first causes have nothing but being in common with the mutable things they cause—like us and the objects of our experience... 9 thus we see that originally the term ‘metaphysics’ denoted the exploration and description of the deep, core, fundamental structures of reality, at the very deepest level it has to do with the unchanging ‘stuff’ of reality which gives rise to the changing phenomena of our experiential world. furthermore, it is clearly essential that metaphysics also elucidates the relationship between ‘pure being’ and the phenomena that arise from its changeless essence. in buddhist yogācāra terminology, as we have seen, ‘pure being’ is dharmata, and the manifested phenomena are dharmas. today, however, the metaphysical task has been handed over to physics, despite baggott’s mistaken notions. we shall see that baggott’s rigid distinction between physics and metaphysics is mistaken. indeed, the significant physicist abner shimony referred to the experimental investigation of the deepest quantum layer of reality accessible to us, in experiments of bell-type inequalities, precisely as “experimental metaphysics.” 10 in this case, then, wherein physics investigates and describes the deepest quantum level of reality, we see that physics dissolves into metaphysics. indeed, there is a fuzzy, hazy boundary between physics and metaphysics. and, furthermore, it is important to be cognisant of the fact that originally physics was based on a metaphysical commitment to materialism, a commitment which its own development has now crucially undermined. the notion that physics and metaphysics can be sharply separated is, then, mistaken. furthermore, the notion that it is invalid to draw metaphysical conclusions, such as that of the anthropic principle, on the basis of the evidence of physics and the other sciences is equally misguided. dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 12-43 smetham, g. p., why us: trespassing on an anthropic lawn (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 15 baggott’s use of the term ‘metaphysics’ is not of the aristotelian kind. his use has more to do with the use of the term by the twentieth century ‘logical positivists’, for whom the meaning of a scientific statement consisted entirely in the predictions it made about possible experience, and any statements which went beyond such statements were asserted to be meaningless ‘metaphysical’ statements. baggott claims that: there is as yet no observational or experimental evidence for many of the concepts of contemporary theoretical physics, such a super-symmetric particles, superstrings, the multiverse, the universe as information, the holographic principle, or the anthropic cosmological principle. for some of the wilder speculations of the theorists there can by definition never be any such evidence. 11 however, whilst it may be the case that “some of the wilder speculations” are completely devoid of evidential backing, it can be shown that this is not true of the anthropic principle. in fact the opposite is the case, there is overwhelming evidence for an anthropic principle, which asserts that the development of sentience and consciousness is a primary and fundamental feature of the process of reality. in his chapter on the anthropic principle, baggott clearly indicates that he rules out the anthropic principle purely on the grounds of what is called the ‘copernican principle’, which is the dogmatic assertion that the universe cannot be anthropic. this assertion is not based on any evidential grounds. baggott indicates that he is uneasy with the fact that the anthropic principle clearly has religious and spiritual implications. but baggott presents no evidence which counters or undermines the anthropic principle, he simply dogmatically rules it out as being unscientific in principle. the ‘copernican principle’ is named after the renaissance mathematician and astronomer nicolaus copernicus, who realized that the earth is not the center of the solar system, as was thought at the time, but, rather, the sun has that central role. it is thought by supporters of the copernican principle that the erroneous notion of the earth being the center was an example of the people at the time overestimating their own importance, rather than just making a mistake based upon the evidence available at the time. supporters of the copernican principle claim that any assertion which seems to privilege human life in any way must be considered anti-scientific, whatever the evidence. when applied to the anthropic principle, the copernican principle has become a dogmatic decision on the part of a large section of the scientific community to disregard, and even suppress by nefarious means, evidence suggesting that consciousness is not only a primary feature of the process of reality, but also has a role in creating what appears to be the ‘material’ world and the sentient organisms within it. baggott describes the copernican principle (or prejudice): the universe is not organized for our benefit and we are not uniquely privileged observers. science strives to remove ‘us’ from the centre of the picture, making our existence a natural consequence of reality rather than the reason for it. empirical reality is therefore something that we have learned to observe with detachment, without passion. scientists ask fundamental questions about how reality works and seek answers in the evidence from observation and experiment, irrespective of their own personal preferences, prejudices and beliefs. 12 dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 12-43 smetham, g. p., why us: trespassing on an anthropic lawn (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 16 the problem with this presentation, however, is that it seems to suggest that a failure to “remove ‘us’ from the centre of the picture” is a result of a lack of detachment, a pandering to “personal preferences, prejudices and beliefs.” but nothing can be further from the truth, as roger penrose has pointed out with regard to the relationship between quantum theory and consciousness: quantum theory was not wished upon us by theorists. it was (for the most part) with great reluctance that they found themselves driven to this strange and, in many ways, philosophically unsatisfying view of the world. 13 the early explorers of the quantum realm did not consciously seek to erect some form of mystically inspired physical theory, to begin with they were shocked by their discoveries. however, the evidence moved towards an inescapable endpoint, as master quantum physicist john wheeler, toward the end of his life, concluded: the question is what is the question? is it all a magic show? is reality an illusion? what is the framework of the machine? darwin’s puzzle: natural selection? where does space-time come from? is there any answer except that it comes from consciousness? what is out there? t’is ourselves? 14 physicist anton zeilinger has written in appreciation of wheeler’s: …realisation that the implications of quantum physics are so far-reaching that they require a completely novel approach in our view of reality and in the way we see our role in the universe. this distinguishes him from many others who in one way or another tried to save pre-quantum viewpoints, particularly the obviously wrong notion of a reality independent of us. 15 so, whereas baggott claims that we must keep ‘us’ out of the scientific picture whatever the evidence, wheeler and zeilinger claim that the evidence of quantum physics indicates the central significance of ‘us’ in the process of reality. and they are not alone, physicist and philosopher bernard d’espagnat, for another example, writes that: the doctrine that the world is made up of objects whose existence is independent of human consciousness turns out to be in conflict with quantum mechanics and with facts established by experiment. 16 there is a dramatic amount of evidence that consciousness is fundamentally significant in the process of reality and the evolution of life and the universe. in other words wheeler and others have drawn the conclusion, based upon quantum theory and the fact of a seemingly miraculous fine-tuning of physical parameters, that ‘us’ or some form of intelligence is somehow involved in the evolution of life and the universe. one example of spectacular fine-tuning of the physical constants of the universe is the generation of carbon in the process of stellar nucleosynthesis. the cosmologist fred hoyle famously stated in this context: dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 12-43 smetham, g. p., why us: trespassing on an anthropic lawn (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 17 would you not say to yourself, “some super-calculating intellect must have designed the properties of the carbon atom, otherwise the chance of my finding such an atom through the blind forces of nature would be utterly minuscule? a common sense interpretation of the facts suggests that a superintellect has monkeyed with physics, as well as with chemistry and bio logy, and that there are no blind forces worth speaking about in nature. the numbers one calculates from the facts seem to me so overwhelming as to put this conclusion almost beyond question.” 17 the notion of a “super-calculating intellect,” of course, moves us in the direction of theism. however this is not a necessity in the anthropic context, wheeler, for instance, thought of the process of the self-production of the universe as being the result of the intersubjective collective perceptual activities of all sentient beings: directly opposite to the concept of universe as machine built on law is the vision of a world self-synthesized. on this view, the notes struck out on a piano by the observer participants of all times and all places, bits though they are in and by themselves, constitute the great wide world of space and time and things. 18 in order to graphically represent this perspective wheeler employed his ‘self-perceiving universe image (figure 1), in this case the self-perceiving u does represent ‘us’. in this context it is worth pointing out that the anthropic principle, a term coined in 1974 by the theoretical physicist brandon carter, is often misrepresented as being the claim that it is solely human life that is the end point of the anthropic process, rather than sentient life in general. as the philosopher nick bostrom has pointed out: figure 1 the term “anthropic” is a misnomer. reasoning about selection effects has nothing to do with homo sapiens, but rather with observers in general. carter himself regrets not having chosen a better name. 19 it is also necessary to point out the distinction between the so-called weak anthropic principle which simply states that the universe we find ourselves in must be anthropic because we exist, but it might have been otherwise, and the strong anthropic principle which asserts that it is the dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 12-43 smetham, g. p., why us: trespassing on an anthropic lawn (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 18 very nature of the universe to be anthropic. on this view, life and sentience are the reason for the universe’s existence, so to speak, and there is an innate intelligence and fundamental awareness and internal consciousness which unfolds within the process of the evolution of life and the universe. however, there is a deep reluctance, verging on a dogmatic prejudice, against allowing such evidence to be entertained because the implications, especially in the sphere of spirituality, are significant and important. and this antagonism has been enshrined in the so-called ‘copernican principle’ which has been elevated by some to an inviolable principle of the scientific method. baggott for example writes: i don’t think we need to waste time debating whether the strong anthropic principle, or indeed any similarly structured principle, is scientific. any structure designed to completely overturn the copernican principle and restore some kind of privileged status to intelligent observers (be they human or not) goes against the grain of nearly five hundred years of scientific practice. 20 however, in making such a sweeping and dogmatic statement baggott is clearly ignoring the most crucial feature of the scientific method which is that, as baggott himself writes in his book, scientists should “seek answers in the evidence from observation and experiment, irrespective of their own personal preferences, prejudices and beliefs.” 21 there is, however, absolutely no “evidence from observation and experiment” which supports the copernican principle, it is much more akin to “personal preferences, prejudices and beliefs.” 22 as brandon carter pointed out about the copernican dogma: unfortunately there has been a strong (not always subconscious) tendency to extend this to a most questionable dogma to the effect that our situation cannot be privileged in any sense. 23 the evolutionary biologist richard lewontin stated a particularly egregious version of the copernican principle which indicates that materialism must be adhered to, whatever the evidence against it, in order to further science’s supposed intellectual war with religion: our willingness to accept scientific claims that are against common sense is the key to an understanding of the real struggle between science and the supernatural. we take the side of science in spite of the patent absurdity of some of its constructs, in spite of its failure to fulfill many of its extravagant promises of health and life, in spite of the tolerance of the scientific community for unsubstantiated just-so stories, because we have a prior commitment, a commitment to materialism. it is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. moreover, that materialism is absolute, for we cannot allow a divine foot in the door. 24 lewontin, like baggott, seems oblivious to the scientific requirement to take observations and evidence seriously. dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 12-43 smetham, g. p., why us: trespassing on an anthropic lawn (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 19 this antagonism towards any evidence which points towards the fundamental and innate presence of awareness, consciousness, intelligence and design (not necessarily of a theistic nature) in the evolution and development of life and the universe runs very deep in some western intellectual cadres. it derives from certain political, social and academic forces in the late nineteenth and early twentieth centuries, forces which favoured materialist darwinism in the face of any contrary evidence. in the most extreme form it manifests in the ridiculous strident and pugilistic assertions of crude materialism and crude darwinian fundamentalism as displayed by the likes of richard dawkins and friends. but the intellectually undermining influence of academic materialism, crude or subtle, permeates and exercises an influence upon a great deal of modern intellectual, academic and popular culture, thus the great popular taste for the writings of dawkins, even though his many of his metaphysical claims can be shown to be dubious. such is the pervasiveness of this fundamentalist materialism that it pervades works such as gefter’s tel, even though the very metaphysical accounts conveyed to gefter by various physicists are entirely contrary to any materialist account of the process of reality. in gefter’s hands they are sanitised for the materialist cause by gefter’s stubborn refusal to figure out that the notion of an ‘observer’ without the presence of consciousness is absurdly incoherent. gefter appears to have a detailed understanding of the groovy, weird and wonderful things that current physics indicates about the nature of reality, yet she fails to appreciate that any moderately metaphysically coherent intellect would consider the perspectives described to her by most of the physicists she interviews to be antithetical to any form of materialism. consider for example, the physical-metaphysical perspective proposed by wheeler as described by physicist paul davies, gefter writes concerning wheeler’s notion of “a participatory universe”: if measurements built the universe bit by bit, as wheeler suspected, then observers were somehow implicated in the creation of reality a radical picture that, if true, would mean ours was a participatory universe. as the physicist paul davies wrote, “wheeler seeks to … turn the conventional explanatory relationship matter→information →observers on its head, and place observership at the base of the explanatory chain: observers→information→matter … could it somehow be that observers turn nothing into something? the idea seemed impossible from the start, because where would the observers come from? what would even count as an observer? surely it did not have to be conscious or human … but what? 25 the fact that it appears that “measurements built the universe bit by bit” derives from the quantum situation that prior to a “measurement” being carried out by an “observer” there is only a quantum realm of potentiality, which is not a “nothing” gefter, like some others, is very slap-dash with some of her terminology regarding the ground quantum state. this quantum realm of potentiality becomes an experienced, and apparently ‘material’, reality when a measurement “collapses” the quantum wavefunction of potentiality. on this view, the activity of a multitude of acts of observation are required to build an experiential-material universe over time. this was wheeler’s fundamental view. and it is a view which clearly requires the acceptance that observership, and therefore consciousness, is a fundamental and primary aspect of the process of reality. in other words, there must be some kind of internal pressure of “observership,” not fully individuated and conscious at the ground dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 12-43 smetham, g. p., why us: trespassing on an anthropic lawn (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 20 level of course, but having the nature of undifferentiated primordial consciousness. the process of the deeper levels of “observership” eventually produces the multitude of sentient organisms which continue to maintain the universe through their observations. such a view is clearly strongly anthropic. gefter refers to such an anthropic perspective as “top-down” as opposed to the conventional “bottom-up” approach. it is “top-down” in the sense that, like mensky's notion of a “lifeprinciple” operating at the quantum level in order to unfold the potentialities for life which are a fundamentally innate aspect of the quantum realm, this perspective requires that we accept that life and consciousness are internal, and primary, aspects of the ground of the process of reality. gefter writes about this: anthropic coincidences are problematic for bottom-up cosmology because you are starting with an initial state that’s completely independent of observers; the universe evolves forwards in time until observers like us just happen to arise, a fluky by-product of physics and happenstance. given random initial conditions some 14 billion years ago, of course we’re scratching our heads and asking, what were the odds that the universe would just happen to have every minute ingredient to cook up the fragile stew of life? top-down cosmology, on the other hand, doesn’t raise the question … top down cosmology starts with observers … and if you start with life, you are bound to end up with a life-friendly universe. why an anthropic principle? … because the universe is observer dependent. such jewel-toned thoughts about life made me nervous any theory which relied on humans or consciousness as being some kind of “special” ingredient struck me as crackpot. 26 so, here we have it, gefter dismisses the notion of a top-down development of life and the universe, not on the basis of evidence or cogent reasoning, but, rather, she kind of feels in her bones, so to speak, that such a notion must be “crackpot.” it does not occur to her that, not only does the evidence support this psycho-metaphysical viewpoint, it is also the only logically coherent possibility. the notion that life and consciousness can emerge from entirely lifeless and entirely blankly non-conscious fundamental aspects of reality is absolutely logically incoherent and therefore definitely “crackpot.” at the same time as gefter revels in the frisson of an “observer-dependent” reality, she, as we shall see, also, inconsistently, supports the current academic prevalence of crude materialist dogma. like many others she seems to be incapable of drawing obvious conclusions because of a preformed dogmatic prejudice concerning any viewpoint which draws spiritual conclusions from the modern discoveries on the part of physics. bizarre and contradictory it may be but, at the same time as she seems to support her father’s view that the universe is some kind of illusion generated from a “homogeneous state” of “nothingness” (which itself is a misuse of the term “nothingness” which should mean absolute zilch – not even a glimmer of potentiality), and that the process of reality and the universe is “observer-dependent,” she also upholds the materialist worldview, supporting a crude materialist darwinism. gefter also holds to the view that consciousness has nothing to do with the fundamental observer-dependency of the universe. in her worldview consciousness is asserted to be generated by material brain processes: dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 12-43 smetham, g. p., why us: trespassing on an anthropic lawn (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 21 wheeler thinks that consciousness could be the criterion for an observer, but that's obviously bullshit. i mean, consciousness is just a physical process in the brain. it’s not magic. 27 this means that, in her universe, which she asserts is “observer-dependent,” observation can take place without the presence or activity of consciousness. according to gefter: it was also clear that we needed to give careful consideration to the meaning and role of “observers” in general. both relativity and quantum theory had changed the role that observers played in physics – not observers as humans or conscious creatures, but observers as in points of view. 28 such bizarre formulations indicate the remarkable philosophical incompetence on gefter’s part. the notion of free-floating “points of view,” having no reference to any kind of experiential substrate able to experience and be aware of the “point of view” is incoherent. this claim elevates the notion of a “point of view” to an elementary feature of the process of reality, a claim which is philosophically unacceptable precisely because the concept of a “point of view” requires the experiential medium of consciousness. however, this attempted objectification of the notion of a “point of view” indicates what is going on here. this move amounts to what zeilinger calls an attempt to “save pre-quantum viewpoints, particularly the obviously wrong notion of a reality independent of us.” 29 in the scientific revolution of the seventeenth century mind and consciousness were removed from the scientific description because of not being amenable to mathematical quantification. subsequently the notion of consciousness became problematic and, due to the remarkable achievements of the scientific method in investigating, harnessing and controlling the phenomena of material reality, it was assumed that matter was the ultimate substance and consciousness was considered to be derivative. consciousness, then, was simply assumed to be irrelevant to any ultimate description of the process of reality. this assumption, however, was overturned within the quantum revolution wherein consciousness was shown to have a subtle interconnection with the quantum realm, interacting with it in order to produce experienced ‘material’ reality. as physicists bruce rosenblum and fred kuttner write in their book quantum enigma: physics encounters consciousness: …physics’ encounter with consciousness, demonstrated for the small, applies to everything. and that ‘everything’ can include the entire universe. 30 this indicates the primary nature of consciousness. however, resistance to this conclusion is still prevalent amongst a rearguard community of adherents to the metaphysical worldview of materialism, and in order to “save the appearances” of this outmoded worldview adherents simply rearrange language to suit their purposes. thus “points of view” become active agents on their own behalf, having, according to gefter’s up-side-down and inside-out perspective, no connection with consciousness. gefter writes: “observers” didn’t mean people, and “observer-dependency” didn’t mean subjective. but i could imagine how it could all be misconstrued. 31 but, as we shall see, wheeler did mean “people” (and animals). it might be true that the universe is not entirely subjective, wheeler’s perspective requires us to consider it to be an intersubjective dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 12-43 smetham, g. p., why us: trespassing on an anthropic lawn (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 22 creation. however, gefter’s absurd misconstrual here is the confident, and mistaken, assertion that “observers” and “observer-dependency” have nothing to do with consciousness. gefter has great admiration for wheeler, praising his poetic approach to exploring some of the deepest mysteries of physics and existence, but at the same time she is wary of his views on the issue of the agency of consciousness. wheeler asserted that the universe has been built up, bit by bit, from the quantum “smoky haze of possibility” (not “nothingness”) by acts of observation made by sentient beings. gefter observes: but what exactly did wheeler mean by an observer? without careful clarification observer was a dirty word. … wheeler himself acknowledged the problem. “any exploration of the concept of ‘observer’ and the closely associated notion of ‘consciousness’ is destined to come to a bad end in an infinite mystical morass,” he wrote. and yet at times he teetered dangerously on the banks of the morass, his view of observers skewed far more towards minds than rods or clocks. 32 and it is true that wheeler did tread a very fine line, it may even be said that at earlier times in his career he hedged his bets, and it is interesting and illuminating to consider why this might have been the case. in a 1983 article law without law, wherein he described the delayed choice experiment, which demonstrates how an observation can determine the nature of reality backwards in time, wheeler wrote the following observations: we are inescapably involved in bringing about that which appears to be happening. 33 and: many investigators, believing that the greatest insights are to be won from nature’s strangest features are … giving fresh coverage of the strange “observer-participancy” forced to our attention by the quantum. 34 and: useful as it is under everyday circumstances to say the world exists “out there” independent of us, that view can no longer be upheld. there is a strange sense in which this is a “participatory universe.” 35 and: is the term “big bang” merely a shorthand way to describe the cumulative consequence of billions upon billions of elementary acts of observer-participancy reaching back into the past... 36 and: yes, oh universe, without you i would not have been able to come into being. yet you, great system, are made of phenomena; and every phenomena rests on an act of observation. you could never even exist without elementary acts of registration such as mine. 37 and: beyond particles, beyond fields of force, beyond geometry, beyond space and time dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 12-43 smetham, g. p., why us: trespassing on an anthropic lawn (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 23 themselves, is the ultimate constituent the still more ethereal act of observerparticipancy? 38 and yet, despite these stirring and repeated assertions of the “observer-participatory” nature of the universe, wheeler also asserted in this article that: we cannot speak in these terms without a caution … the caution: “consciousness” has nothing to do with the quantum process. we are dealing with an event which makes itself known by an irreversible act of amplification, by an indelible record, an act of registration. 39 but one must ask in this context: how does wheeler know this? what possible result or results of quantum experimentation validate this conclusion? none! if observer-participation is clearly required for the manifestation of the universe, and the most natural assumption is that observation is a phenomenon that requires consciousness, then the most obvious conclusion is that consciousness is implicated. so why does wheeler, in this 1983 article, issue such a stern warning? in order to appreciate a possible answer it is useful to look into the intellectual climate and expectations within the physics establishment at that time and the years preceding. rosenblum and kuttner are physicists who have no doubt about the connection between consciousness and the quantum ground of reality: consciousness and the quantum enigma are not just two mysteries; they are the two mysteries; first, our physical demonstration of the quantum enigma, faces us with the fundamental mystery of the objective world ‘out there;’ the second, conscious awareness, faces us with the fundamental mystery of the subjective, mental world ‘in here.’ quantum mechanics seems to connect the two. 40 they also indicate the intellectual climate of mainstream physics since the 1950’s, extending down to recent times: in physics departments a conforming mindset increasingly meant that an untenured faculty member might endanger a career by serious interest in the fundamentals of quantum physics. even today it is best to explore the meaning of quantum mechanics while also working a ‘day job’ on a mainstream physics topic. 41 in his excellent book how the hippies saved physics david kaiser indicates that in the 1960’s and 70’s physics in the united states was a conservative profession not enamored of metaphysical speculation or research. the general attitude amongst working physicists was that of “shut up and calculate,” the idea being that it was the practical results of research that mattered, and speculation about exactly what quantum theory implied about the metaphysical nature of reality was to be avoided. the ethos was very different to that which held sway during the early development of quantum theory when discussions between einstein, bohr, heisenberg, schrödinger and the other ‘founding fathers’ were replete with puzzled philosophical speculations as to what the weird behaviour of the quantum realm might actually indicate about the nature of reality. kaiser observes that later in the united states: the quarter century during which this cold war style reigned witnessed an extraordinary buildup of calculating skill. at the same time, an intellectual trade-off slipped by unnoticed, with wide-ranging implications. for every additional calculation of baroque dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 12-43 smetham, g. p., why us: trespassing on an anthropic lawn (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 24 complexity that physics students tackled during the 1950’s and 1960’s, they spent correspondingly less time puzzling through what all of those fancy equations meant, what they implied about the world of electrons and atoms. the fundamental strangeness of quantum reality had been leeched out. 42 interest in quantum philosophical and metaphysical issues was a fringe activity. later, however, this anti-metaphysical attitude changed. the fundamental fysiks group (ffg) was founded in san francisco in may 1975 by two physicists, elizabeth rauscher and george weissmann, at the time both graduate students at the university of california, berkeley. the group held informal discussions on friday afternoons to explore the philosophical implications of quantum theory. leading members included fritjof capra, john clauser, philippe eberhard, nick herbert, jack sarfatti, saul-paul sirag, henry stapp, and fred alan wolf. according to kaiser: the ways and means of being a physicist came unmoored in a way they hadn’t been for two generations. no longer would the attitude of “shut up and calculate” hold sway unchecked. sitting around the large conference table at the lawrence berkeley laboratory with few other demands on their time, they sought to recapture the sense of excitement, wonder, and mystery that had attracted them to physics in the first place, just as it had animated the founders of quantum mechanics. 43 amongst this fringe group an interest in connections between quantum phenomena, consciousness and psychic phenomena was central, figure 2 shows a ‘roadmap’ drawn out by a member of the group for their research and metaphysical explorations. jack sarfatti was one of the few physicists who was very enthusiastic about wheeler’s metaphysical speculations at that time. he wrote: in my opinion, the quantum principle involves mind in an essential way …. the structure of matter may not be independent of consciousness. some component in the quantum probability involves the turbulent creative sublayer of ideas in the mind of the “participator.” 44 wheeler, however, kept his distance from these wayward fringe physicists. sarfatti and wolf were keen to work with wheeler but wheeler “politely declined” 45 their requests. so it would seem that wheeler at that time was keen not to veer too far from academic respectability. it can be seen from the ‘roadmap’ for explorations based on the important implications of quantum entanglement that the ffg were aware that the new emerging quantum worldview might support the existence of phenomena such as esp and psychokinesis, phenomena that were dogmatically ruled out within a ‘classical’ worldview. they saw the possible implications of an “observercreated world.” wheeler’s disavowal of the role of consciousness at this time actually lacks credibility as he also wrote in law without law: are billions upon billions of acts of observer-participancy the foundation of everything? we are about as far as we can be today from knowing enough about the deeper machinery of the universe to answer this question. increasing knowledge about detail has bought increasing ignorance about plan. the very fact that we can ask such a dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 12-43 smetham, g. p., why us: trespassing on an anthropic lawn (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 25 strange question shows how uncertain we are about the deeper foundations of the quantum and its ultimate implications. 46 in the light of such “uncertainty” about “deeper foundations of the quantum and its ultimate implications” it is difficult to see how wheeler could be so certain at that time that “consciousness has nothing to do with the quantum process.” it seems very likely that such statements were made with deference to academic respectability. as we know he later changed his mind on this issue and he connected up the notion of observership with consciousness: unless the blind dice of mutation and natural selection lead to life and consciousness and observership at some point down the road the universe could not have come into being in the first place... 47 figure 2. the ffg’s ‘roadmap’ of quantum possibilities for the paranormal. in other words the universe could not come into being without the emergence of “consciousness and observership.” but what wheeler failed to see, at least at this point, is that life and consciousness must have been already implicit or potential at the point of the big bang, which was actually a quantum fluctuation in a vast quantum field of potentiality, a field that mensky terms the ‘alterverse’ – the vast pool of possible alternative histories of the universe. furthermore, because consciousness is involved in the unfolding of the universe, the process cannot be driven by “the blind dice of mutation and natural selection.” the materialist darwinian worldview is entirely out of place in wheeler’s quantum psycho-metaphysics, as we have seen in a previous wheeler quote he indicated that “darwin’s puzzle: natural selection … comes from consciousness.” and in this case the kind of “natural selection” involved cannot be the random “blind watchmaker” variety, for the unfolding of life requires that consciousness dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 12-43 smetham, g. p., why us: trespassing on an anthropic lawn (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 26 steers in the direction of life through some sort of quantum ‘look-ahead’ mechanism such as mensky’s ‘postcorrection’ mechanism. wheeler described the meaning of his “universe as a self-excited circuit” graphic image (figure 1) as follows: beginning with the big bang, the universe expands and cools. after eons of dynamic development it gives rise to observership. acts of observer-participancy – via the mechanism of the delayed choice experiment – in turn give tangible “reality” to the universe not only now but back to the beginning. to speak of the universe as a selfexcited circuit is to imply once more a participatory universe. 48 and the caption for the image is: starting small (thin u at upper right), it grows (loop of u) and in time gives rise (upper left) to observer-participancy – which in turn imparts “tangible reality” … to even the earliest days of the universe. 49 physicist kip thorne explained wheeler’s perspective to gefter as follows: from a certain point of view, which wheeler adopts, systems can become classical only when observed. they behave quantum mechanically … until observed, and the observation collapses the wavefunction. so wheeler conceives of the universe as having been born and having evolved quantum mechanically until it naturally generates life. then that life performs the observation that collapses the state of the universe to make it classical. it is self-excited in the sense that the observation comes from within the universe, not from the outside. 50 gefter then asks thorne: “does it have to be biological life that makes the observation?” and thorn tells her that this was wheeler’s view. wheeler, however, did not at this point seem to be aware that “observer-participancy” could not have suddenly sprang into operation from nowhere, it must have been implicit or potential from the beginning. furthermore, the mechanism of “observer-participancy” must have been operative in some form even when fully organic beings where not yet fully evolved. in other words the mechanism of self-excitation, self-observation, or self-registration must be a fundamental mechanism employed by a deep non-individuated primordial consciousness, and the employment of this mechanism results in the development and evolution of the universe and the sentient beings it contains. in other words, primordial consciousness is able to individuate through a wheeler-type mechanism of universal internal self-perception. this wheeler-type mechanism corresponds in an important way with mensky’s psycho-metaphysics, in both perspectives evolutionary choices are made through a quantum mechanism involving consciousness from the reference point of a future point in time. and, as we saw in the first chapter the same is true of the quantum metaphysics outlined by hawking & mlodinow in their book the grand design. gefter, however, seems dogmatically predisposed to reject notions of consciousness being at all involved in the development of the universe and the sentient life within it: dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 12-43 smetham, g. p., why us: trespassing on an anthropic lawn (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 27 i couldn’t see how bringing consciousness into the mix could possibly help not least of all because scientists don’t know what consciousness is. whatever it is, it’s governed by the same laws of physics and composed of the same particles, fields, or informationtheoretic bits as everything else. 51 here we find gefter stating her own prejudices, admittedly derived from the deep-seated materialism that pervades so much scientific and academic discourse, as if they were backed by evidence or reasoning, which they are not. her views on the nature of consciousness are nothing other than materialist dogma. consciousness cannot be composed of ‘particles’ precisely because particles come into being when consciousness interacts with quantum wavefunctions of potentiality. so consciousness is more fundamental than particles. it may be possible to consider consciousness as a quantum field, but in this case it would be a fundamental quantum field capable of interacting with other quantum fields in creative ways. this would render consciousness as being an essential creative feature of the ‘physical’ world. the quantum cosmologist andre linde has mused in this context: is it possible that consciousness, like spacetime, has its own intrinsic degrees of freedom and that neglecting these will lead to a description of the universe that is fundamentally incomplete? what if our perceptions are as real as (or maybe, in a certain sense, are even more real) than material objects? 52 and linde has also observed: the universe and the observer exist as a pair. ... the moment you say that the universe exists without any observers, i cannot make any sense out of that. i cannot imagine a consistent theory of everything that ignores consciousness. a recording device cannot play the role of an observer, because who will read what is written on this recording device? in order for us to see that something happens, and say to one another that something happens, you need to have a universe, you need to have a recording device, and you need to have us. it’s not enough for the information to be stored somewhere, completely inaccessible to anybody. it’s necessary for somebody to look at it. you need an observer who looks at the universe. in the absence of observers, our universe is dead. 53 furthermore, in the absence of conscious observers the universe is only quantum potentiality, no ‘classical’ world exists. such a viewpoint, which was accepted by several of the ‘founding fathers’ of quantum theory, and is accepted today by scientists such as linde, roger penrose, stuart hameroff, henry stapp, amit goswami, mensky and others, is, it seems, rejected by gefter without rhyme or reason. gefter’s claim that most scientists assert that they do not know what consciousness is, on the other hand, true. but the reason for this is that scientists in general approach the phenomenon of consciousness with a ridiculous methodology, expecting to be able to examine it “out there” as if it were some kind of externally existing fluid-like ‘stuff’. this, of course, is not possible. if we want to directly know what consciousness is there is only one way to know, and that is to experience directly through advanced meditation techniques such as exist in the buddhist tradition. in buddhist psycho-metaphysics there are levels or degrees of consciousness, which can be directly experienced by advanced meditation techniques. the basic division is that between jnana, which is fundamental nondual consciousness or wisdom-awareness, and vijnana dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 12-43 smetham, g. p., why us: trespassing on an anthropic lawn (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 28 or divided, dualistic everyday consciousness. everyday consciousness is the “glow of the ground of being” 54 manifesting in the dualistic world. the west’s understanding is primitive in comparison to buddhist psycho-metaphysics. if we require a definition of consciousness, then one derived from buddhism will suffice. here is a description of the fundamental nature of mind or consciousness given by the dalai lama: the knowing nature, or agency … is called mind and this is non-material … cognitive events possess the nature of knowing because of the fundamental nature of clarity that underlies all cognitive events. this is … the mind’s fundamental nature, the clear light nature of mind. 55 if we want to know where the “clear light nature of mind,” which provides the functionality of knowing and cognizing, arises from then, as mensky points out: …the phenomena of life and consciousness cannot be mechanistically reduced to the action of the laws of science as they are found in the course of exploring [inanimate] matter. the explanation of these phenomena on the basis of quantum mechanics requires [the] addition of a special independent element to the set of quantum concepts and laws. such a new element of theory should directly connect quantum concepts with the concepts characteristic of life. the simplest way to find this element is to consider the phenomenon of consciousness and compare it with the description of observation (measurement) in quantum mechanics. 56 the fundamental qualitative aspect of fundamental awareness which manifests as individuated consciousness must reside at the quantum level. as physicist nick herbert (one of the members of the fundamental fysiks group) has pointed out: ...every quantum system has both an ‘inside’ and an ‘outside’, and … consciousness both in humans as well as in other sentient beings is identical to the inner experience of some quantum system. a quantum system’s outside behavior is described by quantum theory, it’s inside experience is the subject matter of a new ‘inner physics’…. 57 as mensky indicates, the required ‘inner physics’ actually already exists within buddhist psycho-metaphysics. consciousness is, then, the internal qualitative aspect of the quantum functioning of the ‘ground of being’. according to buddhist psycho-metaphysics a continuous direct experience of the ground level of awareness is an experience of buddhahood, or enlightenment: when the true face of the ground aspect of buddhahood a state of purity and mastery of the ground of being … timeless awareness the innate glow of the ground of being subside into an inner glow whose radiance is directed outwards … 58 advanced buddhist meditation involves the dissolving of the dualistic everyday levels of the functioning of consciousness and the activation of deeper levels of a more universal consciousness. as buddhist practitioner-writer b. alan wallace has pointed out: this brings us to primordial consciousness, the ultimate level of mind that buddhists seek to penetrate. the substrate consciousness can be compared to a relative vacuum. it is relatively empty, but still possesses structure and energy, characterized by such attributes as bliss (spiritual joy or rapture), luminosity (an internal radiance), and a muted dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 12-43 smetham, g. p., why us: trespassing on an anthropic lawn (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 29 sense of duality between subject and object. primordial consciousness characterized as the absolute ground, the most basic state of consciousness could then be characterized as the absolute vacuum of consciousness. like the absolute vacuum of modern physics, it entails the lowest possible state of mental activity but the highest possible potential and degree of freedom. furthermore, whereas the substrate consciousness is conscious of the substrate the relative inner space or vacuum of the mind primordial consciousness is indivisibly aware of the absolute space of all phenomena (dharmadhatu), which is beyond the duality of external and internal space. out of this space emerge all the phenomena that make up all worlds of experience the whole universe, inside and out, subjective and objective. all appearances of external and internal space, time, matter, and consciousness emerge from the dharmadhatu and consist of nothing other than configurations of this absolute or true vacuum. 59 furthermore, final buddhahood, or complete enlightenment with a continuous awareness of the nondual ground of being, is the endpoint of the evolution and development of a sentient being. wheeler’s quantum conclusions were entirely consistent with buddhist psycho-metaphysics. he summarized his conclusions in his article ‘thoughts on the origin of spacetime’ as follows: in what medium does spacetime itself live and move and have its being? is there any other answer than to say that consciousness brings all of creation into being, as surely as spacetime and matter brought conscious life into being? is all this great world that we see around us a work of imagination? 60 figure 3 in other words we must conceive of a ground level universal energy-awareness-potentiality, also designated within buddhism as shunyata, or emptiness (not nothingness) which, through the medium of “spacetime and matter,” “creates” a manifested realm of individuated sentient beings within the apparently material world in order to embody individuated consciousness. through this process the universe can explore and discover its own meaning (figure 3). such a viewpoint is suggested by the recent notion of a “self-explaining universe” that the physicist paul davies has written about in his book the goldilocks enigma: …a good case can be made that life and mind are fundamental physical phenomena, and so must be incorporated into the overall cosmic scheme. one possible line of dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 12-43 smetham, g. p., why us: trespassing on an anthropic lawn (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 30 evidence for the central role of mind comes from the way in which an act of observation enters into quantum mechanics. it turns out that the observation process conceals a subtle form of teleology. 61 such a universe would necessarily contain organisms that embody the capacity for cognition, which is to say consciousness, precisely because the purpose of ‘self-explanation’, to use davies’ terminology, or self-cognition, is fundamental to the universe. it is part of the “teleology” of the universe. quantum physics seems increasingly to point towards the operation of an infinitely fertile universal “imagination,” to use wheeler’s term, which can actually bring into being an extraordinary appearance of a vast ‘material’ universe containing infinite varieties of consciousness, all of which inhabit an individualized field of meaning-values. as physicist david bohm pointed out: we can say that human meanings make a contribution to the cosmos, but we can also say that the cosmos may be ordered according to a kind of ‘objective’ meaning. new meanings may emerge in this overall order. that is we may say that meaning penetrates the cosmos, or even what is beyond the cosmos. for example there are current theories in physics that imply that the universe emerged from the ‘big bang’. in the earliest phase there were no electrons, protons, neutrons, or other basic structures. none of the laws that we know would have had any meaning. even space and time in their present welldefined form would have had no meaning. all of this emerged from a very different state of affairs. the proposal is that, as happens with human beings, this emergence included the creative unfoldment of generalized meaning. 62 each sentient being is an individualized structure of experiential meaning-values embodied within individualised consciousness, each sentient being embodies a fundamental evolutionary impetus to maximise the overall meaning value of the individualized meaning-matrix, the final endpoint being enlightenment, wherein the limited awareness of a sentient being dissolves into its universal source. this dramatic psycho-metaphysical perspective is articulated within the buddhist dzogchen tradition in texts such as you are the eyes of the world, composed by the remarkable fourteenth century practitioner-yogi longchenpa: listen, because all you beings of the three realms were made by me, the creativity of the universe, you are my children, equal to me. because you and i are not separate, i manifest in you. 63 this “creativity of the universe” can be seen in what paul davies indicates as a quantum “teleology,” an internal purpose, which brings into existence a vast field of individuated sentient beings all of which partake of the infinite capacity of the ultimate source. according to longchenpa: out of the state of pure and total presence, the impetus for everything from which come the five great elements whose very being is this state, i, the creativity of the universe, dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 12-43 smetham, g. p., why us: trespassing on an anthropic lawn (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 31 arise as teacher, in five forms of pure and total presence. 64 these “five teachers,” which are generated by the “creativity of the universe which fashions everything,” 65 are earth, water, fire, wind and space, in other words all the factors which make up the material dualistic world of experience. and: if i [the state of pure and total presence which is the creativity of the universe] did not exist, you would not exist. when you do not exist, the five teachers [i.e. the dualistic and material world of experience] also do not come about… 66 it is intriguing to compare these observations with some of wheeler’s, such as: yes, oh universe, without you i would not have been able to come into being. yet you, great system, are made of phenomena; and every phenomena rests on an act of observation. you could never even exist without elementary acts of registration such as mine. 67 what wheeler refers to as the “imagination” of a primordial consciousness that “brings all of creation into being,” corresponds precisely to longchenpa’s “majestic creativity [of the universe] which fashions everything.” 68 according to another buddhist dzogchen philosopher: in the human context, intelligence reaches into man’s life as his spirituality, constituting itself as human subjectivity. the latter, therefore, is not an immutable essence; rather it is a product of an overall evolutionary force moving in an optimizing direction, thereby enabling the subject to transcend itself by overcoming its limited domains. this force is felt as giving meaning to man’s life and is experienced as having existential significance. 69 in the buddhist dzogchen worldview, which is fully in accord with modern physics, we have a remarkable vision of the universe as a meaning-machine, or meaning-organism, using sentient beings both as creative agents and also agents of transcendence reaching towards ever greater vistas of universal meaning-values. this perspective indicates a universal directedness towards ever more universal modes of experience within consciousness, the ultimate experience being ‘enlightenment’. what is enlightenment? it is the direct nonconceptual understanding of the ground of being by the fundamental cognizant aspect of the ground of being itself. in other words enlightenment occurs when the ground of being fully and directly and nonconceptually cognizes, comprehends and understands its own nature through the agency of a sentient human being (assuming that animals cannot become enlightened). this is brilliantly explained in the excellent dzogchen text wonders of the natural mind by tenzin wangyal rinpoche. the ground of being is characterized within dzogchen as an ‘empty’ energy field of potentiality which has an internal spontaneous cognizant quality. the field of potentiality is designated ‘emptiness’ and the internal spontaneous cognizant quality is designated ‘luminosity’ or ‘clarity’. tenzin wangyal rinpoche writes: who then understands emptiness? there is the self-understanding of emptiness by emptiness itself, by the clarity aspect of emptiness that enables understanding by direct perception. understanding is not separate from emptiness. emptiness understands itself dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 12-43 smetham, g. p., why us: trespassing on an anthropic lawn (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 32 and illuminates itself, ... herein lies the inseparability of emptiness and clarity; selfunderstanding is self-clarity or self-awareness. 70 in mensky’s terminology we may say that within enlightenment the alterverse has a direct and full understanding of its own infinite capacity and nature. in buddhist terminology this is the “ultimate reality intuitive wisdom (dharmadhatu-jnana)” 71 by which the dharmadhatu, the ultimate space of phenomena – mensky’s ‘quantum alterverse’, directly cognizes its own nature. this vision of enlightenment as the final aim of the process of reality, and the evolution of the universe and sentient beings within it, is a natural endpoint of wheeler’s quantum psychometaphysics. his self-perceiving universe graphic indicates that as the universe evolves the degree and power of “observership” increases over time. the final and most complete act of observership can only be the omniscient knowledge of the true nature of all phenomena. in this context it is worth pointing out that the kind of ‘omniscience’ within enlightenment suggested by mensky, wherein an enlightened being has “access to the entire set of parallel worlds,” which is the entire ‘alterverse’, corresponds to what the buddhist scholar sara l. mcclintock calls “capacity omniscience”: on this model, which we find articulated … by vasubandhu, one may be omniscient in the sense that one may attain an unlimited capacity to know whatever one wishes simply by directing one’s attention to the object in question; omniscience is not a matter of knowing all things simultaneously. according to this model, the buddha may be called “all-knowing” by virtue of the fact of his unlimited capacity to know any knowable thing to which he directs his attention… 72 one important aspect of this omniscient capacity is the ability to directly see the rebirth history of any sentient being. such a view, that the process of evolution is directed towards an omniscient endpoint, has been called by some the final anthropic principle. quantum researcher david deutsch, who views the universe as a vast quantum computer, has speculated that in the distant future mankind will form a kind of supermind that will in some sense unite with the universe, forming a god-like entity. he describes the final anthropic principle: in the final anthropic principle or if anything like an infinite amount of computation taking place is going to be true, which i think is highly plausible one way or another, then the universe is heading towards something that might be called omniscience. ... but yes, there’s something like that, the concept that we’ve found that is most like a religious concept is providence. the fine-tuning of the universe, whatever it’s due to, is very like providence. but again, the role that this providence plays in physics is very different from the role that religious providence plays in religion, because in religion providence is supposed to be an explanation for why things are as they are. and that’s no good, because you’ve got to explain why providence did this and it just makes matters worse not better. in thinking about fine-tuning and trying to explain it, what we’re looking for is something that explains the fine-tuning. in other words, providence is not a proposed solution, it’s an interesting problem, which is going to be explained by something else, if at all. 73 however, the notion that the universe is merely a computational machine is yet again a dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 12-43 smetham, g. p., why us: trespassing on an anthropic lawn (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 33 manifestation of the materialist prejudice which seeks to undermine the notion that consciousness is a primary and the fundamental driving force of the process of reality. as gyatrul rinpoche has pointed out: today people tend to spend many hours working on computers rather than gaining the inner quality of experiential realization. a computer may have a tremendous amount of information loaded onto it, but we have yet to see a computer that has obtained liberation or omniscience. 74 it is the primordial consciousness of the process of reality that becomes omniscient of its own nature with the ‘achievement’ of enlightenment by a sentient being. because, like many scientists, deutsch has a mistrust of religious metaphysics he rejects the obvious conclusion that the fundamental existence of a primordial field of non-individuated awareness is a “providential” given. just as we cannot go beyond the fact of the existence of the eternal quantum fields underlying the process of reality, so too, we cannot go beyond the fact of the “providential” existence of primordial awareness or nondual awareness-consciousness. deutsch’s perspective clearly strays into the realm of religion, and it seems to correspond in essence with buddhist perspectives and it also reiterates the psycho-metaphysical perspective of the great twentieth century french jesuit theologian pierre teilhard de chardin who postulated that the process of the universe was directed towards a collective omniscient endpoint he called the “omega point.” in his book the phenomenon of man he wrote: … evolution is an ascent towards consciousness… therefore it should culminate forwards in some sort of supreme consciousness. but must not that consciousness, if it is to be supreme, contain in the highest degree what is the perfection of our consciousness – the illuminating involution of the being upon itself. 75 this notion that the “supreme consciousness” results when individuated consciousness directly cognizes its own nature is remarkably close to the buddhist view. however, de chardin, similar to deutsch, suggested that the final endpoint of the process of the universe resides at a distant future point in a super-personal universal collective consciousness: the very centre of our consciousness, deeper than all its radii; that is the essence which omega, if it is to be truly omega, must reclaim. and this essence is obviously not something of which we can dispossess ourselves for the benefit of others as we might give away a coat or pass on a torch. for we are the very flame of that torch. to communicate itself, my ego must subsist through abandoning itself or the gift will fade away. the conclusion is inevitable that the concentration of a conscious universe would be unthinkable if it did not reassemble in itself all consciousnesses as well as all the conscious; each particular consciousness remaining conscious of itself at the end of the operation, and even … each particular consciousness becoming still more itself and thus more clearly distinct the closer it gets to them in omega 76 . according to the psycho-metaphysical perspective presented by de chardin, then, the omega endpoint is one in which each individuated consciousness “abandons” its limited ego centered perspective, and in so doing it both becomes more fully “still more itself” whilst at the same time becoming co-extensive with all other consciousnesses. whilst this view initially appears consistent and coherent with buddhist psycho-metaphysics, it is in fact far more akin to the hindu notion of a substantial universal self (atman-brahman). buddhism, apart, perhaps, for the dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 12-43 smetham, g. p., why us: trespassing on an anthropic lawn (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 34 jonang school, denies such a substantialist-idealist point of view. de chardin referred to “the primacy accorded to the psychic and to thought in the stuff of the universe.” 77 the ultimate dependency upon consciousness of the apparently external material world is also clearly indicated by physicist wojciech zurek when he writes that the: “ultimate evidence for the choice of one alternative resides in our illusive “consciousness”. 78 but zurek also tells us that at the level of the everyday world consciousness seems to have little impact. quantum experimentation has shown without question that at the level of a single quantum state consciousness influences the ‘choice’ of which alternative reality comes into being. however, at the same time it also appears that on the large scale of the structures of the everyday world individuated consciousness has no choice, the material world seems to exist under its own momentum. this apparently independent weight of the apparently ‘external’ world of materiality is maintained, according to zurek, by the phenomenon of ‘decoherence’. according to zurek there is a kind of quantum template of the material world which “advertises” itself by producing a multitude of copies which are accessed by the conscious-nesses of all sentient beings. he likens this vast ‘template’ as a quantum “advertising billboard” which “decoheres” quantum states under its own momentum. in his “quantum darwinism” proposal zurek suggests that the quantum “advertising billboard” springs into existence advertising classical reality when quantum correlations become “robust enough”: the main idea of quantum darwinism is that we almost never do any direct measurement on anything … the environment acts as a witness, or as a communication channel. … it is like a big advertising billboard, which floats multiple copies of the information about our universe all over the place. 79 in other words there is a kind of quantum ‘matrix’ of the classical ‘material’ world which has become resistant to obliteration through the process of observation, it “floats” so many copies of itself all over the quantum environment that it becomes the source of the apparent ‘objectivity’ of the classical world. zurek explains the emergence of “objectivity” from “intersubjectivity” to gefter as follows: my view of reality has to do with what philosophers call intersubjectivity. that’s what quantum darwinism is all about. reality is what we agree on. in that sense it’s what’s invariant. but that invariance – and hence, quantum reality – is not fundamental, it’s emergent and approximate. 80 and: to understand objectivity. in a quantum universe we do not measure anything directly. if i were to make a direct measurement of a system, i could disturb its state. but i never do that, because usually the environment does the measuring for me. it decides on the set of states that get found out and get disseminated, and i never interact with the system directly, i just use the environment as a witness. the observer gets hold of the information that is already advertised all over the place. 81 in this discussion zurek makes a distinction between the “advertising billboard,” which is the quantum template of the universe that “floats” copies of itself “all over the place,” and the environment which acts as a “communication channel” which conveys quantum information dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 12-43 smetham, g. p., why us: trespassing on an anthropic lawn (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 35 about the template to observers. in this way the original “advertising billboard” does not get disturbed. on this view, ‘decoherence’ is the way that the “advertising billboard” maintains itself in the quantum environment and the “quantum darwinism” extra is the notion of the environment acting as a “witness” in conveying information to observers, as zurek explains: quantum darwinism goes beyond decoherence. it recognizes that we don’t measure anything directly. we just find out from the environment. 82 as gefter points out, this view eliminates wheeler’s notion of observer-dependency because the maintenance of the “intersubjective” “objective” world becomes the responsibility of decoherence, the “environment” then conveys the information to the observer, so the observer is isolated from the quantum template of the material world. zurek replies that: usually the measurement is done for you by the environment. but there are situations in which you deal with quantum systems hands-on. in that case, the choice is up to you how you want to set up your apparatus and decide what you’re going to measure. 83 thus it appears that zurek erects a rigid division between the case wherein quantum experiments are performed to demonstrate the “ultimate” dependency upon consciousness, and the case of the everyday material world which appears, in this presentation, to be entirely independent of consciousness. so zurek’s viewpoint does indeed appear to undermine wheeler’s “participatory universe.” although zurek says that: “the universe is quantum to the core,” he seems hell bent on giving it a fully classical demeanor, by isolating his quantum “advertising billboard” from the tampering effects of conscious observation. zurek’s approach, then, seems to eliminate the operation of consciousness. as john campbell, in his article quantum darwinism as a darwinian process, says of zurek’s work: hopefully this treatment will finally lay to rest the interpretational confusion around the role of a human observer in quantum measurements that has been prevalent in many treatments and taken to anthropomorphic extremes by some such as wigner. zurek’s work makes it clear that decoherence takes place whenever there is an information transfer to the environment. no human observer need be in attendance. 84 eugene wigner was a quantum physicist who was entirely convinced of the necessity of the quantum operation of consciousness: when the province of physical theory was extended to encompass microscopic phenomena, through the creation of quantum mechanics, the concept of consciousness came to the fore again: it was not possible to formulate the laws of quantum mechanics in a fully consistent way without reference to the consciousness. all that quantum mechanics purports to provide are probability connections between subsequent impressions (also called “apperceptions”) of the consciousness, and even though the dividing line between the observer, whose consciousness is being affected, and the observed physical object can be shifted towards the one or the other to a considerable degree, it cannot be eliminated. it may be premature to believe that the present philosophy of quantum mechanics will remain a permanent feature of future physical theories; it will remain remarkable, in whatever way our future concepts may develop, that the very study of the external world led to the conclusion that the content of the consciousness is an ultimate reality. 85 dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 12-43 smetham, g. p., why us: trespassing on an anthropic lawn (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 36 campbell’s desperate rush to dismiss the efficacy of consciousness on the basis of zurek’s treatment is, however, mistaken. zurek’s presentation is only a partial picture. physicist erich joos has pointed out: does decoherence solve the measurement problem? clearly not. what decoherence tells us, is that certain objects appear classical when they are observed. but what is an observation? at some stage, we still have to apply the usual probability rules of quantum theory. 86 and dieter zeh: decoherence by itself does not yet solve the measurement problem … this argument is nonetheless found widespread in the literature … it does seem that the measurement problem can only be resolved if the schrödinger dynamics … is supplemented by a nonunitary collapse… 87 zurek’s account is deficient, it does not, for instance, address the issue of the probabilities within quantum theory. and neither does it give an account of how the quantum “advertising billboard” came into being. at the point of the big bang there was only a vast set of quantum possibilities and no established “advertising billboard,” so where did it come from? if zurek really considers that his “view of reality has to do with what philosophers call intersubjectivity” and “reality is what we agree on,” 88 then should not the “advertising billboard” also be intersubjective in true wheeler-type sense? however, apparently wheeler had problems reconciling himself with a quantum metaphysics which involved multiple observers. the problem is highlighted by the quantum conundrum of “wigner’s friend,” a thought experiment concocted by wigner. if ‘wigner’s friend’ collapses the wavefunction of an atom inside a laboratory, then from the point of view of the friend both atom and friend are not in a state of quantum superposition. but from wigner’s point of view, standing outside the lab, both atom and friend are in a state of quantum superposition. so it seems that when we look at the situation involving multiple observers a contradiction arises. as gefter writes: wigner took the paradox to mean that consciousness plays some special role in physics – that while atoms and photographic plates … could be in superpositions, conscious people could not. 89 so wheeler too was forced to accept a special role for consciousness. gefter writes: wheeler was stuck. the only way to have multiple observers living in the same universe without having to give up the observer’s ability to create reality was to afford some special role for consciousness, however reluctant he was to do it. that opened up a host of bizarre but unavoidable questions “what level of consciousness?” “does a worm qualify?” “what about household appliances?” 90 dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 12-43 smetham, g. p., why us: trespassing on an anthropic lawn (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 37 figure 4. wigner's friend gefter’s absurd quip about “household appliances” is irrelevant because they are not sentient beings. quips such as these simply indicate that the author has given up using coherent reasoning and is resorting to attempted sarcasm. a worm, on the other hand, is a sentient being, although the level of consciousness of such an organism is clearly very low, in fact its level is likely to be virtually unconscious and automatic. this indicates a problem with western concepts of consciousness and unconsciousness when viewed from a buddhist perspective. for buddhist psycho-metaphysics what the west calls the ‘unconscious’ is still a state of consciousness, although it is not accompanied (usually) by self-awareness. within buddhist psycho-metaphysics even dreamless sleep is a state of consciousness, it is the clear light mind. for ordinary human beings this state is a state of blankness, but advanced buddhist practitioners can achieve self-awareness even within the clear light mind of deep sleep. gefter’s quip about the worm, which is clearly an attempt at irony which she thinks indicates the silliness of the notion that consciousness has an important role in the creation of the universe, can be easily defused. all sentient beings, even worms which have barely a glimmer of sentience, are animated by the primordial consciousness of the process of reality. it is this primordial consciousness which creates sentient beings and their environments and then acts through sentient beings to maintain the universe and evolve the sentient beings within it towards greater levels of self-awareness. the phenomenon of the ‘collapse of the wavefunction’ is not necessarily evidence that all sentient beings are individually creating reality by beaming single rays of consciousness, so to speak, at quantum wavefunctions, but, rather, it indicates that a deep level of primordial consciousness is operating through the community of sentient beings of all levels of consciousness in order to “create” the process of reality. thus the “intersubjective” creation of the universe is coherently coordinated by a deep level of primordial consciousness. in this way primordial consciousness acts upon the quantum potentialities in order to produce a coherent world of manifestation. this is the origin of zurek’s dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 12-43 smetham, g. p., why us: trespassing on an anthropic lawn (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 38 quantum “advertising billboard.” and from the point of view of individual sentient beings individual consciousness has little individual impact upon the edifice of the apparently material world precisely because it is an intersubjective collective creation generated by primordial consciousness, eventually acting through the agency of all sentient beings. so, although zurek is correct when he says that “there is every indication that the choice occurs much before” consciousness gets involved, this remark applies to individual consciousness. this does not detract from the fact that ultimately primordial consciousness, acting through the collective agency of sentient beings, orchestrates the process. gefter, however, is antagonistic to such notions: why drag consciousness into it all? i wondered. wheeler knew it was a mystical morass, and that one gap in understanding couldn’t be plugged by another. observers, sure – but why not stick with einsteinian observers, just reference frames, coordinate systems, rods and clocks? … the observer, conscious or not, had to be built out of ordinary physics, not fairy dust. 91 the answer to gefter’s question about why wheeler was drawn to the notion of the significance of consciousness perhaps lies in the fact that wheeler was probably aware that “reference frames, coordinate systems, rods and clocks” are not the kind of things which are capable of observing, observations require consciousness. as to the final “fairy dust” remark, the employment of prejudicial language does not count as evidence or reasoning. what ultimately is “ordinary physics?” it certainly is not the classical physics of ‘matter’. quantum fields are immaterial fields of potentiality, and evidence and reasoning indicates they are animated by a primordial quantum consciousness. the tactic of using insulting language rather than coherent argument has a hallowed tradition in the materialist academic camp. it is possible that gefter took inspiration for her use of the term “fairy dust” from the ardent materialist patricia churchland who tried to pour scorn on the penrose-hameroff proposal concerning consciousness and quantum coherence in brain microtubules: pixie dust in the synapses is about as explanatorily powerful as quantum coherence in the microtubules. 92 however, evidence is now emerging that penrose and hameroff may be correct to some extent. 93 churchland, like many ardent materialists, seems to think that concocting insults, without bothering with evidence and reasoning, against viewpoints they dislike constitutes an argument. gefter seems to have inherited this materialist trait. gefter interviews a few other significant physicists and philosophers, there is no need to cover all of them. the crucial issue we are concerned with is gefter’s treatment of the notion of the significant role of consciousness in the creation of the dualistic world and her attitude, as well as the attitude of some others, to the anthropic principle and religion. in the second chapter of tel she writes concerning the physics and ultimate reality symposium that she gatecrashed, posing as a science journalist, that: throughout the symposium. there had been a giant elephant in the room: the anthropic principle. ... anthropic had become a four letter word because it veered uncomfortably dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 12-43 smetham, g. p., why us: trespassing on an anthropic lawn (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 39 close to religion … as if the universe, somehow, were built just for us. 94 gefter has little patience with religion, she has pitched her intellectual tent with the anti-religion materialist camp. thus in a piece published in the new scientist entitled “how to spot a hidden religious agenda” she wrote: as a book reviews editor at new scientist, i often come across so-called science books which after a few pages reveal themselves to be harbouring ulterior motives. i have learned to recognise clues that the author is pushing a religious agenda. as creationists in the us continue to lose court battles over attempts to have intelligent design taught as science in federally funded schools, their strategy has been forced to… well, evolve. that means ensuring that references to pseudoscientific concepts like id are more heavily veiled. so i thought i’d share a few tips for spotting what may be religion in science’s clothing. red flag number one: the term “scientific materialism”. “materialism” is most often used in contrast to something else – something nonmaterial, or supernatural. proponents of id frequently lament the scientific claim that humans are the product of purely material forces. at the same time, they never define how non-material forces might work. i have yet to find a definition that characterises non-materialism by what it is, rather than by what it is not. the invocation of cartesian dualism – where the brain and mind are viewed as two distinct entities, one material and the other immaterial – is also a red flag. and if an author describes the mind, or any biological system for that matter, as “irreducibly complex”, let the alarm bells ring. misguided interpretations of quantum physics are a classic hallmark of pseudo-science, usually of the new age variety, but some religious groups are now appealing to aspects of quantum weirdness to account for free will. beware: this is nonsense. 95 this passage clearly indicates gefter’s antagonism to the intelligent design (id) perspective and her adherence to ‘scientific materialism’. but how does this endorsement of materialism sit with her trespassing (tel) conclusion that: the message was clear: having a finite frame of reference creates the illusion of a world, but even the reference frame itself is an illusion. observers create reality, but observers aren’t real. there is nothing ontologically distinct about an observer, because you can always find a frame in which that observer disappears... 96 if adopting a “finite frame of reference creates the illusion of a world” then the apparent ‘material’ in that illusory world must also be illusory, so how can someone holding to such a conclusion coherently preach a crude materialism, which asserts the ultimate ontological primacy of ‘matter’, conceived of as independent extended ‘stuff’. furthermore, how can “unreal” observers create an “illusory,” and yet “material,” reality through the mechanism of their observation without being endowed with consciousness? after all, zurek and other significant physicists state that the “ultimate” “choice” of quantum alternative realities resides within consciousness? gefter seems to preside over a remarkable morass of contradictory claims, indicating a lack of awareness of logical coherence, or a lack of intellectual integrity. and yet gefter, as she proudly informs us, is the book reviews editor for new scientist, and in this position she attempts to pour scorn on non-materialist works. gefter says that “some religious groups are now appealing to aspects of quantum weirdness to account for free will.” but there are also significant quantum physicists such as mensky, stapp, dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 12-43 smetham, g. p., why us: trespassing on an anthropic lawn (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 40 goswami and others who also claim this. in his paper entitled free will stapp writes that: a criterion for the existence of human free will is specified: a human action is asserted to be a manifestation of human freewill if this action is a specific physical action that is experienced as being consciously chosen and willed to occur by a human agent, and is not determined within physical theory either in terms of the physically described aspects of nature or by any non-human agency. 97 and the paper then presents an account of how the “orthodox quantum mechanics that flows from john von neumann’s analysis of the process of measurement in quantum theory” leaves a “causal gap” which is closed by the presence of free will. stapp’s account is far from “new age” and is detailed and precise. stapp points out that the “orthodox quantum mechanics” that derives from john von neumann’s presentation of the process of measurement in quantum theory is in terms of three processes that indicate a fundamental “three-level conception of reality.” von neumann’s “process 2” is the deterministic evolution of the probabilities of the quantum realm of idea-like potentiality, this is described by the schrödinger equation. “process 1” is a “psychophysical probing action whose psychologically described aspect is an increment in the knowledge of a probing agent/observer.” “process 3,” is “a choice on the part of nature,” which is a “response to such a probing action.” in other words, in “process 1” an experimenter or group of experimenters perform a “probing action” by deciding upon and then setting up a quantum experiment which can have various outcomes which have associated probabilities. because the choice of experiment determines what the possible outcomes can be, spin up-down or spin left-right for example, this probing action determines what responses “nature” can give. when the experiment is performed “nature” then makes a “choice,” and thereby the “probing knowledge-acquiring agents” get their knowledge. this, stapp says, constitutes “an idea-based quantum triality,” and: ...the dynamical structure of quantum theory contains certain causal gaps. in particular, the process-1 agent-generated choices of probing actions are determined, within the theory, neither by the physically described aspects of nature, nor by any non-human agency. thus, within the framework of orthodox quantum mechanics, the process-1 probing actions are, according to the specified criterion, manifestations of human free will... 98 stapp has also pointed out that this situation applies not just in quantum experiments but also in everyday life. 1 sarfatti, jack ‘wheeler’s world: it from bit?’ internet science education project, san francisco, ca. 2 gefter, amanda (2014), 281 3 mensky (2010), 15 4 the observer (january 25th, 1931) 5 https://www.kirkusreviews.com/book-reviews/amanda-gefter/trespassing-on-einsteins-lawn/ 6 http://www.math.columbia.edu/~woit/wordpress/?p=6532 7 ibid dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 12-43 smetham, g. p., why us: trespassing on an anthropic lawn (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 41 8 baggott, jim (2014), 2 9 http://plato.stanford.edu/entries/metaphysics/ 10 shimony, a. [1984] "contextual hidden variables theories and bell's inequalities", brit ish journal for philosophy of science 35: 25-45 11 baggott, jim (2014), x 12 baggott, jim (2014), 23 13 penrose, roger (1999) p295 14 sarfatti , jack ‘wheeler’s world: it from bit?’ internet science education project, san francisco, ca.. 15 barrow, john d., davies, paul c. w., harper, charles l. (eds) (2004) p201 – anton zeilinger: ‘why the quantum? “it” from bit”? a participatory universe? three far-reaching challenges from john archibald wheeler and their relation to experiment.’ 16 d'espagnat, bernard, ‘the quantum theory and reality’ scientific american, nov. 197 17 fred hoyle, "the universe: past and present reflections." engineering and science, november, 1981. pp. 8–12 18 barrow john d., davies, paul c. w., harper, charles l. (eds) (2004) p577 – wheeler, j a (1999) ‘information, physics, quantum: the search for links.’ in feynman and computation: exploring the limits of computers, ed a. j. g. hey, p309 (314). cambridge, ma: perseus books. 19 bostrom, nick, anthropic bias: observation selection effects in science and philosophy, 6 20 baggott, jim (2014), 278 21 baggott, jim (2014), 23 22 ibid. 23 carter, 1974, p. 291 large number coincidences and the anthropic principle in cosmology. in: longair, m. (ed.), confrontation of cosmological theories with observational data. reidel, dordrecht, pp. 291-298. 24 http://www.nybooks.com/articles/archives/1997/jan/09/billions-and-billions-of-demons/ 25 gefter, amanda (2014), 21 26 gefter, amanda (2014), 209 27 gefter, amanda (2014), 281 28 gefter, amanda (2014), 44 29 barrow, john d., davies, paul c. w., harper, charles l. (eds) (2004) p201 – anton zeilinger: ‘why the quantum? “it” from bit”? a participatory universe? three far-reaching challenges from john archibald wheeler and their relation to experiment.’ 30 rosenblum, bruce and kuttner, fred (2006), 201 31 gefter, amanda (2014), 52 32 gefter, amanda (2014), 101 33 wheeler, j, a, ‘law without law’, 185 http://www.forizslaszlo.com/tudomany/wheeler_law_without_law.pdf 34 ibid. 35 wheeler, j., a., ‘law without law’, 194 36 wheeler, j., a., ‘law without law’, 197 37 wheeler, j., a., ‘law without law’, 199 38 ibid. dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 12-43 smetham, g. p., why us: trespassing on an anthropic lawn (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 42 39 wheeler, j., a., ‘law without law’, 196 40 rosenblum, bruce and kuttner, fred (2006), 179 41 rosenblum, bruce and kuttner, fred (2006), 139 42 kaiser, d (2011), 19-20 43 kaiser, d (2011), 23 44 kaiser, d (2011), 65 45 kaiser, d (2011), 80 46 wheeler, j., a., ‘law without law’, 199 47 gefter, amanda (2014), 101 48 wheeler, j., a., ‘law without law’, 209 49 ibid. 50 gefter, amanda (2014), 216 51 gefter, amanda (2014), 101 52 barrow, john d., davies, paul c. w., harper, charles l. (eds.) (2004), 451 53 http://discovermagazine.com/2002/jun/featuniverse 54 lingpa, dudjom (2002), 95 55 dalai lama, herbert benson, robert thurman, howard gardner, daniel goleman (1999), 21 56 mensky (2010), 12 57 herbert, nick: ‘holistic physics -orintroduction to quantum tantra’ – internet document (www.southerncrossreview.org/16/herbert.essay.htm) 58 lingpa, dudjom (2002), 95 59 wallace, b. alan (2008) p192 60 http://adsabs.harvard.edu/abs/2003aps..apr.b6003w 61 davies, paul (2007), 275 62 bohm, david (2003), 180 63 longchenpa (2000,2010), 38 64 longchenpa (2000,2010), 37 65 longchenpa (2000,2010), 36 66 longchenpa (2000,2010), 39 67 wheeler, j., a., ‘law without law’, 199 68 longchenpa (2000,2010), 36 69 guenther, herbert v. (1984). 33 70 wangyal, tenzin rinpoche (2000) p181 71 thurman, robert a. f. (1991), 71 72 mcclintock sara, l. (2010), 31 73 deutsch, d., (2006) http://www.abc.net.au/radionational/programs/scienceshow/the-anthropic-universe/3302686#transcript 74 gyatrul rinpoche (trans. wallace, b. a.) (1998) 19 75 de chardin, pierre teilhard (2008), 258 76 de chardin, pierre teilhard (2008), 261 77 de chardin, pierre teilhard (2008), 30 78 zurek wojciech h.(2002). ‘ decoherence and the transition from quantum to classical – revisited’ in los alamos science number 27 2002 dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 12-43 smetham, g. p., why us: trespassing on an anthropic lawn (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 43 79 ‘the evolution of reality’ – www.fqxi.org/community/articles/display/122 (the foundational questions institute) november 10, 2009. 80 gefter, amanda (2014), 227 81 gefter, amanda (2014), 224 82 gefter, amanda (2014), 222 83 gefter, amanda (2014), 225 84 campbell, john, ‘quantum darwinism as a darwinian process’ http://arxiv.org/ftp/arxiv/papers/1001/1001.0745.pdf 85 wigner, eugene ‘remarks on the mind-body question’, http://philpapers.org/rec/eugwro 86 joos – quoted in http://pilotscholars.up.edu/cgi/viewcontent.cgi?article=1011&context=phy_facpubs 87 joos et al., 2003 ch.2 – quoted in schlosshauer, m., (ed.) (2011) 88 gefter, amanda (2014), 227 89 gefter, amanda (2014) 90 gefter, amanda (2014), 279-280 91 gefter, amanda (2014), 275 92 http://www.timeshighereducation.co.uk/features/does-consciousness-emerge-from-quantumprocesses/92981.article 93 http://www.sciencedaily.com/releases/2014/01/140116085105.htm 94 gefter, amanda (2014), 28-29 95 http://sciencenotes.wordpress.com/2009/03/15/amanda-gefter-how-to-spot-a-hidden-religious-agenda/ 96 gefter, amanda (2014), 392 97 stapp, h. – ‘free will’ http://www-physics.lbl.gov/~stapp/fw.pdf 98 ibid. (continued on part ii) login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal 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home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 101-123 101 pitkänen, m., molecular signaling from the tgd viewpoint article molecular signaling from the tgd viewpoint matti pitkänen 1 abstract the findings of elowitz et al lead to a formal model suggesting that ligands of type bmp (bone morphogenetic protein) have interactions. the interactions would be non-local so that it is difficult to imagine that they could have chemical origin. the tgd based model for these long range interactions is based on dark photon resonance. for the simplest, receptors would correspond to fixed bio-harmonies. in a single ligand system the ligand would have the bio-harmony of its preferred receptor. the interaction between ligand magnetic bodies would be re-tuning and could replace the preferred bio-harmonies assignable to the participating ligands with distributions of bio-harmonies. therefore the ligands of the multi-ligand system would couple by bio-resonance also to other than preferred receptors. the model stimulates questions, which lead to a rather detailed model for the re-tuning and tuning processes at the level of codons and amino acids. the model suggests that the tuning to a given bioharmony for the dark counterparts of basic biomolecules and its stabilization involves epigenetic control based on the methylation of some special dna and rna nucleotides and amino-acids acting as analogs of tuning forks. the proposal that bioharmonies are molecular correlates for emotions suggests that this process involves minimal number of methylations, which define the seed of phase transition to a bioharmony in the scale of the basic unit of genome (such as gene), mrna sub-unit (splicing) and protein sub-unit. 1 introduction i learned recently about interesting findings about communications of information molecules. the quanta magazine article ”biologists rethink the logic behind cells molecular signals” (https://cutt.ly/ia28lqn) summarizes the findings of elowitz et al described in the article ”the context-dependent, combinatorial logic of bmp signaling” [4] (https://cutt.ly/ya8r07b). 1.1 observations messenger molecules attaching to receptors are thought to be responsible for chemical communications. intercellular communications would involve first messengers (hormones, neurotransmitters,...) and intracellular communications second transmitters, which are not proteins but rather light molecules. the standard interpretation has been that messenger molecules themselves define the message. lockkey hypothesis states that the ligand has a special region (key), which attaches to the receptor in a context independent way determined by the geometries of these regions. induced-fit hypothesis states that the regions in question can modify their surfaces to achieve a perfect fit. for bacteria only intracellular communications are possible and for them there is evidence that in some special cases lock-and-key principle works as was demonstrated by michael elowitz, the leader of the research group behind the recent work. the findings of the elowitz and his coworkers force them to conclude that this model fails for the multi-cellulars. 1. the group studied so-called bone morphogenetic proteins (bmp) (https://cutt.ly/oa7kzna), which regulate how cells proliferate and differentiate in various tissues by directing them to turn sets of genes on and off. these proteins have many other functions than bone growth. 1correspondence: matti pitkänen http://tgdtheory.com/. address: rinnekatu 2-4 a8, 03620, karkkila, finland. email: matpitka6@gamail.com. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://cutt.ly/ia28lqn https://cutt.ly/ya8r07b https://cutt.ly/oa7kzna http://tgdtheory.com/ mailto:matpitka6@gmail.com dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 101-123 102 pitkänen, m., molecular signaling from the tgd viewpoint 2. bmps are so-called 1st messengers and mediate communications between cells. bmps attach to the receptors of various types at the surface of the cell. this step is followed by signal transduction actinating the corresponding signalling pathway. eventually this leads to a generation of transcription factors in the cell nucleus controlling the genetic response. the work concentrated on the study of the binding of bmps to the receptors at the cell membrane. 3. mammals have genes that encode 11 or more distinct bmp proteins. bmps occurs dimeres of the same or different proteins and also these pairs can pair up. the family of bmp proteins sticks to the associated family of receptor proteins, which also appear as dimers of pairs of them. bmp molecules are not very selective but given bmp sticks to several dimer pairs of receptors. several interesting findings were made. 1. the response of a cell to several ligands is not simply the sum of responses of individual ligands. the lock-key mechanism assuming 1-1 correspondence between ligands and receptors fails in the presence of several ligands whereas for a single ligand there is strongly preferred receptor for a giveng ligand. the simplest chemical (and thus local) explanation that in presence of several ligands the affinities kijk of ligands li to the receptors rjk formed by dimers (j,k) of homologous or nearly homologous molecules change so that approximate 1-to-1 correspondence becomes 1-to-many. this is called promiscuity. the responses as concentrations at the cell membrane for the activated signalling pathways pijk associated with receptor i+jk would be still linear in concentrations of li but the matrix characterizing the rate for the creation of pijk would not be diagonal matrix anymore with respect to pairs (i, jk). 2. this situation is easy to model mathematically but it is difficult to understand the physical mechanism behind the promiscuity. 3. the affinities are context dependent in the sense that they depend on the target cell and the developmental stage of the cell. 4. one can classify the ligands in terms of whether they tend to increase or reduce receptor expression. ligands can be also classified in terms of their positive, or negative synergies with other ligands. in the simplest situation one studies all possible pairs of ligands and finds their responses. two ligands li and li are regarded as equivalent if the responses for the pairs (li, lk) and (lj , lk) are identical for all k. this defines functional equivalence. sequence similarity (biological homology) does not in general reflect the functional equivalence. the effects of the ligands in equivalence classes depend on the context (cell type and cell age correlating with receptor concentrations). however, it is found that the equivalence classes are context independent. the proposal is that a single linear parameter could characterize the equivalence classes for bmps considered. 5. this inspires a chemical model for the situation. the basic parameters would be affinitieskijk telling the tendency of ligand li to attach to dimer (j, k), signal complex activities εijk characterizing the rate for the formation of signal complex pijk. also the receptor concentrations ai and bi for the receptors of type i and ii appear as parameters. the empirical data makes it possible to find the best fit for the parameters. promiscuity is the basic predictions. the model could be understood in terms of the competition of ligands for receptors (j,k). an inverse relationship between affinities and activities is predicted. small number of affine ligands with weak activity or vice versa. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 101-123 103 pitkänen, m., molecular signaling from the tgd viewpoint 1.2 tgd view about the findings what can one say about the situation in the tgd framework? here only the key ideas of the tgd inspired quantum biology are described. more detailed summaries can be found in various articles related to dark variant of biochemistry [40, 31, 37], to dark realizations of genetic code [29, 34, 33, 36, 39], and to the models for cell membrane as generalized josephson junction [17, 18, 19, 28], of pollack effect [30], and of water memory and morphogenesis [23, 38]. 1. the basic notion is magnetic body (mb) carrying dark matter as heff = nh0 phases of the ordinary matter and behaving quantum coherently in length scale proportional to heff . mb would control biomatter. communications to mb, sensory input, would be in terms of generalized dark josephson radiation from the cell membrane and the control by mb in terms of dark cyclotron radiation. the sensory input would be from the entire cell membrane and induced by the attachment of the ligands to the receptors. the earlier proposal was that the control signals from mb affect directly the genome. the existing chemical picture based on signal pathways activated at the cell membrane however suggests that the situation is not so simple. the control signal arrives from mb to the receptors and activates signal pathways. at the nuclear membrane similar processes would occur and lead to the activation of transcription factors by similar signal pathways. 2. if the mb determines the response of receptors in a non-local way, promiscuity could be only effective. another option is that mb can control the affinities of receptors (by modifying their surface geometries as in the induced fit model) so that the diagonal l-r matrix becomes nondiagonal. 3. context dependence would conform with the idea that mb determines the response and changes during aging. the aging can be understood in the tgd framework as slow thermalization of mb so that its temperature approaches the hagedorn temperature of magnetic flux tubes. physiological temperature would be related very closely to hagedorn temperature of mb. the almost computer program-like determinism of biochemistry is in a sharp conflict with the stochasticity expected to result from the locality and statistical nature of chemistry. 1. in the tgd framework and at a given level of scale hierarchy the dynamics of the space-time surface as a preferred extremal is deterministic apart from small violations of determinism. spacetime region as a preferred extremal is a minimal surface with singularities, which would bring in the failure of determinism. soap film with frames serves as a good analogy. 2. the notion of a magnetic body having flux tubes as body parts leads to a model of bio-catalysis in which molecules are replaced with nodes of flux tube network. molecules can find each other as part of this dynamical network involving reconnection of u-shaped flux tubes and their shortening in a reduction of heff liberating energy making to overcome the potential wall making the reaction low. 3. one can argue that the second law implies stochasticity in molecular scales. zero energy ontology (zeo) is another possible source of determinism. in so called ”big” state function reductions (bsfrs) the arrow of time changes and the time evolution leads to the direction of geometric past so that for the observer with the standard arrow of time the time evolution obeys second law in wrong time direction and looks like self-organization which is basic characteristic of living matter and usually thought to involve metabolic energy feed in an essential manner. in fact the time reversed time evolution would change dissipation as loss of energy with extraction of energy from the environment. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 101-123 104 pitkänen, m., molecular signaling from the tgd viewpoint the findings of elowitz et al [4] lead to a formal model suggesting that ligands of type bmp have interactions. the interactions would be non-local so that that they could have chemical origin. the tgd based model for these long range interactions is based on dark photon resonance. for the simplest, receptors would correspond to fixed bio-harmonies. in a single ligand system the ligand would have the bio-harmony of its preferred receptor. the nteraction between ligand magnetic bodies would be re-tuning and could replace the preferred bio-harmonies assignable to the participating ligands with distributions of bio-harmonies. therefore the ligands of the multi-ligand system would couple by bio-resonance also to other than preferred receptors. the model stimulates questions, which lead to a rather detailed model for the re-tuning and tuning processes at the level of codons and amino acids. the model suggests that the tuning to a given bioharmony for the dark counterparts of basic biomolecules and its stabilization involves epigenetic control based on the methylation of some special dna and rna nucleotides and amino-acids acting as analogs of tuning forks. the proposal that bioharmonies are molecular correlates for emotions suggests that this process involves minimal number of methylations, which define the seed of phase transition to a bio-harmony in the scale of the basic unit of genome (such as gene), mrna sub-unit (splicing) and protein sub-unit. 2 bio-harmony and context dependence also bio-harmony might relate to context dependence if fundamental communication and control signals take place at the dark level that is between daas instead of aas (amino acids) as parts of proteins by energy and frequency resonances. daas would pair with aas and communicate with energy resonance. 2.1 bio-harmony consider first the bio-harmony [29, 33, 34, 39] in more detail. 1. z6, z4, and z2,rot or z2,refl act as symmetry groups for the 3 icosahedral hamiltonian cycles. each cycle, one of type xz6, one of type z4, and one of type z2, defines 12-note scale and 20 3-chords identified as icosahedral faces and dna codons. the notes along the cycle are obtained as a quint cycle, that is by scaling the frequency of the note by factor 3/2 at each edge of the oriented cycle. the orbits of faces under zn are assigned with amino-acids (aas). this assumption has a concrete interpretation in terms of resonance mechanism for bio-communications [39]. this gives 60 3-chords and the numbers of triangles at the orbits of triangles and the numbers of triangles at orbits correspond nicely to the numbers of dna codons coding for aas. 4 codons are however missing. the fusion with a unique tetrahedral code gives 64 chords and a dark 3-photon realization of the genetic code. also the identification of dtrna, dtrna, and daa in terms of icosahedral code is possible as found quite recently [39]. also the dark realization of genetic codons in terms of dark proton triplets allows this. 2. z6 allows unique icosahedral harmony defined by 12-note scale realized as an icosahedral hamiltonian cycle. the corresponding aas correspond to 3 dna 6-plets and one dna 2-plet. z4 corresponds to 2 bioharmomies with 5 amino-acids which correspond to dna 4-plets. z2,rot and z2,refl correspond to 10 2-plets both. z2,rot corresponds to 3 icosahedral harmonies and z2,refl to 5 icosahedral harmonies. this makes 1× 2× (3 + 5) = 16 bio-harmonies if the common key of the 12-note scale for the 3 icosahedral harmonies does not matter and the orientation of the hamiltonian cycle does not matter. one can also consider the possibility that the key and the orientation of the cycle for the 3 icosahedral harmonies matter. the change of the orientation replaces quint cycle with quart cycle (cg corresponds to quint and cf to quart). issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 101-123 105 pitkänen, m., molecular signaling from the tgd viewpoint 3. the interpretation of bioharmonies is as correlates for moods, emotional states. there is evidence for this interpretation from the strange finding that rna is able to transmit conditioning based on negative or positive emotions generated by stimulus (https://cutt.ly/6sulnqk) discussed in the tgd framework in [32, 35]. the interpretation would be that drna represents the effect of stimulus by its bio-harmony characterizing emotional state, and can induce molecular emotional expression in ddna-dna pairing and also in daa-aa pairing and dx-x pairing in general. dx-x pairing by energy resonance mechanism would correspond to emotional expression. something in x would depend on bio-harmony. in the case of dna and rna this something could be the methylation state and its analogs so that there would be a direct connection with epigenesis. epigenesis would realize the dynamics of emotional expression. one can raise several questions about bio-harmony. 1. how fast is the dynamics of the molecular and higher level emotions and moods? if epigenetics controls the dynamics of emotions, it could be rather fast at the molecular level. note that the hierarchy of planck constants predicts a hierarchy of time scales. 2. how large parts of a given organism a given bio-harmony could characterize? biomolecules, cell nucleus, cell, organelle, ...? is there a hierarchy of harmonies so that the harmonies in different scales need not be identical? concerning molecular bio-harmonies, epigenetics could help to answer the question. for instance, one can ask whether bio-harmony characterizes individual bio-molecules such as enzymes and receptors. 3. could bio-harmony explain at least part of the context dependence found in the ligand-receptor dynamics by the group of? it would seem that bio-harmony appears as an additional aspect of the ligand-receptor pairing involving geometric constraints modelled in terms of lock-key or induced-fit mechanisms. the enzyme and substrate would be like daters. the resonance mechanism would allow e and s to meet and geometric constraints would determine whether this can lead anywhere. 4. this inspires several questions. could the affinities and signal complex activities be determined by the molecular emotional state of the l-r composite coded by the bio-harmony of the dx-x complex? could the ”emotional” state dx-x control affect the state of x complex? how? could this coupling have interpretation as emotional expression in a generalized sense? 5. for the simplest model this would predict that for z4 the 5 aas coded by 4 dna codons would have two emotional states and for z2 10 daa-aa pairs could have 3 resp. 4 emotional states depending on whether one has z2,rot resp. z2,refl. 2.2 could ligand interactions reduce to a re-tuning of ligand harmonies? the notion of ligand interaction has been introduced as a purely formal notion in the article and it is difficult to imagine a local chemical realization for it. however, the fact is that ligands change their behavior in the presence of other ligands. could the ligand interactions be realized at the level of their mbs? 2.2.1 ligand interactions as re-tuning could ligand interactions reduce to the re-tuning of ligand harmonies by the resonant dark photon interactions between daa flux tubes? issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://cutt.ly/6sulnqk dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 101-123 106 pitkänen, m., molecular signaling from the tgd viewpoint 1. assume that ligands and receptors can have several bio-harmonies but that free ligands (single ligand situation) and in the absence of other ligands they correspond to single preferred bio-harmony. assume that each receptors corresponds to a single bio-harmony (also this assumption could be relaxed). free energy minimization could imply preferred bio-harmonies for both receptors and ligands. assume that ligands can only pair with receptors with the same bio-harmony. the immediate question is whether the 3+4 receptors assigned with bmps could relate to 3+5 z2 type harmonies. the problem is that one z2,refl harmony would not correspond to a receptor. 2. interactions between two ligands l1 and l2 with different bioharmonies could induce a re-tuning of l1 to the bio-harmony of l2 or vice versa. this tuning must respect the symmetry group zn, n = 6, 4, 2 in question. the zn orbits would be preserved but the corresponding 3-chords would be modified. some findings about water memory [38] support re-tuning as a basic mechanism of communications between dark biomolecules and it is very natural in the resonance picture. note that re-tuning is a basic mechanism in radio communications. re-tuning would replace the ensemble of ligands with an ensemble in which also non-preferred l-r pairings are possible. it would make the affinity matrixki(jk) and activity matrix εi(jk) non-diagonal and induce promiscuity. probability distribution for bio-harmonies of ligands would emerge in this way. 3. the large-scale quantum coherence at the level of mbs inspires the question whether the quantum superposition of bioharmonies could occur for daas. could quantum superposition allow to understand the observation that the increase of the parameters ki(jk) is accompanied by the decrease of εi(jk) and vice versa. could one think that with a suitable normalization one has ∑ (jk)ki(jk)εi(jk) = constant. in zeo one could regard the entire signal complex, which involves both ligand, receptor and what it induces, as a single zero energy state as a superposition of deterministic time evolutions. if the formation of signal complexes involves a quantum transition from a single ligand-receptor pair to a their quantum superposition involving delocalization at the cell membrane followed by state function reduction involving localiation that is selection of the complexes, the condition∑ (jk)ki(jk)εi(jk) = constant could reflect probability conservation. 4. re-tuning of the icosahedral harmony for z4 and z2 should have a counterpart affecting the physics of aas. could the re-tuning be generated at the level of daa and result from the variation of flux tube thickness as a motor action of mb? or could it be induced by re-tuning at the level of ddna? tuning must be visible at the level of aas since dx-x resonance energies must be modified. 2.2.2 tuning and re-tuning at the level of dx-x pairing what could the re-tuning mean for the dx-x pairing? 1. for ddna-dna pairing dark cyclotron photons must couple to some degrees of freedom of dna. in the tgd framework, dna can be magnetized [38]. the pairing with ddna flux tubes carrying a monopole flux with dna strands is expected to induce magnetization along dna due to the ring currents of electron pairs of the aromatic rings analogous to cooper pairs. the simplest candidates for re-tuned frequencies are cyclotron frequencies for magnetized nucleobases. in re-tuning the cyclotron frequencies for electron pairs) assignable to aromatic rings of nucleotides would be modified in re-tuning. the change of the thickness of the monopole flux tubes defining the 12-note scale would automatically induce the re-tuning at dna level. the re-tuning could be induced by ddna, drna, and dtrna and would not require chemistry. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 101-123 107 pitkänen, m., molecular signaling from the tgd viewpoint 2. what about the daa-aa tuning? the only aas with aromatic rings are phe, tyr and trp. could daa-aa resonance coupling between cyclotron radiation of daa and vibrational modes of aa with energies in the range .45-.045 ev spanning slightly more than 3 octaves? the general forms of the vibrational and cyclotron energy spectra are the same and for a proper value of heff the scale of the daa spectrum is the same and resonance is possible. re-tuning would require change of the conformations of the aas so that the elastic constants would be modified. mb could induce this re-tuning as a kind of entrainment. as already proposed, this could be achieved at the level of dna by methylation of the start codon fixing the bio-harmony. 2.2.3 could special 3-chords act as tuning forks physical model for the tuning and re-tuning should be based on resonance model. 1. tuning to a particular 3-chord or 3-chords should force the entrainment to the bio-harmony. these 3-chords would serve as an analog of a tuning fork. the simplest, and perhaps unrealistic, option is that the met 3-chord associated with the start codon alone fixes the bio-harmony uniquely. the met 3-chord should be different for all z2 harmonies. 2. the chords fixing the bio-harmony (the tables for the 3-chords of bio-harmonies are given in [29]) should be very special and thereindeed are very special chords in the icosahedral harmonies. the epigenetic modification of the amino-acids corresponding to these 3-chords could force the re-tuning of the bio-harmony. the triangles, whose edges do not belong to the hamiltonian cycle, define 0-quint 3-chords containing no quint. these chords include dissonant chords possibly having semitones or tones intervals between the notes (octave equivalence and quit cycle along the hamiltonian cycle is assumed). there are 8 different types of 0-quint chords with basic note x in 12-note scale labeled as xexk, k = 1, .., 8, if the key does not matter. 1. from the appendix one learns that there the first possess no 0-quint chords z4 harmony. in this case, one could argue that the bit defined by the presence or absence of the 0-quint chord defines the tuning fork, which could correspond to a methylation of some codon coding for one of the 5 aas coded by dna 4-plet. it is not clear, whether the choise of the codon matters. 2. by looking at the tables of 3-chords in the chord tables of the appendix, one finds that if key matters, it is easy to distinguish between harmonies using a single 0-quint chord. if the key does not matter, it is in principle almost possible to assign different 0-quint chords to, say, met. there are 2 z2,refl harmonies with 2 0-quint chords, which cannot be distinguished in this manner. if one introduces a fixed key or uses a second special 0-quint chord as a turning fork, also z2,refl harmonies can be distinguished from each other. interestingly, the number of bmp receptors possibly assignable to z2,refl is 4 rather than 5. 3. also tetrahedral codons define special chords in the sense that the intervals are separated by minor third. these 3-chords are identical under the octave equivalence. in the model considered in [39], 3 of them correspond to stop codons whereas the remaining codon corresponds to trp. 2.2.4 re-tuning as an epigenetic process re-tuning is an epigenetic process and can be seen as a control of mb. methylation and its analogs are basic tools of epigenesis. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 101-123 108 pitkänen, m., molecular signaling from the tgd viewpoint 1. mrna methylation (https://cutt.ly/1srm06f) occurs after transcription and is controlled by genes coding the needed enzymes. the methylated rna nucleobase is often called the ”fifth rna” base. start codon aug coding for met is methylated as also the 3-prime untranslated regions (3’-utrs) immediately after the stop codon. this region post-transcriptionally influences gene expression. 2. the findings that the rna of a conditioned sea snail scattered over neurons of second sea snail in petri dish generate neuronal correlates of conditioning (https://cutt.ly/6sulnqk), discussed from the tgd point of view in [32, 35], support the view that the magnetic body of the rna of sea snail infects the emotion/mood related to the conditioning. the emotional state, mood, of dna and rna would affect gene expression. epigenesis could be based on emotional states lasting for several generations. this is natural in zeo [29, 35]. hints about how the methylation could be involved with the tuning to a particular bio-harmony comes from the research of the group led by matthias soller [3] (https://cutt.ly/osegnju). 1. post transcriptional methylation is known to occur for the few nucleotides of mrna following the cap of mrna, whose function has remained poorly understood. soller and collaborators demonstrated that the two enzymes coding for the methylation of these nucleotides played an important role in the animals’ reward learning process. the flies without the genes coding for the methylation showed a defect in their ability to learn the association of a specific odour with a sugar reward. 2. earlier work by one of paper’s co-authors, prof. rupert fray, has demonstrated that that cap modifications are highly dynamic in mice and that these modifications played a role in transporting the mrnas to synapses. 3. the lack of methylation implies a lack of the desired conditioning. conditioning involves emotions, perhaps also at the molecular level: could the bio-harmony of proteins involved with the process differ from that associated with the protein activated by the odour molecules? the proteins would be out-of-tune and conditioning would not happen. the role of cap modifications in the mrna transport would conform with the assumption that dark photon resonance allows the mrna to find synapses. if the bioharmony for them is wrong there is no resonance and the transport fails. these findings suggest the following interpretation in the tgd framework. 1. the resonance mechanism would force ddna and dmrna to have the same bio-harmony. the post-transcriptional methylation of the first rna codon could re-tune and stabilize mrna bioharmony. stabilization could involve a methylation of a large enough number of special rna codons so that it would serve as a seed of a phase transition forcing the same bio-harmony for all codons. if bioharmonies correspond to molecular moods, this would be analogous to the spread of an emotional mood in crowd. the special codons as signatures of the mood could be especially effective inducers of this phase transition. 2. could a 0-quint 3-chord assigned to met in the beginning of mrna fix the z2 harmony almost uniquely by acting as a tuning fork. z4 harmony could be fixed by the absence of methylation in some mrna nucleotide in codon coding for one of the 5 aas [(val,pro,thr,ala,gly)] coded by 4 codons. note that the methylation of 2 aug nucleotides of met affecting the cyclotron frequencies of aug could in principle select between the 16 bio-harmonies predicted by the simplest model. this issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://cutt.ly/1srm06f https://cutt.ly/6sulnqk https://cutt.ly/osegnju dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 101-123 109 pitkänen, m., molecular signaling from the tgd viewpoint estimate is however based on counting of bits and bio-molecules need not see each other as bit sequences as we do. the methylation of the mrnas associated with several 0-quint chords could help to stabilize the z2 harmony at the level of dmrna. could the proteins obtained by splicing and involving methylation in the beginning of mrna portions coding them consist of functional sub-units with different bioharmony? 3. what about dna? could the methylation of the start codon also now help to stabilize the z2 bio-harmony. only a and c dna nucleotides of dna strand can be methylated (as also t and g nucleotides of the conjugate strand). note that a and g appear often in dna repeats defining part of what was called junk dna. one can ask whether the methylation of a and c could stabilize the bio-harmony and dna level. the corresponding rna codon contains at most one u or g nucleotide. note that met corresponds to aug whereas agu corresponds to cys which together with trp (coded by tetrahedral codon) are the only sulphur containing amino-acids. met is special in the sense that it belongs to a symmetry broken codon doublet for which ile has replaced met. 4. the first mrna codon aug codes for met so that the d(aug)-dmet pairing could induce the daa bio-harmony and affect the vibrational frequencies of aa. this is perhaps enough for the stability of the bio-harmony. could pretein methylation help to stabilize the bio-harmony of proteins? according to wikipedia (https://cutt.ly/usivact), protein methylation is a type of posttranslational modification featuring the addition of methyl groups to proteins. it can occur on the nitrogen-containing side-chains of arginine and lysine but also at the aminoand carboxy-termini of a number of different proteins. one can imagine 2 options for changing the bio-harmony at daa-aa level. for the bureaucratic option, the re-tuning would occur at the dna level. this would require enzymes coded by appropriate genes to re-tune the first codon of mrna coding for aa. for the non-bureaucratic option, daa would re-tune aa directly by entrainment and this could involve re-methylation. 2.3 an attempt to concretize the model of ligand interactions the following is a very naive first attempt to concretize the idea about ligand interactions as a re-tuning, whhich affects the matrices ki(jk) and εi(jk). reader should take the following considerations as as free associations. 1. bmps couple to 4+3 receptors. there are 3 hamiltonian cycles with z2,rot symmetry and 5 cycles with z2,refl symmetry assignable to 10 amino-acids coded by 2 or single dna (met) have 3. there are 4+3 receptors and 5+3 bioharmonies: could it be that the considered 4 receptors correspond to 4+3 z1 harmonies with the same z4 harmony and that there is also a fifth receptor of this kind but not considered? a priori, any protein could correspond to any bio-harmony but the correlation of daa and bioharmony could be forced by dynamics since the daa-aa resonances might be possible only for certain z2 harmonies (and only for one of the 2 z4 harmonies). suppose that the receptors indeed correspond to one particular z2 harmony each. 2. if the binding sites for bmp-receptor pairs correspond to single aa (in analogy with trna-mrna binding), the binding site for z2 harmonies should correspond to a aa which is one of the 10 aas coded by dna doublet or singlet. the reduction of correspondence to the level of binding site aa would conform with the finding that the functional similarity of bmps does not very closely correspond to the sequence similarity. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://cutt.ly/usivact dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 101-123 110 pitkänen, m., molecular signaling from the tgd viewpoint in the code table there are 9 doublet aas and 1 singlet. symmetry breaking is present [39]. it is not quite clear which doublets correspond to z2. for instance, phe could correspond to the doublet for z6 leaving 8 doublet aas plus (ile,met) as a doublet with a broken z2 symmetry. ugg coding for trp and 3 stop codons would correspond to the tetrahedral cycle. by resonance condition, at most 3 receptors should correspond to more than 1 bmp as their preferred receptor. there are also chemical constraints on the aas acting as a binding site. resonance condition for daas implies that pairing aas are identical. the pairing aas must be neutral and must be coded by dna doublets or singlets. this leaves the following cases under consideration. 1. two amino acids have amide side-chains. • asparagine (asn): nh22coch2• glutamine (gln): nh22coch22ch2 these side-chains do not ionize in the normal range of ph. 2. two side-chains contain sulfur atoms, of which one ionizes in the normal range. • cysteine (cys): hsch2• glutamine (gln): nh2-coch2-ch23. three amino acids have aromatic ring structures as side-chains. of these, tyrosine ionizes in the normal range; the other two do not. • phenylalanine (phe) • tyrosine (tyr) • tryptophan (trp) this would give 2+2+3 =4+3 aas. in the above mentioned option phe is however assigned with z6 harmony but any other doublet aa could correspond to z6 harmony. this would suggest that aas with amide side chains and containing sulphur correspond to 4 z2,rot harmonies. there are 10 bmps with the decomposition 10=3+3+2+1+1. using the standard biological notation, this correspondings to the decomposition [gdf5,gdf6,gdf7], [bmp5,bmp6,bmp7], —bmp2,bmp4],[bmp9], [bmp10]) to functional equivalence classes [4]. could the two 3:s correspond to the 3 z2,rot harmonies and 2+1+1 to 4 of the 5 z2,refl harmonies? the two triplets [gdf5,gdf6,gdf7] resp. [bmp5,bmp6,bmp7] are weak resp. strong activators. both gdfs (growth differentiation factors) and bmps (bone morphogenetic proteins) belong to the transforming growth factor beta superfamily (tgf). if gdfs are excluded the correspondence between bmps and receptor proteins is 1-to-1. 2.4 could the dark matter hierarchy relate to the bio-harmony? one can wonder how the hierarchy of algebraic extensions and algebraic evolution defining the evolutionary state for a given layer of mb affects the l-r pairings. 1. 3n-photons and 3n-nucleons as dark variants of basic information molecules would correspond to galois confined states for which the 4-momenta for components are algebraic integers summing up to ordinary integer when the momentum unit is defined by the p-adic length scale associated with the extension. also frequencies would correspond to rational integers for galois confined states. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 101-123 111 pitkänen, m., molecular signaling from the tgd viewpoint table 1: notation of chords inspired by popular music notations. ceg ≡ c , cd]g ≡ cm , cd]f] ≡ co , ceg] ≡ caug , cfg ≡ c4 , cf]g ≡ c4+ , cgg] ≡ c6− , cga ≡ c6 , cgb[ ≡ c7 , cgb ≡ cmaj7 , cgc] ≡ c9− , cgd ≡ c9 . (3.1) 2. these states depend on the algebraic extension of rationals defining n = heff/h0 as its dimension although mass squared values and momenta are integer valued as also frequencies. this would give an additional context dependence. for instance, organisms at higher levels of evolution could have larger values of heff associated with the dark variants of the basic biomolecules. 3 appendix: tables of basic types of 3-chords for icosahedral harmonies 3.1 icosahedral harmonies as hamiltonian cycles one can find the list of hamiltonian cycles at http://tinyurl.com/yacgzm9x. the edge {1, 2} is fixed and cycles are oriented so that there are 1024 of them. all of them are relevant from the point of music interpretation and the change of orientation corresponds to major-minor duality, albeit not in the simplest sense. note that this duality does not affect the characteristics listed above. the general following general results hold true as one can learn at http://tinyurl.com/pmghcwd. one can classify the cycles using their symmetries which can correspond to isometries of icosahedron leaving them fixed or to a reflection taking the vertex n at the cycle to vertex 12− n. this symmetry is not same as change of orientation which is purely internal operation and cannot change the cycle. one can even find images of the cycles possessing symmetries at http://tinyurl.com/y8ek7ak8 and deduce the triplets n and p characterizing them by visual inspection. also one can write explicitly the 3-chords defined by the three kinds of faces. i have deduced the triplets n and the 3-chords defining the harmony by the inspection of the images. ”bio-harmony” (4, 8, 8) forced by the model of extended genetic code involving also the 21st and 22nd amino-acids is of special interest.the classes of cycles with symmetries 6-fold rotational symmetry and two distinct reflection symmetries realize it. before continuing some terminology and notation is in order. take c as the major key. submediant or relative minor corresponds to am, subdominant (sharp or flat) to f major (f ) or fminor (fm), dominant to g. the notation for chords is such that quints correspond to subsequent notes in the chord. for 1-quint chords this means that first two notes define the quint. table 1 summarizes the notation inspired by the popular music notation. the basic difference is that the third is in most cases excluded so that the emotional character of the chord is not fixed. besides these notions it is convenient to introduce additional notations for various dissonant chords appearing as 0-quint chords. cc]d ≡ cex1 , cc]d] ≡ cex2 , cdd] ≡ cex3 , cde ≡ cex4 , cd]e ≡ cex5 , cc]e ≡ cex6 , cdf] ≡ cex7 , cdg] ≡ cex8 . (3.2) clearly, the sets {ex1}, {ex2, ex3}, {ex4, ex5, ex6}, {ex7}, {ex8}, corresponds to the span of 2, 3, 4, 6, 8 half notes for the chord. the following summarizes the results. note that cex7 can be seen as part of d7 chord. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/yacgzm9x http://tinyurl.com/pmghcwd http://tinyurl.com/y8ek7ak8 dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 101-123 112 pitkänen, m., molecular signaling from the tgd viewpoint 1. there are 6 collections of cycles without any symmetries containing 48 cycles each: these 48 cycle are mutually isometric so that one can say that there 6 different harmonies. 2. there is a collection with 6-fold rotational symmetry, 48/6=8 examples. n = (2, 12, 6). the chords of this scale define 6-note scale involving only total steps. cdf and its 6 translates by integer number of steps define 6 1-quint chords. ce[g (cm) and its 6 translates (they obviously correspond to the 6-fold rotational symmetry) define also 6 1-quint chords. the reflection transforms these series to those defined by gb[g and its translate and byfac (f major) and its translates. impressionists like debussy used 6-note scale of this kind. half-octave shift is an exact symmetry. 1-chords lack the third so that one cannot assign to 3-chords any emotional quality. the extension to 4-chord can however bring either ”happy” or ”sad” quality. clearly, these harmonies have ”jazzy” character. 0-quint chords are faug ≡ fac] and gaug ≡ ghd] are transformed to each other by both half-octave shift and inversion. 3. there are 2 collections with 2 distinct reflectional symmetries with 12=48/4 representatives in each. half-octave scaling is a symmetry of both these scales as one might guess. the first cycle (see fig. 3.3 ) has n = (0, 16, 4) so that there are no 0-quint chords which in general are dissonant. second cycle (see fig. 3.3 ) realizes n = (4, 8, 8) bio-harmony and deserves some comments. it will be discussed in detail later. (a) the 8 2-quint chords consist of b[fg ≡ b[9, c9, f9, g9 and their half-octave scalings. clearly, the simple four-note scale appears here. (b) using the popular notion introduced earlier, 1-quint chords consist of two 4-plets dmaj7, e9−, a7, a6 and g]maj7, b[9−, d]7, d]6 related by half-octave shift. the harmony contains no ”simple” major or minor chord and only the extension to tetrahedral harmony can provide them. the same is true for the second bio-harmony. (c) the 4 0-quint chords are cex3 ≡ cdd] and eex2 ≡ efg and their half-octave scalings f]ex3 ≡ f]g]a and b[ex2 ≡ b[bc]g. 4. there are 3 collections with z2 rotational symmetry with 48/2 = 24 representatives in each. the triplets n are (0, 16, 4) (see fig. 3.3 ), (2, 12, 6) (see fig. 3.3 ), and (4, 8, 8) (see fig. 3.3 ). all these harmonies are symmetric with respect to half-octave shift (tritonus), which obviously corresponds to the z2 rotation. tritonus would not have been tolerated by catholic church! this symmetry characterizes all 3 harmonies. basic 3-chords do not contain pure minor and major chords. the reflection of the scale does not leave the collection of chords invariant but it is not clear whether this corresponds only to a change of scale, probably not. consider the (4, 8, 8) case (see fig. 3.3 ). (a) the 8 2-quint chords appear as four-plet h9, c]9, d]9, f9 and its half octave shift (tritonus interval) acting as a symmetry of the harmony. 2-quint chords are always of type x9 (note that the third is missing) but also 1-quint chord can be of form x9 as explicit construction of chords demonstrates: i have denoted these 1-quint chords by symbol x4 (cdg is obviously equivalent with cdg). (b) using the popular music notation introduced earlier, the 8 1-quint chords ared7, amaj7, a4+, e7 and their half-octave shifts g]7, d]7, d]4+, b[7. no major and minor chords are included and only the extension to tetra-icosahedral harmony can provide them and also break the symmetry giving rise to well-defined key. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 101-123 113 pitkänen, m., molecular signaling from the tgd viewpoint table 2: table gives various types of 3-chords for harmonies with z6 rotational symmetry. note that half-octave shift is an exat symmetry. note that gaug = ceg], f aug act as bridges between the groups related by half octave shift. the chords have been arranged so that they form orbits of z6. ”amino-acid chords” correspond to preferred chords at the orbits. (n0,n1,n2) 0-chords 1-chords 2-chords (2, 12, 6) (faug,gaug) (cm,dm,em,f]m,g]m,b[m), (c9, d9, e9, f ]9, g]9, b[9). (f6, g6, a6, b6, c]6, d]6). 5. the four 0-quint chords appear in two types. d]ex2 ≡ d]ef] and its half-octave shift aex2 ≡ ab[c plus hex3 ≡ hc]g and its half-octave shift fex3 ≡ fgc]. according to usual thinking these chords involve dissonances. this dissonance character is a rather general phenomenon for the harmonic loners and classical views about harmony would exclude them as asocial cases! in the case of maximally symmetric harmony the loners are diminished chords and thus not so dissonant. in some cases there are no 0-quint chords. there are 5 collections of 20 chords with z2 reflection symmetry (see figs. 3.3, 3.3, 3.3, 3.3, 3.3 ). the integer triplets n are (2, 12, 6), (2, 12, 6), (4, 10, 6), (2, 12, 6), (2, 12, 6). bio-harmony has a representative also in this class (see fig. 3.3 ). the half-octave scaling symmetry is broken for these harmonies. some comments (4, 8, 8) case are in order (see fig. 3.3 ). 1. 2-quint chords appear as reflection related multiplets c9, d9, h]9, d]9 and c]9, h9, f9, b[9. 2. 1-quint chords appear as symmetry related mutiplets g,d7, amaj7, e7 and c]m,f]6, h6−, e6. key g major and c] minor would be natural looking keys even without tetrahedral extension. for the mirror image b[ minor and e major would be the natural looking keys. for extension e major would be the key. to sum up, half octave shift is a symmetry of all harmonies expected those having only z2 reflection symmetry, and fails thus also for the corresponding bio-harmonies. the tables below give list for the three types of 3-chords for the 11 harmonies possessing symmetries. a 3-chord with n quints is called n-quint chord. the harmonies are labelled by integer triplets (n0, n1, n2), ni gives the number of n-quint chords. the reversal of the orientation for the cycle induces the transformation c ↔ c, f] ↔ f], h ↔ c], f ↔ g, d ↔ b[, e ↔ g], a↔ d] and produces a new scale with minor type chords mapped to major type chords and vice versa. the standard notation of chords used in popular music is used. one must however remember that all 3-chords except those which are simple majors or minors lack the third so that their emotional tone remains uncharacterized. for instance, c6 does could be replaced with cm6 and g7 with gm7. the reader can check the chords by direct inspection of the figures. the convention used is that vertex number 1 in hamiltonian cycle corresponds to c note. 3.2 tables for the 3-chords of icosahedral harmonies the following tables give the 3-chords of the icosahedral harmonies. 3.3 illustrations of icosahedral hamiltonian cycles with symmetries the figures below illustrate the hamiltonian cycles involved. quite generally, the zn symmetry acts by a shift by 12/n quints along the cycle and the orbits of chords consist of at most n chords of same type as the reader is encouraged to verify. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 101-123 114 pitkänen, m., molecular signaling from the tgd viewpoint table 3: table gives various types of 3-chords for the two harmonies with z4 = zrot 2 × zrefl 2 symmetry. 4-plets represent the orbits. first cycle has no harmonic loners. second cycle gives rise to bio-harmony (4, 8, 8) for which 0-quint chords are dissonant. both cycles have z2 rotation symmetry acting as a vertical reflection symmetry in figures and realized also as half-octave shift so that 4-plets contains chords and their half-octave shifts. the genuine reflection symmetry acts as a horizontal reflection symmetry in figures. the cycles correspond to figures 3.3, 3.3 . (n0,n1,n2) 0-chords 1-chords 2-chords (0, 16, 4) (d7, d6, g]7, g]6), (b[9, b9, e9, f9). (g4+, a9−, c]4+, d]9−), (emaj7, gmaj7, b[maj7, c]maj7), (c9−, a9−, f ]9−, d]9−). (4, 8, 8) (cex3, eex2, f ]ex3, b[ex2). (dmaj7, e9−, a7, a6), (b[9, f9, c9, g9). (g]maj7, b[9−, d]7, d]6). (e9, b9, f ]9, c]9). table 4: table gives various types of 3-chords for harmonies with z2 rotation symmetry acting as halfoctave shift. the doublets represent 2-chord orbits. the cycles correspond to figures 3.3, 3.3, and 3.3. (n0,n1,n2) 0-chords 1-chords 2-chords (0, 16, 4) (em,b[m), (cm,f]m), (d9, g]9), (g6, c]6), (a6, d]6), (e9, b[9). (d4+, g]4+), (b4+, f4+), (cmaj7, f ]maj7), (g6−, c]6−). (2, 12, 6) (aex4, d]ex2). (am,d]m), (g9−, c]9−), (c9, f ]9), (c4, f ]4), (e4+, b[4+), (a9, d]9), (dmaj7, g]maj7), (d9, g]9). (bmaj7, fmaj7). (4, 8, 8) (aex2, hex8, d]ex2, f ex8). (d7, g]7), (amaj7, d]maj7), (g9, c]9), (a9, d]9), (a4+, d]4+), (e7, b[7). (b9, f9), (e9, b[9). table 5: table gives various types of 3-chords for harmonies with single reflection symmetry. the cycles correspond to figures 3.3, 3.3, 3.3, 3.3, 3.3. (n0,n1,n2) 0-chords 1-chords 2-chords (2, 12, 6) (f]ex3, hex4), (am,d]), (a6, d]7), (c9, f9), (b9, f ]9), (d7, b[6), (g6−, fmaj7), (e9, c]9). (d4+, b[9−), (e9−, g]4+), (2, 12, 6) (dex4, hex4). (f, fm), (c6−, b[maj7), (c9, d]9), (d7, g]6), (gmaj7, d]6−). (d]9, c]9), (c]4−, a4+), (e4+, f ]6). (e9, b9). (4, 8, 8) (fex1, d]ex3, g]ex1, aex2). (e7, e6), (amaj7, b9−), (d9, b9), (c9, c]9), (g,c]m), (d7, f ]6). (f9, g]9), (d]9, b[9). (2, 12, 6) (hex3, eex7). (d7, g]6), (g,d]m), (c9, d]9), (f, fm), (c6−, b[maj7), (d9, c]9), (a9−, c]4+), (e7, f ]6). (e9, b9). (2, 12, 6) (f]ex2, f ex3). (f,b[m), (c7, g]6), (b[9, d]9), (amaj7, b9−), (e6, e7), (c9, c]9), (g,c]m), (d7, b6). (d9, h9). issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 101-123 115 pitkänen, m., molecular signaling from the tgd viewpoint figure 1: (n0, n1, n2) = (2, 12, 6) hamiltonian cycle with 6-fold rotation symmetry acting shifts generated by a shift of 2 quints. figure 2: (n0, n1, n2) = (0, 16, 4) hamiltonian cycle with 4 reflection symmetries generated by reflections in vertical and horizontal directions. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 101-123 116 pitkänen, m., molecular signaling from the tgd viewpoint figure 3: (n0, n1, n2) = (4, 8, 8) hamiltonian cycle with 4 reflection symmetries. figure 4: (n0, n1, n2) = (0, 16, 4) hamiltonian cycle with 2-fold rotational symmetry realized as 6-quint shift along the cycle. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 101-123 117 pitkänen, m., molecular signaling from the tgd viewpoint figure 5: (n0, n1, n2) = (2, 12, 6) hamiltonian cycle with 2-fold rotation symmetry. figure 6: (n0, n1, n2) = (4, 8, 8) hamiltonian cycle with 2-fold rotation symmetry. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 101-123 118 pitkänen, m., molecular signaling from the tgd viewpoint figure 7: (n0, n1, n2) = (2, 12, 6) hamiltonian cycle with 2-fold reflection symmetry realized as horizontal reflection figure 8: (n0, n1, n2) = (2, 12, 6) hamiltonian cycle with 2-fold reflection symmetry. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 101-123 119 pitkänen, m., molecular signaling from the tgd viewpoint figure 9: (n0, n1, n2) = (4, 8, 8) hamiltonian cycle with 2-fold reflection symmetry. figure 10: (n0, n1, n2) = (2, 12, 6) hamiltonian cycle with 2-fold reflection symmetry. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 101-123 120 pitkänen, m., molecular signaling from the tgd viewpoint figure 11: (n0, n1, n2) = (2, 12, 6) hamiltonian cycle with 2-fold reflection symmetry. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 101-123 121 pitkänen, m., molecular signaling from the tgd viewpoint received april 4, 2022; accepted july 23, 2022 references [1] nottale l da rocha d. gravitational structure formation in scale relativity, 2003. available at: http://arxiv.org/abs/astro-ph/0310036. 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[35] pitkänen m. epigenesis, inherited memories and moods lasting over several generations. available at: https:/tgdtheory.fi/public_html/articles/amoebamemory.pdf., 2019. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https:/tgdtheory.fi/pdfpool/eegdark.pdf https:/tgdtheory.fi/pdfpool/eegii.pdf https:/tgdtheory.fi/pdfpool/eegii.pdf https:/tgdtheory.fi/pdfpool/prebio1.pdf https:/tgdtheory.fi/pdfpool/prebio2.pdf https:/tgdtheory.fi/pdfpool/geesink.pdf https:/tgdtheory.fi/pdfpool/homeoc.pdf https:/tgdtheory.fi/pdfpool/biophotonslian.pdf https:/tgdtheory.fi/pdfpool/biophotonslian.pdf https:/tgdtheory.fi/pdfpool/persconsc.pdf https:/tgdtheory.fi/pdfpool/persconsc.pdf https://link.springer.com/chapter/10.1007/978-3-319-55612-3_11 https://link.springer.com/chapter/10.1007/978-3-319-55612-3_11 https:/tgdtheory.fi/public_html/articles/adelephysics.pdf https:/tgdtheory.fi/public_html/articles/adelephysics.pdf https://tgdtheory.fi/public_html/articles/mseeg.pdf https://tgdtheory.fi/public_html/articles/mseeg.pdf https:/tgdtheory.fi/public_html/articles/harmonytheory.pdf https:/tgdtheory.fi/public_html/articles/harmonytheory.pdf https:/tgdtheory.fi/public_html/articles/pollackyoutube.pdf https:/tgdtheory.fi/public_html/articles/pollackyoutube.pdf https:/tgdtheory.fi/public_html/articles/valenceheff.pdf https:/tgdtheory.fi/public_html/articles/philosophic.pdf https:/tgdtheory.fi/public_html/articles/gcharm.pdf https:/tgdtheory.fi/public_html/articles/gcharm.pdf https://tgdtheory.fi/public_html/articles/bioharmony2020.pdf https://tgdtheory.fi/public_html/articles/bioharmony2020.pdf https:/tgdtheory.fi/public_html/articles/amoebamemory.pdf dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 101-123 123 pitkänen, m., molecular signaling from the tgd viewpoint [36] pitkänen m. is genetic code part of fundamental physics in tgd framework? available at: https://tgdtheory.fi/public_html/articles/tih.pdf., 2021. [37] pitkänen m. revolution in chemistry. https://tgdtheory.fi/public_html/articles/ newchemistry.pdf., 2021. [38] pitkänen m. tgd view about water memory and the notion of morphogenetic field . https: //tgdtheory.fi/public_html/articles/watermorpho.pdf., 2022. [39] pitkänen m. the realization of genetic code in terms of dark nucleon and dark photon triplets. https://tgdtheory.fi/public_html/articles/darkcode.pdf., 2022. [40] pitkänen m and rastmanesh r. the based view about dark matter at the level of molecular biology. available at: https:/tgdtheory.fi/public_html/articles/darkchemi.pdf., 2020. [41] pitkänen m. a model of protocell based on pollack effect. available at: https:/tgdtheory.fi/ public_html/articles/pollackoparin.pdf., 2020. [42] pitkänen m. time reversal and the anomalies of rotating magnetic systems. available at: https: //tgdtheory.fi/public_html/articles/freereverse.pdf., 2021. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://tgdtheory.fi/public_html/articles/tih.pdf https://tgdtheory.fi/public_html/articles/newchemistry.pdf https://tgdtheory.fi/public_html/articles/newchemistry.pdf https://tgdtheory.fi/public_html/articles/watermorpho.pdf https://tgdtheory.fi/public_html/articles/watermorpho.pdf https://tgdtheory.fi/public_html/articles/darkcode.pdf https:/tgdtheory.fi/public_html/articles/darkchemi.pdf https:/tgdtheory.fi/public_html/articles/pollackoparin.pdf https:/tgdtheory.fi/public_html/articles/pollackoparin.pdf https://tgdtheory.fi/public_html/articles/freereverse.pdf https://tgdtheory.fi/public_html/articles/freereverse.pdf introduction observations tgd view about the findings bio-harmony and context dependence bio-harmony could ligand interactions reduce to a re-tuning of ligand harmonies? ligand interactions as re-tuning tuning and re-tuning at the level of dx-x pairing could special 3-chords act as tuning forks re-tuning as an epigenetic process an attempt to concretize the model of ligand interactions could the dark matter hierarchy relate to the bio-harmony? appendix: tables of basic types of 3-chords for icosahedral harmonies icosahedral harmonies as hamiltonian cycles tables for the 3-chords of icosahedral harmonies illustrations of icosahedral hamiltonian cycles with symmetries login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x microsoft word fiscalettidavide2_v10n2 dna decipher journal | november 2020 | volume 10 | issue 2 | pp 67-82 fiscaletti, d., perspectives on the origin of life in exoplanets as a phenomenon generated by a 3d quantum vacuum issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 67 article perspectives on the origin of life in exoplanets as a phenomenon generated by a 3d quantum vacuum davide fiscaletti * spacelife institute, italy abstract a model of the origin of life in exoplanets as a phenomenon generated by a quantum potential of a three-dimensional quantum vacuum acting as a reservoir of heat is proposed, which implies that the probability of life in exoplanets is determined by the heat that describes the interaction between the living organism and its environment, the surface temperature of the planet and the fluctuations of the quantum vacuum energy density in the region into consideration. it is shown how, in this picture, not only the parameters of the planet and the star influence the habitability of a planet and the duration of the habitability, but also a quantum term associated with the action of the quantum potential of the vacuum which implies that life is a global non-local property which can transmit instantaneously from a region to another of the universe. keywords: origin of life, exoplanet, 3d quantum vacuum, quantum potential, non-local propery. 1. introduction for several decades, researchers have been studying exoplanets, including the so-called earth-like planets, rocky planets with a radius between 1 and 1.75 times that of the earth and whose orbit is located within the habitability zone of a similar star to the sun, at a distance compatible with the presence of liquid water on the planet’s surface. since the discovery of the planet 51 pegasi b orbiting a solar-type star in 1995, several exoplanets have been discovered. today, the number of confirmed exoplanets is about 4000 with over 600 planetary systems possessing more than one exoplanet and among them there are several earth-like exoplanets. the search for exoplanets today certainly represents one of the most advanced frontiers of astrophysics, which stimulates scientists to use their resources in order to find biosignatures as well as technosignatures, in order to answer two crucial questions that humanity has been asking for millennia, namely "are we alone in the universe?" and "what is the origin of life?". habitability of an exoplanet can be defined as the potential of an environment (past or present) to support life of any kind and is thus a function of a multitude of environmental parameters whose study is influenced by the effects that biology has on these parameters. despite the immense difficulties and challenges one has to face as regards the problem of identifying extraterrestrial life, the simplest way to treat this topic remains to search for “life as we know it” on a planet that shares the basic physical properties of the earth. water is conventionally regarded as one of the most essential requirements for * correspondence: davide fiscaletti, spacelife institute, san lorenzo in campo (pu), italy. e-mail: spacelife.institute@gmail.com note: this article was first published in 2020 in scientific journal journal, 11(6): pp. 359-375. dna decipher journal | november 2020 | volume 10 | issue 2 | pp 67-82 fiscaletti, d., perspectives on the origin of life in exoplanets as a phenomenon generated by a 3d quantum vacuum issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 68 life on earth by virtue of its unusual physicochemical properties [1]. as a consequence, many studies tend to adopt a “follow the water” approach, namely to search for planets where liquid water could exist on their surfaces. since the pionieristic works of hart [2, 3] till the more recent ones by kasting et al. [4] and kopparapu et al. [5], this “surface liquid water” criterion has been used to define the habitable zone as that range of distances from a parent star in which an earth-like planet could maintain liquid water on its surface and so potentially host a surface biosphere. although subsurface liquid water is entirely possible and may even be common — as suggested by the interior oceans of the icy moons in our solar system — detecting that water, and any subsurface biosphere supported by it, is very difficult with remote-sensing telescopic observations. consequently, the search for habitability and life on exoplanets will focus on telescopic observations of planetary atmospheres and surfaces, where a surface biosphere will be more apparent. in fact, another important condition which must be satisfied in order to guarantee the possibility of a planet to host life lies in the fact that the planet needs to retain an atmosphere since water ice transforms directly into gas phase in vacuum. on the basis of our current knowledge, one can utilize the term “habitable zone” in order to identify the region around a star where an orbiting planet has the highest probability of being detectably habitable, for remote-sensing studies. although we do not currently have a means of observing markers of surface habitability on exoplanets, these capabilities are expected in the near future. on the other hand, the habitable zone of a planet depends not only on stellar properties but also a wide range of planetary properties. as the field of astrobiology develops, it is becoming clearer that multiple factors, characteristics and processes, can impact whether a planet can acquire and maintain liquid water on its surface. these include the properties of the planet (such as atmospheric composition, atmospheric escape/retention, volatile inventory and delivery, cycling of elements between surface and interior, planetary magnetic field, planet mass and size), star (which can include: stellar spectral energy distribution, activity, stellar winds, age, x-ray/ultraviolet emission, magnetic field, and stellar multiplicity) as well as planetary system (in particular, orbital architecture of planets in the system and the presence of giant planets), and how these factors interact over time [6]. as regards the planet’s environment, its mass, radius, orbit, interior, surface and atmosphere are elements that affect its habitability. once life has evolved on a habitable world, it becomes a planetary process that can also impact its environment [7-10]. 1.5 �⊙ radii is the upper limit for an exoplanet to be more likely to have a predominantly rocky composition [11-13]. a planet’s mass impacts planetary habitability in multiple ways, by providing radiogenic heating from long-lived radionuclides to drive internal heating and tectonics [14] as well as generation of a magnetic field [15], which is a key parameter that determines atmospheric retention [16-18]. planetary mass, via planetary gravity, also rules atmospheric scale height, which can modify the rate the planet radiates to space, as well as its climate and the limits of the habitable zone [19]. the planetary orbital parameters, such as semi-major axis, eccentricity, obliquity, and rotation rate, affect planetary habitability through their control on the stellar radiation received by a planet over its orbit, and associated feedbacks on the climate system. an active and dynamic interior plays a crucial role in determining the habitability of a planet, by driving the generation of a magnetic field [20, 21] and outgassing [22], which are key factors in order to produce and maintain a secondary atmosphere. magnetic fields are another important factor when considering the habitability of a planet, since they may protect planets from losing volatiles (such as water) through stellar wind interactions [16, 23, 17, 21, 24, 25], even if recent studies suggest that there dna decipher journal | november 2020 | volume 10 | issue 2 | pp 67-82 fiscaletti, d., perspectives on the origin of life in exoplanets as a phenomenon generated by a 3d quantum vacuum issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 69 is a complex relationship between magnetic field and atmospheric escape, in terms also of the strength of the planet’s intrinsic magnetic field and the incoming stellar wind pressure [18]. on the other hand, the host star’s features have a huge influence on a planet’s environment and habitability. stellar mass and radius determine many of the star’s fundamental characteristics, such as temperature and lifetime. stellar luminosity evolution drives strong climate change and may result in atmospheric or ocean loss, which is a compositional change and often a threat to habitability. the stellar spectrum and activity levels influence atmospheric escape and climate, provide the most abundant surface energy source for the majority of planets of the habitable zone, and photochemically modify the planet’s atmospheric composition. moreover, also the interactions among the planet, its host star, and its planetary system constitute another category of factors that in part determine whether a planet is and can remain habitable. radiative interactions with the host star can modify planetary atmospheric compositions by driving the photochemical production of aerosols or gas species. these modifications of the atmosphere subsequently affect planetary climate and the ultraviolet flux incident at the planet’s surface, both of which directly affect habitability. gravitational interactions between the host star, planet and the planetary system can modify orbital properties which in turn modulate insolation levels and therefore climate. gravitational interactions also may be responsible for late volatile deliveries from comets deflected into the inner part of stellar systems. tidal interactions between bodies in the system can influence planetary interiors, ruling the magnetic dynamo and plate tectonics, both of which play significant roles in the maintenance and retention of secondary atmospheres on terrestrial planets. the characteristics and processes which play a relevant role regarding the maintenance of surface liquid water on a terrestrial planet are broad, interdisciplinary and interconnected, and both theoretical modelling and astronomical observations will be needed to understand them. at this time, our best first-order assessment method for establishing whether or not a planet is likely to be habitable has been to check whether a newly discovered exoplanet is in the size range that is likely to be terrestrial, and is in the habitable zone of its parent star. as we have said before, in the light of our current knowledge, we can say that habitability is maintained via the interplay of the planet, of the stellar and planetary system characteristics over the planet’s lifetime. in particular, within this new framework, r.k. kopparapu, e.t. wolf and v.s. meadows have recently suggested that the habitable zone of a planetary system can be seen as a 2-dimensional slice in stellar type and semi-major axis through a multi-dimensional parameter space, that understanding how the balance between outgassing and atmospheric escape sculpts the resulting terrestrial planet atmosphere, and potentially replenishes an ocean, will be an important new frontier in terrestrial exoplanet evolution and habitability and that an interdisciplinary system science approach will be needed to fully explore the depth and complexity of planetary habitability [26]. as regards the problem of determining the habitability of a exoplanet, by considering the detection of biosignatures (or technosignatures) on an earth-like planet (a planet with basic physical parameters similar to earth) orbiting (i) an arbitrary star with a general mass �∗, and (ii) a g-type star of approximately solar mass �⊕, in the recent paper “optimal target stars in the search for life” lingam and loeb estimated the probability to find life in a given planet with the parameter: ∝ �ρ (1) dna decipher journal | november 2020 | volume 10 | issue 2 | pp 67-82 fiscaletti, d., perspectives on the origin of life in exoplanets as a phenomenon generated by a 3d quantum vacuum issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 70 where � denotes denotes the probability that the chosen planet has life, and ρ is the probability that the biosignatures arising from this exolife are detectable. moreover, they compared the relative benefits of the strategies (i) and (ii) through the variable: δ = �⋆�⨀ = � �⋆�⨀� � �⋆�⨀� (2) from (2) it derives that the value of δ depends on the ratio: � = �⋆�⨀ (3) which quantifies the ratio of the probabilities of life-bearing planets around stars of mass �∗ and �⨀. in order to provide an estimate of the value of �, which can be interpreted as the relative likelihood of life in a given planet, the most common procedure is to utilize physical constraints on habitability regarding bioactive ultraviolet radiation, magnetic fields, planetary magnetospheres, atmospheric erosion, water loss, which according to recent studies seem to indicate that life-bearing planets around m-dwarfs are likely to be rare with respect to sun-like stars [27, 4, 28-30]. however, if one considers atmospheric escape driven by the stellar wind [31] as well other constraints (e.g. stellar ultraviolet radiation and lifetime) which can be incorporated in a similar fashion [32], the relative likelihood of life may be expressed as: � ≈ � �⋆�⨀� � �⋆�⨀� (4) where � denote the corresponding luminosity of the planet. in this paper our purpose is to suggest new scenarios as regards the estimate and interpretation of the quantity (3), introduced by lingam and loeb in order to evaluate the likelihood of life in a planet, inside a model of a three-dimensional quantum vacuum defined by rs processes of creation/annihilation of virtual particles occurring in correspondence to elementary energy density fluctuations. this paper is structured in the following way. in chapter 2 we will show in what sense the origin of life in an exoplanet is determined by a quantum potential of the three-dimensional quantum vacuum. in chapter 3 we will compute the probability of life in an exoplanet inside our model. finally, in chapter 4 we summarize the results of the paper underlining the perspectives of our model. 2. on the role of the quantum potential of the vacuum in the origin of life in a planet our uncertainty about the origin of life can be associated with our ignorance in calculating the probability, for matter, to give place to a transition from non-living to living state. the knowledge of this parameter is important not only for understanding life on earth, but also for estimating the distribution of life in the universe [33]. today we have got a number of explicit models which provide clues regarding the emergence of life, and how the traditional tools of physics can help us to give a solution to this problem. however, we are dna decipher journal | november 2020 | volume 10 | issue 2 | pp 67-82 fiscaletti, d., perspectives on the origin of life in exoplanets as a phenomenon generated by a 3d quantum vacuum issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 71 far from a resolution to our question “how is it that life can emerge from non-living matter?”. most work on fundamental properties of life focuses on the concept of information [34, 35] which plays an important role for quantitative theories of life’s origins too [36]. the mathematical relationship between shannon and boltzmann entropies suggests a potentially deep connection between information and thermodynamics [37]. this connection has been explored by substantial work over the last decade (see, for example, [38] for a recent review of this topic). on the other hand, schrödinger was aware of the link between information and life in his considerations on biology, coining the term “negentropy” in order to describe life’s ability to seemingly violate the 2 nd law of thermodynamics. yet, he still felt that something was missing and ultimately suggested the perspective that “other laws” might be necessary for the description of life [39]. von neumann was one of the first to consider the possibility that information plays a key role in living systems [40]. he recognized that one cannot explain the origin of the complexity of living systems (which he hoped to emulate in artificial systems), in terms only of the copying information (even with mutation and selection), but at this purpose the concept of constructability must additionally be introduced [41]. copying and construction as introduced by von neumann are two fundamentally different physical processes, although they may ultimately lead to the same effective result, namely the reproduction of information stored in one physical media in another. in the case of copying, the information is replicated from one media to another of the same physical stuff (or nearly so) [42]. constructors by contrast perform transformations on physical objects, such that one physical media may be transformed into another. the concept that living systems (and their artefacts) mediate transformations that do not violate known laws of physics, but are at the same time not predicted by them, may be considered as one of the most fundamental features of life, suggesting that an explanation for life does not lie in explaining the states themselves, but instead the paths [43]. this view is consistent with an emerging emphasis in nonequilibrium thermodynamics on trajectories rather than states. marletto has recently underlined that an important feature of life is that life not only copies information but also uses it to construct itself and can utilize information to construct other objects [44]. this implies that, if one wants to model the origin of life, the concept of life as “information that copies itself” must be intended in the sense that “simple machines that can make slightly more complicated machines” [45]. in other words, one has to invoke the existence of non-trivial replicators that process information in an active sense, enabling the system’s dynamics to (in part) be directed by the current informational state (“program”) of the system. this is the key idea which underlies the philosophical concept of top-down causation [36, 35, 46]. living systems can be seen as embedded hierarchies, with complex flows of information between scales of organization [47] that do not generally permit this layer-by-layer decomposition of causation (information flows from 'higher' to 'lower' levels). that is, life could be regarded as a hierarchy of ‘constructors’, or at least information flows that mediate which transitions occur and when. it is widely recognized that the procedure of coarse-graining (which defines some of the relevant “informational” degrees of freedom) plays a foundational role in how biological systems are structured, by defining the biologically relevant macrostates [48]. however, it is not clear how those macrostates arise, if they are objective or subjective [49], or whether they are in fact a fundamental aspect of biological organization. dna decipher journal | november 2020 | volume 10 | issue 2 | pp 67-82 fiscaletti, d., perspectives on the origin of life in exoplanets as a phenomenon generated by a 3d quantum vacuum issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 72 the emergence of life can be re-stated as a problem of explaining how (biological) hierarchies emerge (these should be distinguished, for example, from re-normalization group flows or other ‘hierarchies’ in physics, since in biology the individual 'levels' are not self-similar). the mechanisms through which topdown causation, if indeed it is a real and not just apparent property of nature, could operate in biology would most likely be through information (in an as yet unspecified manner) acting as a causal agent. the idea of information is itself abstract, but it must be emphasized that each bit of information is instantiated in physical degrees of freedom: “information is physical!”, if we want to use an icastic sentence of rolf landauer [50]. whether fundamental or an epiphenomenon, the causal role of information in biology represents indeed one of the hardest explanatory problems for solving the origins of life. in [36] walker and davies presented a framework for understanding the origin of life as a transition in causal structure, and information management and control, whereby information gains causal efficacy over the matter it is instantiated in. the walker and davies approach suggests that a rigorous distinction between life and non-life is most likely to derive from the distinctive mode of information management and control displayed by living systems. while both the traditional digital-first and analogue-first viewpoints neglect the active (algorithmic or instructional) and distributed nature of biological information, in the walker and davies model, the real challenge of life’s origin is to explain how instructional information control systems emerge naturally and spontaneously from mere molecular dynamics and the key distinction between the origin of life and other ‘emergent’ transitions is the onset of distributed information control, enabling context-dependent causation, where an abstract and non-physical systemic entity (algorithmic information) effectively becomes a causal agent capable of manipulating its material substrate [46, 51]. the advantage of this perspective is that it provides a foundation for identifying the origin of life as a well-defined transition, by shifting emphasis to the origins of information control, rather than, for example, the onset of darwinian evolution or the appearance of autocatalytic sets. walker’s and davies’ approach also permits a broader view of life, where the same underlying principles would permit understanding of living systems instantiated in different chemical substrates (including potentially nonorganic substrates). but, how does this transition occur? what does it explain the distributed nature of biological information in living systems, where information gains causal efficacy over the matter it is instantiated in? while in walker’s and davies’ approach this transition shift in the efficacy of information gaining of living systems over matter remains an open question, the model of the there-dimensional (3d) quantum vacuum developed by the author in several papers [52-55] has the merit to introduce interesting perspectives about these issues. in particular, here a starting-point consideration is that processing systems with delocalized information are evolutionarily robust, in other words that there exists a delocalized information in the form of a non-local connection between living systems and the elementary vibratory states of the 3d quantum vacuum. let us review briefly, before all, the essential features and results of the model of the 3d quantum vacuum. in the model proposed by the author in [52-55], all the events of our everyday life are the explicit manifestations of more elementary processes of a fundamental, deep arena, a three-dimensional (3d) timeless non-local quantum vacuum characterized by rs processes of creation/annihilation of virtual particles corresponding to opportune fluctuations of the quantum vacuum energy density. in this dna decipher journal | november 2020 | volume 10 | issue 2 | pp 67-82 fiscaletti, d., perspectives on the origin of life in exoplanets as a phenomenon generated by a 3d quantum vacuum issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 73 model, each material particle, which is revealed in the experiments, is associated to a specific excited state of the 3d quantum vacuum characterized by a diminishing of the quantum vacuum energy density )( qvepeqve   and corresponding to opportune elementary rs processes of creation/annihilation of virtual particles, where the planck energy density: 3 2 p p pe l cm   (5) defines the ground state of the vacuum and v cm peqve 2   (6) is the energy density of quantum vacuum inside the particle, pm is planck’s mass, � is the light speed and pl is planck’s length. here, the rs processes of creation/annihilation of the virtual particles of the medium, which give rise to the appearance of a material particle of mass obtained from equation (6), can be described by a wave function � = �� ! at two components satisfying a time-symmetric extension of the klein-gordon quantum relativistic equation: 0 0 0        c h h (7) where          2 2 2 2 qve c v h   h . equation (7) may be considered as the fundamental equation ruling the behaviour of the excited states of the 3d quantum vacuum. the crucial feature of the 3d quantum vacuum lies in its non-local character, which is associated with a quantum potential of the vacuum of the form:                                            iq iq iq iq qve iq tc tc v c q , ,2 2 2 2 , ,2 2 2 2 22 22 , 1 1      h (8) the quantum potential of the vacuum (8) is the fundamental entity which the guides, in a non-local way, the occurring of the processes of creation or annihilation in space. in the light of the results obtained in [56], the non-local information encoded in the 3d quantum vacuum is a crucial element which explains the origin of life, which explains the distinctive features of living systems, providing a rigorous distinction between life and non-life at a fundamental level. in this regard, the key element is represented by a quantum potential of the vacuum which has the role of dna decipher journal | november 2020 | volume 10 | issue 2 | pp 67-82 fiscaletti, d., perspectives on the origin of life in exoplanets as a phenomenon generated by a 3d quantum vacuum issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 74 generating an additional density of physical space in a living system. in other words, a quantum interaction between a living organism with its environment is generated which is determined by a quantum potential of the vacuum that acts as a heat reservoir, and this quantum potential of the vacuum acting as a heat reservoir produces an “additional density” of physical space in a living organism (living matter) with respect to inert matter. the quantum potential of the vacuum acting as a reservoir heat that is responsible for the origin of life in a planet, in the relativistic domain, is expressed by equation: " = ℏ$%$ &$'∆)*+,-$ ∇$/01ℏ2 (9) while in the non-relativistic domain is: " = − ℏ$%$4&∆)*+, ∇$/01ℏ2 (10) where ℏ5/2 is the average kinetic energy associated with the vibratory states of the 3d quantum vacuum and hfq is the heat that describes and regards the interaction between the living organism and its environment. by following grössing’s thermodynamic approach to the quantum potential [57, 58], in our approach of a 3d non-local quantum vacuum as fundamental origin of physical processes, the quantum potential of the 3d quantum vacuum which rules the interaction between a living organism and its environment acts as a heat reservoir, as a thermal energy in the sense that generates the appearance of bio-photons which act non-locally in the environment itself. the instantaneous action of the bio-photons produced by the thermalized quantum potential of the vacuum implies that the distributions of the vibratory states in the environment under consideration contribute in their totality to the form of the heat distribution in the overall system and thus to the evolution of the living organism, leading to a promising perspective for a deeper understanding, in a global picture, of the origin of life in the universe. in other words, in our approach, we can say that the distributed nature of biological information in living systems, where information gains causal efficacy over the matter it is instantiated in, is determined just by the action of the quantum potential of the 3d quantum vacuum as a heat reservoir, that generates the appearance of bio-photons which act non-locally in the environment itself. we can therefore give the following answer as regards the transition in the causal structure, as regards the ability of information management and control, the origins of information control, inside living systems: these elements, which are distinctive of living systems, are generated just by the fact that the quantum potential of the vacuum, acting as a heat reservoir, produces an “additional density” of physical space in a living organism with respect to inert matter. the action of the quantum potential of the vacuum as a thermal energy which generates the appearance of bio-photons which act non-locally in the environment, explains in what sense information plays a key role in living systems, in what sense living systems are characterized by complex flows of information between scales of organization, in what sense life may be regarded as a hierarchy of ‘constructors’, or at least as information flows that mediate which transitions occur and when. the key of explanation of all these informational processes characterizing living systems lies in the quantum potential of the vacuum. now, a fundamental consequence of this model is that the non-local action of the quantum potential of the vacuum makes life as a property that ultimately has a global feature, namely acts non-locally itself. dna decipher journal | november 2020 | volume 10 | issue 2 | pp 67-82 fiscaletti, d., perspectives on the origin of life in exoplanets as a phenomenon generated by a 3d quantum vacuum issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 75 in other words, we can say that, in the light of the quantum potential of the vacuum (27) (or (26)), life is a property of all universe, is a cosmic property. the non-local features of life may also be characterized by introducing an appropriate bell length associated with the quantum potential of the vacuum (9): ��899 = : ℏ$%$4∆)*+,&/ (11) namely, ��899 = :− %ℏ2∇$/01 (12) namely, taking account of (9): ��899 = :− 4%∆)*+,&;∇$/01 (13) the condition " = 0, i.e. ��899 = ∞ provide the points where the action of the 3d quantum vacuum acting as a heat reservoir expressing the interaction between a living organism and its environment, namely where the additional density of physical space present in living matter, is delocalized, thus implying the evolution of life and equation (30) shows that this happens when: >2�∆?@ab c> ≥ >n∇4"fg> (14) equation (14) is a plausible physical condition which, for a great number of rs processes of creation/annihilation of quanta corresponding to a great number n of virtual particles/antiparticles of the vacuum, practically occurs in a specific macroscopic volume v. this means in other words that the propagation of life in the universe, owed to the action of the thermalized quantum vacuum which functions as a heat reservoir, as a thermal energy which appear then as bio-photons which act nonlocally in the environment itself, occurs instantaneously in all the points of the universe, namely that life is indeed a global property which is able to transmit itself in the entire universe. moreover, other relevant considerations may be made by taking account of the metabolic theory of ecology. in the picture of the metabolic theory of ecology several ecological parameters – such as the production and turnover of biomass, the rates of genetic divergence and speciation, species diversity and coexistence – are determined by the metabolic rate b of organisms given by: ∝ hi/jklm �− bnop� (15) where h is the mass of the organism, q� is the boltzmann constant, r is the absolute temperature and s is the average activation energy which is associated to the appropriate rate-limiting step in metabolism [59]. therefore, since here the activation energy s associated with the metabolism in a planet is ultimately generated the quantum potential of the vacuum acting as a reservoir heat which supports the interaction between the living organism and its environment, equation (15) can be opportunely expressed as: dna decipher journal | november 2020 | volume 10 | issue 2 | pp 67-82 fiscaletti, d., perspectives on the origin of life in exoplanets as a phenomenon generated by a 3d quantum vacuum issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 76 ∝ �∆)*+,&%$ �i/j klm t ℏ$u$$v∆w*+,∇$x01ℏynop z (16) as a consequence, taking account that for life as we know it in our planet, the earth-referenced temperature-dependent likelihood function” �p = klm[−26,7_` − 1abc_r − r�ac_rd − ra (17) (where c is the heaviside function which assures that the likelihood becomes for r < r� and r > rd, rd and r� are the limits over which the boltzmann factor is valid and the temperature range r� < r < rd is not expected to exceed the earth-based photosynthesis limits for life-as-we-know-it) holds, and that the auxiliary parameter ` in equation (17) is expressed by relation: ` = bb⨁ p⨁p ∼ p⨁p (18) where s⨁ = 0,66kc and r⨁ = 287j are the corresponding values for the earth, and here s ∼ s⨁, one obtains the following condition for the quantum potential of the vacuum as a reservoir heat relative to the parameters of the planet earth: ℏ$u$$v∆w*+,∇$x01ℏynop = 26,7 t ℏ$u$$v∆w*+,∇$x01ℏyb⨁ p⨁p + 1z 19) namely, ∇4"fg = 4&∆)*+,2b⨁nopℏ%$b⨁l4m,nℏ%$nop⨁ (20) which expresses the link between the heat ∇4"fg that describes and regards the interaction between the living organism and its environment, the surface temperature of the planet and the fluctuations of the quantum vacuum energy density in the region into consideration. an interesting advantage of equation (20) is that it reproduces correctly the fact that “origin of life”-type events are determined by the parameters of the surrounding environment and not necessarily by the global properties (such as the global temperature) of the planet. 3. the role of the quantum potential of the vacuum with regards to the probability of life in exoplanets and the duration of habitability in our approach, life in an exoplanet is produced by a thermalized vacuum acting as a reservoir of heat. in particular, taking account of the results obtained by lingam and loeb in [60], the likelihood function of life in exoplanets may be expressed through the following equations: dna decipher journal | november 2020 | volume 10 | issue 2 | pp 67-82 fiscaletti, d., perspectives on the origin of life in exoplanets as a phenomenon generated by a 3d quantum vacuum issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 77 a) � = klm t ℏ$u$$v∆w*+,∇$x01ℏynop z c_r − r�ac_rd − ra � �opqrs� �tut⨁� �〈w,xv〉〈w⨁〉 �lp (21) if the lifetime of the planet’s atmosphere is less than the timescale of atmospheric loss for unmagnetized planets, and b) � = klm t ℏ$u$$v∆w*+,∇$x01ℏynop z c_r − r�ac_rd − ra � �opqrs� � qpzd�4 �tut⨁�lp,n � {| ⋆{| ⨀�lp (22) if the lifetime of the planet’s atmosphere is bigger than the timescale of atmospheric loss for unmagnetized planets. in equations (21) and (22), �} = ~{���j�tu$ is the surface pressure of the atmosphere (�qrs is the mass of the atmosphere, �� is the radius of the planet), 〈�bd&〉 is the average extreme ultraviolet flux, �⨁ is the value of 〈�bd&〉 for the earth, �⨁ is the radius of the earth, � is the semimajor axis of the planet, �| ⋆ is the stellar mass loss rate, �| ⨀ is the sun’s mass loss rate. the advantage of the functions (21) and (22) lies in the fact that they allow us to determine the likelihood of a planet being conducive to life with respect to earth in terms of parameters which are direct observables, or can be deduced indirectly, by means of numerical simulations (except for uncertainties concerning the surface pressure and the surface temperature). as regards the approach based on equations (21) and (22), the crucial point is that, despite the presence of some terms that for a given exoplanet seem to provide values which differ with respect to those of earth (as lingam’s and loeb’s research demonstrate), this does not necessarily mean that the exoplanet into consideration does not host life because the quantum term klm t ℏ$u$$v∆w*+,∇$x01ℏynop z associated with the quantum potential of the vacuum, as a consequence of its non-local action, makes life a non-local property which can originate also in that peculiar exoplanet. in other words, in this picture, one can say that the habitability of an exoplanet is determined by the synergy of different parameters: some parameters regarding the planet into consideration (such as its atmosphere) and its star, as well as the quantum term klm t ℏ$u$$v∆w*+,∇$x01ℏynop z associated with the quantum potential of the vacuum, which indicates the role of life as a global non-local phenomenon. therefore, a suggestive perspective introduced by the approach based on equations (21) and (22) is that a given exoplanet will be habitable and thus will host life when the term klm t ℏ$u$$v∆w*+,∇$x01ℏynop z prevails with respect to the other terms appearing in (21) and (22), in particular the heaviside function, the surface pressure of the atmosphere, the average extreme ultraviolet flux and the stellar mass loss rate. the considerations we have made here allow us now to throw new light as regards the probabilities of life-bearing planets around stars of mass �∗ and �⨀, in the sense that the likelihood function of life in exoplanets may be expressed through simple equations where the value of the parameter dna decipher journal | november 2020 | volume 10 | issue 2 | pp 67-82 fiscaletti, d., perspectives on the origin of life in exoplanets as a phenomenon generated by a 3d quantum vacuum issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 78 klm t ℏ$u$$v∆w*+,∇$x01ℏynop z must be put in comparison with the other terms appearing in these equations. the quantity � = �⋆�⨀, which represents the ratio of the probabilities of life in exoplanets around stars of mass �∗ with respect to earth, can be expressed through the following equations: a) � = 8�� ⎝ ⎜⎛ ℏ$u$$v∆w*+,∇$x01ℏy�o� ⎠ ⎟⎞� uo�������u�⨁!�〈�,xv〉〈�⨁〉 !�� 8��[l4m,n_�lpab (23) if the lifetime of the planet’s atmosphere is less than the timescale of atmospheric loss for unmagnetized planets, and through the following equation: b) � = 8�� ⎝ ⎜⎛ ℏ$u$$v∆w*+,∇$x01ℏy�o� ⎠ ⎟⎞� uo������ ���x�$��u�⨁!��,�� �| ⋆�| ⨀!�� 8��[l4m,n_�lpab (24) if the lifetime of the planet’s atmosphere is bigger than the timescale of atmospheric loss for unmagnetized planets. clearly, as regards the probability of life in an exoplanet – which can be expressed through equations (23) or (24) – one must take into account that the upper bound on the habitability of a planet is the stellar lifetime and that the maximum duration that the planet remains habitable is less than the stellar lifetime for a simple reason: the stellar luminosity increases over time, and the planet will eventually enter a runaway greenhouse phase and become uninhabitable (like venus). thus, the duration of habitability is essentially specified by the temporal extent of the continuously habitable zone. by using the knowledge about the inner and outer boundaries of the habitable zone in conjunction with stellar evolution models, one can estimate the total duration of time (���) that an earth-analog will remain inside the habitable zone as a function of the stellar mass �∗. by following [61], one obtains: ��� ≈ 0,55�⊙ � {∗{⊙!l4 if �∗ > �⊙ (25) ��� ≈ 0,55�⊙ � {∗{⊙!lp if 0,5�⊙ < �∗ < �⊙ (26) ��� ≈ 0,55�⊙ � {∗{⊙!lp,4� if �∗ < 0,5�⊙ (27) where �⊙ ≈ 10��� and �⊙ is the solar mass. by analysing (25)-(27), it follows that low-mass stars are characterized by continuous habitable zones that last for a longer duration of time, which is along expected lines since they have longer main-sequence lifetimes [62, 63]. now, in our approach of 3d quantum vacuum, the interesting perspective is opened that the total duration of habitability of a planet dna decipher journal | november 2020 | volume 10 | issue 2 | pp 67-82 fiscaletti, d., perspectives on the origin of life in exoplanets as a phenomenon generated by a 3d quantum vacuum issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 79 is itself determined by the synergy of the values of the parameters appearing in equations (21) and (22), namely the parameters regarding the planet into consideration (such as its atmosphere) and its star, as well as the quantum term klm t ℏ$u$$v∆w*+,∇$x01ℏynop z associated with the quantum potential of the vacuum. in other words, it is the evolution of the values of the parameters appearing in equations (21) and (22) which contribute to make a given exoplanet habitable or non-habitable and, therefore, influences the total duration of habitability of that exoplanet. finally, it must be emphasized that the quantum term klm t ℏ$u$$v∆w*+,∇$x01ℏynop z associated with the quantum potential of the vacuum and which makes life a global property which has the potential to transmit instantaneously from one region to another, allows us to throw new light also as regards the computation of the number of planets which host life in a given region of the universe. in this regard, in [64] lingam and loeb estimated the number of planets with life in a particular volume through relation: �� =  }¡¢ ∙ ¤8 ∙ ¤9 (28) where  }¡¢ is the number of stars that can be covered by a state-of-the-art telescope like the jswt, ¤8 is the fraction of “habitable” planets per star, and ¤9 is the probability that a “habitable” planet is actually inhabited. if in lingam’s and loeb’s approach, ¤8 is an unknown quantity since we do not currently know the list of necessary and sufficient criteria for habitability, in our approach things are different because life is a non-local global property generated by the action of the quantum potential of the 3d quantum vacuum as a heat reservoir and klm t ℏ$u$$v∆w*+,∇$x01ℏynop z is the fundamental term which is responsible of this. as a consequence, in our model of 3d quantum vacuum as origin of life in an exoplanet, the unknown coefficient ¤8 of lingam’s and loeb’s approach can be replaced with the term klm t ℏ$u$$v∆w*+,∇$x01ℏynop z which indeed makes life a global property which has the potential to emerge everywhere in the universe. therefore, in our model the number of planets with life in a particular volume can be expressed through the following relation: �� =  }¡¢ ∙ klm t ℏ$u$$v∆w*+,∇$x01ℏynop z ∙ ¤9 (29) in summary, equations (21), (22), (23) and (29) have the potential to determine relevant perspectives in order to explore the possibilities of life in the different exoplanets and different galaxies and stellar systems existing in the visible universe. these equations indeed introduce a field which is all to be explored. in this regard, further research will give you more information. dna decipher journal | november 2020 | volume 10 | issue 2 | pp 67-82 fiscaletti, d., perspectives on the origin of life in exoplanets as a phenomenon generated by a 3d quantum vacuum issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 80 4. conclusions and perspectives in this paper, we have examined the likelihood function of life in exoplanets, we have estimated the number of planets with life in a given volume of the universe, and we have made considerations about the duration of the habitability of an exoplanet, in the context of a 3d quantum vacuum model where life is originated by the action of a quantum potential of the vacuum as a heat reservoir, thus providing an additional density of physical space in a living organism. the crucial result of this approach lies in the perspective that life is a non-local global property which has the potential to transmit instantaneously from one region to another and thus that the habitability of an exoplanet is determined not only by the parameters of the planet and of its star, but also depends on a quantum term associated with the action of the quantum potential of the vacuum as a heat reservoir, thus implying the idea that life is a global property. the next step regards the computation of the probability of the development of intelligent species in a given region and thus the estimation of the number of technological extraterrestrial species. in this regard, in july 2015 a 10-year program has been announced, named breakthrough listen initiative, which has the aim to quantify the distribution of advanced, technologically 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for laser line emission”, arxiv:1812.10161 [astro-ph.im] (2018). 67. v. gajjar et al., “the breakthrough listen search for extraterrestrial intelligence”, arxiv:1907.05519 [astroph.im] (2019). login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x dna decipher journal | june 2016 | volume 6 | issue 2 | pp. 115-119 115 pitkänen, m. progress on the notion of magnetic body & metabolism in tgd framework exploration progress on the notion of magnetic body & metabolism in tgd framework matti pitkänen 1 abstract the notion of magnetic body, pollack’s mechanism modelled in tgd as transfer of protons to dark protons at magnetic flux tubes, and remote metabolism predicted by zero energy ontology are key elements of tgd-based quantum theory of consciousness and biology. the recent finding that brain hemispheres of persons having no corpus callosum are in synchrony supports the notion of magnetic body as intentional agent. the assumption that a modification of pollack’s mechanism is involved with cellular metabolism leads to the proposal that the energy of solar photons fed into electron transport chain is used to pump dark protons at magnetic flux tubes through thylakoid membrane. the finding that visible and uv light can provide metabolic energy for animal cells leads to a proposal how animal cells can perform the analog of photosynthesis using essentially same basic mechanism. the finding that gut cells without any mitochondria can survive leads to a concrete cell level model for remote metabolism based on sending of negative energy photons to a energy storage. keywords: metabolism, magnetic body, transfer of proton, magnetic flux, zero energy, tgd framework. 1 evidence for the notion of magnetic body from brain synchrony without corpus callosum the notion of magnetic body is central for the entire tgd based approach to living matter and it would be important to find experimental support for it. quite recently i received a link to a rather baffling finding about brain [?] (see http://tinyurl.com/3gjhtgb). neuroscientists have believed that the two hemispheres communicate via the neural pathways associated with corpus callosum: kind of communication cables would be in question. many areas of brain behave synchronously, which has led to the notion of resting state network. the team led by michael tyszka, associate director of caltech brain imaging center, has however discovered that the resting state network seems to work normally in people born without corpus callosum! as if brain hemispheres were communicating by some other means than neural signalling! this finding challenges not only the views about the origin of brain synchrony as being created by neural circuits but also the models of autism and schizophrenia explaining them in terms of impaired communications between hemispheres. one can for instance speculate with the possibility that there is electromagnetic communication between brain hemispheres. this does not look a bad idea at all: nowadays it is possible to extract information about eeg so that pilots are able to control the flight of tiny flying object by imagining what the object should do. technological applications will probably appear in the market soon so that anyone can have robots controllable by thoughts. this mechanism is consistent with the tgd inspired view about brain. this view however encourages to consider also a more imaginative explanation. in tgd universe living system involves besides organism and environment also magnetic body (mb) acting as an intentional agent receiving sensory input from 1correspondence: matti pitkänen http://tgdtheory.com/. address: köydenpunojankatu 2 d 11 10940, hanko, finland. email: matpitka@luukku.com. isbn: issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/3gjhtgb http://tgdtheory.com/ mailto:matpitka@luukku.com dna decipher journal | june 2016 | volume 6 | issue 2 | pp. 115-119 116 pitkänen, m. progress on the notion of magnetic body & metabolism in tgd framework organism and controlling it. mb has hierarchical onion-like structure. for instance, brain hemispheres have their own mbs, and entire brain its own mb serving as a ”boss” for the mbs of hemispheres. communications between magnetic body and part of organism take place using dark photons having non-standard value heff = n×h of planck constant and thus energy e = hefff , which should correspond to ordinary photons with energies above thermal energy: otherwise quantal effects are masked by thermal fluctuations. bio-photons in the visible and uv range could result in the transformation of dark photons to ordinary photons. the frequency range of dark photons depends on the level of the layer of mb characterized by heff and wavelength corresponds to the size scale of the layer. in the case of brain the transfer of sensory information to mb would be realized as eeg wavelength of 7.8 hz radiation is order of the circumference of earth so that mbs for brain would be really large. in zero energy ontology (zeo) control signals would be realized as negative energy signals propagating backwards in geometric time and having phase conjugate laser light as a counterpart in ordinary physics. this explains libet’s finding that neural activity precedes conscious decision. coordination by using eeg rhythms would be part of control analogous to work songs. the mb of entire brain controls it and could naturally do this via the intermediate control of brain hemispheres forcing them to operate in the same rhythm. brain synchrony and resting network would not be produced by resonant neuro-circuits as usually believed but by the spatiotemporal coherence of the eeg radiation from the mb of entire brain forcing brain hemisphere mbs to oscillate in the same rhythm and in turning synchronizing the brain hemispheres. this would be like forcing soldiers to march in the same pace and brain hemispheres could co-operate without any neural communication between hemispheres. the communication between hemispheres would be needed for more refined collaboration involving ”discussion” between hemispheres: hemispheres of a person without corpus callosum would be like soldiers obeying blindly the orders. this might be also an essential element of autism and schizophrenia. 2 progress in tgd based model of metabolism a considerable progress in the understanding of tgd based model of metabolism has taken place. 2.1 generalization of pollack’s mechanism and photosynthesis pollack’s mechanism involves charge separation [?, ?, ?] (see https://www.youtube.com/watch?v=i-t7tcmudxu). pollack’s mechanism creates in presence of radiation and water bounded by a gel at the boundary of water and gel an ez, which is a layer negatively charged water with effective stoichiometry h1.5o consisting of layers with hexagonal structure. the tgd inspired proposal is that hydrogen bonded pairs of h2o molecules are formed and that each of them loses one proton as dark proton at magnetic flux tubes outside ez [?] [?]. the notion of many-sheeted space-time and topological ield quantization are essential elements of the proposal. same phenomenon could be caused also by irradiation by sun light. charge separation occurs also in photosynthesis as water molecules split to give o2 plus protons and electrons. the obvious question is whether pollack’s mechanism could be precursor of photosynthesis. the electrons in photosynthesis are however free and transferred to electron transport chain so that recent photosynthesis should be a generalization of pollack’s process and produce besides dark protons also free (possibly dark) electrons. that dark protons would be transferred through thylakoid membrane via magnetic flux tubes conforms with the general model for channels and pumps in tgd inspired quantum biology. electron transport chain appears also in cell respiration. this can be used to explain the reports that that solar radiation and also ir radiation on skin can transfer metabolic energy to the cell so that animal cell would effectively perform photosynthesis. in the case of ir radiation the mechanism could be remote metabolism (quantum credit card mechanism) possible in zero energy ontology. the light dependent step 2h2o → 4h++4e−+o2 of photosynthesis pumps protons through thylakoid mebranes (for an illustration see https://en.wikipedia.org/wiki/light-dependent_reactions). the isbn: issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://www.youtube.com/watch?v=i-t7tcmudxu https://en.wikipedia.org/wiki/light-dependent_reactions dna decipher journal | june 2016 | volume 6 | issue 2 | pp. 115-119 117 pitkänen, m. progress on the notion of magnetic body & metabolism in tgd framework electrons excited by photons of sunlight are transferred along electron transport chain and lose energy used to pump protons through the thylakoid membrane and being thus transferred from stroma to grana against electric gradient. adp transforms to atp as these protons return to back through atp synthase. this step is repeated again and again. could dark protons created by the analog of pollack’s mechanism be involved with photosynthesis? in what step the protons are transformed to dark protons by this mechanism? 1. the model of cell membrane leads to a proposal that pumps and channels quite generally are dark magnetic flux tubes and protons (and also other ions) are transferred through them as dark protons (dark ions). this would imply almost dissipationless transfer. 2. the protons are pumped as dark protons through the thylakoid membrane along dark magnetic flux tubes serving as pumps using the energy provided by electrons flowing down in the electron chain. the dark protons return from grana through atp synthase as dark protons as atp is generated and transform with some rate back to ordinary protons in stroma. otherwise the fraction of dark protons would steadily increase. 3. this leaves two options under consideration. already the step 2h2o → 4h+ + 4e− + o2 step 2h2o → 4h+ + 4e− + o2 creates dark protons by a generalization of pollack’s mechanism or this step creates ordinary protons transformed by pollack’s mechanism to dark protons as they are transferred to dark magnetic flux tubes serving as pumps. the first option looks more plausible. 2.2 the analog of photosynthesis in animal cells? what is interesting is the electron transport chain is involved also with the cellular respiration. there are various light therapies using red or ir light, and they seem to provide basically metabolic energy. cells would act like plant cells and the analog of photosynthesis could be in question. this would explain the claims that the members of some religious cults can practically live utilizing only sunlight. i have actually proposed that analog of photosynthesis storing the energy by adp + pi → atp type process using standard machinery could be actually involved and transfer the energy of ir light to metabolic energy further distributed by atp. the metabolic machinery for cellular respiration contains so called oxidative phosphorylation (op) as a basic step: op adds to adp a phosphate giving metabolic currency atp. atp in turn distributes the metabolic energy further. op uses electron transport chain to transfer metabolic energy from nadh by nadh → nad+h+ + 2e−. the electrons go through the electron transport chain as in photosynthesis and transfer protons outside the mitochondrial membrane very much like through thylakoid membrane in photosynthesis. the protons return through atp-synthase and induce adp + pi → atp . the metabolic energy must come from somewhere and op indeed follows krebs cycle in which the energy is extracted from nutrients and given to the nadp molecule. the photon energy could be feeded directly to op electron transport chain just as photon energy is transferred to this chain in photosynthesis. the presence of electron transport chain is necessary and one must feed the electrons and protons to this chain somehow. 1. could the analog of photosynthetic reaction 2h2o → 4h++4e−+o2 with visible photons replaced with ir photons produce dark protons? whether this is energetically possible and whether the electrons have high enough energies to drive the dark protons through the membrane is far from clear. one can of course imagine, that the number of pumped protons per electron is lower than usually. 2. a mechanism that i have called quantum credit card or remote metabolism [?] looks more plausible. the splitting 2h2o → 4h+ + 4e− + o2 could occur not by absorption of positive energy photon but by emission of negative dark ir photon with the energy of visible photon. cell would actively isbn: issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | june 2016 | volume 6 | issue 2 | pp. 115-119 118 pitkänen, m. progress on the notion of magnetic body & metabolism in tgd framework suck metabolic energy from ir light source. the emitted dark negative energy ir photon would decay to ordinary ir photons in reverse time direction, which would look like fusion in standard time direction and is thermodynamically non-favoured. zeo predicting kind of syntropic processes to occur in living matter would be an essential prerequisite. at deeper level metabolic energy might correspond to negentropic entanglement and thus information. information could be the basic metabolic currency. 2.3 gut cells without mitochondria can survive: a proof for the notion of remote metabolism? gut cells can survive without mitochondria [?] (see http://tinyurl.com/j7p49cn for the article in current biology and http://tinyurl.com/hqq79th for a popular representation). there are many other strange findings. visible and ir light energize human skin cells transferring energy for the cells the analog of photosynthesis. some spiritual groups and also traditionally the people called saints are reported to survive by using only sunlight as their source of metabolic energy. nasa has studied sleigh dogs able to run for days without eating and showing no signs of getting tired. could the analog of photosynthesis work also in animal mitochondrial cells? the basic mechanism could be essentially the same: electron transfer chain providing energy to pump protons through cell membrane against potential gradient. this is the key step of both photosynthesis and cellular respiration. after that protons flow spontaneously back through atp synthase and liberate energy to build atp from adp. this is like power plant. in plants solar photons provide the energy for electrons. in the animal cells dark photons with large heff = n × h (transforming now and then to biophotons) could do it. in the case of ir metabolism electrons could send to the energy source dark negative energy ir photons, which decay to ordinary ir photons. this would be an active variant of metabolism and time reversal of the usual mechanism: i have called it quantum credit card mechanism or remote metabolism [?]. now even mitochondria are missing! could remote metabolism work also without mitochondria? adp → atp transformation should occur since atp is the universal energy currency. could it take place as remote metabolism by sending negative energy photons to the cells having the mitochondria. the electron transfer chain is preceded by krebs cycle extracting the energy from nutriens: could the absorption of negative energy photons induce the decay of nutrient without transfer of energy to electron chain of the mitochondria. the hungry gut cell without mitochondria would be allowed to eat in the table of the luckier ones. again one quantum objection against vulgar darwinism. this would be like kicking laser from population reversed state to ground state by phase conjugate negative energy irradiation. references [1] the fourth phase of water : dr. gerald pollack at tedxguelphu. available at: https://www. youtube.com/watch?v=i-t7tcmudxu, 2014. [2] zhao q pollack gh, figueroa x. molecules, water, and radiant energy: new clues for the origin of life. int j mol sci available at: http://tinyurl.com/ntkfhlc, 10:1419–1429, 2009. [3] pollack gh zheng j-m. long-range forces extending from polymer-gel surfaces. phys rev e available at: http://tinyurl.com/ntkfhlc, 68:031408–, 2003. [4] a eukaryote without a mitochondrial organelle. current biology.available at: http://tinyurl. com/j7p49cn, 26(10):1274–1284, 2016. [5] [6] tyszka jm et al. intact bilateral resting-state networks in the absence of the corpus callosum. the journal of neuroscience. available at:http://tinyurl.com/3gjhtgb, 2011. isbn: issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/j7p49cn http://tinyurl.com/hqq79th https://www.youtube.com/watch?v=i-t7tcmudxu https://www.youtube.com/watch?v=i-t7tcmudxu http://tinyurl.com/ntkfhlc http://tinyurl.com/ntkfhlc http://tinyurl.com/j7p49cn http://tinyurl.com/j7p49cn http://tinyurl.com/3gjhtgb dna decipher journal | june 2016 | volume 6 | issue 2 | pp. 115-119 119 pitkänen, m. progress on the notion of magnetic body & metabolism in tgd framework [7] pitkänen m. macroscopic quantum coherence and quantum metabolism as different sides of the same coin: part i. in bio-systems as conscious holograms. onlinebook. available at: http: //tgdtheory.fi/public_html/hologram/hologram.html#metab, 2006. [8] pitkänen m. pollack’s findings about fourth phase of water : tgd view. available at: http: //tgdtheory.fi/public_html/articles/pollackyoutube.pdf, 2014. isbn: issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.fi/public_html/hologram/hologram.html#metab http://tgdtheory.fi/public_html/hologram/hologram.html#metab http://tgdtheory.fi/public_html/articles/pollackyoutube.pdf http://tgdtheory.fi/public_html/articles/pollackyoutube.pdf dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 5-23 5 pitkänen, m. many-sheeted dna: basic ideas article many-sheeted dna: basic ideas matti pitkänen 1 abstract the problems of how genes code information about the morphology of organism and how this information is expressed, belong to the great puzzles of the developmental biology. a closely related mystery is the differentiation of cells. the notion of the genetic program is far from precise and it is not clear how close the analogy with a computer program is. there are also several problems which challenge the basic dogmas of genetics. 1. only 1 per cent of dna of human genome actually codes polypeptides. eukaryote genes contain intron sequences which are transcribed into hnrna but snipped of when hnrna is transformed mrna in process called slicing. the higher the evolutionary level of organism, the higher the fraction of introns is. molecular darwinists see introns as ”junk dna” but there is evidence that introns are far from junk. for instance, the splicing of intron contribution from hnrna to give mrna can give several different outcomes depending on the stage of development of the organism and introns are crucial for the effectiveness of immune system. hence one can wonder whether intronic mrna and protein mrna could both form the real output of gene subprograms serving in some sense as input for other gene subprograms. this interpretation obviously conflicts with ”gene-single protein” dogma in its basic form. 2. there are large amounts of highly repetitive dna which is silent. one can wonder whether there is some fundamental mis-understanding involved. could it be that this dna is analogous to control dna not transcribed to rna and therefore not all useless. there is also active repetitive dna. 3. there is large amount of silent dna in control sections between genes. could it be that this silent dna expresses itself in some nonchemical manner? chemical expression is very slow, translation rate being twenty aminoacids per second, and one can wonder whether life might have invented faster modes of gene expression and control of gene expression. 4. plant genome is often by a factor of hundred longer than human genome. one could argue that the complexity of organism is measured by the length of the shortest program coding the organism. it is however not at all obvious how the genome of plants could be more redundant than human genome since repetitive sequences common to all animals are present. introns are in fact more frequent in human genome. this suggests that some new unidentified degrees of freedom giving rise to complexity might be present and that the chemistry of dna in the sense of standard physics is perhaps not all that is needed to understand genetic program. 5. various self-organization process such as self-assembly and de-assembly are very frequent in living systems. the problem how genes give rise to morphology of the organism is poorly understood. this forces to challenge the dogma of genetic determinism. one should be able to understand what is determined by genes and what is determined by self-organization and whether the genes of the standard physics are enough. in the first part of the article basic facts about genetics are introduced and the notion of manysheeted dna is introduced as a possible solution of the above discribed problems. in the second part of the article a model of genetic program will be developed and some tgd inspired ideas about regulation of morphogenesis are discussed. 1correspondence: matti pitkänen http://tgdtheory.com/. address: köydenpunojankatu 2 d 11 10940, hanko, finland. email: matpitka@luukku.com. issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.com/ mailto:matpitka@luukku.com dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 5-23 6 pitkänen, m. many-sheeted dna: basic ideas 1 introduction the problems of how genes code information about the morphology of organism and how this information is expressed, belong to the great puzzles of developmental biology. a closely related mystery is the differentiation of cells. the notion of genetic program is far from precise and it is not clear how close the analogy with a computer program is. there are also several problems which challenge the basic dogmas of genetics. 1. only 1 per cent of dna of human genome actually codes polypeptides. eukaryote genes contain intron sequences which are transcribed into hnrna but snipped off when hnrna is transformed mrna in a process called slicing. the higher the evolutionary level of organism, the higher the fraction of introns is. molecular darwinists see introns as ”junk dna” but there is evidence that introns are far from junk. for instance, the splicing of the intron contribution from hnrna to give mrna can give several different outcomes depending on the stage of the development of the organism and introns are crucial for the effectiveness of the immune system [4] . hence one can wonder whether intron mrna and exon mrna could both form the real output of gene subprograms serving in some sense as input for other gene subprograms. this interpretation obviously conflicts with ”gene-single protein” dogma in its basic form. 2. there are large amounts of highly repetitive dna which is silent. one can wonder whether there is some fundamental mis-understanding involved. could it be that this dna is analogous to control dna not transcribed to rna and therefore not at all useless. there is also active repetitive dna. 3. there is large amount of silent dna in control sections between genes. could it be that this silent dna expresses itself in some nonchemical manner? chemical expression is very slow, translation rate being twenty aminoacids per second, and one can wonder whether life might have invented faster modes of gene expression and control of gene expression. also the question whether there is a relation to the typical frequency scales of brain consciousness of order 10 hz, which can be related to the magnetic transition frequencies, can be raised. 4. plant genome is often by a factor of hundred longer than human genome. one could argue that the complexity of organism is measured by the length of the shortest program coding the organism. it is however not at all obvious how the genome of plants could be more redundant than human genome since repetitive sequences common to all animals are present. introns are actually more frequent in human genome. this suggests that some new unidentified degrees of freedom giving rise to complexity might be present and that the chemistry of dna in the sense of standard physics is perhaps not all that is needed to understand genetic program. 5. various self-organization process such as self-assembly and de-assembly are very frequent in living systems. the problem how genes give rise to morphology of the organism is poorly understood. this forces to challenge the dogma of genetic determinism. one should be able to understand what is determined by genes what is determined by self-organization and whether the genes of the standard physics are enough. the reason why the above mentioned problems have turned out to be so untractable might be due to a wrong view about space-time. many-sheeted space-time concept of tgd might be absolutely crucial for the expression of genetic code. dna itself might involve many-sheeted space-time structures coding faithfully the topology of the body parts. this many-sheeted structure of dna could allow to understand the miraculous looking features of dna replication and differentiation of cells. tgd based view of evolution as p-adic evolution implied by the basic quantum theory, should be a crucial element of the picture. together with the p-adic length scale hypothesis it leads to precise quantitative predictions and a general model for genetic program based on the many-sheeted space-time concept. the model explains also why introns are present only in eukaryotic genome. most importantly, it seems that the statements issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 5-23 7 pitkänen, m. many-sheeted dna: basic ideas represented by the dynamical intron-exon decompositions of genes and defining boolean algebra, could represent our conscious beliefs and thus affect our behavior as conscious beings. notice the beautiful connection between matter and mindgenes code the information, not only about the material structure of organism, but also about its belief system. thus without introns, the pariah class in the society of bio-molecules regarded as ’junk dna’ by always-so-imaginative reductionistic materialists, we would have no world views and belief systems! in this article one possible tgd inspired view about genetic code and its realization is discussed in detail. 1.1 the notions of magnetic body and dark matter the notion of magnetic body is central in the tgd inspired theory of living matter. every system possesses magnetic body and there are strong reasons to believe that the magnetic body associated with human body is of order earth size and that there could be hierarchy of these bodies with even much larger sizes. therefore the question arises what distinguishes between the magnetic bodies of earth and human body. the vision about dark matter hierarchy labelled partially by a hierarchy of values of planck constant coming as ~eff = n~. the original proposal was that the favored values of the integer n are n = λk, λ ' 211 (near to the ratio of proton and electon masses) but this assumption is un-necessarily restrictive. even without this assumption one ends up with to a rather concrete view about the hierarchy of magnetic bodies and implies a natural generalization leading to the notion of superand hyper genes. tgd inspired biology in its recent form (see the chapters in [17]) involves also other tgd inspired concepts, which are barely mentioned in this two-part article for the simple reason that the articles were written first time for about eighteen years ago and have been gradually updated since then. mention only the notions of zero energy ontology (zeo) and negentropic entanglement. the most recent summary about tgd inspired theory of consciousness highly relevant also to quantum biology in tgd universe can be found in [19]. the chapter about dark photons as biophotons [18] should also give a view about the role of electromagnetic fields in tgd based quantum biology. in particular, a rather detailed view about the central role of magnetic body emerges. it would be highly rewarding to process the material of these articles in light of the updated vision about living matter. 1.2 many-sheeted dna the replacement of the dna of standard physics with many-sheeted dna suggest surprisingly simple model for how organism’s morphology is coded and decoded to dna. 1. how the morphology of body is coded? the most striking feature of dna is its one-dimensionality. according to work of mae-wan ho, living systems are liquid crystals [1] . liquid crystals are effectively one-dimensional since the layers of the liquid crystal consist of homogenous liquid phase determined by macroscopic characteristics such as ph, temperature, ionic concentrations and electric fields. this suggests that the structural information coded into dna could be essentially information about the macroproperties of the layers of liquid crystal. this would make 1-dimensional coding of the body plan using dna sequences very natural. kind of contraction of the body parts to dna sequences having many-sheeted structure could be in question! this coding would preserve the topological structure of the many-sheeted space-time surface representing the expression domain of the gene. the structure of the expression domains of maternal genes and hox genes [8] controlling morphogenesis supports this picture. 2. how dna is expressed? the very naive first guess is that during growth various thin space-time sheets associated with dna gradually grow and are glued together by the join along boundaries contacts and form the spacetime sheets associated with their expression domains. somewhat exaggerating, many-sheeted dna would represent only a particular developmental period of organism in which it is contracted to a issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 5-23 8 pitkänen, m. many-sheeted dna: basic ideas thin thread. for instance, the cells determined to develop into eye are glued to the space-time sheet representing future eye and replication products belong also to this space-time sheet. clearly, the gluing to the space-time sheet of the future expression domain would generate the needed long range correlation between cells in the expression domain. it must be emphasized that self-organization should play key role in this process: for instance, liquid crystal nature of the living matter should determine morphology to a high extent. 3. what makes differentiation and control of the morphogenesis possible? differentiation must be explainable as a selective activation of transcription and although a local process, involves also top-down control making possible a precise timing. concentration gradients for the transcription factors, that is proteins controlling transcription, are certainly crucial in this respect. when the concentration of the protein falls below a critical value, the truth value of a statement representing input to some gene program modules changes. this leads obviously to spatial patterns of gene expression resulting from branching of gene programs. for instance, the development of organs should result as a combination of genetic control of this kind plus self-organization. join along boundaries bonds between gene space-time sheets and larger space-time sheets or genes and control regions of chromosome make possible quantum control of genetic expression based on phase gradients of the super conducting order parameters and resonant josephson frequencies which correspond to magnetic transition frequencies of genes, control regions or related substructures. it could also be that the # contacts (wormhole contacts) from genes to various space-time sheets representing body parts provide the interaction with the classical fields of the macroscopic space-time sheets representing body arts and controlling the activity of a particular gene. in any case, the fact is that the action mechanisms of transcription factor proteins in eukaryotes are not understood. the mechanism is not purely chemical one since transcription factors are often located quite far from the promoter region. electromagnetic oscillations with resonant frequencies could be in question. in absence/presence of oscillation gene is activated. 2 background the foundations of genetics were discovered by george mendel in 1866, but remained generally unknown until 1900. during the first half of nineteenth century it was gradually realized that genes play major roles in the functioning and evolution of organisms. the discovery of dna revealed the principles of heredity and how genes store hereditary information and transmit it from generation to next. hereditary information is contained within the nucleotide sequence of dna. organization, expression and evolution of the hereditary information are the main aspects of genetics. hereditary information is organized into chromosomes consisting of dna sequences. it is expressed via transcription to mrna followed by a translation to protein. the evolution of the hereditary information involves basically sexual breeding in one chromosome from the chromosome pairs of both parents combine to form chromosome pair. also recombination of the members of the chromosome pairs is possible during meiosis. also other mechanisms, such as fusion or fission of chromosomes and modification of dna sequences, are possible. there are excellent books about topics [4] but for the convenience of the reader the basics of genetics are very briefly summarized in the following. 2.1 dna and rna dna add rna provide a manner to store and organize genetic information [4] . 1. genetic information is stored in nucleic acids, which are long sequences of nucleotide serving as letters of genetic code: three nucleosides form single world of code. there are four different nucleotides so that the number of different words is 64. issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 5-23 9 pitkänen, m. many-sheeted dna: basic ideas 2. nucleotide consists of three basic units joined by covalent bonds: nucleotide= nucleoside+sugar+5′phosphate. the units are sugar, which is deoxiribose in case of dna and ribose in case of rna, phosphate and nucleoside (nucleic acid). nucleosides are the information carrying part of dna and rna. 3. dna and rna sequences contain 4 different nucleosides. in case of dna they correspond to c(ytocine), t(ymine), a(denine) and t(ymine). in case of rna t is replaced by u(racil). u, t and c are purines containing one carbon ring and a and g are pyrimidines containing two carbon rings. 4. dna molecules/nucleic acids/polynucleotides are formed as very long sequences of nucleotides bound together by phospho-diester bonds. dna double helix consists of two dna strands , which are conjugates of each other, conjugation being defined as a ↔ t , c ↔ g. the helices are bound by hydrogen bonds between a and t and c and g respectively. sequences of dna triplets form genes, which represent basic units of hereditary information revealed as traits of the organism. each gene involves also additional dna sequences serving as control structures in the transcription of gene to mrna. in prokaryotes there is only single chromosome in the form of a circular double strand. in eukaryotes the chromosomes are located in nucleus and appear in homologous pairs. eukaryotic chromosome is a complicated helical structure resembling beads in thread formed by dna. dna is wound around nucleosomes with diameter d ' 10 nanometers. nucleosomes consist of octamer formed from 4 different histones. chromosome structure will be considered in more detail later. rna appears both inside nucleus and cell. there are several types of rna. 1. messenger rna (mrna) is the outcome of transcription of dna inside nucleus and is translated to proteins outside the nucleus. 2. transfer rna (trna) is involved in the translation of mrna to protein: trna molecules bind specific aminoacids and glue them to specific mrna triplets in a manner dictated by genetic code. rrna appears as a building block protein of ribosomes playing the role of reading head in the translation of mrna to proteins. 3. in case of eukaryotes transcription involves intermediate state in which dna is transcribed to hnrna which contains also the transcriptions of introns (”junk dna”), which are split in so called splicing process cutting away intron rna to form rna-protein complexes which remain inside nucleus. 2.2 proteins proteins are in a vital role in organisms. the diversity and complexity of life is largely due to the diversity and complexity of proteins. some proteins act as transcription factors controlling genetic expression. some proteins are used by cells in chemical communication between cells: hormones serve as signalling proteins; various receptor proteins serve as receptors of chemical signals and hormone-receptor complexes serve as transcription factors. neural transmitters appear in the synaptic communication between neurons. some proteins act as enzymes catalyzing biochemical reactions. other proteins serve as structural building blocks, either by themselves or in association with nucleic acids (nucleoproteins), polysaccharides (glycoproteins) or lipids (lipoproteins). some proteins, such as myoglobins and hemoglobins are associated with metal-containing organic molecules. proteins consists of polypeptides, which are polymers of 20 different aminoacids. genetic code assigns unique polypeptide to a given gene. with single exception aminoacids share the same basic structure. hydrogen atom h, carboxyl group cooh and amino group nh2 and radical r linked to carbon atom. r determines exclusively the chemical properties of protein. 8 aminoacids are nonpolar (hydrophobic) and issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 5-23 10 pitkänen, m. many-sheeted dna: basic ideas 12 of them are polar (hydrophilic). of the twelve polar aminoacids 7 are neutral, 3 are basic (tending to become positively charged) and 2 and acidic (tending to become negatively charged) under physiological conditions. carboxyl and amino groups tend to become ionized at physiological ph; -cooh group tends to lose its proton and nh2 group tends to gain a proton. in polypeptides, which are products of gene translation, aminoacids are linked to each other by peptide bonds formed when nh2 group of one aminoacid and cooh group of next aminoacid are linked (h2o molecule is snipped away in this process). polypeptide chains spontaneously adopt so called secondary structure determined by the nature of the r groups along the backbone. backbone forms alpha helix, a coil containg 3.6 aminoacid redidues per turn. another secondary structure is the beta pleated sheet configuration consisting of rows of polypeptide chains hydrogen bonded with each other. polypeptide can also adopt the form of a random coil. proline, because of its unique structure, causes a kink in the polypeptide backbone. polypeptides have also tertiary structure. how the tertiary structure is determined by the chemistry of aminoacids is poorly understood. one of the big problems of biology is to understand who protein is able to fold to such a unique configuration. tgd suggests that tertiary structure might not be determined solely by the standard chemistry and that many-sheeted nature of protein might be crucial in determining the final result of the folding. there is also quaternary structure associated with proteins formed by polypeptide sequences. the formation of higher level structures, such as micro-tubules, micro-filaments, cell membranes and collagen fibers involves self-organization and living matter seems to behave as a liquid crystal whose basic properties depend only on very general properties of protein. 2.3 replication, transcription, translation information processing in living matter involves three basic processes: replication, transcription and translation. replication of dna means replication of dna double helices and is essentially copying of genetic information. replication involves unwinding of the parental strands of dna double helix. they serve as templates on which the growing complementary daughter strands are synthesized. the direction of the synthesis is opposite for the two strands and only the second (leading) strand can be synthetized continuosly whereas the synthesis of the second strand occurs discontinuously and results in disjoint pieces of dna containing approximately 1000 nucleotide pairs (okazaki fragments of length about 34 nanometers), which later combine to form connected dna strand. dna can be transcribed to mrna molecules (messenger rna) translated to proteins; to trna (transfer rna), which is the rna molecule affecting the coding of rna triplets to aminoacids and to rrna, which is the building block of the machinery affecting the translation. in case of prokaryotes the transcription of dna to mrna occurs directly. the rules for the transcription are a→ u , t → a , c → g , g→ c . in case of eukaryotes the transcription involves two steps since eukaryote genes in general decompose into exons translated to protein plus introns. first the entire gene is transcribed to hnrna sequence. after this so called splicing occurs and gives rise to mrna, which corresponds to the dna sequence formed by the exons. in the splicing process intron sequences are split off and wind around specific proteins which do not leave the nucleus. there are different pathways for slicing meaning that the decomposition to exons and introns is not unique. dynamical exon-intron decomposition is essential for the working of immune system. transcription is a complicated process involving the action of several enzymes. rna polymerase i is involved in the transciption of large rrna molecules, rna polymerase ii with the transcription of hnrna, rna polymerase iii with transcription of small 5s-rrna molecules and trna molecules. usually so called heavy strand is transcribed. light strand can be transcribed to some trna molecules at least. gene is preceded by aug triplet. in eukaryote cells rna polymerase ii copies sequences containing issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 5-23 11 pitkänen, m. many-sheeted dna: basic ideas 6000-8000, sometimes even 20.000 nucleotides. the average length of mrna sequence is 1500 nucleotides and the aminoacid corresponds to a sequence of average length of 1200 nucleotides. rna ii polymerase binds to the promotor region preceding the gene. promotor region contains at least two binding sites, so called tata block and ccat sequence regognized by rna polymerase. between promotor site and gene are operator site in which repressor enzymes bind and make translation impossible. tac sequence denotes the beginning of that part of gene which is translated to protein (apart from introns). at the end of the gene there is rather long a · · ·aaa control sequence preceided by tga sequence signifying the end of the part of the gene to be translated. introns which are not translated begin with ac and end with ca. the translation of mrna to polypeptide occurs outside the nucleus. translation involves trna molecules, which are about 80 nucleotides long. each trna contains a specific triplet which is anticodeword for the corresponding codeword in mrna and binds only to this codeword in translation process. each trna molecule binds with a specific aminoacid molecule and each aminoacid has at least one trna binding to it. the allowed bindings of trna and aminoacid molecules define genetic code. in translation trna carrying aminoacid attaches to an mrna codeword to its own anticodeword and the aminoacid forms a peptide bond with the polypeptide sequence already translated at rrna. genetic code assigns to 64 rna triplets 20 aminoacids so that there is a considerable degeneracy involved. the largest number of dna codewords mapped to same aminoacid is six. three codewords are interpreted as stoppping sign for the translation. genetic code is universal for the nuclear dna of all eukaryotes and prokaryotes. the mitochondrial genetic codes of various eukaryotes however differ slightly from the universal genetic code. for instance, 4 dna triplets can correspond to stopping sign. replication, transcription and translation are not the only information transfer processes occurring in living matter. 1. reverse transcription rna → dna is known to occur in some cases and is also involved with the homing phenomonen of introns. reverse transcription might have led from a system of rna and proteins to system involving dna sequences and primitive form of genetic code. the simplest starting system of this kind would consist of dna coding rna coding a protein which catalyzes both transcription and reverse transcription. this kind of system might have gradually evolved to a more complex dna sequences. 2. rna replication can occur in cells infected by viruses. what happens is that viral rna strand which can be either single or double stranded, is replicated to its complement which in turn serves as a template for the synthesis of progeny rna molecules. 3. direct translation of dna to protein without transcription has been observed only in vitro. this process probably never occurs in living cells. 2.4 introns, pseudogenes, repetitive dna, silent dna the genes in nuclei of the eukaryote cells contain introns, sequences consisting of 10-1000 nuclotides interspersed with the exon parts of dna which is translated to a protein coded by gene [2] . molecular darwinist could compare introns with the commercials appearing between tv program or simply as selfish dna. one could see them also unused parts of a computer program separated from the program code by comment signs in front of each line corresponding now to dna nucleotide. the latter metaphor is consistent with the observation that intron can begin even in the middle of dna triplet and that the transcription to mrna is not unique so that same gene can give rise to several proteins. the content of intron sequences seem to be unrelated to the exon sequences: as if two separate interspersed computer codes would be in question. only one prokaryote cell, photosynthetic cyanobacterium fischerella, is known to contain introns [2] . usually also the genes of cell organelles (such as mitochondria of human cell) contain only very few introns. fungi are however an exception in this respect [4] . the higher the evolutionary level of the issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 5-23 12 pitkänen, m. many-sheeted dna: basic ideas eukaryote cell, the higher the fraction of introns in the genome is. for humane genome the fraction of exons is about one per cent. during transcription both introns and exons are transcribed to hnrna, intron sections are snipped away in a process called splicing and the resulting mrna for the protein coded by exons is transferred from the nucleus and translated to a protein coded by the gene. it is possible to snip off the introns from genome but the mrna coded by these genes is not transferred from nucleus, which suggests that introns have some role in genetic program. the addition of introns does not seem to have any dramatic effects on the genetic program. introns are a headache of molecular darwinism. the nickname ”junk dna” tells the basic attitude towards introns. introns represent selfish dna living as parasites of the genome. there are two opposite schools concerning how introns have appeared. 1. the first school claims that introns came early. somewhat surprisinly, this school sees bacteria as results of a long evolution which has gradually snipped off the introns from a primitive cell in order to achieve maximal rate of dna transcription. one can of course wonder why the same thing has not happened to the cell nuclei also. 2. second school tells that introns came late: this view conforms with the observations about the fraction of introns in genome. introns seem to start from preferred sites and exons seem often to correspond to a modular decomposition of the protein they code. on basis of this it has been also proposed that introns separate modular parts of proteins from each other. the facts that introns can appear in the middle of protein module and even split single dna triplet are not however consistent with this interpretation. one can criticize the identification of introns as junk dna. 1. it is difficult to see how human genome containing so high per cent of junk dna could work with such a fantastic precision while viruses, second form of junk dna, are often lethal. there are several pathways for slicing. exon-intron transformation has been found to occur: exon and intron parts of gene simply change their roles [2, 7] ! this suggest that exon-intron property is additional dynamical degree of freedom in genone and might have deep meaning. exon↔exon transformation is indeed crucial for the working of immune system. 2. mrna produced by intronless gene does not get out of nucleus. it seems that the presence of introns somehow initiates a module of genetic program taking care that protein mrna gets out of the nucleus. introns seem thus to be necessary for the functioning of the cell and could be in some sense regarded as an output of gene interpreted as a genetic subprogram. note however that intron mrna which winds around spherical proteins in the process of splicing, have not been reported to serve as transcription factors. 3. the positions of the intron sequences in similar genes are not same for various species. there are wandering introns which can move even from cell to another one. there is a phenomenon called homing [2, 6] : the rna coded by intron inserts itself into dna sequence and builds by inverse transcription its complement in complementary dna strand. retrohoming in turn means that introns can carry and install long pieces of rna to dna sequences to dna [5] . this suggests that introns might provide a new mechanism for the evolution of the genome and provide a mechanism for modifying the program code of genetic programs. it is also known that there are long range correlations (in scale of one micro-meter) in genes containing introns [3] . this suggests that introns are essential element in the organization of dna to larger structures. all these properties of introns suggest that their role in genetic program is badly misunderstood in the framework provided by molecular darwinism and the basic dogmas of genetics. besides introns there are pseudogenes of various types, which by definition code no proteins. for instance, eukaryote genes from which introns have been snipped off, behave as pseudogenes. pseudogenes issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 5-23 13 pitkänen, m. many-sheeted dna: basic ideas can also contain ”programming errors”: for instance, the dna triplet signifying the beginning of gene has changed. genetic program metaphor suggests interpretation of pseydogenes as unused program modules. the idea about two interspersed program codes could explain the program errors as only apparent program errors. of course, every experienced computer programmer would suggests the possibility of also genuine program errors! also the interpretation as control structure affecting transcription via long range interactions rather than via chemical contact interactions might make sense. it is indeed known that so called enhancers and silencers act as transcription factors in this manner. genetic code contains large amounts of repetitive dna. 1. five per cent of genome of the eukaryotes consists of highly repetitive dna consisting of 5-300 nucleotides (even 106 copies are possible). in particular satellite dna, containing less than 10 nucleotides belongs to this class. this dna are active during mitosis and meiosis [4] . 2. 30 per cent of dna is moderately repetitive. the first class corresponds to rrna, 5srna, trna and histogenes (10-100 copies). these genes are concentrated in certain chromosomes. in case of genes coding rrna, trna the repetition of genes is understandable since translation making possible large number of aminoacid copies does not occur. the fact is however that also genes coding proteins appear as very many copies and there is no obvious explanation for this. so called sine segments have length not longer than 103 np and are interspersed through the entire genome as 104 − 105 copies. line-segements consist about 3 × 103 np: there are about 104 copies are interspersed through the entire genome. part of these sequences are transposons (see below). 3. 65 per cent of dna are present in only few (1-15) copies. both exons and introns belong to this group of dna and exons form only one percent of human genome. 4. the control regions between genes are rather long and seem to contain dna with no obvious function. also second strand of dna can be regarded as silent dna since its presence is not absolutely necessary for the storage of genetic information. the question is whether this silent dna has some hitherto unidentified function. the genome of both prokaryotes and eukaryotes contains transposons, which are movable dna sequences able to insert themselves to dna with the help of insertion sequences. insertion sequences are short (less than 2000 nucleotides) and do not code proteins. insertion sequences can carry also promotor and repressor sequences with them. transposons could be important for evolution. 2.5 is central dogma an absolute truth? the central dogma of molecular biology states that each gene corresponds to a unique polypeptid. there are several observations challenging central dogma. 1. it is known that many alternate pathways of transcript splicing are possible and give rise to different protein outcomes called isoforms. this would suggest that transformation of some introns to exons and vice versa occurs routinely in gene expression. using computer program analogy, this transformation would mean that the program part represented by introns becomes active and the part represented by exons becomes passive. 2. the phenomenon of superimposed genes [4] . there are genes nested inside genes and translation can start also in the middle of gene producing shorter protein than the gene usually. these phenomena were first observed for bacteriophage φx174, whose genome is known in its entirety. it is known that gene is transcribed as a whole and that different proteins result from frame shift. gene can also overlap the dna sequences formed by two subsequent genes as first observed in bacteriophage g4. these observations suggest that the standard notion of gene fails somehow. 3. it is known that also the ”nonsense” strand of dna can serve as template for transcription [4] . issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 5-23 14 pitkänen, m. many-sheeted dna: basic ideas 2.6 is life nothing but biochemistry? it is not at all obvious whether the hypothesis ”life is nothing but biochemistry” holds true. 1. it is not known whether protein folding is coded into the chemistry of dna. the problem is mathematically unattractable due to the occurrence of combinatorial explosion. it seems more probable that folding might be self-organization type phenomenon and thus affected by the conditions of environment: protein development can be regarded as hopping in spin glass type energy landscape leading to some deep valley of free energy valley. tgd suggest that folding is the quantum analog of this kind of process. in particular, p-adic length scale hierarchy and many-sheeted space-time concept suggest that one cannot understand protein folding in terms of dna chemistry alone. 2. dna is essentially one-dimensional structure. this suggests that gene codes only one-dimensional skeleton of its expression domain and that self-organization by quantum jumps could take care of the rest. indeed, the work of mae-wan ho [9] shows that living organisms are liquid crystals which can be regarded as one-dimensional crystals and two-dimensional liquids, whose properties can be characterized by some global parameters. perhaps genes code the properties of various layers of the liquid crystal. one of the basic characteristics of liquid crystals is self-assembly and de-assembly. depending on ph, ionic concentrations, temperature, electric fields,... liquid crystals organize to micelle like structures (cell membranes, collagen fibers,....) and effectively one-dimensional layered structures [1] . 3. one can wonder how morphology is coded in dna and how it is decoded from dna. it is not at all obvious that dna chemistry, which is purely local, is enough to code morphology. 4. so called enhancers and silencers are transcription factors, which encourage or disencourage gene expression in eukaryotes. the position of these proteins or orientation in dna does not seem to be important [4] . for instance, they can bind to introns and the distance of the binding site from gene promotor regions can be thousands of nucleotide pairs. this would suggest that the mechanisms of enhancing and silencing are not purely chemical if chemical at all. this would suggest the generalization of the notions of gene expression and transcription factor. chemical expression takes place very slowly. non-chemical expression modes yielding nonchemical transcription factors could make possible very fast running of genetic programs and there could be even connection between many-sheeted genome and nerve pulse activity. 5. the naive expectation is that the size of the genome should correlate with the evolutionary stage of the species. eukaryotes indeed have genome which is typically 103 times longer than prokaroyote genome. the table below however shows that the total length of genome does not correlate with the complexity of the organism faithfully. the genome of plants is typically 10-100 times longer than human genome. the genome of amoeba is by two orders of magnitude longer than that of human! the genomes of monkeys and men are almost identical. this suggests that there might be some unindentified degree of freedom associated with dna which explains these differences. organism human mus amoeba marbled musculus lungfish n(dna)/109 3 3 670 139 organism salamander onion trumpet lily n(dna)/109 81 18 90 table 1. the amount of total genome measured as the number of dna triplets. issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 5-23 15 pitkänen, m. many-sheeted dna: basic ideas 3 many-sheeted dna the notion of many-sheeted dna suggest a profoundly new manner to understand how the morphology of the organism is coded to and decoded from dna. p-adic length scale hypothesis leads to quantitative predictions for the number of levels of genetic program as function of a suitably defined size of the organ. the proposed model for introns inspires the interpretation of gene as a representation for boolean algebra and to the proposal that genes realize not necessarily conscious-to-us boolean mind at the basic level. many-sheeted dna suggests also new forms of gene expression and of control of gene expression. for instance, nerve pulse patterns could affect also genetic program of postsynaptic cell via the classical em and z0 field patterns associated with them and genes could affect cell membrane via conformational waves propagating along micro-tubules connecting nucleus to cell membrane. 3.1 many-sheeted dna as hierarchy of genetic programs many-sheeted dna allows to realize genetic subprogram hierarchy in an elegant manner. many-sheeted dna and proteins are like a hierarchy of ordinary dna and proteins effectively living in different spacetimes corresponding to body parts. one can consider the possibility that subprograms correspond to p-adic space-time sheets and subprogram hierarchy corresponds to the hierarchy of p-adic space-time sheets. the gene program in a given length scale would selectively activate programs in shorter length scale, etc.. dna sequences with the same chemical structure correspond to different genetic programs since the many-sheeted structure of dna affects its functioning. analogous conclusion is true about proteins. one can assign to gene a unique p-adic prime as the prime characterizing the largest p-adic sheet at which gene has # contacts. the number of levels in subprogram hierarchy could be deduced from the size of the organism. gene can have # contacts to several space-time sheets characterized by p-adic primes p ' 2k, k power of prime. denote by kg the largest value of k associated with gene. kg characterizes the position of gene in subprogram hierarchy. gene can have # contacts with space-time sheets k < kg also. gene can be characterized by the p-adic kg labelling the largest space-time sheet to which it has # contacts. ”comment sign” marking each nucleotide of intron could correspond to a direction of classical field at some space-time sheet characterized by p-adic prime p ' 2k, k = ki . the only sensible assumption seems to be ki = kg. the other # contacts of gene must be assumed to be on space-time sheets with k < kg = ki . this implies that given program can call only programs which are in the lower level of the hierarchy. this would suggest that programs belonging at the lower level of hierarchy cannot call program at higher level. does this imply that growth process in which larger and larger space-time sheets are activated can only occur by self-organization? this would mean that dna space-time sheets with increasing value of kg expand in phase transition like manner and fuse to form space-time sheets corresponding to various body parts. on the other hand, it is not at all obvious that growth process could not start from higher level and lead to gradual differentation at lower levels. in fact, embryogenesis seems to occur in this manner [4] . also proteins can be classified by the the number kp characterizing the largest space-time sheet to which protein has # contacts. proteins must mediate program calls to gene modules g1 with various values of kg1 < kg. this suggests that protein activating gene characterized by kg1 must have same kp = kg1 . this would automatically guarantee that chemically identical proteins activate only the genes belonging to the level of the fractal hierarchy they represent. the notion of many-sheeted dna has immediate applications. 1. many-sheeted dna provides a possible explanation for why dna triplets act as codewords of the genetic code. if members of each dna triplet are glued to space-time sheet containing only # contacts from the nucleotides of the triplet, codewords have a clear geometrical meaning. issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 5-23 16 pitkänen, m. many-sheeted dna: basic ideas 2. the notions of many-sheeted dna and many-sheeted protein suggests also an explanation for how enhancers and silencers are able to regulate gene expression. interaction with classical em or z0 fields via wormhole contacts would provide a nonchemical interaction mechanism. second mechanism is based on josephson currents running along join along boundaries contacts. since an interaction with much larger length scale is involved, these interaction mechanisms are not too sensitive to the position of the transcription factor and the distance of the binding site from gene promotor regions can be thousands of nucleotide pairs. this mechanism explains also the observe issue specificity of some transcription factors. proteins with same chemical structure can be quite different trascription factors if they have contacts to different space-time sheets. 3.2 possible answers to the basic questions many-sheeted dna suggests stupifyingly simple coding of body’s morphology. the genes would be obtained by simply contracting the many-sheeted space-time representing expression domains of genes to one-dimensional structure. decoding of the morphology means the growth of this structures to their orginal size. of course. this hypothesis is oversimplified but its extreme simplicity makes it worth of testing. 3.2.1 how the structure of expression domain of the gene is coded in the structure of gene? the p-adic length scale of the gene correlates trivially with the p-adic length scale of the protein coded by it. already protein folding implies that the correlation with the size of the structure coded by dna is not so straightforward. furthermore, proteins are not mere building blocks but can have quite abstract functions like regulating gene expression of genes. consider now various aspects of the idea that expression the domain of gene is coded into the structure of gene and this that correspondence could be also realized at functional level. 1. the first thing that comes into mind is that the p-adic length scale of the gene correlates with the p-adic prime of the space-time sheet which corresponds to the expression domain of the gene during early phases of the embryogenesis. gene clusters, say hox cluster, would represent kind of a miniature of the body and every gene of hox cluster would give rise to a space-time sheet which would be a scaled down model of the expression domain of the gene. thus the expression domains of various genes in the genome could correspond to the extended space-time sheets at the level of the genome and the topology of these genome level expression domains, in particular, their ordering, would be consistent with that for the actual expression domains. expression domain corresponds most naturally to a join along boundaries condensate generated by the formation of the join along boundaries bonds between the extended space-time sheets associated with the genes. this means that the p-adic prime of the expression domain can be much smaller than one could conclude it to be on basis of its size. 2. one could test the hypothesis that the total length of the region occupied by gene and by the dna controlling its activity in the genome could correlate with the size of its expression domain at the stage of the development when the gene is expressed. note that many genes affecting morphogenesis are expressed in a very early stage: many of them in the embryonic stage when no cell formation has yet occurred. this stage corresponds to the p-adic length scale of a fertilized cell about 10−4 meters. of course, the correlation between the content of the gene program and the size of its expression domain, is not necessary and might be even un-desirable. 3. fractality suggests that the communication by expression factor proteins at the level of genome might mimick the hormonal communication occurring at the level of the entire organism. this could mean that the hormonal communication between the expression domains of two genes is issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 5-23 17 pitkänen, m. many-sheeted dna: basic ideas equivalent with the presence of a transcription factor communication between corresponding genes at the level of nucleus. hormonal communication between cells involves the formation of hormonereceptor complex acting as a transcription factor. the length of human genes ranges to thousands of nucleotides. this would mean that the longest p-adic length scales of human gene would correspond to l(173) ∼ 16 micro-meters. the total length of a human chromosome is about 75× 106 dna triplets. the corresponding p-adic length scale is l(193) ∼ 2 cm. the next length scales correspond to the pair (197, 199) and correspond roughly to the size of brain hemisphere and brain. the total length of dna in chromosomes is 48×l(193) ∼ 1 meter, the size scale of human body. many-sheeted space-time concept suggests that genes actually correspond to dna sequences glued to a larger space-time sheet defining the gene. hox clusters could be one example of this. the geometry of the organism might be coded to these secondary, tertiary, etc. space-time sheet structures of the dna sequence guaranteing the coding the topology of the body plan to the topology of the multi-sheeted dna. these structures are be labelled by p-adic primes and their number would be quite limited. the linearity of dna suggests that also the plan of the expression domain should be essentially linear such that each cross section of each module of the expression domain is essentially homogenous phase and its structure is determined by a self organization process constrained by the p-adic length scale hypothesis rather than purely genetically. according to mae-wan [9, 10] living systems are liquid crystals and the basic characteristic of the liquid crystals is that they have crystal like structure in one dimension and are liquids in transversal dimensions [1] forming. thus layer-like structures. this suggests that p-adic selforganization determines the size of the transversal layer and that dna only codes some general properties of the liquid phase for a given layer. the sizes for the expression domains of the genes should form a hierarchy. effective expression domain can be much larger than the p-adic length scale characterizing it since join along boundaries condensates are possible. for instance, the modularization of the genetic programs of plants is perhaps stopped at the level k = 167 so that expression domains for plant cells could be regarded as join along boundaries concept of of k = 167 plant cells. at the level of organism this perhaps corresponds to the emergence of cell walls hindering the formation of higher level structures formed from cells: plant could perhaps be regarded as a large join along boundaries condensate of k = 167 plant cells surrounded by a wall. besides the length of the genome, the number of the p-adic hierarchy levels in the space-time sheet hierarchy of dna is a natural candidate for a measure of the complexity of the organism. 3.2.2 how the information about morphology is expressed? one of the fundamental questions of the developmental biology is how the information of genes stored into dna is translated to the geometry and topology of the organism. the idea of many-sheeted dna suggests an immediate answer to this question. expression is ’nothing but’ the reversal of the coding. the expression domain of the gene contracted effectively to one-dimensional dna-thread grows back to the expression domain with non-uniqueness and flexibility brought in by self-organization depending on external parameters. this means that various space-time sheets associated with dna grow during grow to space-time sheets representing actual organs. this process involves the formation of join along boundaries bonds between growing space-time sheets associated with various dna molecules so that coherent macroscopic quantum phases become possible. one can ask how the growth plan is coded into dna. or how much of it is coded into the chemistry of dna? the idea that dna is essentially body contracted to a thin thread suggests that the chemical control of dna is restricted to the local properties of tissues. the space-time sheets of replicating dna at various body parts simply grow and fuse to form join along boundaries condensates growing and giving rise to various organs. the replication of dna would in turn be quantum self-organization process involving essentially self-hierarchy starting from atomic level and ending up the level of entire organism. issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 5-23 18 pitkänen, m. many-sheeted dna: basic ideas 3.2.3 what makes cell differentiation possible? cell differentiation is one of the great mysteries of biology. it is known that only part of dna is active in a cell located in a given part of body and that selective activation of the genome gives rise to differentiation. the problem is to understand the mechanism of activation. especially difficult challenge for the view about life as mere chemistry is the interaction between large length scales with gene level making possible precise timing of genetic activity. in tgd framework cell differentiation should correspond to a selection of branch in the the flow diagram describing genetic program. this occurs during the growth since the concentrations of the proteins representing the inputs of the gene programs evolve during the growth and generate also spatial gradients. therefore different branches of the genetic program are activated in different parts of the developing organism. also the genes associated with space-time sheet of increasing size are activated during growth and this brings in new and higher control levels. very probably the mechanism involves interaction between microscopic degrees of freedom for dna and between macroscopic degrees of freedom representing body part where dna resides. the control and coordination based on josephson currents between gene space-time sheets and larger space-time sheets is very probably involved as is suggested by the general time scales of genetic activity. also the interaction with the classical fields of the space-time sheet of the body part to which dna has wormhole contacts provides an obvious mechanism of activation. the frequencies of the coherent oscillations of em fields involved could be important in both interaction mechanisms. this kind of interactions with larger spacetime sheets makes possible to understand induction phenomenon, which corresponds signalling between cells and entire cells groups. this kind of signalling could be crucially important for morphogenesis. many-sheeted space-time thus provides explanation for the ability of cells to form organs. the notion of cell cohesion is introduced to explain this: the cohesion would correspond to the formation of join along boundaries condensate of extended gene space-time sheets. 3.3 what is the number of the levels in program hierarchy? the obvious idea is that the size of the organism determines the largest p-adic prime contributing to the program hierarchy. it is however not obvious whether to define the size of organism as the ’physical’, visible size or as electromagnetic size, which is well defined notion in tgd framework. 3.3.1 does the visible size of the organism determine the number of hierarchy levels? the simplest working hypothesis is that the number of the levels in the program hierarchy is the number of p-adic length scales between atomic length scale and body size. the larger the visible size of the organism, the larger the number of the levels in the genetic program hierarchy, if this hypothesis is correct. this number is testable characteristic of species and could be valuable guide in attempts to understand how genetic code functions. one can identify the hierarchical level of the gene by looking how many genes it activates before building block protein is coded. it must be however emphasized that visible size need not be a correct criterion: the point is that join along boundaries condensates are possible and give rise to a much larger body size than one might conclude from the value of largest p-adic prime involved. it is instructive to look the numbers of hierarchy levels in some specific examples assuming that the visible size of the organism determines the number of hierarchy levels. it is assumed that k = 139 is the first level which counts as a hierarchy level. 1. viruses could have 4 hierarchy levels if k = 139, 149, 151, 157. proteins, lipid layers of cell membrane and cell membrane and genes coding building block proteins. it could be that only k=149 is present for the simplest viruses since the formation of the envelope is self-organization process. 2. bacteria should have 5 levels. k = 139, 149, 151, 157, 163. 3. home fly should have 12 levels since its size is below l(197) ' 1.6 cm. issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 5-23 19 pitkänen, m. many-sheeted dna: basic ideas 4. animals with size between l(199) ' 16 cm and l(211) ' 10 m have 15 hierarchy levels. note the large gap between l(199) and l(211) = 64l(199). 5. the next level corresponds to the level of dinosauri and whales having sixteen levels unless they correspond to join along boundaries condensates formed from smaller structures which is quite possible. the next level is l(223) and corresponds to size of 640 m! 3.3.2 does the electromagnetic size of of organism determine the number of hierarchy levels? there is a large gap between l(199) and l(211) and the next twin length scale corresponds to a length scale of one kilometer. this suggests that new levels of hierarchy possibly emerged after l(199) cannot correspond to the physical growth of body. mere large size does not guarantee intelligence. furthermore, if the visible size of the organism determines the number of the hierarchy levels, then dinosauri would have been in a well defined sense more intelligent animals than we! these arguments suggest that the visible size of the organism need not determine the number of genetic program levels. 1. it could be that dna codes and even controls also the electromagnetic structure of the organism realized as topologically quantized electromagnetic field, ”aura”, characterizing the organism. 2. an alternative option inspired by the notion of memetic code, which is next level in the hierarchy of genetic codes predicted by the tgd inspired simple model of abstraction process, is that there are higher hierarchy levels present but they are not controlled by the genetic program but call it as a subprogram. a natural working hypothesis is that eeg correlates with the electromagnetic size of the organism. eeg has emerged rather lately in the evolution and is possessed only by vertebrates. in case of humans it becomes fully developed only at the age of 18. meditation in general tends to increase the amplitudes of low frequency waves with 8 hz (alpha wave s) and also waves with lower frequencies (theta wave s). this suggests that growth in electromagnetic degrees of freedom can continue all the lifetime and could be identified as what is called ”spiritual growth”. it could continue also after the physical death so that the protein based state of life would be only a part of much longer lasting process of self-organization analogous to the development of butterfly. indeed, in tgd based picture about geometric time the death of the physical body does not mean the end of life. schumann resonances are resonances of em fields in the wave cavity defined by the 80 km thick layer between earth’s surface and ionosphere. the frequency range in question correspond to the frequency range of eeg. a hypothesis worth of considering is that human body generates via schumann resonances topological field quanta, which define electromagnetic sub-selves having the size of earth. one could even consider the possibility that the highest value of kg depends on individual and people having tendency to have religious and mystical experiences have exceptionally large value of kg. the length scale corresponding to alpha waves is 3.8 × 107 meters and corresponds is roughly 3.75 times the length scale l(251). if levels up to l(257) are present in the human genome then the number of hierarchy levels is 22, not too large number. l(251) ∼ 107 m corresponds to a frequency of 37.5 hz and is quite near to the 40 hz frequency claimed by koch and crick to be crucial for the visual consciousness! the frequency associated with k = 257 corresponds to the frequency of 5 hz, which also belongs to eeg. the electromagnetic size of the organ increases rapidly with the number of levels present in the hierarchy as the following table demonstrates. k 227 229 233 239 241 lp/m 2.5e + 3 5e + 3 2e + 4 1.6e + 5 3.2e + 5 k 251 257 263 269 271 lp/m e + 7 8e + 7 6.4e + 8 5e + 9 e + 10 issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 5-23 20 pitkänen, m. many-sheeted dna: basic ideas table 2. table of p-adic length scales above l(211) ' 10 meters. l(151) = 10−8 meters is assumed. there are even more explicit observations about the importance of elf em fields for the functioning of living matter and these observations finally led to a breakthrough in tgd based model of conscious brain. the observations about the special effects of elf em fields on brain at cyclotron frequencies of ions na+, cl−,k+ and ca++ in endomagnetic fields bend = 2be/5 = .2 gauss were made already at 1983 [12] . these experiments suggest that these ions/their cooper pairs form are confined in the magnetic field of earth and form bound states with macroscopic size of order cell size and with extremely small binding energy corresponding to frequency of order 10 hz. this is impossible in the standard physics framework but can be understood as resulting from the dropping of ions and electrons from the atomic space-time sheet to the space-time sheet of the cell where the density of the matter is very low. also electron cooper pairs of high tc electronic super conductor as well as cooper pairs of neutrino super conductor are important. besides magnetic cyclotron frequencies z0 magnetic cyclotron frequencies and wormhole cyclotron frequencies make sense: z0 currents for ions indeed induce automatically also ionic currents. one can argue that there is very cold, dry and silent at the cellular space-time sheets and this makes possible macroscopic quantum phases formed by cooper pairs of ions na+, cl−,k+ and electron as well as well as ca++ ions. later the argument was modifiedthe large values of planck constant [14, 13] imply that cyclotron energy scale is above thermal energy at room temperature even if thermal equilibrium of dark space-time sheets with ordinary ones is allowed. also other ions are possible but these ions are especially important for nerve pulse generation. these super conductors must be effectively onedimensional (otherwise gap energy is extremely small) and the needed confinement in the transversal degrees of freedom is caused by the presence of bend which could be in tgd framework interpreted as the dark companion of the earth’s magnetic field responsible for controlling biomatter possibly also associated with the personal magnetic body. one could regard these super conductors as associated with the flux quanta of bend having radius 25 µm (the size of a large neuron) by flux quantization and serving as templates for the formation of biostructures. when the josephson frequency (potential difference) associated with the weakly coupled super conductors of this kind corresponds to a magnetic transition frequency, quantum jumps between states of either super conductor occur and change the charge distributions and hence potential differences associated with other josephson junctions associated with either super conductor. quantum jumps can lead to ’wake-up’ of either or both super-conductor sub-self giving rise to a mental image. also emission of elf photons with resonance frequency is involved. the topological field quanta associated with these photons have typically size of order earth’s circumference. the fact that multiples of the cyclotron frequencies correspond directly to the most important frequencies of eeg and also to some important schumann frequencies suggests very strongly that the ’elf selves’ associated with these topological field quanta represent also selves in our self hierarchy. this leads to a general model for quantum control and for how the space-time sheets representing the self-hierarchy are coupled by join along boundaries bonds serving as josephson junctions, to a detailed model for the quantum correlates of the sensory qualia and to a model of boolean mind. elf selves are a crucial factor of all these models [15, 16] . the work of michael persinger shows that elf em fields and elf modulated em fields, affect also gene expression [11] . thus it seems that elf levels, rather than being controlled by gene level, actually control and coordinate gene level rather via the formation of join along boundaries bonds between gene spacetime sheets and elf space-time sheet. whether gene level actually codes also elf levels of the organism is an interesting question. the idea about genome as the entire many -sheeted organism contracted to a thin thread would support this view. on the other hand, the notion of the memetic code identified as the next level of abstraction hierarchy suggests that elf level corresponds to something genuinely new not reducible to gene level. elf level could be even seen as a different life form next to the biological life living in symbiosis with biological life. one must also remember that higher levels could couple with gene level only via join along boundaries contacts and that the development of organism could be seen as a ’social’ process in the sense that growing organism gradually builds join along boundaries contacts issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 5-23 21 pitkänen, m. many-sheeted dna: basic ideas to the space-time sheets representing higher level selves. whether the number of the hierarchy levels in the genetic program hierarchy is larger than the visible size of organism, might be perhaps tested sooner or later by deciphering the number of hierarchy levels in the genetic program. to check the hypothesis about eeg, it is enough to study simplest verterbrates possessing eeg. the identification the levels of various genes in program hierarchy would mean a tremendous boost in the understanding of genetic code and dramatic change in world view. 3.4 band structure of chromosomes as an evidence for many-sheeted dna? in prokaryotes dna is arranged in single chromosome forming closed circular double strand whereas in eukaryotes dna genome is organized into chromosome pairs. chromosome is believed to correspond to single dna thread which has beads in thread structure. beads are spherical nucleosomes of diameter 10−8 meters (l(151)!) consisting of histones of 4 different types forming histone octamer. dna is wound very tightly around nucleosomes, there is about 70 nanometers (slightly less than l(157) of dna per nucleosome. chromosome forms a helical coil with diameter found to be 30 nm. in interphase chromosomes are coiled once more to a hollow tube of diameter 200 nm (slightly less than l(167)) a helix of thickness about 10−7 meters. the transition from interphase chromosome to metaphase chromatid is accompanied by a winding to a helical coil of diameter about 600 nm (slightly more than l(169)). a possible interpretation of these transformations is as generation of new space-time sheets. chromosome banding was discovered already in eighteenth century by metzner. chromosome banding characterizes both the chromosome and the method used to produced the banding structure and there are many methods for revealing the band structure. increasing resolution implies the division of band structures to smaller structures in fractal like manner. the band structures can be divided into two classes. 1. the highly localized heterochromatic bands, nucleolar organizers and kinetochores appear in all organisms. the latter two structures seem to reflect the purely geometrical organization, ”packing”, of genome rather than the internal organization of genome. the main features of heterochromatic banding are its universality, diversity and variability. heterochromatic banding is present in all eukaryotes and can differ widely for closely related species and be very similar to widely different species. heterochromatin seems to correspond to highly repetitive short dna sequences of 10 nucleotid pairs (106 copies) located near the centromere of the chromosome. this dna is not transcribed to dna. pairs are often duplicated and duplication leads to various physiological defects. soma cells of some organisms appear to have ability to get rid of of heterochromatin whereas it is present in germ cells. these facts suggest that the regions of chromosome near its center regulate gene expression and that highly repetitive dna sequences represent sites for genes at which repressor proteins bind. abnormally large duplication of repressor sites would lead to stronger repression is more effective and could lead to abnormal development. 2. the chromosomes of the eukaryotes contain also non-localized bands called euchromatic bands. patterns of euchromatic bands resemble closely to the patters of dna replication and patterns correlate very strongly with species. thus euchromatic bands correspond to active rna. the moderately repetitive dna which is transcribed corresponds corresponds to euchromatin. it is known that there are several types of euchromatic banding. banding patterns can be used as diagnostic tools to identify various chromosome fusions and splittings. various bandings are of enormous value in providing manner to locate genes in genome. in tgd framework a natural interpretation of various types euchromatic banding provide evidence for the many-sheeted dna. thus euchromatic banding should reflect the modular structure of the genetic program as well as the interspersing of control regions and transcribed regions of genes corresponding to the basic structure ”if a then b” of the gene. issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 5-23 22 pitkänen, m. many-sheeted dna: basic ideas references condensed matter physics [1] liquid crystals on line. http://www.lcionline.net/. biology [2] introns. http://en.wikipedia.org/wiki/introns. [3] ivan amato. dna shows unexplained patterns. science, page 747, 1992. [4] f. j. ayuala and jr. j. a. kiger. modern genetics. benjamin cummings, 1984. [5] benoit et al. (nine others) cousineau. retrohoming of a bacterial group ii intron: mobility via complete reverse splicing, independent of homologous dna recombination. cell, 94:456–462, 1998. [6] j. yang et al. efficient integration of an intron rna into double-stranded dna by reverse splicing. nature, 1996. [7] k. t tycowski et al. a mammalian gene with introns instead of exons generating stable rna products. nature, 379:464–466, 1996. [8] stephen gaunt. hox genes: regulators of animal design. http://www.bi.bbsrc.ac.uk/world/ sci4alll/gaunt/gaunt2.html, 1999. [9] m. w. ho. the rainbow and the worm. world scientific, singapore, 1993. [10] m. w. ho. coherent energy, liquid crystallinity and acupuncture. http://www.consciousness. arizona.edu/quantum/archives/uploads/mifdex.cgi?msgindex.mif, 1994. neuroscience and consciousness [11] j. hitt. this is your brain on god. wired. http: // www. wired. com/ wired/ archive/ 7. 11/ persinger_ pr. html , 1999. [12] d. yarrow. spin the tale of the dragon. http://www.ratical.org/reatvlle/rofd2.html, 1990. books and articles related to tgd [13] m. pitkänen. dark matter hierarchy and hierarchy of eegs. in tgd and eeg. onlinebook. http://tgdtheory.com/public_html/tgdeeg/tgdeeg.html#eegdark, 2006. [14] m. pitkänen. does tgd predict the spectrum of planck constants? in towards m-matrix. onlinebook. http://tgdtheory.com/public_html/tgdquant/tgdquant.html#planck, 2006. [15] m. pitkänen. general theory of qualia. in bio-systems as conscious holograms. onlinebook. http://tgdtheory.com/public_html/hologram/hologram.html#qualia, 2006. issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. http://www.lcionline.net/ http://en.wikipedia.org/wiki/introns http://www.bi.bbsrc.ac.uk/world/sci4alll/gaunt/gaunt2.html http://www.bi.bbsrc.ac.uk/world/sci4alll/gaunt/gaunt2.html http://www.consciousness.arizona.edu/quantum/archives/uploads/mifdex.cgi?msgindex.mif http://www.consciousness.arizona.edu/quantum/archives/uploads/mifdex.cgi?msgindex.mif http://www.wired.com/wired/archive/7.11/persinger_pr.html http://www.wired.com/wired/archive/7.11/persinger_pr.html http://www.ratical.org/reatvlle/rofd2.html http://tgdtheory.com/public_html/tgdeeg/tgdeeg.html#eegdark http://tgdtheory.com/public_html/tgdquant/tgdquant.html#planck http://tgdtheory.com/public_html/hologram/hologram.html#qualia dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 5-23 23 pitkänen, m. many-sheeted dna: basic ideas [16] m. pitkänen. genes and memes. in genes and memes. onlinebook. http://tgdtheory.com/ public_html/genememe/genememe.html#genememec, 2006. [17] m. pitkänen. tgd based view about living matter and remote mental interactions. onlinebook. http://tgdtheory.com/public_html/tgdlian/tgdlian.html, 2012. [18] m. pitkänen. are dark photons behind biophotons?. in tgd based view about living matter and remote mental interactions, 2013. [19] m. pitkänen. comparison of tgd inspired theory of consciousness with some other theories of consciousness. in tgd based view about living matter and remote mental interactions. onlinebook. http://tgdtheory.com/public_html/pdfpool/consccomparison.pdf, 2013. issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.com/public_html/genememe/genememe.html#genememec http://tgdtheory.com/public_html/genememe/genememe.html#genememec http://tgdtheory.com/public_html/tgdlian/tgdlian.html http://tgdtheory.com/public_html/pdfpool/consccomparison.pdf introduction the notions of magnetic body and dark matter many-sheeted dna background dna and rna proteins replication, transcription, translation introns, pseudogenes, repetitive dna, silent dna is central dogma an absolute truth? is life nothing but biochemistry? many-sheeted dna many-sheeted dna as hierarchy of genetic programs possible answers to the basic questions how the structure of expression domain of the gene is coded in the structure of gene? how the information about morphology is expressed? what makes cell differentiation possible? what is the number of the levels in program hierarchy? does the visible size of the organism determine the number of hierarchy levels? does the electromagnetic size of of organism determine the number of hierarchy levels? band structure of chromosomes as an evidence for many-sheeted dna? dna decipher journal | august 2015 | volume 5 | issue 1 | pp. 74-77 74 pitkänen, m., a possible quantum control mechanism in tgd-inspired biology exploration a possible quantum control mechanism in tgd-inspired biology matti pitkänen 1 abstract the idea that tgd universe is quantum critical, is the corner stone of quantum tgd and fixes the theory more or less uniquely since the only coupling constant parameter of the theory kähler coupling strength is analogous to critical temperature. also more than one basic parameter are in principle possible maximal quantum criticality fixes the values of all of them but it seems that only kähler coupling strength is needed. tgd universe is a quantum critical fractal: like a ball at the top of hill. quantum criticality allows to avoid the fine tuning problems plaguing as a rule various unified theories. in this article the recent discovery of that smbr6 behaves simultaneously as a conductor and insulator in external magnetic field led to a tgd based model relying on quantum criticality. quantum criticality corresponds to a situation in which landau orbits emerges as an orbit at the surface of the magnetic flux tube and should lead to generation of large heff phases if tgd based view about quantum criticality holds true. this also leads to an identification of quantum bio-control mechanism based on the variation of the thickness of magnetic flux tubes inducing by flux conservation the variation of field strength controlling quantum critical currents flowing along the flux tubes. this mechanism is expected to play a central role in living matter. 1 quantum criticality the meaning of quantum criticality at the level of dynamics has become only gradually clearer. the development of several apparently independent ideas generated for about decade ago have led to the realization that quantum criticality is behind all of them. behind quantum criticality are in turn number theoretic vision and strong forms of general coordinate invariance and holography. 1. the hierarchy of planck constants defining hierarchy of dark phases of ordinary matter corresponds to a hierarchy of quantum criticalities assignable to a fractal hierarchy of sub-algebras of super-symplectic algebra for which conformal weights are n-ples of those for the entire algebra, n corresponds to the value of effective planck constant heff/h = n. these algebras are isomorphic to the full algebra and act as gauge conformal algebras so that a broken super-conformal invariance is in question. 2. quantum criticality in turn reduces to the number theoretic vision about strong form of holography. string world sheets carrying fermions and partonic 2-surfaces are the basic objects as far as pure quantum description is considered. also space-time picture is needed in order to test the theory since quantum measurements always involve also the classical physics, which in tgd is an exact part of quantum theory. space-time surfaces are continuations of collections of string world sheets and partonic 2-surfaces to preferred extremals of kähler action for which noether charges in the sub-algebra of supersymplectic algebra vanish. this condition is the counterpart for the reduction of the 2-d criticality to conformal invariance. this eliminates huge number of degrees of freedom and makes the strong form of holography possible. 1correspondence: matti pitkänen http://tgdtheory.com/. address: karkinkatu 3 i 3, 03600, karkkila, finland. email: matpitka6@gmail.com. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.com/ mailto:matpitka6@lgmail.com dna decipher journal | august 2015 | volume 5 | issue 1 | pp. 74-77 75 pitkänen, m., a possible quantum control mechanism in tgd-inspired biology 3. the hierarchy of algebraic extensions of rationals defines the values of the parameters characterizing the 2-surfaces, and one obtains a number theoretical realization of an evolutionary hierarchy. one can also algebraically continue the space-time surfaces to various number fields reals and the algebraic extensions of p-adic number fields. physics becomes adelic. p-adic sectors serve as correlates for cognition and imagination. one can indeed have string world sheets and partonic 2-surfaces, which can be algebraically continued to preferred extremals in p-adic sectors by utilizing p-adic pseudo constants giving huge flexibility. if this is not possible in the real sector, figment of imagination is in question! it can also happen that only part of real space-time surface can be generated: this might relate to the fact that imaginations can be seen as partially realized motor actions and sensory perceptions. 1.1 quantum criticality and tgd inspired quantum biology in tgd inspired quantum biology quantum criticality is in crucial role. first some background. 1. quantum measurement theory as a theory of consciousness is formulated in zero energy ontology (zeo) and defines an important aspect of quantum criticality. strong form of nmp states that the negentropy gain in the state function reduction at either boundary of causal diamond (cd) is maximal. weak form of nmp allows also quantum jumps for which negentropic entanglement is not generated: this makes possible ethics (good and evil) and morally responsible free will: good means basically increase of negentropy resources. 2. self corresponds to a sequence state function reductions to the same boundary of cd and heff does not change during that period. the increase of heff (and thus evolution!) tends to occur spontaneously, and can be assigned to the state function reduction to the opposite boundary of cd in zero energy ontology (zeo). the reduction to the opposite boundary means death of self and living matter is fighting in order to avoid this even. to me the only manner to make sense about basic myth of christianity is that death of self generates negentropy. 3. metabolism provides negentropy resources for self and hopefully prevents nmp to force the fatal reduction to the opposite boundary of cd. also homeostasis does the same. in this process self makes possible evolution of sub-selves (mental images dying and re-incarnating) state function by state function reduction so that the negentropic resources of the universe increase. 1.2 a new mechanism of quantum criticality consider now the mechanisms of quantum criticality. the tgd based model [5] for the recent paradoxical looking finding [1] that topological insulators can behave like conductors in external magnetic field led to a discovery of a highly interesting mechanism of criticality, which could play a key role in living matter. 1. the key observation is that magnetic field is present. in tgd framework the obvious guess is that its flux tubes carry dark electrons giving rise to anomalous currents running in about million times longer time scales and with velocity, which is about million times higher than expected. also supra-currents can be considered. the currents can be formed of the cyclotron energies of electrons are such that they correspond to energies near the surface of the fermi sphere: recall that fermi energy for electrons is determined by the density of conduction electrons and is about 1 ev. interestingly, this energy is at the lower end of bio-photon energy spectrum. in the field of 10 tesla the cyclotron energy of electron is .1 mv so that the integer characterizing cyclotron orbit must be n ' 105 if conduction electron is to be transferred to the cyclotron orbit. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | august 2015 | volume 5 | issue 1 | pp. 74-77 76 pitkänen, m., a possible quantum control mechanism in tgd-inspired biology 2. the assumption is that external magnetic field is realized as flux tubes of fixed radius, which correspond to space-time quanta in tgd framework. as the intensity of magnetic field is varied, one observes so called de haas-van alphen effect (https://en.wikipedia.org/wiki/de_haasvan_ alphen_effect) used to deduce the shape of the fermi sphere: magnetization and some other observables vary periodically as function of 1/b (for a model for the quantum critical variant of the effect see [2]). this can be understood in the following manner. as b increases, cyclotron orbits contract. for certain increments of 1/b n + 1:th orbit is contracted to n:th orbit so that the sets of the orbits are identical for the values of 1/b, which appear periodically. this causes the periodic oscillation of say magnetization. 3. for some critical values of the magnetic field strength a new orbit emerges at the boundary of the flux tube. if the energy of this orbit is in the vicinity of fermi surface, an electron can be transferred to the new orbit. this situation is clearly quantum critical. if the quantum criticality hypothesis holds true, heff/h = n dark electron phase can be generated for the critical values of magnetic fields. this would give rise to the anomalous conductivity perhaps involving spin current due to the spontaneous magnetization of the dark electrons at the flux tube. even super-conductivity based on the formation of parallel flux tube pairs with either opposite or parallel directions of the magnetic flux such that the members of the pair are at parallel flux tubes, can be considered and i have proposed this a mechanism of bio-superconductivity and also high tc super-conductivity. 2 a new mechanism of quantum bio-control the quantum criticality of the process in which new electron orbit emerges near fermi surface suggests a new mechanism of quantum bio-control by generation of super currents or its reversal. 1. in tgd inspired quantum biology magnetic body uses biological body as motor instrument and sensory receptor and eeg and its fractal variants with dark photons with frequencies in eeg range but energy e = hefff in the range of bio-photon energies make the necessary signalling possible. 2. flux tubes can become braided and this makes possible quantum computation like processes [3]. also so called 2-braids defined by knotted 2-surfaces imbedded in 4-d space-time surface are possible for the string world sheets defined by flux tubes identified to be infinitely thin, are possible. as a matter fact, also genuine string world sheets accompany the flux tubes. 2-braids and knots are purely tgd based phenomenon and not possible in superstring theory or m-theory. 3. it is natural to speak about motor actions of the magnetic body. it is assumed that the flux tubes of the magnetic body connect biomolecules to form a kind of indra’s web explaining the gel like character of living matter. heff reducing phase transitions contract flux tubes connecting biomolecules so that they can find each other by this process and bio-catalysis becomes possible. this explains the mysterious looking ability of bio-molecules to find each other in the dense molecular soup. in fact the dark matter part is far from being soup! the hierarchy of planck constants and heff = hgr hypothesis imply that dark variants of various particles with magnetic moment are neatly at their own flux tubes like books in shelf. reconnection of the u-shaped flux tubes emanating from two subsystems generates a flux tube pair between them and gives rise to supracurrents flowing between them. also cyclotron radiation propagating along flux tubes and inducing resonant transitions is present. this would be the fundamental mechanism of attention. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. https://en.wikipedia.org/wiki/de_haas–van_alphen_effect https://en.wikipedia.org/wiki/de_haas–van_alphen_effect dna decipher journal | august 2015 | volume 5 | issue 1 | pp. 74-77 77 pitkänen, m., a possible quantum control mechanism in tgd-inspired biology 4. i have proposed that the variation of the thickness of the flux tubes could serve as a control mechanism since it induces a variation of cyclotron frequencies allowing to get in resonance or out of it. for instance, two molecules could get in flux tube contact when the cyclotron frequencies are identical and this can be achieved if they are able to vary their flux tube thickness. the molecules of immune system are masters in identifying alien molecules and the underlying mechanism could be based on cyclotron frequency spectrum and molecular attention. this would be also the mechanism behind water memory and homeopathy [4] which still is regarded as a taboo by mainstreamers. 5. finally comes the promised new mechanism of bio-control. the variation of the magnetic field induced by that of flux tube thickness allows also to control whether there is quantum criticality for the generation of dark electron supra currents of electrons. the fermi energy of the conduction electrons at the top of fermi sphere is the key quantity and dictated by the density of these electrons. this allows to estimate the order of magnitude of the integers n characterizing cyclotron energy for ordinary planck constant and the maximal value of heff/h = n cannot be larger than n . references [1] s. e. sebastian et al. unconventional fermi surface in an insulating state. science. http: // www. sciencemag. org/ content/ early/ 2015/ 07/ 01/ science. aaa7974 , 349(6243):605–607, 2015. [2] d. m. hofman s. a. hartnoll. generalized lifshitz-kosevich scaling at quantum criticality from the holographic correspondence. phys. rev. b. http: // journals. aps. org/ prb/ abstract/ 10. 1103/ physrevb. 81. 155125 , 81(151125), 2010. [3] m. pitkänen. dna as topological quantum computer. in genes and memes. onlinebook. http: //tgdtheory.fi/public_html/genememe/genememe.html#dnatqc, 2006. [4] m. pitkänen. homeopathy in many-sheeted space-time. in bio-systems as conscious holograms. onlinebook. http://tgdtheory.fi/public_html/hologram/hologram.html#homeoc, 2006. [5] m. pitkänen. does the physics of smb6 make the fundamental dynamics of tgd directly visible? http://tgdtheory.fi/public_html/articles/smb6.pdf, 2015. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. http://www.sciencemag.org/content/early/2015/07/01/science.aaa7974 http://www.sciencemag.org/content/early/2015/07/01/science.aaa7974 http://journals.aps.org/prb/abstract/10.1103/physrevb.81.155125 http://journals.aps.org/prb/abstract/10.1103/physrevb.81.155125 http://tgdtheory.fi/public_html/genememe/genememe.html#dnatqc http://tgdtheory.fi/public_html/genememe/genememe.html#dnatqc http://tgdtheory.fi/public_html/hologram/hologram.html#homeoc http://tgdtheory.fi/public_html/articles/smb6.pdf quantum criticality quantum criticality and tgd inspired quantum biology a new mechanism of quantum criticality a new mechanism of quantum bio-control login dna decipher journal open journal systems journal help subscription login to verify subscription give 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~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x untitled dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 213-216 campbell, r., part i: a critique of river out of eden: introduction issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 213 article part i: a critique of river out of eden: introduction robert campbell * abstract darwinism as generally interpreted in the modern scientific paradigm claims that chance events and rare random mutations, only a few of which bestow a survival advantage, shape the evolution of life in the biosphere. we have all experienced accidents and know that we must be careful to anticipate and avoid them if we can. we do have the intelligence to learn from past experience and behave accordingly in the present in our efforts to ensure a positive future. in this way we have an evolving capacity to span and integrate events in space and time. the darwinian paradigm however denies that the evolutionary process possesses any capacity to adjust according to feedback from past experience. only blind accidental mutations determine the course of evolutionary events over great spans of time, it is claimed. only a rare few of these mutations bestow a survival advantage that select in favor of the branching limbs of the evolutionary tree. the arguments in favor of this belief as expressed by richard dawkins are critically assessed and shown to be lacking in supporting evidence. key words: charles darwin, theory of evolution, cosmic order, intellegent direction, spirituality, atheist, richard dawkins. in the academic world it is usual for scientific contributions to be assessed by a peer review process that for all of its weaknesses is better than nothing. a peer review process can cut both ways, however. biases inevitably come to play, as they do in all human endeavors, and a peer review process can often serve as much to promote them as to expose them. it is only over time, sometimes over periods of centuries, that biases gradually get weeded out from our garden of acceptable ideas. in our current social environment, there is a tendency for certain academic ideas to get publicly extolled in popular editions, asserting views as established truth without confirming evidence to support them. this is a little disconcerting, since lay people have been educated to believe that science is a highly disciplined search for truth, based upon solid empirical evidence. we have seen the results. we drive cars. we have television sets and computers. it may therefore come as a surprise to some of us that strong biases and political pressures often prevail in scientific circles. in part one of this series of articles, we will be examining scientific biases that are currently favored in evolution theory. richard dawkins [3-5] is to be commended for his popular writing in this regard, for he has attempted to publicly address many questions posed by skeptics of the evolutionary process as viewed by darwinists. in doing so he has opened the way for public * correspondence: rober campbell, independent researcher. website: http://www.cosmic-mindreach.com e-mail: bob@cosmic-mindreach.com note: the articles presented in this issue are based on my book “downsizing darwin: an intelligent face for evolution” self-published in 1996 [1]. more information is available at my website [2]. dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 213-216 campbell, r., part i: a critique of river out of eden: introduction issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 214 examination of the issues involved, for they concern us all. darwinism is taught in our schools and it inevitably influences the thinking of future generations and the direction that our cultures will take. since literary works of a popular kind sometimes use the mantle of science to cloak biased views in the guise of truth, it is important that they be critically assessed. the scientists that write them have no conscious intention to deceive the public. they believe in the social value of what they are doing and they are conscientiously committed to their jobs. that’s why they write. however subtle their biases may be they also wish to swing the tide of public opinion behind them. science must sell itself as a worthy endeavor, as it should. we cannot get along without science. the public, of course, is usually in no position to assess the merits of ideas preached from the pulpit of science. these are learned people who are experts in their field and highly respected. they must be right. since there is normally no peer review in the public domain there is a good chance that many will believe the views that an expert expresses. in the interests of a little balance it should therefore be permissible for someone to take an academic writer to task over ideas that he publicly champions as truth. i don’t mean to single out richard dawkins for personal criticism. i’m sure he is a conscientious man who is very committed to doing his job well. he also shows signs of being inconsistent with some of he extreme views he expresses in his book “river out of eden.” [3]. and he may well have moderated his views since his still popular book was first published in 1995. the book is nevertheless instructive because of the ideas it promotes that warrant the most critical examination. as one of the most vocal proponents of views that have become firmly entrenched in the academic community, the book betrays a powerful scientific bias, without the support of empirical evidence. richard dawkins is the author of a number of popular books including the blind watchmaker [4] and the selfish gene [5], books that by their title tell where he is coming from. he is promoting the darwinian concept that the evolutionary process is the blind indifferent result of rare random mutations, a few of which accidentally endow a survival advantage that environmental selection pressures consequently favor. some darwinists have taken a more moderate line in recent decades, but not those of dawkins’ persuasion. as dawkins himself claims, they have all but achieved a closed shop in scientific circles and they are promoting their beliefs as gospel to the general public, as we might expect. the comments offered here are not intended to contest that chance events play a part in the evolution of life. we know from our own experience that accidents happen and some of us have a better capacity to cope with them than others, resulting in a certain survival advantage. there is every reason to believe that similar influences have helped to shape the development and adjustment of species in the natural environment. what is contested is the exclusive view that this is the only creative agent at work in the universe, or that it is the most important. in the case of human experience most of us assume there is an intelligent process at work in the human mind that allows us to cope creatively with random accidents. but darwinists deny that there is any intelligence whatever at work in the evolutionary dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 213-216 campbell, r., part i: a critique of river out of eden: introduction issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 215 process. they believe that the universe is a vast sea of random atomic, molecular and radiation collisions, with no coherent universal order behind it other than these local chance collisions. this is a universal world view that they implicitly accept as the only foundation of the entire universe. there is no evidence, much less proof, to support such an extreme position. it is a blind belief, a rock solid bias [6]. accidents happen. they must be accommodated and adjustments made for life to continue. but we may not correctly assume from this that all events are determined by accident. there is also a system of order that pervades the universe, from atoms to galaxies and stars, and from the simplest bacterium to plants and animals and humans. all things in the universe are interrelated and interdependent, whether by gravity, light and electromagnetism, or by the chemical bath that we swim in. there is gravitational and electromagnetic communication between the stars just as there is physical and chemical communication between living species. this is only part of the picture. we shall see that there is also tensional communication between the galaxies and stars. there is a synchronicity to their collective being and to the atomic synthesis that takes place in the centers of stars in the process of integrating space and time. there is also communication between the species through universal hierarchies that are an expression of an evolutionary order to the creative process on every level. self-similarity pervades the structure of all phenomena through which we are able to integrate and make sense of our everyday experience. in touching on some of this as we go along, we shall see that the cosmic order that pervades the universe is implicitly intelligent. the nature of this system of order has been explored elsewhere1, however we shall see here that there are persistent clues as to how intelligence works right under our noses, with the evidence spread far and wide. because there is no practical paradigm of how intelligence works currently available, science is left with accidental cause as the only alternative. it is this bias that will be under critical examination here. it will also be shown that an alternate paradigm is possible that can find practical application in science and that offers a far grander view of the universe with an intelligent role for humans to play. 2 1 the “system” inherent in the cosmic order was first introduced in a general way by the author in fisherman’s guide: a systems approach to creativity and organization, new science library (shambhala), boston, 1985. it has been developed in more rigorous fashion in science and cosmic order: a new prospectus, and in many articles freely available at www.cosmic-mindreach.com. 2 the bias began to form with the emergence of western science three to four centuries ago, but its origins reach back to aristotle. the essence of the bias is a refusal to acknowledge that universal influences are operative in the cosmic order of things. in the development of physics, for example, action-at-a-distance has been shunned like the plague. all events are believed to be the result of local influences operative in a space-time continuum. general relativity theory has reduced space and time to a continuous field with a curvature to account for apparent gravitational action-at-a-distance. more recent experimental evidence of quantum events confirm quantum correlation-at-a-distance. universal influences in the natural order of things do keep cropping up, despite our most ingenious inventions to dispense with them. dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 213-216 campbell, r., part i: a critique of river out of eden: introduction issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 216 with these thoughts in mind, one of richard dawkins’ books, entitled river out of eden, will be critically reviewed point by point and chapter by chapter, beginning with the preface. this book will thus serve as a basis for a critical review of darwinist ideas in general. references 1. robert campbell, downsizing darwin: an intelligent face for evolution. mindreach library (1996). 2. http://www.cosmic-mindreach.com 3. richard dawkins, river out of eden: a darwinian view of life. basic books (1996). 4. richard dawkins, the blind watchmaker: why the evidence of evolution reveals a universe without design. w. w. norton & company (1996). 5. richard dawkins, the selfish gene. oxford university press (1990). 6. http://www.cosmic-mindreach.com/truth_bias.html login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x dna decipher journal | october 2015 | volume 5 | issue 2 | pp. 144-148 144 pitkänen, m. are there direct evidence for dark dna? essay are there direct evidence for dark dna? matti pitkänen 1 abstract sciencedaily tells about extremely interesting finding related to dna. what has been found (http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14580.html) is that knockout (removing parts of gene to prevent transcription to mrna) and knock-down of gene (prevent protein translation) seem to have different consequences. removing parts of gene need not have the expected effect at the level of proteins! does this mean that somehow dna as a whole can compensate the effects caused by knock-out but not those by knock-down? this explanation is natural in the standard conceptual framework and is proposed in the article. or could tgd provide explanation in terms of more fundamental representation of genetic codons as states of dark protons forming analogs of dark nuclei identified as string like objects accompanying ordinary dna? could all basic biopolymers be accompanied by their dark analogs identified in this manner and could transcription and translation occur at dark level and could their chemical counterparts be kind of shadow processes? 1 introduction sciencedaily tells about extremely interesting finding related to dna (http://www.sciencedaily.com/ releases/2015/07/150722101813.htm. the finding is just what breakthrough discovery should be: it must be something impossible in the existing world view. what has been found [4] (http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14580. html) is that knock-out (removing parts of gene to prevent transcription to mrna) and knock-down of gene (prevent protein translation) seem to have different consequences. removing parts of gene need not have the expected effect at the level of proteins! does this mean that somehow dna as a whole can compensate the effects caused by knock-out but not those by knock-down? this explanation is natural in the standard conceptual framework and is proposed in the article. could this be explained by assuming that genome is a hologram as gariaev et al (http://www. wavegenetics.jino-net.ru) [3, 1] have first suggested? also tgd leads to a vision about living system as a conscious hologram [5]. small local changes of genes could be compensated. somehow the entire genome would react like brain to a local brain damage: other regions of brain take the duties of the damaged region. could the idea about dna double strand as nano-brain having left and right strands instead of hemispheres”help here. does dna indeed act as a macroscopic quantum unit? the problem is that transcription is local rather than holistic process. something very simple should lurk behind the compensation mechanism. 2 could transcription transform dark dna to dark mrna? also the tgd based notion of dark dna comes in mind [7, 9] (http://www.tgdtheory.fi/public_html/ hologram/hologram.html#homeoc, http://www.tgdtheory.fi/public_html/neuplanck/neuplanck.html# nuclstring). dark dna consists of dark proton sequences for which states of single dna proton correspond to those of dna, mrna, aminoacids, and trna. dark dna is one of the speculative ideas of tgd inspired quantum biology getting support from pollack’s findings (https://www.youtube.com/ watch?v=i-t7tcmudxu [2],[11]). ordinary biomolecules would only make their dark counterparts visible: 1correspondence: matti pitkänen http://tgdtheory.com/. address: köydenpunojankatu 2 d 11 10940, hanko, finland. email: matpitka@luukku.com. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14580.html http://www.sciencedaily.com/releases/2015/07/150722101813.htm http://www.sciencedaily.com/releases/2015/07/150722101813.htm http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14580.html http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14580.html http://www.wavegenetics.jino-net.ru http://www.wavegenetics.jino-net.ru http://www.tgdtheory.fi/public_html/hologram/hologram.html#homeoc http://www.tgdtheory.fi/public_html/hologram/hologram.html#homeoc http://www.tgdtheory.fi/public_html/neuplanck/neuplanck.html#nuclstring http://www.tgdtheory.fi/public_html/neuplanck/neuplanck.html#nuclstring https://www.youtube.com/watch?v=i-t7tcmudxu https://www.youtube.com/watch?v=i-t7tcmudxu http://tgdtheory.com/ mailto:matpitka@luukku.com dna decipher journal | october 2015 | volume 5 | issue 2 | pp. 144-148 145 pitkänen, m. are there direct evidence for dark dna? dark biomolecules would serve as a template around which ordinary biomolecules such as dna strands are formed in tgd universe. all basic biomolecules of genetics would be pairs of ordinary biomolecule and its dark proton analog. although ordinary dna is knocked out of ordinary gene, dark gene would still exist! if dark dna actually serves as template for the transcription to mrna, everything is still ok after knockout! could it be that we do not understand even transcription correctly? could it actually occur at the level of dark dna and mrna?! dark mrna would attach to dark dna after which ordinary mrna would attach to the dark mrna. one step more! damaged dna could still do its job! dna transcription would would have very little to do with bio-chemistry! if this view about dna transcription is correct, it would suggest a totally new manner to fix dna damages. these damages could be actually at the level of dark dna, and the challenge of dark genetic engineering would be to modify dark dna to achieve a proper functioning. 3 could dark genetics help to understand the non-uniqueness of the genetic code? also translation could be based on pairing of dark mrna and dark trna. this suggests a fresh perspective to some strange and even ugly looking features of the genetic code. are dna and mrna always paired with their dark variants? do also amino-acids and anticodons of trna pair in this manner with their dark variants? could the pairings at dark matter level be universal and determined by the pairing of dark amino-acids with the anticodons of dark rna? could the anomalies of the code be reduced to the non-uniqueness of the pairing of dark and ordinary variants of basic bio-molecules (pairings rna–dark rna, amino-acid– dark amino-acid, and amino-acid–ordinary amino-acid in trna). 1. there are several variants of the genetic code differing slightly from each other: correspondence between dna/mrna codons and amino-acids is not always the same. could dark-dark pairings be universal? could the variations in dark anticodon anticodon pairing and dark amino-acid-aminoacid pairing in trna molecules explain the variations of the genetic code? 2. for some variants of the genetic code a stop codon can code for amino-acid. the explanation at the level of trna seems to be the same as in standard framework. for the standard code the stop codons do not have trna representatives. if stop codon codes for amino-acids, the stop codon has trna representation. but how the mrna knows that the stop codon is indeed stop codon if the trna associated with it is present in the same cell? could it be that stop codon property is determined already at the level of dna and mrna? if the dark variant of genuine stop codon is missing in dna and therefore also in mrna the translation stops if it is induced from that at the level of dark mrna. could also the splicing of mrna be due to the splitting of dark dna and dark mrna? if so genes would be separated from intronic portions of dna in that they would pair with dark dna. could it be that the intronic regions do not pair with their dark counterparts. they would be specialized to topological quantum computations in the tgd inspired proposal [6]. start codon (usually aug coding met) serves as a start codon defining the reading frame (there are 3 possible reading frames). dark dna would naturally begin from this codon. 3. also two additional amino-acids pyl and sec appear in nature. gariaev et al have proposed that the genetic code is context dependent so that the meaning of dna codon is not always the same. this non-universality could be reduced to the non-uniqueness of dark amino-acid–amino-acid pairing in trna if genetic code is universal. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2015 | volume 5 | issue 2 | pp. 144-148 146 pitkänen, m. are there direct evidence for dark dna? 4 could dark genetics help to understand wobble base pairing? wobble base pairing (https://en.wikipedia.org/wiki/wobble_base_pair) is second not-so-well understood phenomenon. in the standard variant of the code there are 61 mrnas translated to amino-acids. the number of trna anticodons (formed by the pairs of amino-acid and rna molecules) should be also 61 in order to have 1-1 pairing between trna and mrna. the number of ordinary trnas is however smaller than 61 in the sense that the number of rnas associated with them is smaller than 45. trna anticodons must be able to pair with several mrna codons coding for given amino-acid. this is possible since trna anticodons can be chosen to be representative for the mrna codons coding a given amino-acid in such that all mrna codons coding for the same amino-acid pair with at least one trna anticodon. 1. this looks somewhat confusing but is actually very simple: genetic code can be seen as a composite of two codes: first 64 dnas/mrnas to are coded to n < 45 anticodons in trna, and then these n anticodons are coded to 20 amino-acids. one must select n anticodon representatives for the mrnas in the 20 sets of mrna codons coding for a given amino-acid such that each amino-acid has at least one anticodon representative. a large number of choices is possible and the wobble hypothesis of crick pose reduce the number of options. 2. the wobble hypothesis of crick states that the nucleotide in the third codon position of rna codon of trna has the needed non-unique base pairing: this is clear from the high symmetries of the third basis. there is exact u-c symmetry and approximate a-g symmetry with respect to the third basis of rna codon (note that the conjugates of rna codons are obtained by a↔u and c↔g permutations). 3. the first two basis in the codon pair in 1-1 manner to the second and third basis of anticodon. the third basis of anticodon corresponds to the third letter of mrna codon. if it is a or c the correspondence is assumed to be 1-to-1: this gives 32 trnas. if the first basis of anticodon is g or u the 2 mrna basis can pair with it: they would be naturally a for g and c for u by symmetry. one would select a from a-g doublet and c from u-c double. this would give 16 anticodons: 48 anticodons altogether, which is however larger than 45. furthermore, this would not give quite the correct code since a-g symmetry is not exact. smaller number of trnas is however enough since the code has almost symmetry also with respect to a and c exchange not yet utilized. the trick is to replace in some cases the first basis of anticodon with inosine i, which pairs with 3 mrna basis. this replacement is possible only for those aminoacids for which the number of rnas coding the amino-acid is 3 or larger (the amino-acids coded by 4 or 6 codons). 4. it can be shown at least 32 different trnas are needed to realize genetic code by using wobble base pairing. full a-c and g-u symmetry for the third basis of codon would give 16+16=32 codons. one can ask whether trna somehow realizes this full symmetry? how dark variants of could help to understand wobble base pairing? suppose for a moment that the visible genetics be a shadow of the dark one and fails to represent it completely. suppose the pairing of ordinary and dark variants of trna anticodons resp. amino-acids and that translation proceeds at the level of dark mrna, dark anticodons, and dark amino-acids, and is made visible by its bio-chemical shadow. could this allow to gain insights about wobble base pairing? could the peculiarities of trna serve for some other essentially bio-chemical purposes? the basic idea would be simple: chemistry does not determine the pairing but it occurs at the level of the dark mrna codons and dark trna anticodons. there would be no need to reduce wobble phenomenon to biochemistry and the only assumption needed would be that chemistry does not prevent isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. https://en.wikipedia.org/wiki/wobble_base_pair dna decipher journal | october 2015 | volume 5 | issue 2 | pp. 144-148 147 pitkänen, m. are there direct evidence for dark dna? the natural dark pairing producing standard genetic code apart from the modifications implied by nonstandard dark amino-acid–amino-acid pairing explaining for different codes and the possibility that stop codon can in some situation pair with dark mrna. one can consider two options. 1. the number of dark trnas is 64 and the pairings between dark mrna and dark anticodons and dark anticodons and dark amino-acids are 1-to-1 and only the pairing between dark rna codons and anticodons in trna is many-to-1. 2. the model of dark genetic code [7] suggests that there are 40 dark proton states, which could serve as dark analogs of trna. this number is larger than 32 needed to realize the genetic code as a composite code. i have cautiously suggested that the proposed universal code could map dark mrna states of the same total spin (there is breaking of rotational symmetry to that around the axis of dark proton sequences) to dark trna/dark amino-acid states with the same total spin projection. the geometric realization would in terms of color flux tubes connecting the dark protons of corresponding dark proton sequences. also in ordinary nuclei the nucleons are proposed to be connected by color flux tubes so that they form nuclear strings [9] and dark proton sequences would be essentially dark variants of nuclei. one should understand the details of the dark mrna–trna anticodon correspondence. one can also ask whether the dark genetic code and the code deduced from the icosahedral model for music harmony [10] [12] are mutually consistent. this model implies the decomposition of 60+4 dna codons to 20+20+20+4 codons, where each ”20” corresponds to one particular icosahedral hamilton’s cycle with characteristic icosahedral symmetries. ”4” can be assigned to tetrahedron regarded either disjoint from icosahedron or glued to it along one of its faces. this allows to understand both the standard code and the code with two stop codons in which exotic amino-acids pyl and sec appear. one should understand the compositeness 64 → 40 → 20 of the dark genetic code and and whether it relates to the icosatetrahedral realization of the code. i have proposed [8] (http://www.tgdtheory.fi/public_html/hologram/hologram.html#molephoto) that dark variants of transcription, translation, etc.. can occur and make possible kind of r&d laboratory so that organisms can test the consequences of variations of dna. if ordinary translation and transcription are induced from their dark variants it would not be surprising and if dark biomolecules could also appear as unpaired variants, these processes could occur as purely dark variants. organisms could indeed do experimentation in the virtual world model of biology and pairing with ordinary bio-molecules would make things real. references [1] brief introduction into wavegenetics. its scope and opporturnities. http://www.wavegenetics. jino-net.ru. [2] the fourth phase of water: dr. gerald pollack at tedxguelphu. https://www.youtube.com/ watch?v=i-t7tcmudxu, 2014. [3] p. gariaev et al. the dna-wave biocomputer, volume 10. chaos, 2001. [4] y.r. steinier et al. genetic compensation induced by deleterious mutations but not gene knockdowns. nature. doi:10.1038/nature14580, 2015. [5] m. pitkänen. bio-systems as conscious holograms. in bio-systems as conscious holograms. onlinebook. http://tgdtheory.fi/public_html/hologram/hologram.html#hologram, 2006. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. http://www.tgdtheory.fi/public_html/hologram/hologram.html#molephoto http://www.wavegenetics.jino-net.ru http://www.wavegenetics.jino-net.ru https://www.youtube.com/watch?v=i-t7tcmudxu https://www.youtube.com/watch?v=i-t7tcmudxu http://tgdtheory.fi/public_html/hologram/hologram.html#hologram dna decipher journal | october 2015 | volume 5 | issue 2 | pp. 144-148 148 pitkänen, m. are there direct evidence for dark dna? [6] m. pitkänen. dna as topological quantum computer. in genes and memes. onlinebook. http: //tgdtheory.fi/public_html/genememe/genememe.html#dnatqc, 2006. [7] m. pitkänen. homeopathy in many-sheeted space-time. in bio-systems as conscious holograms. onlinebook. http://tgdtheory.fi/public_html/hologram/hologram.html#homeoc, 2006. [8] m. pitkänen. macroscopic quantum coherence and quantum metabolism as different sides of the same coin: part ii. in bio-systems as conscious holograms. onlinebook. http://tgdtheory.fi/ public_html/hologram/hologram.html#molephoto, 2006. [9] m. pitkänen. nuclear string hypothesis. in hyper-finite factors and dark matter hierarchy. onlinebook. http://tgdtheory.fi/public_html/neuplanck/neuplanck.html#nuclstring, 2006. [10] m. pitkänen. quantum model for hearing. in tgd and eeg. onlinebook. http://tgdtheory. fi/public_html//tgdeeg/tgdeeg/tgdeeg.html#hearing, 2006. [11] m. pitkänen. quantum gravity, dark matter, and prebiotic evolution. in genes and memes. onlinebook. http://tgdtheory.fi/public_html/genememe/genememe.html#hgrprebio, 2014. [12] m. pitkänen. geometric theory of harmony. http://tgdtheory.fi/public_html/articles/ harmonytheory.pdf, 2014. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.fi/public_html/genememe/genememe.html#dnatqc http://tgdtheory.fi/public_html/genememe/genememe.html#dnatqc http://tgdtheory.fi/public_html/hologram/hologram.html#homeoc http://tgdtheory.fi/public_html/hologram/hologram.html#molephoto http://tgdtheory.fi/public_html/hologram/hologram.html#molephoto http://tgdtheory.fi/public_html/neuplanck/neuplanck.html#nuclstring http://tgdtheory.fi/public_html//tgdeeg/tgdeeg/tgdeeg.html#hearing http://tgdtheory.fi/public_html//tgdeeg/tgdeeg/tgdeeg.html#hearing http://tgdtheory.fi/public_html/genememe/genememe.html#hgrprebio http://tgdtheory.fi/public_html/articles/harmonytheory.pdf http://tgdtheory.fi/public_html/articles/harmonytheory.pdf introduction could transcription transform dark dna to dark mrna? could dark genetics help to understand the non-uniqueness of the genetic code? could dark genetics help to understand wobble base pairing? login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 72-80 72 pitkänen, m., on magnetic body, bio-harmonies, morphogenesis & epigenetics exploration on magnetic body, bio-harmonies, morphogenesis & epigenetics matti pitkänen 1 abstract in tgd, magnetic body is an intentional agent using biological body as a sensory receptor and motor instrument. tgd also provides various mechanism used by magnetic body for control and communication purposes, and the notion of bio-harmony suggests itself as a correlate for quantum coherence at the level of basic bio-molecules. how magnetic body and bio-harmony could help to understand biology? can one identify biological phenomena making these notions compelling? in this article some candidates for phenomena of this kind are briefly discussed. the finding that behavioral patterns of planaria can be remembered also by the piece of split planaria without brains is consistent with the idea that replication of magnetic body coding for behaviors is behind biochemical replication. that alleles of the same gene have different expression could be understood if the bio-harmony assignable to gene carries additional information besides the biochemical information. these notions might help to understand the mechanisms epigenetic. histone modification and dna methylation are believed to involve geometric locking preventing transcription. they could also affect the frequency assignable to dna codon or some key unit so that the resonance condition making possible reconnection of u-shaped flux tubes allowing biomolecules to get in contact and for transcription to proceed fails to be satisfied. epigenetic inheritance could reduce to inheritance of bio-harmony: the magnetic bodies of cells of offspring get in tune with those of parent. 1 introduction what tgd can possibly give to biology is the vision about magnetic body [8] as an intentional agent using biological body as a sensory receptor and motor instrument and about various mechanism used by magnetic body for control and communication purposes. a new element is brought in by zero energy ontology: magnetic body is 4-dimensional and thus correlate for a behavioral pattern rather than 3d state for part of organism. also the notion of bio-harmony [9] [7] suggests itself as a correlate for quantum coherence at the level of basic bio-molecules. how magnetic body and bio-harmony could help to understand biology? can one identify biological phenomena making these notions compelling? in this article some candidates for phenomena of this kind are briefly discussed. the finding that behavioral patterns of planaria can be remembered also by the piece of split planaria without brains is consistent with the idea that replication of magnetic body coding for behaviors is behind biochemical replication. that alleles of the same gene have different expression could be understood if the bio-harmony assignable to gene carries additional information besides the biochemical information. these notions might also provide a fresh approach to epigenetics. histone modification and dna methylation are believed to induce kind of geometric locking preventing transcription. they could also affect the frequency assignable to dna codon or some key unit so that the resonance condition making possible reconnection of u-shaped flux tubes allowing biomolecules to get in contact fails and transcription cannot proceed. epigenetic inheritance could reduce to the inheritance of bio-harmony: the magnetic bodies of cells of offspring get in tune with those of parent. to how high degree magnetic body and bio-harmony are inherited? this becomes the key question. 1correspondence: matti pitkänen http://tgdtheory.com/. address: köydenpunojankatu 2 d 11 10940, hanko, finland. email: matpitka@luukku.com. isbn: issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.com/ mailto:matpitka@luukku.com dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 72-80 73 pitkänen, m., on magnetic body, bio-harmonies, morphogenesis & epigenetics 1.1 the notions of 4-d magnetic body and bio-harmony recall first some key ideas of tgd inspired quantum biology. 1. in tgd framework magnetic body extends the pair formed by organism and environment to a kind of holy trinity. magnetic flux tubes and the realization of genetic code in terms of dark proton sequences has been the key hypothesis. the model for cold fusion (see http://tgdtheory. fi/public_html/articles/cfagain.pdf) [?] suggests that also more general dark nuclei must be allowed. dark neutron sequences could correspond to genes separated by dark protons. dark weak interactions with large value of heff effectively massless below neuron size scale would play central role and induce large parity breaking effects (chiral selection). the chemistry would not be all that matters. dna-nuclear/cell membrane as topological quantum computer with braided magnetic flux tubes would explain why organisms with virtually identical genomes are so different (we and our ancestors for instance). the hierarchy of magnetic bodies would be responsible for the development of intelligence and for cultural evolution. flux tubes connecting dna and mrna as well as mrna and trna molecules are present but it is difficult to say anything concrete. 2. ontogeny could be seen as a kind of editing process for the text defined by the dna. control of control of... is involved so that situation is very complex. who performs the editing? does dna edit itself and is the editing process defining evolution of genome coded by genome? or is the editing performed by darwinian selection at cell level (see https://en.wikipedia.org/wiki/cellular_ differentiation)? or is the magnetic body the editor using genome also as its tool as tgd would suggest? what is important that in tgd framework self-organization in 4-d sense implied by zero energy ontology replaces ordinary self organization leading to asymptotic spatial patterns and select spatiotemporal patterns as asymptotic behavioral patterns defining various biological functions. the role of magnetic body is central in this process. 3. magnetic body contains cyclotron bose-einstein condensates and cyclotron frequencies determined by the strength of magnetic field would give for dna and other biomolecules additional characteristics. in tgd based model for musical harmony dna codons would correspond quite concretely to 3-chords but played using dark photons (also ordinary music represented as sounds could be transformed to dark photon music). if one accepts the icosahedral model of bio-harmonies predicting genetic code correctly, there would be 256 fundamental harmonies characterised by the allowed collection of 3-chords and they would add to the information carried by dna molecules. i have constructed a program building random sequences of the allowed chords using the additional harmonic rule that two subsequent chords contain at least one common note and this music sounds rather harmonic (albeit boring in absence of any other elements!) 4. could one distinguish between different states/phases of dnas, mrnas, trnas, and amino acids in terms of harmony? could their functioning depend on the harmony? with the inspiration coming from the connection of emotions and musical harmonies i have proposed that the harmony associated with a gene or organ could correlate with something analogous to an emotional state or mood maybe micro-mood or microemotion could be the proper notion. could amino-acids be happy, hilarious, melancholic, sad, depressed? could one distinguish between different phases of dna, rna, trna, aminoacid collections characterized by the harmony in turn characterizing the of a cell, organelle, organ, or even organism? trna defines the map of the harmony associated with dna codons to amino-acid harmony. is the information about dna codon and about corresponding 3-chord represented at the level of magnetic body of amino-acidthat is as the 3-chord, which it represents, and realized as the rules telling with which trnas amino-acid can reconnect? in contrast to dna codons, which represent local information, harmony could represent holistic information and characterize entire genes or their intronic portions. isbn: issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.fi/public_html/articles/cfagain.pdf http://tgdtheory.fi/public_html/articles/cfagain.pdf https://en.wikipedia.org/wiki/cellular_differentiation https://en.wikipedia.org/wiki/cellular_differentiation dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 72-80 74 pitkänen, m., on magnetic body, bio-harmonies, morphogenesis & epigenetics 1.2 problem there is however a problem. dna codons coding for the same amino-acid correspond to different 3-chords of harmony. one of these chords corresponds to amino-acid itself and the codons coding for amino-acid correspond to the orbit of this chord under subgroup of isometries of icosahedron moving the triangles of icosahedron along the orbit. this would apply also to mrna and maybe also to trna. the chords at the orbit of amino-acid are isomorphic (intervals are same) and obtained as transposes of each other. the chords are isomorphic but not identical and this leads to the problem with resonance paradigm unless one gives up the idea that amino-acid corresponds to a unique dna codon and assumes that there is analog of gauge invariance allowing to choose the preferred codon freely. 1. the assumption about preferred dna codon could be given up if one can choose the preferred dna codon freely so that also the magnetic bodies of amino-acids are characterized by 3-chords and thus carry information about what dna codon coded them. this is possible if one has the analog of fiber space structure with dna codons coding for amino-acid defining the fiber and amino-acids defining the base. this fiber structure with discrete gauge invariance is strongly suggestive and i have proposed it for two decades ago but it seems that it poses strong conditions on the orbits of the subgroups of isometries of icosahedron. this condition is very restrictive. simplifying somewhat: one considers 60 codons decomposing into 20+20+20 codings and each group of 20 codons codes for amino-acids belonging to different groups. there are twenty of them. the 20 triangles of icosahedron correspond to 3 dna codons each and each of them corresponds to one and only one amino-acid. one has 3 subgroups of isometries corresponding to 20+20+20 decomposition. can one perform a global gauge transformations realized as isometries and moving triangles along the orbits of one of the 3 subgroups involved say isometry g1 of g1? these transformations would move the entire orbits of 2 subgroups involved call them g2 and g3. what happens to the chords of g2 and g3: is their character changed completely so that these harmonies would be destroyed? it seems that this cannot work. should one replace g2 and g3 with their automorphs g1g2g −1 1 and g1g3g −1 1 . does this make sense? 3-chords defining give orbit should be invariant under automorphisms of gi? this does not seem to be a realistic condition. 2. could different automorphs correspond to different collections of chords physically just as global gauge transformations generate different physical situations? isometries of groups gi would therefore define physically different realizations of bio-harmonies such that for each of them only one of the dna codons coding for given amino-acid could actually perform the coding. ordinary genetic code with many-to-one correspondence would make sense in statistical sense only. if this is true, the cyclotron frequency 3-chord assignable to amino-acid depends on the dna coding it and implies physical distinctions. 3. one can consider also a third alternative. dna codon with same 3-chord as coding for amino-acid is in special role in that only it can resonate with the amino-acid! could dna codons codons correspond to same cyclotron frequency triplet (magnetic fields) but different value of heff so that one would have chord with respect to energy rather than frequency. different values of heff for dna codons coding for the same amino-acid would scale their cyclotron frequencies to the same amino-acid frequency while keeping cyclotron energies invariant? cyclotron energy ratios for codons correspond to rational valued ratios ei/ej = heff (i)/heff (j) = n(i)/n(j). amino-acid would correspond to fixed heff and this creates a problem: can dna codon code for amino-acid with different value of heff . this option does not look attractive. second option looks the most plausible one. of course, it is early to talk about a prediction: it might well be that i have mis-understood something. isbn: issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 72-80 75 pitkänen, m., on magnetic body, bio-harmonies, morphogenesis & epigenetics 2 how the notions of magnetic body and bio-harmony could help to understand inheritance next more concrete ideas about magnetic body and bio-harmony in relation to epigenetics and inheritance will be developed. 2.1 questions about bio-harmony one can pose a lot of questions about bio-harmony. 1. it is not necessary to assign any interpretation on the harmony. just the harmony could be enough if it is forced to be same for dna, corresponding mrna, trna, and aminoacids. one can however make questions. is the harmony inherited invariant and could it distinguish between different personality types about which we learned in old books of psychology? or could the harmonies correlate with our own moods? 2. could differentiation selecting particular genes as expressed genes apply also to harmonies so that given gene would correspond only to a particular harmony and different copies of gene could correspond to different harmonies. could this selection rely on the same mechanisms as ordinary differentiation realized in terms of epigenetic mechanisms and dna editing? from the magnetic bodies of genes the harmony would be automatically transferred to the magnetic bodies of mrna, trna and aminoacids since otherwise the transcription and translation do not work since magnetic bodies do not have common resonance frequencies and reconnection and resonant interaction is not possible. 3. does given harmony characterize given gene or the entire cell? all basic biomolecules associated with a gene would naturally correspond to the same harmony. if the rrnas associated with ribosomes are in harmony mutually cellular harmony seems to be the only option. if ribosomes have their own harmonies, only certain ribosomes can translate given gene. this would bring in additional control tool. the most plausible picture is that the situation depends on what happens in the self-organization process. some organs/organisms are more harmonious, others not so harmonious. harmony need not be given fixed to remain the same: magnetic body can have motor actions changing the cyclotron frequencies. moods could reflect the character of harmony at gene level. 4. does magnetic body control the differentiation by posing restrictions on gene expression or vice versa? the idea about magnetic body as intentional agent suggests that the first option is correct. there would be hierarchy of magnetic bodies with magnetic bodies at the higher level controlling bodies at the lower level. the value of planck constant would label the hierarchy levels and also dna codons would be characterized by ”intelligence quotient” defined by heff/h. this would be nothing but the analog for the hierarchy of program modules and i have earlier considered the realization of this hierarchy (see http://tgdtheory.fi/public_html/articles/braidparse.pdf). 5. the selection of harmony could take place and be analogous to cell differentiation. this would be a self-organization process in which magnetic bodies of genes, cells, etc.. tune themselves to resonance with each other by modifying their magnetic fields by controlling their thickness (for monopoles flux the flux is invariant). something analogous to the development of social skills. this could pose resonance as a constraint on processes like replication, transcription, reverse transcription, silencing, enhancing, editing, etc.... it might induce the differentiation at gene level. editing processes for genome could be seen as being induced by the motor actions of the magnetic body involving reconnection and change of the value of heff changing the length of the flux tube and bringing biomolecules near to each other or separating them. this selection would also apply to the intronic part of dna proposed to be responsible for topological quantum computation like isbn: issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.fi/public_html/articles/braidparse.pdf dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 72-80 76 pitkänen, m., on magnetic body, bio-harmonies, morphogenesis & epigenetics processes. the copies of same fragment appearing in intronic portion and copies of genes could correspond to different harmonies. 2.2 can the notions of magnetic body and bio-harmony explain something that ordinary genetic cannot? it would be nice to identify some biological phenomenon difficult to understand in standard framework but having an elegant explanation in terms of magnetic body. 1. the notion of harmony could manifest itself at the level of genes as different expressions for the copies of same gene if they correspond to different notions of harmony. the copies of gene are known as alleles (see https://en.wikipedia.org/wiki/allele). the alleles can indeed give rise to different phenotypic traits such as different pigmentation. 2. morphogenesis provides examples of this kind of phenomena [2, 3, 4]. the first key idea is that dna and cell replication is induced by the replication of magnetic bodies serving as information carriers (see http://tgdtheory.fi/public_html/tgdlian/tgdlian.html#lianpb) [8]. the second key idea is that in zero energy ontology (zeo) magnetic body is 4-dimensional and represents behavioral patterns rather than only 3-dimensional patterns. for instance, memory as behavioral patterns can be inherited by the piece of planaria worm not containing the brain. the explanation could be that the magnetic body carries behavioral patterns replicated in the splitting of the worm. 3. epigenetics studies changes of gene expression not caused by the change of dna itself. epigenome (see https://en.wikipedia.org/wiki/epigenome) is the highly dynamic part of dna controlling expression of the rather stable part of genome. one might regard stable part of genome as hardware and epigenome as topological quantum computer programs assignable to magnetic body and modifying gene expression epigenetically. comment sign in computer code serves as a computer scientific metaphor for epigenetic control by repression. the modelling of epigenesis in terms of magnetic body and bio-harmonies deserves a separate discussion. 1. the modification of transcription rate is the basic tool of epigenetic regulation. there are two basic mechanisms involved. histone modification (see https://en.wikipedia.org/wiki/histone affects the histones of chromatin so that the transcription is repressed or activated. histone modification takes place by several mechanisms. dna methylation occurs for cpg pair and if it occurs for a promoter region it represses the transcription and serves as a kind of gene lock. the degree of methylation serves as a measure for the effectiveness of repression. i do not know whether the locking is absolute at the level of single gene or whether only the transcription rate is reduced. two mechanisms are mentioned in the wikipedia article (see https://en.wikipedia.org/wiki/dna_methylation). methylation can impede geometrically some step in the transcription. methylated site can be also accompanied by proteins affecting histones in chromatin and in this manner impede transcription. 2. the notions of magnetic body and bio-harmony suggest an alternative one might even hope fundamental mechanism of repression. methylation (histone modification) could affect some cyclotron frequency associated with dna codon (histone). in the optimal situation for transcription the dna and protein catalyzing the transcription or mrna are in resonance. when cyclotron resonance condition is not exactly satisfied, the reconnection rate for the u-shaped flux tubes associated with the molecules involved in the process is reduced and also transcription is repressed. i have considered also the radical possibility that the dynamics at the level of magnetic body is fundamental for biology and that magnetic body defines templates for the bio-molecular selforganization making dark matter dynamics visible. this is probably too extremist view and it isbn: issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://en.wikipedia.org/wiki/allele http://tgdtheory.fi/public_html/tgdlian/tgdlian.html#lianpb https://en.wikipedia.org/wiki/epigenetics https://en.wikipedia.org/wiki/epigenome https://en.wikipedia.org/wiki/histone https://en.wikipedia.org/wiki/dna_methylation dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 72-80 77 pitkänen, m., on magnetic body, bio-harmonies, morphogenesis & epigenetics would seem that biochemistry affects the cyclotron frequencies assignable to the magnetic body by affecting the strengths of magnetic fields also at dark magnetic flux tubes. 3. the notions of epigenetic code (see https://en.wikipedia.org/wiki/epigenetic_code) and histone code (see https://en.wikipedia.org/wiki/histone_code) have been proposed. epigenetic code would consist of histone modifications and additional modifications such as dna methylation. the codeword of the epigenetic code could code for some larger unit than protein: say gene or entire cell. the hypothesis is that the chromatin-dna interactions are induced by histone tail modifications (such as methylation, acetylation, adp-ribosylation, ubiquitination, citrullination, and phosphorylation). there are 4 histones and the position of modification varies as well as the modifier (the above modifications are not the only ones) so so that the number of modifications is very large. the addition of bioharmonies to the genetic information could simplify the situation dramatically since the modifications could be seen as defining of of the 256 bio-harmonies with 64 chords each (this for fixed scale which varies if the value of magnetic field strength is varied: biophoton spectrum in visible is proposed to represent the range of values of magnetic field). the most plausible starting hypothesis is that given harmony characterizes the gene. much simpler option would be that the harmony characterizes entire cell or even group of cells. if the modification by kicking cyclotron frequency out of harmony is enough to repress transcription, almost endless number of bio-chemical manners to achieve would exist but the epigenetic code could be very simple at the basic level as tgd would predict. each bio-harmony [?]harmonytheory [7] would provide a representation of genetic code in terms of 3-chords predicting correctly the dnaamino-acid correspondence (there are actually two slightly differing codes explaining the presence of 21st and 22nd amino-acid and deviations from the standard code). the states of dark protons (or neutrons) are also proposed to realize genetic code [6, 5]: it is an open question whether these codes imply each other as they should. 4. the understanding of transgenerational epigenetic inheritance (see https://en.wikipedia.org/ wiki/transgenerational_epigenetic_inheritance) raises difficult challenges. one should understand how histone modification and dna methylation are transferred to daughter cells in cellular division or inherited by the offspring. transgenerational interaction of the genomes seems necessary. in tgd framework the interaction of magnetic bodies of via resonance mechanism could transfer the epigenetic programs to the offspring. offspring could ”learn” the epigenetic programs of the mother by tuning. 5. gregory carey (see http://www.colorado.edu/ibg/people/61) gives nice real life examples about the complexities of epigenesis identified quite generally as gene regulation (see http://tinyurl. com/zb97cgs). he compares the gene regulation involved with the handling of a stressful situation to ”nightmarish rube goldberg mousetrap” and sees the process as extremely ineffective from engineering point of view. for instance, the hormones secreted to blood circulation are distributed to the entire body. the whole thing could be carried out in brain! he also wonders why evolution is so inefficient. all cells have same genome although most of the genes are silenced. second strand of dna is totally un-used and most of dna consists of introns. his explanation is that evolution does not make long term plans but finds just a solution to a particular without thinking it from a wider perspective: ”if it ain’t broke, don’t fix it”. i tend to see this differently. if entire body is coherent quantum entity, engineering based thinking does not make sense. entire body and also magnetic body must be informed from the stress situation since the reaction is holistic. the genes which are not used for gene expression might be used for other purposes. topological quantum computation could be this purpose in tgd framework and repressed genes could be thus used for quantum information processing. information processing could be actually the dominating function of the dna of higher vertebrates. isbn: issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://en.wikipedia.org/wiki/epigenetic_code https://en.wikipedia.org/wiki/histone_code https://en.wikipedia.org/wiki/transgenerational_epigenetic_inheritance https://en.wikipedia.org/wiki/transgenerational_epigenetic_inheritance http://www.colorado.edu/ibg/people/61 http://tinyurl.com/zb97cgs http://tinyurl.com/zb97cgs dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 72-80 78 pitkänen, m., on magnetic body, bio-harmonies, morphogenesis & epigenetics to sum up, magnetic body could be seen as the ”boss” controlling the gene expression and also the evolution of genome in longer scales. magnetic body would use bio-molecular mechanisms for its purposes. this would bring in a new kind of inheritance: bio-harmony would be inherited. the most spectacular almost-prediction would be that genetic code is many-to-one only in statistical sense. 2.3 rna is transferred between soma cells and germ cells the basic question of epigenesis is how the information between soma cells and germ cells is transferred. in standard genetic the transfoer rna or dna molecules is necessary to achieve this. in tgd dark dna, rna, trna, and aminocids consisting of dark nucleons realized as nuclear strings and accompanied by the corresponding biomolecules is one possibility. the extremist view would be that the dynamics of the dark variants of basic bio-molecules induces the dynamics of their molecular shadows making them only visible. also the transfer of information as cyclotron radiation can be considered in tgd framework and cyclotron resonance could serve as a fundamental mechanism of epigenetic control. the above model suggest that epigenetic control mechanisms rely on resonance mechanism for 3-chords associated with dna codons and other biomolecules giving them names is also at work besides purely geometrical silencing. the popular article no sex required: body cells transfer genetic info directly into sperm cells, amazing study finds (see http://tinyurl.com/hhdth5j) summarizing the findings discussed in the article [1] (see soma-to-germline transmission of rna in mice xenografted with human tumour cells: possible transport by exosomes (see http://www.ncbi.nlm.nih.gov/pmc/articles/pmc4081593/) as very interesting concerning this basic question. the abstract of the article gives for a professional a readable summary. mendelian laws provide the universal founding paradigm for the mechanism of genetic inheritance through which characters are segregated and assorted. in recent years, however, parallel with the rapid growth of epigenetic studies, cases of inheritance deviating from mendelian patterns have emerged. growing studies underscore phenotypic variations and increased risk of pathologies that are transgenerationally inherited in a non-mendelian fashion in the absence of any classically identifiable mutation or predisposing genetic lesion in the genome of individuals who develop the disease. non-mendelian inheritance is most often transmitted through the germline in consequence of primary events occurring in somatic cells, implying soma-to-germline transmission of information. while studies of sperm cells suggest that epigenetic variations can potentially underlie phenotypic alterations across generations, no instance of transmission of dnaor rna-mediated information from somatic to germ cells has been reported as yet. to address these issues, we have now generated a mouse model xenografted with human melanoma cells stably expressing egfp-encoding plasmid. we find that egfp rna is released from the xenografted human cells into the bloodstream and eventually in spermatozoa of the mice. tumor-released egfp rna is associated with an extracellular fraction processed for exosome purification and expressing exosomal markers, in all steps of the process, from the xenografted cancer cells to the spermatozoa of the recipient animals, strongly suggesting that exosomes are the carriers of a flow of information from somatic cells to gametes. together, these results indicate that somatic rna is transferred to sperm cells, which can therefore act as the final recipients of somatic cell-derived information. some background is needed to understand this rather technical summary. 1. darwinism has dominated biology since darwin. the rules of classical mendelian inheritance conform with the darwinian view and can be reduced to genetic level. various traits are inherited genetically by sexual reproduction and genome would change during lifetime only through mutations. genome changes exremely slowly by random changes for offspring from which selection pressures choose the survivors. lamarckian view in turn assumed that the external circumstances experienced by organism leave a trace, which can be inherited but it could not be formulated in terms of modern molecular biology whereas the darwinian dogma could be formulated in terms of weissman’s genetic barrier. information flows from germ cells to soma but never in opposite direction. if it would do so, the isbn: issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/hhdth5j http://www.ncbi.nlm.nih.gov/pmc/articles/pmc4081593/ dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 72-80 79 pitkänen, m., on magnetic body, bio-harmonies, morphogenesis & epigenetics soma interacting with environment could transfer information to germ cells and the experiences during lifetime could leave inheritable trace to germ cells. an analogous dogma is that information is always transcribed from dna to rna to proteins but never in opposite direction. it is now known that this takes place in case of viruses and retroviruses: there are so called jumping genes which can also make copies of themselves. 5 per cent of human genome conists of endogenous retroviruses capable of doing the same. the huge genome of maize is due to this kind of proces. 2. the development epigenetics has started to shatter the belief on wessimann’s genetic barrier. gene expression is not fixed by genome alone and can be change even when genes are unaffected. silencing of genes by dna methylation and histone modification allow to modify gene expression. silencing is essentially a locking of gene preventing its expression by transcription followed by translation. it is now known that epigenetic changes in the gene expression can be inherited. the mechanisms are still poorly understood. what seems however clear the genome is more like a slowly changing hardware and gene expression or whatever is behind it is the software and programs can change very rapidly by just adding or deleting comment signs in the code. a deeper understanding of this software is needed. 3. epigenetic inheritance requires that genetic information is transferred from soma cells to germ cells. if only dna or rna are capable of representing genetic information, then dna or rna must be transferred from soma cells to germ cells. no instance of direct dna or rna mediated information from soma to germ cells had been observed before the above mentioned experiments. one can of course challenge the assumption about dna and rna as the only representations of genetic information. the basic idea of the experiment was simple. use a marker for rna by using plasmids (dna strands not belonging to chromosomes) genetically engineered to code for a marker protein making itself visible by fluoresence. then one just follows the fate of these proteins generated in soma cells and looks whether they end up inside germ cells and how this happens. more technically: mouse model was xenografted with human melanoma cells stably expessing egfpcoding plasmid (expressed in a manner possibly evoking emotions: human melanoma cancer tissue was implanted in mouse). egfp-rna is released from xenografted human cells to blood. one just looks whether it eventually ends up to the sperm cells of mice and tries to identify the transfer mechanism. only transfer to sperm cells was studied. one might expect that the transfer of rna can happen also to ovum. i guess that the sperm cells are easier to study. what was observed? 1. the transfer of rna from soma cells to sperm cells was indeed found to occur. the transferred rna can in turn induce epigenetic effects in germ cells known to be inherited by a mechanisms, which however remain poorly understood. epigenetic mechanisms seem to be involved in the cases considered so that dna is not changed, only its expression. 2. the transfer mechanism was identified. the transferred rna is contained by exosomes analogous to synaptic vesicles transferring neurotransmitters from presynaptic to postsynaptic cell. transfer of rna takes place via fusion of the membranes just like transfer of neurotransmitters. maybe genetic engineering using exosomes or analogous structures to transfer the needed material to cells has been tried. the implications of the findings are dramatic but already implied by the earlier work in epigenetics. what is important that lamarckian view can be now defended by a concrete genetic mechanism. lamarckism implies that the time scale of inheritance becomes the time scale for the appearence of a new generation. nutrition, environment, lifestyle and even meditation and similar practices, are already isbn: issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | march 2016 | volume 6 | issue 1 | pp. 72-80 80 pitkänen, m., on magnetic body, bio-harmonies, morphogenesis & epigenetics now known to affect gene expression on daily basis: we are not victims of genetic determinism and are epigenetically responsible for our own well-being. epigenetic information can be transferred also to germ cells so that we responsible also for the well-being of our children. our children suffer our sins and share our sufferings. the precise mechanism of inheritance of epigenetic modifications remains still poorly understood although it seems that the transfer or rna to germ cells occurs. there are also other hints: it is known that alleles (variants of game gene) can express themselves differently. one allele can also induce other allele to express in the same manner. somekind of ”social pressure” like interaction seems to be involved. as explained, tgd suggests the notion of magnetic body and cyclotron resonance as this interaction. the dna of offspring get tuned to the dna of mother during pregnancy and this gives to epigenetic inheritance. various epigenetic mechanisms such as methylation and histone modification could affect cyclotron frequencies besides purely geometric modifications of dna and locking at the level of gene could be accompanied kicking out of tune at the level of magnetic body. in this framework the transfer of rna to germ cells would be necessary to affect the cyclotron frequencies. references [1] cossetti c et al. soma-to-germline transmission of rna in mice xenografted with human tumour cells: possible transport by exosomes. plos one.available at: http://www.ncbi.nlm.nih.gov/ pmc/articles/pmc4081593/ , 9, 2014. [2] levin m. the wisdom of the body: future techniques and approaches to morphogenetic fields in regenerative medicine, developmental biology and cancer. regen med . available at: http: //www.futuremedicine.com/doi/pdf/10.2217/rme.11.69, 6(6):667–673, 2011. [3] levin m. morphogenetic fields in embryogenesis, regeneration, and cancer: non-local control of complex patterning. biosystems. available at: http://www.ncbi.nlm.nih.gov/pubmed/22542702, 109(3):243–261, 2012. [4] levin m somrat t. an automated training paradigm reveals long-term memory in planarians and its persistence through head regeneration. the j experimental biology. available at: http://tinyurl. com/ntlxpep, 216:3799–3810, 2013. [5] pitkänen m. homeopathy in many-sheeted space-time. in bio-systems as conscious holograms. onlinebook. available at: http://tgdtheory.fi/public_html/hologram/hologram.html# homeoc, 2006. [6] pitkänen m. nuclear string hypothesis. in hyper-finite factors and dark matter hierarchy. onlinebook. available at: http://tgdtheory.fi/public_html/neuplanck/neuplanck.html# nuclstring, 2006. [7] pitkänen m. quantum model for hearing. in tgd and eeg. onlinebook. available at: http: //tgdtheory.fi/public_html/tgdeeg/tgdeeg/tgdeeg.html#hearing, 2006. [8] pitkänen m. quantum mind, magnetic body, and biological body. in tgd based view about living matter and remote mental interactions. onlinebook. available at: http://tgdtheory.fi/public_ html/tgdlian/tgdlian.html#lianpb, 2012. [9] pitkänen m. geometric theory of harmony. available at: http://tgdtheory.fi/public_html/ articles/harmonytheory.pdf, 2014. isbn: issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://www.ncbi.nlm.nih.gov/pmc/articles/pmc4081593/ http://www.ncbi.nlm.nih.gov/pmc/articles/pmc4081593/ http://www.futuremedicine.com/doi/pdf/10.2217/rme.11.69 http://www.futuremedicine.com/doi/pdf/10.2217/rme.11.69 http://www.ncbi.nlm.nih.gov/pubmed/22542702 http://tinyurl.com/ntlxpep http://tinyurl.com/ntlxpep http://tgdtheory.fi/public_html/hologram/hologram.html#homeoc http://tgdtheory.fi/public_html/hologram/hologram.html#homeoc http://tgdtheory.fi/public_html/neuplanck/neuplanck.html#nuclstring http://tgdtheory.fi/public_html/neuplanck/neuplanck.html#nuclstring http://tgdtheory.fi/public_html/tgdeeg/tgdeeg/tgdeeg.html#hearing http://tgdtheory.fi/public_html/tgdeeg/tgdeeg/tgdeeg.html#hearing http://tgdtheory.fi/public_html/tgdlian/tgdlian.html#lianpb http://tgdtheory.fi/public_html/tgdlian/tgdlian.html#lianpb http://tgdtheory.fi/public_html/articles/harmonytheory.pdf http://tgdtheory.fi/public_html/articles/harmonytheory.pdf introduction the notions of 4-d magnetic body and bio-harmony problem how the notions of magnetic body and bio-harmony could help to understand inheritance questions about bio-harmony can the notions of magnetic body and bio-harmony explain something that ordinary genetic cannot? rna is transferred between soma cells and germ cells login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > 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register with this site forgot your password? issn: 2159-046x microsoft word robertcampbell9_v2n3 dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 254-267 campbell, r., part i: a critique of river out of eden: our celestial prison issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 254 article part i: a critique of river out of eden: our celestial prison robert campbell * abstract the analogy of supernovae is applied to the information explosion taking place on our planet that he calls the replication bomb, linking it to dna. the exponential growth of information is unrelated to the growth of digitized dna information, because the linear branches of the evolutionary tree are unrelated acccording todawkins’ reckoning. the vast majority of historical species are extinct so the river of genes must be drying up. he cites a simple self replicating chemical of two links in its chain as evidence that life must have started as a chemical accident while dna can have billions of nucleotide links wrapped around complex histone spools. chemical reactions in a cell require protein enzymes that employ non-covalent forces to catalyze them in highly recursive patterns so the cell survives by complex energy patterns that are not chemical in nature. dawkins proceds to identify ten thresholds triggered by the replication threshold, essentially following a process of hierarchical order contrary to the darwinian position of random order that he is otherwise committed to. key words: charles darwin, theory of evolution, cosmic order, intellegent direction, spirituality, atheist, richard dawkins. 5the replication bomb: dawkins begins this chapter of his book with reference to the three supernovas that have been observed in our galaxy since chinese astronomers first documented a star exploding in 1054, to leave the crab nebula in its wake. he applies the analogy to the information explosion that he says has occurred on our planet, and that he calls the replication bomb, linking it to dna. “the reason self-replication is a potentially explosive phenomenon is the same as for any explosion: exponential growth—the more you have the more you get.” double speak creeps in again here for he jumps from dna replication to our technological culture. we have seen that the latter is dependent upon language and is not genetically programmed by accident. it is through us, he says, “—through our brains, our symbolic culture and our technology—that the explosion may proceed to the next stage and reverberate through deep space.” but why, in the first place, are we to assume that there has been an exponential explosion of digitized information via dna survival? if less than one percent of species have survived to the * correspondence: rober campbell, independent researcher. website: http://www.cosmic-mindreach.com e-mail: bob@cosmic-mindreach.com note: the articles presented in this issue are based on my book “downsizing darwin: an intelligent face for evolution” self-published in 1996 [1]. more information is available at my website [2]. dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 254-267 campbell, r., part i: a critique of river out of eden: our celestial prison issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 255 present, this indicates a growing proportionate loss of information that has been accumulating through the evolutionary process. the only way it could be preserved is if some intelligent process could reemploy the information gained from extinct lineages to enhance the evolving characteristics of surviving lineages. the mammals for example diverged early in the reptilian age some 160 million years before the demise of the dinosaurs. we might expect an intelligent process to work in much the same way that we humans are able to reemploy the lessons we learn in one circumstance to help us cope in certain other circumstances that arise in the future, since different experiences are frequently presented to us with inherently similar characteristics. intelligent creatures are endowed with memories and a capacity for recall that permits the spanning of space and time. to the extent that we can understand the ever changing stream of circumstance we can tailor old memories to reapply similar techniques to new situations. memories are not hard wired to the thought process, since the abstract concepts of thought are not hard wired. however, the recall process is tensionally coupled to sensory input such that it is always relevant to the ongoing stream of circumstance. as a simple example, when we see that we are out of groceries, we remember that we must go shopping to stock up for future needs based upon our past experience. we span space and time through our perception of appropriate needs and we respond accordingly. it is in this way that we effect the integration of history, and the evolutionary process is busy at the same endeavor. so is the whole cosmic order that turns the heavens. but all of this is contrary to the darwinian position. so accordingly information digitized by dna must be being lost. dawkins then turns to the origins of life. he concedes that there is no direct evidence of the replication event that started life on the planet, but insists that it must have begun as a chemical event. there is no evidence whatever for that either, but most darwinists seem certain that it was through a series of chemical accidents that biological life got started. that is blind unsubstantiated belief. it is difficult to understand why anyone should volunteer to be so totally committed to a mindless idea that requires their own complete psychic demise at death. after an excursion through right and left handed stereoscopic chemicals that rotate polarized light in opposite directions, and that can act as a template for their mirror image forms, dawkins comes to the work of rebek and colleagues. these researchers demonstrated that true self replication is possible among simple molecules, something that molecules don’t normally exhibit. two small molecules are shown to join in solution to make a third, which then acts as a template to promote the formation of more of itself from the two starting molecules still in solution. the population of the product molecule thus grows exponentially. one of the starting molecules comes in a variety of forms so that there can be competing varieties of the product molecule replicating itself. ultraviolet light can also mutate one of the products into a slightly different form which is more adept at replicating itself and soon dominates the test tube population. dawkins is so sure that rebek and colleagues are on the road to replicating the origins of life that he refers to these simple chemicals as “protocreatures.” one can hardly construe this as impartial science. these “protocreatures” consist of a chain with only two links and the two starting molecules chemically combine to produce them initially, without benefit of their template. one dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 254-267 campbell, r., part i: a critique of river out of eden: our celestial prison issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 256 might as well say that they can jump to jupiter because they can jump a foot. all it takes is a little more practice. dna can have billions of links in its chain and its monomers do not join up spontaneously without benefit of a template and a great deal more. they need enzymes to specifically catalyze thousands of essential chemical reactions in the life of a cell. enzymes are large protein molecules that fold up in specific ways to fit the reactants together in just the right way for them to combine in each reaction. they can speed up the reaction rate millions of times, so that each chemical reaction in a cell needs one. they are produced by the machinery in the cell, with the aid of still other enzymes, according to dna blueprints that encode their amino acid sequences, typically hundreds to thousands of units long for each enzyme. enzymes have active sites that bind reactants by noncovalent forces and they are not themselves chemically altered in the process of catalyzing reactions. they are themselves transcribed and translated with the aid of enzymes so the whole process is a highly recursive energy pattern distinct from the covalent molecular chemistry that forms the cell and its organelles. 1 selection must take place from twenty amino acids that must each be identified and brought into place for assembly in a very precise order. the assembly machinery consists of many ribosomes which are chains of rna, also produced with the aid of still other enzymes from dna, and these are precisely connected and folded into complex nodules. the assembly machines themselves are useless without both transfer and messenger rna, both of which are transcribed with the aid of still more enzymes from dna which must partly unravel from the histone spools it is wrapped around in exactly the right place for this to happen. a host of transcriptions factors and epigenetic factors are essential to the process. messenger rna brings to the ribosomes the section of blueprint from dna that encodes the amino acid sequences for making a specific protein, while transfer rna collects the necessary amino acids and brings them to the ribosomes for assembly. non-coding dna and rna comes into play in a complex variety of ways. it is obvious that migrations throughout the cell must be specifically directed, timed, and integrated, according to an incredibly complex host of needs, yet the direction process is a complete mystery. the cell membrane must also remain in contact with the external environment and for this purpose it has complex proteins embedded in it that contact numerous external chemical messengers and trigger complex internal sets of chemical messengers, many of them in cascades of reactions that transmit chemical instructions to dna. the cell must also acquire essential raw materials and cut them up like vegetables for a stew but in precise ways with the aid of still more enzymes. and the cell must identify and dispose of waste materials as well as repair itself and maintain a membrane together with its internal architecture. then every once in a while it must spontaneously divide itself in two, each half containing precisely one complete set of encoded plans, together with all of the other equipment and enzymes necessary to continue the work. miss out a few critical enzymes and the whole thing won’t work. bacteria typically have a few thousand enzymes to catalyze the necessary chemical reactions. the eukaryotic cells that are the building blocks of all plant and animal life are much more complex, somewhat like comparing a 1 http://www.cosmic-mindreach.com/gene_expression.html dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 254-267 campbell, r., part i: a critique of river out of eden: our celestial prison issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 257 747 to a motorcycle. they have many more enzymes that are required to function in a much more complex environment with a nuclear envelope and a complement of other organelles. but even the simple bacterium has as much traffic within it as a large city crammed with motorcycles, cars, and trucks, each headed for specific destinations to perform a great diversity of tasks and guided by processes that we can hardly guess at. the simple truth is that it remains a complete mystery how these diverse and incredibly complex and interdependent processes ever came together into a functional whole by any means imaginable, much less by accident. the simple truth is that the collective ingenuity of all of the biologists on earth still cannot begin to fathom how the many pieces of the puzzle work together, even after having identified much of the chemistry involved. they have no means at their disposal by which to research how experience itself is organized and integrated. the darwinian paradigm precludes it, since darwinists believe they already know. undaunted, dawkins plods onward. he points out that it is only in the last few decades of our four billion year evolutionary saga that our nervous systems have developed radio technology and now an expanding shell of information-rich radio waves is advancing outward from the planet at the speed of light and might one day be detected by remote civilizations far out in space. he calls it “...the radio threshold—the moment when a proportion of the information overflows from the parent world and starts to bathe neighboring star systems with pulses of meaning.” note the double speak use of the word “meaning.” here richard dawkins unwittingly confirms that he himself believes that there is such a thing as a basis to meaning that is not genetically programmed and that altogether completely transcends dna survival. how else could alien creatures hope to intelligently identify it? he has just finished saying, “the centaurian radio astronomers would report, amid fanfares of excitement, that the star sol had exploded in the informational equivalent of a supernova (they’d guess but might not be sure, that it was actually a planet orbiting sol.)” from this he says we can guess that information explosions “...pass a graded series of thresholds.” he has now begun to talk about the nature of a tiered order that transcends and subsumes random mutation and natural selection, in open contradiction to his own earlier position, which somehow seems to conceal the meaning in his own words from himself. he certainly isn’t a bad fellow at heart. he first identifies five major thresholds in reverse historical order: the radio threshold, the language threshold, the nerve-cells threshold, the many-cells threshold, and the replicator threshold. the last one is now called “...a triggering event that made the whole explosion possible.” from here he jumps back to his old position and uses the example of chain letters to emphasize the enormity of the numbers that result from geometric progressions, and different strategies that people may invent to get the letters duplicated. then he says, with reference to the letters, “it is important to understand that none of these replicating entities is consciously interested in getting itself duplicated.” dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 254-267 campbell, r., part i: a critique of river out of eden: our celestial prison issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 258 of course chain letters are not interested in getting themselves duplicated. that’s exactly the point! neither are inert chemicals like dna. chain letters have intelligent agents behind them, namely people that are manipulating their content in order to achieve their replication. so does dna have intelligent energies working behind it, manipulating its content so that it relates meaningfully to the working machinery of the whole cell, as well as to organs and host in complex multi-celled creatures. like chain letters, living creatures are complex communications systems in intimate contact with themselves and their environment. “but it will just happen that the world will become filled with replicators that are more efficient,” he says, ignoring the fact that people are writing the letters, just as all darwinists ignore so much obvious evidence that intelligence is implicitly at work in the creative process. just because a letter may be left unsigned is no reason to assume that it wrote itself. dawkins adds the example of the “st. jude letter” to show how easily people may be duped into believing, implying that anyone who believes there is anything more than random chemistry at work in the creative process is also easily duped. on the face of the evidence the opposite is true. “a successful replicator molecule will be one that, for reasons of detailed chemical technicality, has what it takes to get duplicated,” says dawkins, implying that although the technical details are beyond most readers, we may take his word for it. “all the organs and limbs of animals; the roots, leaves and flowers of plants; all eyes and brains and minds, and even fears and hopes, are the tools by which successful dna sequences lever themselves into the future,” he says. but you can extract pure dna from a cell and place it floating freely in a jar with all the necessary monomers to replicate itself and it will not do so. naked dna is an inert chemical. that is why it is able to preserve genetic integrity. by stressing this theme over and over dawkins expects us to believe that life got started by simple self-replicating chemicals that by some completely unknown series of accidental steps became dna, a complex chemical that is not remotely similar. but even if we take raw dna or rna as a starting point, we are still no closer to life. we can sprinkle dna in the earth, and streams and lakes and rivers and oceans and organic soups forever and it will not initiate new life. this in fact happens daily on a huge scale, complete with the cellular machinery that surrounds it, every time a leaf falls or a creature bleeds or kills or dies, but new life does not reassemble itself and come creeping out of our graveyards. the host creature is not something physical, and when it dies, the life disappears from the chemistry. the host is a manifestation of the intelligent processes that guide and direct the chemistry of life. the host is a microcosm in the universal chore of integrating history. dawkins next turns back to thresholds for a guess at the steps in the chronology of a life explosion on any planet, anywhere in the universe, the series of thresholds through which life must pass. he is entitled to his guess, even though he is unaware that he is back to sniffing out the nature of hierarchies in the cosmic order. he is talking about deciphering an order to life that transcends and subsumes its primary chemistry. he is also talking to a certain extent about climbing a ladder of sentient awareness to conscious thought. but then, typical of his science training, he reverts to a dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 254-267 campbell, r., part i: a critique of river out of eden: our celestial prison issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 259 linear progression of technical achievements rather than stick with our continued evolution as intelligent beings. he then adds to his initial five thresholds and identifies ten thresholds in all, and some of them are legitimate levels in a universal hierarchy of a higher order than the three levels idea→routine→form identified earlier. he even says that some of these steps are likely to be genuinely universal, while others may be peculiar to our own planet. “it may not always be easy to decide which are likely to be universal and which local, and this question is interesting in its own right.” so dawkins does have some inspiring glimpses into reality. he really does believe in transcending universal influences that are operative in the creative process. he is even attempting to integrate history through the chronology of the thresholds. and him a darwinist no less! before reviewing dawkins’ ten thresholds it is worth diverging for a moment to explain a little about hierarchies. since we all encounter them in business organizations it will be convenient to explain how they become established there. in a one man business there are no hierarchies apparent because they all exist in the intelligence of one man and he does all the physical work. to an outside observer the physical work is all that is seen and we may call this the form level. behavior takes a certain form and gives a specific form to a product. let’s say our businessman is making stainless steel screw nails for the marine industry. lets call him hank. hank has one machine that he operates himself, he purchases and stocks the raw materials he needs, he keeps his own books, he services and repairs the machine, and he makes his own sales and deliveries. he is a factory laborer, purchasing agent, warehouseman, accountant, repairman, salesman and delivery boy all wrapped up in one. all the variety of jobs that hank does are form level work, that we might better call functional work in the case of a business. hank’s business is good and in no time he has twenty machines making stainless bolts and a variety of fittings as well as screw nails, and all the jobs that he used to do have been delegated to fifty or sixty employees. they are divided into departments that each do different kinds of functional work. even the foremen or heads of these small departments are concerned with the form of their final product and thus do functional work through focusing on task cycles. does that mean that hank now has nothing to do? not on your life. now he has headaches with matching up work schedules with sales commitments, and cash flow financing with customer credit, and inventory levels with turnover, and costing with pricing, and quality control verses customer satisfaction, and equipment maintenance versus replacement, and rental space versus purchase, and more, that all used to fall into place simply in his head. now he has to commit plans to paper and keep records that never used to be needed. he has to budget all his resources against all his commitments according to product cycles. this is a new kind of work that does not directly involve the form of the end product that employees in each department produce, whether it be a balance sheet or screw nails. hank’s work dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 254-267 campbell, r., part i: a critique of river out of eden: our celestial prison issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 260 now involves the routines of his business that are predominantly associated with product cycles as opposed to task cycles. we may call this kind of work supervisory work, keeping in mind the special meaning associated here with the word supervisory to distinguish it from functional work. a supervisor in this sense works on a higher level of abstraction than a functional foreman. and now hank has to do hiring, and evaluate pay levels, and train and discipline as well, but this is usually of a functional nature. hank’s business continues to prosper and grow. he has started to cast, forge and machine larger stainless fittings, valves, and small pumps, all for the marine industry. he has put a down payment on factory space and offices that now house five hundred employees. he has had to further delegate the personnel function at the functional level, and he has also had to appoint a plant superintendent responsible for supervisory level work in the operations department, with plant foremen, maintenance foremen, scheduling, quality control inspection, and cost accounting, all at the functional level reporting to this superintendent. he has also had to develop an engineering and design department with delegation of supervisory work to a chief engineer, with design engineers, draftsmen, mold makers, costing and budgeting, scheduling, materials testing, and technical inspection all at the functional level reporting to him. he has also had to delegate work at the supervisory level to a sales manager over a sales department, and to a chief accountant over a treasury department, each with a variety of tasks at the functional level reporting to them. hank himself is now obliged to concentrate primarily on what we will call administrative level work, concerned with the assimilation, maintenance and development of knowledge implicitly essential to the facilities, to the technical and human resources, and to the infrastructure of the organization generally. he is concerned with these kinds of infrastructure cycles, as opposed to product or task cycles. a three level universal hierarchy was previously identified but it subsumes and transcends a four level universal hierarchy in which explicit knowledge becomes distinct from the integrating idea. a four level hierarchy may therefore be described as follows: idea→knowledge→routine→form. four levels are common in large organizations whether economic or biological. hank’s work has now graduated to administrative knowledge level work. it soon becomes apparent to hank, however, that conditions are just right for him to go international and if he doesn’t do so, it could adversely affect his business at home since boats and ships travel the world and they need service. in order to do so he must fill out his line of products, have a network of international distributors and a couple of manufacturing plants abroad. he has to delegate administrative level work to develop the necessary facilities, resources and infrastructure. he also needs a marketing department, probably at the supervisory level, completely distinct from sales, to assess international markets and keep the stream of available products current with market needs. the other five departments, operations, engineering, sales, treasury, and personnel, will probably all be promoted to administrative level work with vice president chiefs. hank has had to move up another level of abstraction in his everyday thinking. as president and managing director, he is now concerned primarily with idea level managerial work. this kind of work integrates, maintains, develops and diversifies, or consolidates his far flung organization. this work gives overall coherence and direction to the organization. it was there when he was a dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 254-267 campbell, r., part i: a critique of river out of eden: our celestial prison issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 261 one man operation too, but he was too busy to give it much notice. nor did he need to. now it requires nearly all of his time. the point in all of this is that every business organization during its growth goes through these same four major stages of delegation up a hierarchy of different levels of work. (in still larger organizations the process starts again with a broader focus, involving considerable diversification.) as delegation proceeds the same six departments always break out, tailored only to the nature of the business they are in. within the larger departments, especially operations, the same six subdepartments break out again within it as it grows. in practice intermediate levels of work creep in and the six departments are not always separately delegated, but invariably when this happens bureaucracy and political in fighting begin to erode the organization from within. the organization loses its transparency and ceases to operate intelligently and responsibly. 2 note, however, that direction in the hierarchy always comes in reverse order to that in which delegation occurs. idea gives direction to knowledge which gives direction to routine which gives direction to form. thus it is also in the evolutionary order. we have evolved up through the plants (cellular form), the invertebrates (motor sensory routine), the vertebrates (cerebral awareness in knowledge), to homo sapiens (idea integrating history). the history of our evolution has been incorporated into our anatomy such that our creative ideas give direction to our accumulated knowledge which gives direction to our motor sensory routines which animates our physical form. but this pattern is surely a reflection of a self-similar pattern to universal intelligence that has directed the evolutionary process in the first place, as the evidence clearly and powerfully indicates, culminating in the delegation of conscious intelligence to humans. when we come to assess the evolutionary process in this light, the futility of the darwinian position becomes apparent. it fatally cripples itself by focusing exclusively on the physical form of chemical processes, which are valid enough in their own right, but they don’t give direction to the evolutionary process. by concentrating exclusively on the lowest level in the hierarchy darwinism has no hope of ever advancing up through the hierarchy to understand the integration of living processes. the more darwinists win, the more we all lose. with these thoughts in mind let’s return to richard dawkins’ ten thresholds. the first threshold, he says is the arising of some kind of self copying system with some rudimentary form of hereditary variation, with occasional random mistakes in copying, which he says will result in a mixed population competing for resources which will become scarce. now the earliest fossil evidence of life has recently been pushed back to nearly four billion years ago, almost immediately after the planet had cooled sufficiently for life to survive, so it didn’t take 2 a full description of the principles involved in structuring a business organization, and how to apply them, is given by the author in enlightened management and the organizational imperative. http://www.cosmicmindreach.com/management.html . see also http://www.cosmic-mindreach.com/organize_structure.html and http://www.cosmic-mindreach.com/three-brains.html dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 254-267 campbell, r., part i: a critique of river out of eden: our celestial prison issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 262 vast spans of geological time for life to evolve, despite infinite odds against it happening by accident. this should lead us to look for another route as to how it began. one reasonable alternate was suggested early in the century by svante arrhenius, and it was promptly ignored. a nobel prize winner in 1903, he suggested that the earth could have been seeded by spores arriving from interstellar space. sir fred hoyle and chandra wickramasinghe have further investigated the possibility and found it quite possible that bacterial spores and perhaps very small eukaryotic spores could survive the rigors of interstellar space and be carried by comets to the inner solar system where solar radiation pressure is sufficient to carry them to a soft landing on planets with atmosphere. it offers a credible mechanism by which life could be seeded on suitable planets from an interstellar gene pool. there are also mechanisms by which dormant spores can be ejected from planets to maintain the pool. asteroid impacts, for example, are common in the early life of planets and they can readily eject spores into interstellar space. these efforts to investigate alternate origins to life on the planet have been largely ignored. the darwinist lobby is powerful. even though the findings make a lot more sense than bacteria forming themselves spontaneously by accident in a primordial inorganic soup, they are dismissed. hoyle and wickramasinghe conservatively computed the odds of producing by chance from twenty amino acids just the two thousand enzymes necessary for a simple bacterium to function. they are 10 40,000 to one, against. there are no names for such vast numbers. it would take ten pages just to type out forty thousand zeros after a one. it is infinitely more than all of the electrons and protons in the universe. (that number can be written in a couple of lines.) and those odds only get us the enzymes. they do not tell us how the enzymes work together with dna and rna to produce the organized machinery of the cell. but darwinists turn their heads and go back to talking about chemical accidents, ignoring odds that a bookmaker wouldn’t take if the planet had a billion billion years to work the result. it’s more possible that life was seeded intentionally by advanced alien civilizations. the appearance of eukaryotic cells is as much a mystery as that of prokaryotes, for their level of complexity is several orders of magnitude greater. even the “miracle” option is more possible than chance. it would entail a transcendent intelligence “moving on the face of the deep,” directly assembling the first living cells and setting them about the task of replicating. there are surely organized energies of some kind at work in the cell that govern the complex migrations of chemicals to the right places at the right times as if they were all in communication in response to mutual needs. but it’s not necessary to invoke this kind of speculation when the panspermia theory of arrhenius, hoyle and wickramasinghe can be tested. 3 in any case the development of the plants and their competition for resources did not deplete the planet’s resources so much as enhance them. plants capture the sun’s energy and store it, in apparent defiance of the second law of thermodynamics, since even in death their decay products leave the environment more ordered. each chemical reaction in a cell or a plant obeys the second law, leading to an increase in disorder, and yet the intelligent integration of all the interdependent 3 a description of the panspermia theory and evidence as to how it may work is given in evolution from space, by f. hoyle and c. wickramasinghe, granada books, london, 1983. dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 254-267 campbell, r., part i: a critique of river out of eden: our celestial prison issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 263 reactions and processes going in a cell, taken together as an integrated whole, generates an increase in order. it cannot be an accidental process attributable to atomic billiards. but however life got started it was a first threshold. we may assume that much. threshold 2 is the phenotype threshold. “on our planet, phenotypes are easily recognized as those parts of animal and plant bodies that genes can influence. that means pretty well all bits of bodies.” now even single celled creatures have a complex cell body, and since we don’t find chemicals in nature replicating themselves nude, including dna or rna, how can this be assumed to be a threshold at all? the living record is replete with surviving examples of every other major step in the evolutionary process. the self-replicating mechanism, as we know it, is utterly dependent upon the complex machinery of the whole cell and there is no sound reason to expect that it has ever been otherwise. there are many hundreds of enzymes in the simplest bacterium that are necessary to catalyze the chemistry essential for replication together with the growth and maintenance of cells generally. let’s set this threshold aside as redundant. threshold 3 is the replicator team threshold, “...which may on some planets be crossed before, or at the same time as, the phenotype threshold. ...the genes work in teams.” genes are obviously organized in some way to integrate information and to produce a coherent result, and again there is no sound reason to expect that it has ever been different. the simplest free-living cells, pleuromona, are estimated to have about a thousand genes, most of them committed to encoding the amino acid sequences in making the protein enzymes that are essential to catalyze the chemistry essential for replication, maintenance and growth. escherichia coli, a more typical bacterium, has about 4000 enzymes. the latter translates to about 4,000,000 base pairs in precise sequence, a far cry from two links in the chain of a self replicating chemical under controlled conditions. a human being has about 2.9 billion base pairs in its genome, and for some strange reason the genome of the south american lungfish is about thirty-five times larger than that of the human. in any case there is a total absence of evidence to indicate a progression from replicating chemicals to a cell body with genes working in isolation, to genes working in teams. the evidence in fact indicates that threshold 3 came at the same time as thresholds 1 and 2, that the living cell is so interdependent on all of its working parts that it somehow appeared on the planet as a functioning whole. but dawkins doggedly pushes his point further: “...it is obviously tempting to leap to the assumption that darwinian selection nowadays chooses among rival teams of genes—to assume that selection has moved up to higher levels of organization. tempting, but in my view wrong at a profound level,” he says. it is hard then to understand why a hundred and sixty million years of prolific reptilian evolution should be wiped out in favor of a few ancient rodents, asteroid catastrophe or not. perhaps there is a fear that selection moving up to higher levels of organization directly implies that there is a more fundamental order to the creative process than random chance. that would be a crack in the armor that would bring down the darwinian edifice. and yet there are hierarchies recognized in gene expression, since homeotic genes are known to activate teams of genes in concert. dawkins identifies threshold 4 as the many-cells threshold. he skips over the big event that made this possible, the appearance of eukaryotic cells. when cells divide, he observes: “if two cells do not separate fully but remain attached to one another, large edifices can form, with cells dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 254-267 campbell, r., part i: a critique of river out of eden: our celestial prison issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 264 playing the role of bricks.” he doesn’t address the question of why cells should not separate fully, but remain in obvious intimate communication with one another and develop diverse specialized functions which mutually cooperate to some collective end. they are obviously more than insentient bricks. he explains that “...many-celled organs acquire their characteristic shapes and sizes because layers of cells (bricks) follow rules about when to stop growing.” really! how are insentient bricks to follow rules? there must be a development plan that is communicated to all cells in the organ and the organism, all of which have identical genes. some communication system must be operative to switch specific genes on and off in each cell at just the right time for it to assume a specialized function in relation to all the other cells. and genes themselves must be hierarchically ordered in an intelligent way if some are to act in a directing capacity over others. it’s good of dawkins to make the admission that “cells must also, in some sense know where they sit in relation to other cells. liver cells behave as if they know that they are liver cells and know, moreover, whether they are on the edge of a lobe or in the middle.” this is a clear admission that a communicative intelligence is at work in the collective organization of cells. one can hardly assume from this, that how intelligence works is local to our planet. on the contrary intelligence displays all of the earmarks of being universal in its operation. but dawkins has only lapsed back into double speak, for he then says, “whatever the details, the methods have been perfected by exactly the same general process as all other improvements: the nonrandom survival of successful genes judged by their effects—in this case, effects on cell behavior in relation to neighboring cells.” this is more jumping to jupiter. dawkins’ bucket just doesn’t hold water. you can’t write off obvious communication between cells as just “a difficult question” to be explained one fine day in the future, not when the evidence so obviously contradicts the only mechanism darwinists allow to explain it. we may nevertheless accept that multicellular threshold 4 represents another level up an intelligent hierarchy that is implicit in the evolutionary process, the first level being the living cell, that is, the combination of thresholds 1, 2 and 3. dawkins now jumps several hundreds of millions of years in the evolutionary process, from the appearance of multicelled plants to the development of the neuron, which emerged with the invertebrates. threshold 5 is the high speed information processing threshold, which on our planet may be called the nervous system threshold. dawkins believes in his theme, “...because now action can be taken on a timescale much faster than the genes, with their chemical levers of power, can achieve directly. predators can leap at their dinner and prey can dodge for their lives, using muscular and nervous apparatus that acts and reacts at speeds hugely greater than the embryological origami speeds with which genes put the apparatus together in the first place.” dawkins doesn’t see anything fundamentally meaningful in this development other than the survival of dna, and the leverage it gains. but dna survives comfortably in creatures without nervous systems, so where is the leverage? dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 254-267 campbell, r., part i: a critique of river out of eden: our celestial prison issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 265 but then again he turns around and among the consequences he acknowledges “...large aggregations of data handling units—‘brains’—capable of processing complex patterns of data apprehended by ‘sense organs’ and capable of storing records of them in ‘memory.’ a more elaborate and mysterious consequence of crossing the neuron threshold is conscious awareness, ...” so richard does after all acknowledge that there is something mysterious going on in that mystic jelly called a brain, at least to the extent that we don’t yet understand it. he calls threshold 6 the consciousness threshold. of course everything is mysterious until we understand it properly. without mystery there wouldn’t be science. we have seen, however, that awareness is associated with the evolution of an autonomic nervous system in concert with cerebral hemispheres, such that the vertebrates are able to reflect emotive patterns of behavior in cerebral awareness. because all vertebrates are anchored to a common skeletal, sensory, motor, and visceral arrangement, we have access to the emotive feelings of others than our isolated physical selves. awareness begins to transcend the self in awareness of others’ feelings. we all empathize with domestic pets, and they with us. now what has that got to do with the blind survival of dna? it’s very difficult to see how it may convey a survival advantage if predators start to empathize with their prey. and if intelligent social creatures have evolved anywhere else in this vast universe, they too must have acquired an ability to reflect on experience and make sense of it. in humans this awareness of other than self is compounded by the development of language and the ability to abstract experience, to think and plan, incurring a need for intuitive insight into the dynamics of experience itself in order to function at all. and the meaning inherent in words is not genetically programmed. it is intuited from general experience that is independent of our individual genetic makeup, whatever the blessings or burdens endowed by the latter may be. dawkins calls threshold 7 the language threshold, which may or may not be crossed on a planet. but if there is no conscious ability to deal with experience in abstraction, as we do with words, there can be no independent creative activity, no ability to consciously plan, and no consciously entertained collective social endeavors. these things are all dependent on three focal points to the process of thought, namely one intuitive, one emotive, and one behaviorally explicit. this allows for the conscious expression of the universal hierarchy idea, routine and form. dawkins sees all of this as a flat, mechanically interconnected networking system “...by which brains ...exchange information with sufficient intimacy to allow the development of a cooperative technology.” notice how he slips in that word intimacy, a value. how can there be intimacy without consciously abstracting meaning from experience and recognizing another as sharing similar conscious intentions? cooperative technology depends upon it. if this is all genetically programmed there is no meaning to the word intimacy. but dawkins goes on to threshold 8, the cooperative technology threshold. “indeed it is possible that human culture has fostered a genuinely new replication bomb, with a new kind of self-replicating entity—the meme, as i have called it in the selfish gene—proliferating and darwinizing in a river of culture.” it is all so easy, once one realizes the hypostatizing power of words. just give cultural traits another name and make it out to be another progression of accidents devoid of any transcending meaning, now even divorced from dna. just pure greed proliferating dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 254-267 campbell, r., part i: a critique of river out of eden: our celestial prison issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 266 through the cosmos! “beautiful and inspiring!” no wonder he calls it “...too big a subject for this chapter.” threshold 9 is the radio threshold, “...the power to make an impact outside the home planet...” may god forbid! it might be better to hope that some alien intelligence may contact us with some constructive advice, especially in the sciences. of course radio messages have been rocketing into space at the speed of light for nearly a century and in a mere sixty or seventy thousand years increasingly faint echoes of our collective global radio racket could begin reaching most star systems in our galaxy, but not in a meaningful form. “after radio waves, the only further step we have imagined in the outward progress of our own explosion is physical space travel itself: threshold 10, the space travel threshold.” but where are we going to go? the moon is barren, mercury or venus would boil our blood, mars would freeze it, the outer planets would crush and smother us, and we can’t work things out where we are. the other planets in our solar system are also very unlikely to be populated by highly evolved intelligent creatures and the next nearest star system is over four light years away. to get there and return with our present understanding of the physics of the universe would take a lifetime, and the relative time distortion would mean that several life times had elapsed on earth in our absence. perhaps it is fortunate that there are built-in restrictions to space travel, lest our own barbaric ways become contagious before we mature to a responsible age. our current science makes a celestial prison of our planet. if interstellar space travel is possible for intelligent beings anywhere in the universe, they must have a vastly superior understanding of the cosmic order than the simplistic understanding we have so far devised. it is very unlikely that space travel could ever be a practical affair for beings anywhere by traveling through space and time. but a proper insight into the cosmic order transcends space and time. in some vastly superior science this may ultimately make quantum leaps through space possible, but this brings with it other restraints. it is highly probable that intelligent insights into the cosmic order present value constraints of powerful proportions, associated with the mutually conscious evolution of beings from different star systems. it would undoubtedly be an awesome mind expanding evolutionary event. if it was not to have negative consequences for either or both parties, one would expect that it would require highly responsible preparation and planning, as yet far beyond our current capacity to comprehend or relate to. for darwinists the outward vision ends on a sadly impotent note, with a space capsule plummeting outward beyond pluto toward the empty reaches of interstellar space, containing a picture of a naked man and woman. the coordinates of our planet are iconically engraved in relation to the galaxy, in the hope that this tiny craft will someday be met by an alien intelligence that can understand the message. the hope is far more remote than slipping a note in a tiny bottle and setting it adrift, for the ocean of space is immense beyond our accustomed conceptions. to a darwinist we are forever condemned to the cell, imprisoned with the survival of dna in the cell, and the whole vast universe can hold no meaning. although the ten thresholds may at first appear to offer hope of more, it seems that dawkins hasn’t grasped the elements of an intelligent hierarchy after all. dawkins’ heart is obviously in the right place, for his hopes are high, but the darwinist logic precludes their realization. dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 254-267 campbell, r., part i: a critique of river out of eden: our celestial prison issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 267 references 1. robert campbell, downsizing darwin: an intelligent face for evolution. mindreach library (1996). 2. http://www.cosmic-mindreach.com 3. richard dawkins, river out of eden: a darwinian view of life. basic books (1996). 4. richard dawkins, the blind watchmaker: why the evidence of evolution reveals a universe without design. w. w. norton & company (1996). 5. richard dawkins, the selfish gene. oxford university press (1990). 6. http://www.cosmic-mindreach.com/gene_expression.html 7. fred hoyle, chandra.wickramasinghe. evolution from space. london: granada books (1983). login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x dna decipher journal | august 2019 | volume 9 | issue 1 | pp 13-21 smith, s. p., a possible holarchy representing morphic resonance as one side of the poised realm issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 13 article a possible holarchy representing morphic resonance as one side of the poised realm stephen p. smith * abstract the theory of morphic resonance is unified with warm-body quantum mechanics following the ontological basis that describes the poised realm that depicts a balancing act involving quantum coherence and decoherence. morphic resonance more properly belongs to the side of quantum coherence, leaving the other side the place where classical mechanics applies. this equally turns time into something two-sided, leaving open the possibility that proto-emotion sources the middle-term that holds the sides together. keywords: holarchy, morphic resonance, poised realm, quantum mechanics, middle term, coherence, decoherence. 1. introduction alfred north whitehead 1 permits duration to impact his process philosophy leading to a panpsychism that time has gotten into; in the sense of an impact that is timeless across the duration. likewise, henri bergson 2 lets duration impact his proposed vitalism that then comes with similar properties. smith (2018) also hypothesized that time got into biological life, and proposed an epigenetic model that regulates dna function based on a proto-emotional driver that comes from a timeless source. time and proto-emotion were completely confounded according to smith, and smith pointed to the vattay and kauffman’s (2012) “poised realm” depiction of warm-body quantum mechanics as a possible supporting ontology. left then out of consideration was sheldrake’s (1995) morphic resonance having to do with remembering past context or forms in the present moment, that is remembering in a broad sense having to do with panpsychism, crystals, biological life, and including mind. the purpose of the present note is to attempt a unification of the three models, smith’s timesensed vitalism, sheldrake’s morphic resonance, and vattay and kauffman’s poised realm. the discussion will necessarily deal with the challenges that come from different semantics, not that the present attempt is completely successful. these challenges typify anything having to do with alternative interpretations of quantum mechanics. note, for example, how quantum nonlocality can substitute for retrocausation, and how retrocausation can explain non-locality. it is to be proposed that sheldake’s resonance that comes from the past is indistinguishable from quantum wave functions in the present moment, and that any distinction is only one of correspondence: stephen p. smith, ph.d., independent researcher. e-mail: hucklebird@aol.com 1 in process and reality. 2 in creative evolution. dna decipher journal | august 2019 | volume 9 | issue 1 | pp 13-21 smith, s. p., a possible holarchy representing morphic resonance as one side of the poised realm issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 14 semantics. nevertheless, the present paper maintains the belief that the future is undetermined, and that foretelling the future is overated as an exact science even as it is possible to forecast the future by using our powers of deduction, induction and intuition. there are no wave functions coming from the undetermined future, alternatively, what is known about the future is only context returning to the big bang in reverse time. likewise, time travel into the past does not permit changing the past 3 , time travel into the past is only at best remembering the past. all of these subtleties fall under semantical meanings that sometimes can conflict, but the goal remains to avoid such conflicts in attempting a unification. this unification is equally a theory of time that comes as something two-sided and comes with a middle-term. arthur koestler (1982) made famous the concept of holon and holarcy, and these are reintroduced in section 2 but by including a time-sense that looks forward and backward in time. the time-sensed holarcy is a necessary building block for the unifying treatment of morphic reasonance that is presented in section 3. the same unification is extended to the poised realm in section 4. concluding remarks are made in section 5, including listing some open questions that can in principal be put to scientific testing. 2. holarchy and time a set of holons, nested in other holons, are represented by figure 1, and showing collectively the holarchy at one snap-shot in time (the present moment). 3 not withstanding the delayed choice experiment, and retrocausation. dna decipher journal | august 2019 | volume 9 | issue 1 | pp 13-21 smith, s. p., a possible holarchy representing morphic resonance as one side of the poised realm issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 15 the static image of the holarchy carries two faces, however: one face looking forward in time (the white areas) and acts as a conduit for a forward flowing determinism; the other face looking to the past (black areas) representing context and form, frequencies and habits. inside the white circles the black holons carry emotions that are found competing with each other, whereas in the black circles the white holons carry the emotion of cooperation with their neighbors. this division of labor is not intended to carry value judgments, however, such as cooperation is good and competition is bad making the black background heaven and the white background hell. these are just arbitrary distinctions that give the holarchy a time sense. a theory of evolution that has been sanitized to remove the slightest hint of emotion will project only the features of competition and cooperation. christian de duve (1995) sees biological evolution as a natural selection that operates only within preset limits, coincidentally hinting of the holarchy described above. in a similar vain, morowitz (2002) sees broad-scale evolution as the operation of pruning rules that are each active in different levels of a natural hierarchy, again hinting of an underlying holarchy of a kind hinted at by figure 1. figure 1 represents a flat-land projection of the real thing that holds an emotional connection among holons, but otherwise the emotional connection becomes invisible 4 when projected on a flat surface. the flow of determinism representing white areas of figure 1 mirrors the second law of thermodynamics where collective organizations degrade into disorder and fragmentation. therefore, the black regions represent pockets of the universe where the second law acts in reverse, where fragments unite into wholes forming order in the chaos, a possibility that agrees with sidis (1925). however, the black areas represent context or form and tend to get ignored given the dominance of the white areas representing content. 5 the black areas point to a return to a larger whole in reverse time, returning to the whole that constitutes the entire universe. the black areas are the cpt inversion 6 of the white areas, making a two-sided time and removing any conflict with known physics. the reverse-time pull to unity (black areas), and the forward-time push to fragmentation (white) areas, act as strange attractors that leave reflections on the substrate of evolution. proto-emotion is placed in the timeless middle-term that holds time’s sides together, and brings with it an evolution that is now emotive. time is not a flow, rather time is a perpetual triad of past, present moment, and undetermined future. to prehend causation and emotion as described by whitehead, is to get caught up in the flow of forward marching causation as a conduit, a flow that can show great passion and can be expressed as a deep deductive chain of thought that anticipates and plans ahead. to surrender emotion, or center emotion, is to fall into the surrounding context, and this practice can carry great compassion and expressive creativity and including inductive thinking by remembering past habits as form. both deduction and induction are activities learned from past habits, but both are used for making a forecast of the undetermined future that is yet to unfold; therefore, deduction and induction as found as emotive 4 in the same way rationalism may incorrectly eliminate emotion from reason. 5 to observe anything requires the synthesis of content with context, a trinitarian version of the holographic principle. 6 cpt is acronym for charge-parity-time. the cpt inverse reality is composed of anti-particles that are mirror reflected and that evolve in reverse time, agreeing with all the action principles that make up unified field theory for the non-inverted state. dna decipher journal | august 2019 | volume 9 | issue 1 | pp 13-21 smith, s. p., a possible holarchy representing morphic resonance as one side of the poised realm issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 16 polarities in their primitive state are highly adaptive qualities of life. a simple nested holarchy is described as dna nested in cells, cells nested in organs, organs nested in organisms, organisms nested in communities, communities nested in the biospheres, and the biospheres nested in the universe. a finer resolution is possible with improved science, but a better classification should be based on quantum entanglement and merge with biochemistry and the pattern of inheritance. note that the holarchy as a snap-shot in time is not necessarily equivalent to an animal pedigree, or the tree of life (showing phylogeny), that are found in time. figure 2 shows phylogeny as a tree. trying to identify holons in time that shows phylogeny would have to account for first emerging phylum and branches that go extinct, and this confounds the apparent nesting as a snap-shot in time. nevertheless, the pattern of inheritance represented by a tree also implies a holon nesting as a snap-shot in time, and this is completely missed in a holarchy based on a simple classification. figure 2. tree of life showing simplified phylogeny (ref: the evidence of evolution by nicholas hotton iii, smithsonian, 1968). dna decipher journal | august 2019 | volume 9 | issue 1 | pp 13-21 smith, s. p., a possible holarchy representing morphic resonance as one side of the poised realm issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 17 3. morphic resonance sheldrake (1995) describes morphic resonance as a memory that emerges from the past that connects to the present moment and becomes available. in effect, the past is found living in the present where forms and context are borrowed again, and reused. the human form, the apple tree from, the star fish form are all examples of general forms that are reused by life presently living. the ontological basis of morphic resonance can be described by a nested system of holons that is depicted by figure 5.9 in sheldrake (1995), that also looks closely like figure 1. figure 1 is different in that it shows dark areas and white areas that represent a time-sense. but both figures are intended to connect back to the past where the contextual nature of any particular holon first appeared. note that a black area in figure 1 indicates contextual information that is available in the present moment, assumed to be there even if it tracks back to the past as sheldrake describes. an alternative formulation is to represent contextual information that first appeared in the past as stored in a holograph, or in the holographic universe (e.g., talbot 1992). while this formulation has some utility, figure 1 is general enough to represent the same storage while allowing for a different feature that is provided by the white areas that show a different side to the time polarity. figure 1 breaks from sheldrake’s formulation because it’s the black areas alone that are responsible for the morphic resonance that reappears in the present moment, leaving the white to carry a forward marching determinism. because proto-emotion holds times sides together, holding black to white in figure 1, it is understood that it’s the emotional connection to the past that makes it possible for memories to resonant in the present moment. in other words, emotions in the past go through a transfiguration and reappear in the present moment as memories. remembering represents a form of time travel into the past, a process that can be facilitated by emotive centering. sheldrake (2012, chapter 8) also recognizes the importance of emotions that can conjure up memories, with sharper memories available when emotions in the present moment are well entangled with past emotions that connect directly to prior context. figure 1 shows by example how emotions (between black and white) are entangled and all connect to the grounding emotion. this returns to the grand view of time, as two-sided with an emotive middle-term. 4. the poised realm as holon and nested holons vattay and kauffman (2012) describe a new model for warm-body quantum mechanics, that is able to maintain itself in a poised realm through a process of self-resonance, maintaining itself between quantum coherence and decoherence. kauffman (2014) describes this model as a triad: actuals; possibles; and mind. the region of actuals is a world showing classical dynamics that is limited to a forward flow of determinism that is controlled by the 2 nd law of thermodynamics, a world of “newtonian billiard balls” that bounce off of each other as kauffman describes. the flow of determinism (or entailment) is well matched to aristotle’s deductive logic where the principle of excluded middle dna decipher journal | august 2019 | volume 9 | issue 1 | pp 13-21 smith, s. p., a possible holarchy representing morphic resonance as one side of the poised realm issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 18 is strictly enforced. when any quantum wave function collapses into decoherence it is the region of actuals that gets enlarged and comes into being. when a wave function collapses, however, it is also re-established and the poised realm is thus maintained. the actuals represent the white areas in figure 1, or figure 3 below. the region of possibles is the world as a quantum wave function and is found in the state of coherence. the wave function is found in the present moment, and represent possible future states of an evolving system. but it is equally a by-product of the past given the actuals that are found in the past. therefore the possibles equally signify the black areas in figure 1 or figure 3, representing sheldrake’s morphic resonance. kauffman’s mind implies a possible panpsychism that carries a “responsible freewill,” sandwiched between the actuals and the possibles. a responsible freewill is one that carries preferences, and therefore its necessarily emotive. this glue that connects the actuals to the possibles is described as the proto-emotion in the present context. a single poised system may be illustrated simply by figure 3; the black area representing the possibles and the white area the actuals. again the emotive middle-term connects black to white. figure 3 may better describe one holon in isolation, but quantum systems don’t actually exist in isolation. poised systems exits in the universe with other poised systems. the collective of poised systems returns to figure 1 again that’s forced into a nesting, but now representing a grand poised system of its own showing time again with its two sides. table 1 represents the poised realm as a particle/wave duality in the present moment that is set to forward time, but also showing itself polarized in forward time and backward time. in forward time (or the present moment) particles will push forward while quantum waves that represent context will pull to the past; therefore, contextualizing form is pulled into being from a memory found in the past. in backward time these qualities are hypothetically reversed, and its theoretically possible 7 for holons to switch orientation when new nesting is added. 7 this futuristic possibility is highly speculative, if not impossible. sidis (1925) did postulate the existence of “pseudo-living organisms” that live in reverse time and are in theoretical reach by returning to figure 1 and turning white to black, and black to white. dna decipher journal | august 2019 | volume 9 | issue 1 | pp 13-21 smith, s. p., a possible holarchy representing morphic resonance as one side of the poised realm issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 19 table 1: showing particle/wave duality as poised realm, showing time’s pulling and pushing actions. poised realm time’s action time mode particle wave particle wave forward a resonance of a -1 pushing forward pulling backward backward a -1 resonance of a pulling backward pushing forward note: a -1 represents cpt inversion of a. the prediction is that the pulling and the pushing relative to time (itself a type of quantum gravity) is being caused by the conduit that is holding the sides of time together, and is otherwise acting as an aether that is beyond law, the possible source of emotion. table 1 describes the wave-function of particle a as the resonance of a -1 , the echo 8 that a makes when it returns through the aether form the other side of time. the appearance of novelty is not well described by morphic resonance alone. however, it can be described 9 with the proposed unification: as an emotive search in the white area that leads to exhaustion; followed by an emotive surrender and release that returns to the black area; in the black area the solution is echoed back, a quantum search 10 takes place that finds a preferred path among a supper-position, where the selected path holds the creative birth that was sought and resolves the crisis. the stipulation is that this dynamic follows a universal grammar, and is repeated on different levels of the holarchy. 5. conclusion despite their variant origins that carry different semantics, morphic resonance (sheldrake 1995), the poised realm describing warm-body quantum mechanics (vattay and kauffman 2012), and the polarizing emotion that’s confounded with time (smith 2018), all permit unification under one ontology. this is remarkable, and provides some justification for each approach taken in isolation. however, there still may be another hypothetical ontology that is more correct that combines what’s right with each approach while avoiding that which is wrong. inventing interesting ontology is a fine hobby, but what is really important is how this particular unification may point to testable science given the connection to emotion, and given the time sense that is implied. sheldrake (2012) has already compiled evidence to support his theory of morphic resonance. there are new questions listed below that are open to scientific testing, and that come from the proposed unification. 8 the echo is intended to provide future context as a possibility wave, be it gravity, quantum gravity, dark matter, dark energy, or the memory of form. 9 described phenomenally, and not an account that can be made into a blueprint if only because protoemotion is taken for granted. 10 a quantum search involving the selection of a sought path among many held in a supper-position is a feature of advanced quantum computing that one day may be perfected. dna decipher journal | august 2019 | volume 9 | issue 1 | pp 13-21 smith, s. p., a possible holarchy representing morphic resonance as one side of the poised realm issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 20 are those proficient in deductive thinking really more passionate and driven? are those proficient in inductive thinking really more compassionate and reflective? do those that are measurably intuitive take pleasure in reading this paper, where others find only revulsion? do organ transplants carry an emotional memory that gets passed to the recipients? when does emotional entanglement permit a transfer of memory from one party to the other? and does it matter if the memory was made before or after the entanglement? when we read a book are we entangling our emotion with the author’s? if the emotional attachment to the present moment is strengthened, is the short-term memory enhanced? how much information can be remembered from the past? and under what conditions and emotional preparation? obviously, proto-emotion is not necessarily educated or even human-like. it is merely emotional 11 , and therefore an intellectual science will have an easier time being objective by studying subtle connections that are more emotional than intellectual. nevertheless, it is clear that morphic resonance can confound our understanding of genes and epigenetics when a wider venue of causation should be considered. dias and ressler (2014) found that when a mouse is trained to become fearful of rose blossom odor, its offspring were more sensitive to that odor, even though the offspring never encountered the odor. is this really an epigenetic effect showing transgenerational inheritance in mice? or was it due to a morphic resonance across generations having to do with a reemerging emotion? or is the answer yes to both of these questions, like the ontology predicts? proto-emotion will have impacts on gene action, and on epigenetics, so hypothesized but also on the immune response, neuroplasticity, homeostasis, and as well on our experience of free choice. how are all these biological behaviors impacted by emotion? references dias, b.g., and k.j. ressler, 2014, parental olfactory experience influences behavior and neural structure in subsequent generations, nature neuroscience, 17, 89-96. de duve, c., 1995, vital dust: the origin and evolution of life on earth, basic books. kauffman, s.a., 2014, beyond the stalemate: conscious mind-body – quantum mechanics free will possible panpsychism possible interpretation of quantum enigma, arxiv achieved, paper # 1410.2127. koestler, a.., 1982, the ghost in the machine, last century media. langan, c., 2017, an introduction to mathematical metaphysics, cosmos and history: the journal of natural and social philosophy, 13 (2), 313-330. morowitz, h.i., 2002, the emergence of everything, oxford university press. sheldrake, r., 1995, the presence of the past: morphic resonance & the habits of nature, park street press. 11 and faithful to a universal grammar, even langan’s (2017) “cognitive-theoretic model of the universe”. dna decipher journal | august 2019 | volume 9 | issue 1 | pp 13-21 smith, s. p., a possible holarchy representing morphic resonance as one side of the poised realm issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 21 sheldrake, r., 2012, science set free: 10 paths to new discovery, deepak chopra books. sidis, w.j., 1925, the animate and the inanimate, the gorham press. smith, s.p., 2018, time, life & the emotive source, journal of consciousness exploration & research, 9 (8), 707-721. talbot, m., 1992, the holographic universe, first harper perennial. vattay, g., s. kauffman and s. niiranen, 2012, quantum biology on the edge of quantum chaos, arxiv achieved, paper# 1202.6433. dna decipher journal | december 2014 | volume 4 | issue 3 | pp. 199-202 christianto, v. & umniyati, y., a graphic plot for a soliton solution of sine-gordon model of dna issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 199 report a graphic plot for a soliton solution of sine-gordon model of dna victor christianto *1 &yunita umniyati2 1 malang institute of agriculture, malang, indonesia 2 swiss german university, tangerang – indonesia abstract there are many models of dna, both the linear ones and the nonlinear ones. one interesting model in this regard is the sine-gordon model of dna as proposed by salerno. it belongs to nonlinear model of dna which is close to realistic model. here we discuss a graphical plot of soliton solution of such a sine-gordon model of dna. key words: soliton solution, sine-gordon, dna, graphic. introduction there are many models of dna, both the linear ones and the nonlinear ones [1]. one interesting model in this regard is the sine-gordon model of dna as proposed by salerno [2], see also daniel and vasumathi [3]. it belongs to nonlinear model of dna which is close to realistic model. a review of physical significance of such a sine-gordon model was given in [6]. here we discuss a graphical plot of soliton solution of such a sine-gordon model of dna. soliton solution of a sine-gordon model of dna assuming the wavefunction ψ to be a function of x and t, then the sine-gordon model of dna can be written as follows: [3, p.7] 𝛹𝑡𝑡 −𝛹𝑧𝑧 + sin⁡(𝛹) = 0 (1) or in mathematica expression: =u[x-c t]; pde=d[,x,x]-d[,t,t]-sin[]0 now we will use mathematica 9.0 to simplify and give graphical plot [3, p.443].to simplify with mathematica: * correspondence:victor christianto, malang institute of agriculture, malang – indonesia. url: http://researchgate.net/profile/victor_christianto. email: victorchristianto@gmail.com http://researchgate.net/profile/victor_christianto mailto:victorchristianto@gmail.com dna decipher journal | december 2014 | volume 4 | issue 3 | pp. 199-202 christianto, v. & umniyati, y., a graphic plot for a soliton solution of sine-gordon model of dna issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 200 −sin[𝑈[𝑧]] + 𝑈′′[𝑧] − 𝑐2𝑈′′[𝑧] = 0 (2) the result is known as kink soliton wave: [3, p.444] 𝛷 = 4arctan[𝑐sinh[𝑥/sqrt[1 − 𝑐^2]]/cosh[𝑐𝑡/sqrt[1 − 𝑐^2]]] (3) or in mathematica: 4arctan [𝑐sech [ 𝑐𝑡 √1 − 𝑐2 ] sinh [ 𝑥 √1 − 𝑐2 ]] differentiating for t, it yields: ∂𝑡 (4arctan [𝑐sech [ 𝑐𝑡 √1 − 𝑐2 ] sinh [ 𝑥 √1 − 𝑐2 ]]) − 4𝑐2sech[ 𝑐𝑡 √1−𝑐2 ]sinh[ 𝑥 √1−𝑐2 ]tanh[ 𝑐𝑡 √1−𝑐2 ] √1 − 𝑐2(1 + 𝑐2sech[ 𝑐𝑡 √1−𝑐2 ]2sinh[ 𝑥 √1−𝑐2 ]2) simplifying the above result, it yields: simplify [− 4𝑐2sech [ 𝑐𝑡 √1−𝑐2 ] sinh [ 𝑥 √1−𝑐2 ] tanh [ 𝑐𝑡 √1−𝑐2 ] √1 − 𝑐2 (1 + 𝑐2sech [ 𝑐𝑡 √1−𝑐2 ] 2 sinh [ 𝑥 √1−𝑐2 ] 2 ) ] − 8𝑐2sinh[ 𝑐𝑡 √1−𝑐2 ]sinh[ 𝑥 √1−𝑐2 ] √1 − 𝑐2(1 − 𝑐2 + cosh[ 2𝑐𝑡 √1−𝑐2 ] + 𝑐2cosh[ 2𝑥 √1−𝑐2 ]) the 3d plot is given below for c= 0.72 dna decipher journal | december 2014 | volume 4 | issue 3 | pp. 199-202 christianto, v. & umniyati, y., a graphic plot for a soliton solution of sine-gordon model of dna issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 201 figure 1. mathematica plot of soliton solution on sine-gordon equation for c=0.72 perturbed sine-gordon equation (sge) perturbed sge come in a variety of forms. one common form is a damped and driven sge [7, p.17]: 𝛹𝑡𝑡 +𝛷𝛹𝑡 −𝛹𝑧𝑧 + sin⁡(𝛹) = 𝐹 (4) in addition, the following two versions of the perturbed sge have been studied in the literature, including: a. directly forced sge: [7, p.19] 𝛹𝑡𝑡 −𝛹𝑧𝑧 + sin⁡(𝛹) = 𝑀𝑓(𝜔𝑡) (5) b. damped and drived sge: 𝛹𝑡𝑡 −𝛹𝑧𝑧 + sin(𝛹) = 𝑀𝑓(𝜔𝑡) − 𝛼𝛹𝑡 + 𝜂 (6) in the meantime, (2+1)d sge with additional spatial coordinate (y) is defined as [7,p.21]: 𝛹𝑡𝑡 = 𝛹𝑥𝑥 +𝛹𝑦𝑦 − sin⁡(𝛹) (7) in their in-depth review of sge, ivancevic and ivancevic [7] discuss potential applications of sge solitons in dna, protein folding, microtubules, neural impulse conduction and muscular contraction soliton. new insights may be expected in the near future in these biological fields, based on sine-gordon equation soliton. conclusion there are many models of dna, both the linear ones and the nonlinear ones [1]. one interesting model in this regard is the sine-gordon model of dna as proposed by salerno [2]. it belongs to nonlinear model of dna which is close to realistic model. here we have discussed a graphical plot of soliton solution of such a sine-gordon model of dna. considering that sine-gordon equation has been used extensively by particle physicists, it would be interesting to study possibility to improve or alter dna using electromagnetic field/pulse such as laser. this may be considered as a dna enhancement method. new insights may be expected in the near future in these biological fields, based on sine-gordon equation soliton. dna decipher journal | december 2014 | volume 4 | issue 3 | pp. 199-202 christianto, v. & umniyati, y., a graphic plot for a soliton solution of sine-gordon model of dna issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 202 references [1] ludmilav. yakushevich.nonlinear physics of dna. second, rev. ed. berlin: wiley-vch verlag gmbh & co., 2004. [2] m. salerno, phys. rev. a 44 (1991) 5292 [3] m. daniel & v. vasumathi. soliton-like base pair opening in a helicoidal dna: an analogy with helimagnet and cholesterics. arxiv:0812.4536 [nlin.ps], 2008. [4] richard h. enns & george c. mcguire.nonlinear physics with mathematica for scientists and engineers. berlin: birkhäuser, 2001, p. 443-445. [5] sadri hassani. mathematical methods using mathematica: for students of physics and related fields. new york: springer-verlag new york, inc., 2003. [6] sara cuenda, angel sanchez, & niurka r. quintero. does the dynamics of sine-gordon solitons predict active regions of dna? physica d 223 (2006) 214-221. [7] vladimir g. ivancevic and tijana t. ivancevic. sine-gordon solitons, kinks and breathers as physical models of nonlinear excitations in living cellular structures. arxiv:1305.0613 [q-bio.ot] dna decipher journal | december 2024 | volume 14 | issue 1 | pp. 62-68 62 pitkänen, m., new findings related to the chiral selection exploration new findings related to the chiral selection matti pitkänen 1 abstract the article ”enantioselective adsorption on magnetic surfaces” of mohammad reza safari et al published in the journal advanced materials (2023) discusses very interesting findings related to the chiral selection. there is a copper conductor with a strong electric field in the normal direction of the conductor. cu is not a magnetic substance. there are very thin cobalt islands at the surface of the conductor. cobalt is a magnetic metal. there are two options: magnetization direction is north or south and it corresponds to either up or down. north up and south down are the options and these could correspond to different chiralities somehow. the molecules drift to the cobalt islands and, depending on their chirality, prefer to bind to either south-up or north-up cobalt islands. are the magnetic fields of islands helical and possess a definite chirality? does the magnetic chirality tend to be the same or opposite to that of the enantiomer that binds to it? the effect is reported to occur already before the cobalt islands in the drifting of molecules to the cobalt islands. counterparts of magnetic fields are not present outside the cobalt islands. it is also found that electrons with a given spin direction prefer to tunnel through the molecules in a direction which correlates with the chirality. chiral selection is a mystery in standard model physics since it represents huge parity violation. tgd suggests a mechanism of parity violation in terms of the hierarchy of effective planck constants labelling phases behaving like dark matter. for a large enough value of heff , the dark weak boson compton length would be a biological scale and below this scale the parity violation would be large. this motivates a concrete model for what occurs in the experimental situation. the model provides support for the generalizations of pollack effect and dark genetic code replacing dark protons with dark electrons. 1 introduction i learned of very interesting empirical findings related to the chiral selection of biomolecules (see the popular article). the article ”enantioselective adsorption on magnetic surfaces” of mohammad reza safari et al [2] is published in the journal advanced materials (2023). 1.1 the findings consider first the experimental arrangement and findings. 1. there is a copper conductor with a strong electric field in the normal direction of the conductor. cu is not a magnetic substance. there are very thin cobalt islands at the surface of the conductor. cobalt is a magnetic metal. there are two options: magnetization direction is north or south and it corresponds to either up or down. north up and south down are the options and these could correspond to different chiralities somehow. 2. the molecules drift to the cobalt islands and, depending on their chirality, prefer to bind to either south-up or north-up cobalt islands. are the magnetic fields of islands helical and possess a definite chirality? does the magnetic chirality tend to be the same or opposite to that of the enantiomer that binds to it? 1correspondence: matti pitkänen http://tgdtheory.com/. address: valtatie 8 as 2, 03600, karkkila, finland. email: matpitka6@gmail.com. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://phys.org/news/2024-02-magnetic-effects-life-difference.html http://tgdtheory.com/ mailto:matpitka6@gmail.com dna decipher journal | december 2024 | volume 14 | issue 1 | pp. 62-68 63 pitkänen, m., new findings related to the chiral selection 3. the effect is reported to occur already before the cobalt islands in the drifting of molecules to the cobalt islands. what does this mean? counterparts of magnetic fields are not present. 4. it is also found that electrons with a given spin direction prefer to tunnel through the molecules in a direction which correlates with the chirality. chiral selection is a mystery in standard model physics since the it represents huge parity violation. tgd suggests a mechanism of parity violation in terms of the hierarchy of effective planck constants labelling phases behaving like dark matter. for a large enough value of heff , the dark weak boson compton length would be a biological scale and below this scale the parity violation would be large. this motivates a concrete model for what occurs in the experimental situation. the model provides support for the generalizations of pollack effect and dark genetic code replacing dark protons with dark electrons. 2 tgd based model for the findings in the sequel, the general ideas about chiral selection in the tgd universe are discussed and at the end a concrete model is proposed. 2.1 the general tgd view of the findings these findings are provide new empirical hints about the nature of chiral selection in living matter. weak interactions are indeed weak and parity violation effects should be extremely small above weak scale so that the standard model fails to explain chiral selection. 1. chiral selection is one of the key empirical facts supporting the tgd prediction of a hierarchy of phases of ordinary matter predicted by the number theoretical vision of tgd [20, 19, 29, 23, 24, 25]. these phases are labelled by effective planck constant heff , which is essentially the dimension of an algebraic extension of rationals. 2. the predicted huge values of heff assignable to classical gravitational and electric fields of astrophysical objects [25] mean that weak interactions become as strong as em interactions below the scale up compton length of weak bosons, which, being proportional to heff , can be as large as cell size. this amplifies parity violation effects visible for instance in hydrodynamics [6]. 3. large heff phases behave like dark matter: they do not however explain the galactic dark matter, which in the tgd framework is dark energy assignable to cosmic strings (no halo and an automatic prediction of the flat velocity spectrum). instead, large heff phases solve the missing baryon problem. the density of baryons has decreased in cosmic evolution (having biological evolution as a particular aspect) and the explanation is that evolution as unavoidable increase of algebraic complexity measured by heff has transformed them to heff ≥ h phases at the magnetic bodies (thickened cosmic string world sheets, 4-d objects), in particular those involved with living matter. 4. the large value of heff has besides number theoretical interpretation [21, 22, 26, 27] also a geometric interpretation. space-time surface can be regarded as many-sheeted over both m4 and cp2. in the first case the cp2 coordinates are many-valued functions of m4 coordinates. in the latter case m4 coordinates are many-valued functions of cp2 coordinates so that qft type description fails. this case is highly interesting in the case of quantum biology. since a connected space-time surface defines the quantum coherence region, an ensemble of, say, monopole flux tubes can define a quantum coherent region in the latter case: one simply has an analog of bose-einstein condensate of monopole flux tubes. the flux tube condensate as a covering of cp2 means a dramatic deviation from the qft picture and is a central notion in the applications of quantum tgd to biology. therefore some examples are in order. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2024 | volume 14 | issue 1 | pp. 62-68 64 pitkänen, m., new findings related to the chiral selection 1. fermi liquid description of electrons relies on the notion of a quasiparticle as an electron plus excitations of various kinds created by its propagation in the lattice. in some systems this description fails and these systems would. have a natural description in terms of space-time surfaces which are multiple coverings of cp2, say flux tube condensates. 2. in high tc superconductors and bio-superconductors [10, 11] the space-time surface could correspond to this kind of flux tube condensates and cooper pairs would be fermion pairs with members at separate flux tubes. the connectedness of the space-time surface having about heff/h = n flux tubes would correlate the fermions. 3. bogoliubov quasiparticles related to superconductors are regarded as superpositions of electron excitation and hole. the problem is that they have an ill-defined fermion number. in tgd, they would correspond to superpositions of a dark electron accompanied by a hole which it has left behind and therefore having a well-defined fermion number. bogoliubov quasiparticle is indeed what can be seen using the existing experimental tools and physical understanding. 4. strange metals would be an example of a system having no description using quasiparticles, as the linear dependence of the resistance at low temperatures demonstrates. i have considered a description of them in terms of cooper pairs at short closed flux tubes [10, 15]: this would however suggest a vanishing resistance in an ideal situation. something seems to go wrong. an alternative description could be in terms of superpositions of dark electrons and holes assignable to the flux tube condensate. strange metal is between fermi liquid and superconductor: this conforms with the fact that strange metals are quantum critical systems. the transition to high tc superconductivity is preceded by a transition to a phase in which something resembling cooper pairs is present. a natural looking interpretation would be in terms of a flux tube condensate and pairs of dark and ordinary electrons. also now the flux tubes could be short. in [8], i have considered the possibility that high tc superconductors could be this kind of ”half-superconductors” but this option seems to be wrong. the phase transitions between ”half-superconductivity” and superconductivity could play a central rol also in living matter. 2.2 how large parity violation could emerge in the tgd framework before proceeding to a detailed model, one must understand how the large parity violation required by the chiral selection could emerge in the tgd framework. 1. since the kähler action does not contain the induced su(2)l weak fields, there should be no direct parity violation at the space-time level. the geometric parity violation as a chiral selection of biomolecules could be however induced from the fermionic dynamics induced by the modified dirac action determined completely the bosonic action. the twistor lift of tgd [16, 13, 7] suggest that this action is a sum of volume term and kähler action. holography realized as generalized holomorphy implies that solutions are minimal surfaces irrespective of action and only the conditions at boundaries and singularities distinguish between different general coordinate invariant actions constructible using the induced geometry. 2. in the standard physics framework one could argue that chern-simons term relates to the parity violation. now the situation is not so straightforward since parity violation for the weak interactions basically occurs at the level of m4 × cp2 and is induced to the space-time level. chern-simons-kähler (csk) action emerges from the topological istanton term j∧j in the exponent defining vacuum functional [9, 12, 14, 18]. the csk term is naturally imaginary whereas the nontopological term defining the kähler function as kähler action would be real. the csk term contains issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2024 | volume 14 | issue 1 | pp. 62-68 65 pitkänen, m., new findings related to the chiral selection two parts corresponding to m4 and cp2 parts of the kähler form. neither kähler action nor csk action contain the induced su(2)l gauge potentials so that parity violation directly induced by weak interactions is not present. csk action is associated with partonic orbits carrying fermion lines identified as the light-like boundaries of the space-time surface and the interfaces of euclidean and minkowskian regions of the space-time surface. 3. csk term contributes also a term to the modified dirac action [18] [28], which is fixed completely by the bosonic action defining the space-time surfaces as a bohr orbit-like preferred extremals satisfying holography, which reduces to a generalized holomorphy [14]. what is crucial is that the covariant derivative acting on the induced spinor fields, obtained by restricting the second quantized h spinor fields to the space-time surface, contains the parity violation weak interaction term so that the parity violation at the level of elementary fermions emerges through it. this parity violation must induce the geometric parity violation at the level of the geometry of space-time surfaces distinguishing between different chiralities in dark weak scales. 4. the model of anomalous electron-positron pairs produced in heavy nucleus collisions [17] assigns dark leptopion condensate to the non-vanishing of the chern-simons term requiring that the induced kähler and electric fields are not orthogonal. the condition that the dark leptopion compton wavelength, which is 1/2 of dark electron compton length, should be of the order of the thickness of the electric flux tube. one must assume that the leptopions are dark in the sense that they have heff ̸= h since otherwise they would be produced in the decays of weak bosons. it will be found that the model provides further support for a generalization of the pollack effect [3, 1, 5, 4]: instead of protons of water molecules, electrons at the conductor surface would be transformed to dark electrons at the magnetic monopole flux tubes. this suggests also a generalization of the dark genetic code discussed already earlier [24]. for this generalization dark proton triplets as a representation of codons would be replaced with dark electron triplets. the universality of the realization of the dark genetic code in terms of the completely unique icosa tetrahedral tessellation of hyperbolic space h3 supports this idea. 2.3 a concrete tgd based model for the findings consider now a concrete model for the findings in the tgd framework. 1. a good guess is that the molecular monopole flux tubes of the molecules and of the magnetic fields assignable with the cobalt islands tend to have the same chirality. this would generalize the chiral selection from the level of biomolecules to the level of dark monopole flux tubes. some kind of condensate of flux tubes of the same chirality as a long scale parity violation would be in question. 2. in the tgd framework, the north up and south up magnetic fields could correspond to helical monopole flux tubes of opposite chiralities. the helical structure is essential and could relate directly to the requirement that the flux tube is closed: one could have a shape of flattened square for which the long sides form a double helix. this would be the case also for dna. 3. parity violation requires a large value of heff . dark z (and w) bosons could generate a large parity violation. dark z boson compton length of order biological scale. the very large value of heff would give the needed large energy splitting between generalized cyclotron energies at the dark flux tube and induce chiral selection. gravitational flux tubes of the earth’s gravitational field or solar gravitational field would do the job. by the equivalence principle, the gravitational compton length λgr,e = .5 cm for earth does not depend on the particle mass and looks like a promising scale. also the cyclotron energies are independent of the mass of the charged particle since ~gr is proportional to particle mass m and cyclotron frequency to 1/m. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2024 | volume 14 | issue 1 | pp. 62-68 66 pitkänen, m., new findings related to the chiral selection 4. also the electric field of the copper surface should have an important role. the electric field orthogonal to cu conductor would correspond to electric flux tubes. the consistency condition for the electric flux tube thickness with charged at the bottom (conductor) reads as λem(d) ∼ d. ~em = ne2/β0, n the number of electrons at the bottom. there is roughly one electron per atom. n ∼ 104 per flux tube area of 100 nm2 having radius about 10 nm. λem = ne2/β0λe is about 1 nm for β0 = 1. the value of ~em are rather small and it seems that it cannot contribute to the chiral selection. one can however consider also the electric field of earth, and in this case the situation could be different. the effect occurs already before the cobalt islands. furthermore, electrons with a given spin direction prefer to tunnel through the molecules in a direction dicrated by the chirality. what could this mean? 1. the counterparts of magnetic fields are present as dark magnetic fields inside the magnetic bodies of the drifting molecules. suppose that dark molecular gravitational monopole tubes are indeed present and give rise to closed spin current loops with a direction determined by the chirality of the molecule. this would give rise to the large parity violation but how to understand the occurrence of the effect already before the cobalt islands? 2. could one assign a definite chirality also to the electric flux tubes assignable to the cu surface and assume that the molecular chirality tends to be the same (or opposite) to this chirality? do also these closed monopole flux tubes carry dark electric current? the spin direction of the current carrying electrons would correlate with the magnetization direction so that the magnetic body of the molecule would prefer a pairing with the electric body with a preferred spin direction. the preferred pairing would explain the drift to a correct cobalt island: the paths leading to the cobalt island would be more probable. 3. in the case of water, the pollack effect [3, 1, 5, 4] transfers part of the protons of water molecules to dark protons at monopole flux tubes. now there are no protons available. does this require a generalization of the pollack effect? could the electric flux tubes be gravitational flux tubes carrying electrons instead of protons? gravitational compton length would be the same. could electronic pollack effect for conductors as a dual of pollack effect for water be in question. 4. in the tgd inspired quantum biology, one assigns genetic code with dark proton triplets. could one assign a dark realization of the genetic code to dark electron triplets? could the electric counterparts of gravitational flux tubes carrying dark realization of the genetic code define dark genetic code? codons would correspond to dark electron triplets instead of dark proton triplets. could the analogs of the ordinary genetic codons correspond to the triplets of electron holes at the conductor surface? the tgd based vision about universal genetic code suggests the existence of a 2-d analog of dna realized in terms of mathematically completely unique hyperbolic icosa tetrahedral tessellation. could this genetic code be associated with the metal surfaces? the implications of this hidden genetic code for computers might be rather dramatic. received july 1, 2024; accepted december 31, 2024 references [1] the fourth phase of water: dr. gerald pollack at tedxguelphu, 2014. available at: https: //www.youtube.com/watch?v=i-t7tcmudxu. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://www.youtube.com/watch?v=i-t7tcmudxu https://www.youtube.com/watch?v=i-t7tcmudxu dna decipher journal | december 2024 | volume 14 | issue 1 | pp. 62-68 67 pitkänen, m., new findings related to the chiral selection [2] safari mr et al. enantioselective adsorption on magnetic surfaces. advanced materials, 2023. available at: https://doi.org/10.1002/adma.202308666. [3] pollack g. cells, gels and the engines of life. ebner and sons, 2000. available at: https: //www.cellsandgels.com/. [4] zhao q pollack gh, figueroa x. molecules, water, and radiant energy: new clues for the origin of life. int j mol sci, 10:1419–1429, 2009. available at: https://tinyurl.com/ntkfhlc. [5] pollack gh zheng j-m. long-range forces extending from polymer-gel surfaces. phys rev e, 68:031408–, 2003. available at: https://tinyurl.com/ntkfhlc. [6] pitkänen m. hydrodynamics and cp2 geometry. in tgd and condensed matter. https:// tgdtheory.fi/tgdhtml/btgdcondmat.html. [7] pitkänen m. about tgd counterparts of twistor amplitudes. in quantum tgd: part iii. https: //tgdtheory.fi/tgdhtml/btgdquantum3.html. available at: https://tgdtheory.fi/pdfpool/ twisttgd.pdf, 2023. [8] pitkänen m. comparing berry phase model of super-conductivity with tgd based model. in tgd and condensed matter. https://tgdtheory.fi/tgdhtml/btgdcondmat.html. available at: https://tgdtheory.fi/pdfpool/scberrytgd.pdf, 2023. [9] pitkänen m. identification of the wcw kähler function. in quantum physics as infinitedimensional geometry. https://tgdtheory.fi/tgdhtml/btgdgeom.html. available at: https: //tgdtheory.fi/pdfpool/kahler.pdf., 2023. [10] pitkänen m. quantum model for bio-superconductivity: i. in tgd and quantum biology: part i. https://tgdtheory.fi/tgdhtml/bqbio1.html. available at: https://tgdtheory.fi/pdfpool/ biosupercondi.pdf, 2023. [11] pitkänen m. quantum model for bio-superconductivity: ii. in tgd and quantum biology: part i. https://tgdtheory.fi/tgdhtml/bqbio1.html. available at: https://tgdtheory.fi/pdfpool/ biosupercondii.pdf, 2023. [12] pitkänen m. recent view about kähler geometry and spin structure of wcw . in quantum physics as infinite-dimensional geometry. https://tgdtheory.fi/tgdhtml/btgdgeom.html. available at: https://tgdtheory.fi/pdfpool/wcwnew.pdf, 2023. [13] pitkänen m. some questions related to the twistor lift of tgd. in quantum tgd: part iii. https://tgdtheory.fi/tgdhtml/btgdquantum3.html. available at: https://tgdtheory.fi/ pdfpool/twistquestions.pdf, 2023. [14] pitkänen m. symmetries and geometry of the ”world of classical worlds”. in quantum physics as infinite-dimensional geometry. https://tgdtheory.fi/tgdhtml/btgdgeom.html. available at: https://tgdtheory.fi/pdfpool/wcwsymm.pdf, 2023. [15] pitkänen m. tgd and condensed matter physics. in tgd and condensed matter. https: //tgdtheory.fi/tgdhtml/btgdcondmat.html. available at: https://tgdtheory.fi/pdfpool/ tgdcondmatshort.pdf, 2023. [16] pitkänen m. the classical part of the twistor story. in quantum tgd: part iii. https://tgdtheory. fi/tgdhtml/btgdquantum3.html. available at: https://tgdtheory.fi/pdfpool/twistorstory. pdf, 2023. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://doi.org/10.1002/adma.202308666 https://www.cellsandgels.com/ https://www.cellsandgels.com/ https://tinyurl.com/ntkfhlc https://tinyurl.com/ntkfhlc https://tgdtheory.fi/tgdhtml/btgdcondmat.html https://tgdtheory.fi/tgdhtml/btgdcondmat.html https://tgdtheory.fi/tgdhtml/btgdquantum3.html https://tgdtheory.fi/tgdhtml/btgdquantum3.html https://tgdtheory.fi/pdfpool/twisttgd.pdf https://tgdtheory.fi/pdfpool/twisttgd.pdf https://tgdtheory.fi/tgdhtml/btgdcondmat.html https://tgdtheory.fi/pdfpool/scberrytgd.pdf https://tgdtheory.fi/tgdhtml/btgdgeom.html https://tgdtheory.fi/pdfpool/kahler.pdf https://tgdtheory.fi/pdfpool/kahler.pdf https://tgdtheory.fi/tgdhtml/bqbio1.html https://tgdtheory.fi/pdfpool/biosupercondi.pdf https://tgdtheory.fi/pdfpool/biosupercondi.pdf https://tgdtheory.fi/tgdhtml/bqbio1.html https://tgdtheory.fi/pdfpool/biosupercondii.pdf https://tgdtheory.fi/pdfpool/biosupercondii.pdf https://tgdtheory.fi/tgdhtml/btgdgeom.html https://tgdtheory.fi/pdfpool/wcwnew.pdf https://tgdtheory.fi/tgdhtml/btgdquantum3.html https://tgdtheory.fi/pdfpool/twistquestions.pdf https://tgdtheory.fi/pdfpool/twistquestions.pdf https://tgdtheory.fi/tgdhtml/btgdgeom.html https://tgdtheory.fi/pdfpool/wcwsymm.pdf https://tgdtheory.fi/tgdhtml/btgdcondmat.html https://tgdtheory.fi/tgdhtml/btgdcondmat.html https://tgdtheory.fi/pdfpool/tgdcondmatshort.pdf https://tgdtheory.fi/pdfpool/tgdcondmatshort.pdf https://tgdtheory.fi/tgdhtml/btgdquantum3.html https://tgdtheory.fi/tgdhtml/btgdquantum3.html https://tgdtheory.fi/pdfpool/twistorstory.pdf https://tgdtheory.fi/pdfpool/twistorstory.pdf dna decipher journal | december 2024 | volume 14 | issue 1 | pp. 62-68 68 pitkänen, m., new findings related to the chiral selection [17] pitkänen m. the recent status of lepto-hadron hypothesis. in p-adic physics. https:// tgdtheory.fi/tgdhtml/bpadphys.html. available at: https://tgdtheory.fi/pdfpool/leptc. pdf, 2023. [18] pitkänen m. wcw spinor structure. in quantum physics as infinite-dimensional geometry. https://tgdtheory.fi/tgdhtml/btgdgeom.html. available at: https://tgdtheory.fi/pdfpool/ cspin.pdf, 2023. [19] pitkänen m. does valence bond theory relate to the hierarchy of planck constants? available at: https://tgdtheory.fi/public_html/articles/valenceheff.pdf., 2017. [20] pitkänen m. quantum self-organization by heff changing phase transitions. available at: https: //tgdtheory.fi/public_html/articles/heffselforg.pdf., 2019. [21] pitkänen m. a critical re-examination of m8 −h duality hypothesis: part i. available at: https: //tgdtheory.fi/public_html/articles/m8h1.pdf., 2020. [22] pitkänen m. a critical re-examination of m8 −h duality hypothesis: part ii. available at: https: //tgdtheory.fi/public_html/articles/m8h2.pdf., 2020. [23] pitkänen m. comparison of orch-or hypothesis with the tgd point of view. https://tgdtheory. fi/public_html/articles/penrose.pdf., 2022. [24] pitkänen m. how animals without brain can behave as if they had brain. https://tgdtheory.fi/ public_html/articles/precns.pdf., 2022. [25] pitkänen m. about long range electromagnetic quantum coherence in tgd universe. https: //tgdtheory.fi/public_html/articles/hem.pdf., 2023. [26] pitkänen m. new findings related to the number theoretical view of tgd. https://tgdtheory. fi/public_html/articles/m8hagain.pdf., 2023. [27] pitkänen m. a fresh look at m8 − h duality and poincare invariance. https://tgdtheory.fi/ public_html/articles/tgdcritics.pdf., 2024. [28] pitkänen m. modified dirac equation and the holography=holomorphy hypothesis. https: //tgdtheory.fi/public_html/articles/moddir.pdf., 2024. [29] pitkänen m and rastmanesh r. the based view about dark matter at the level of molecular biology. available at: https://tgdtheory.fi/public_html/articles/darkchemi.pdf., 2020. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://tgdtheory.fi/tgdhtml/bpadphys.html https://tgdtheory.fi/tgdhtml/bpadphys.html https://tgdtheory.fi/pdfpool/leptc.pdf https://tgdtheory.fi/pdfpool/leptc.pdf https://tgdtheory.fi/tgdhtml/btgdgeom.html https://tgdtheory.fi/pdfpool/cspin.pdf https://tgdtheory.fi/pdfpool/cspin.pdf https://tgdtheory.fi/public_html/articles/valenceheff.pdf https://tgdtheory.fi/public_html/articles/heffselforg.pdf https://tgdtheory.fi/public_html/articles/heffselforg.pdf https://tgdtheory.fi/public_html/articles/m8h1.pdf https://tgdtheory.fi/public_html/articles/m8h1.pdf https://tgdtheory.fi/public_html/articles/m8h2. pdf https://tgdtheory.fi/public_html/articles/m8h2. pdf https://tgdtheory.fi/public_html/articles/penrose.pdf https://tgdtheory.fi/public_html/articles/penrose.pdf https://tgdtheory.fi/public_html/articles/precns.pdf https://tgdtheory.fi/public_html/articles/precns.pdf https://tgdtheory.fi/public_html/articles/hem.pdf https://tgdtheory.fi/public_html/articles/hem.pdf https://tgdtheory.fi/public_html/articles/m8hagain.pdf https://tgdtheory.fi/public_html/articles/m8hagain.pdf https://tgdtheory.fi/public_html/articles/tgdcritics.pdf https://tgdtheory.fi/public_html/articles/tgdcritics.pdf https://tgdtheory.fi/public_html/articles/moddir.pdf https://tgdtheory.fi/public_html/articles/moddir.pdf https://tgdtheory.fi/public_html/articles/darkchemi.pdf introduction the findings tgd based model for the findings the general tgd view of the findings how large parity violation could emerge in the tgd framework a concrete tgd based model for the findings dna decipher journal | october 2019 | volume 9 | issue 2 | pp. 71-80 71 pitkänen, m., some applications of tgd inspired quantum biology: biochemistry, metabolism & replication article some applications of tgd inspired quantum biology: biochemistry, metabolism & replication matti pitkänen 1 abstract tgd replaces einsteinian space-time with many-sheeted space-time, and gauge and gravitational fields with purely geometric induced fields leading to the notion of field body. tgd also forces to generalize quantum theory by introducing the hierarchy of planck constants explaining dark matter and providing universal mechanism of evolution as increase of algebraic complexity and intelligence. zero energy ontology in turn solves the basic problem of quantum measurement theory and allows to understand ”free will” with conflict with the laws of physics. the implications for quantum biology are rather dramatic. in this article some problems related to biochemistry based approach, metabolism, and replication will be discussed in this framework. examples from bio-chemistry are bio-catalysis with application to dna replication, the selection of bio-molecules, and genetic code. metabolism is second topic i have included also a universal purely thermodynamical model of remote metabolism relying on zero energy ontology. generalization of point like particle to 3-d surface allows to understand replication basically as analog of particle decay taking place at the level of magnetic body. 1 introduction tgd replaces einsteinian space-time with many-sheeted space-time, and gauge and gravitational fields with purely geometric induced fields leading to the notion of field body. tgd also forces to generalize quantum theory by introducing the hierarchy of planck constants explaining dark matter and providing universal mechanism of evolution as increase of algebraic complexity and intelligence. zero energy ontology in turn solves the basic problem of quantum measurement theory and allows to understand ”free will” with conflict with the laws of physics. the implications for quantum biology are rather dramatic. in this article some problems related to biochemistry based approach, metabolism, and replication will be discussed in this framework. examples from bio-chemistry are bio-catalysis with application to dna replication, the selection of bio-molecules, and genetic code. metabolism is second topic i have included also a universal purely thermodynamical model of remote metabolism relying on zero energy ontology. generalization of point like particle to 3-d surface allows to understand replication basically as analog of particle decay taking place at the level of magnetic body. the path leading to this article was following. i wrote a new chapter ”getting philosophical: some comments about the problems of physics, neuroscience, and biology” [?] to the book ”tgd based view about consciousness, living matter, and remote mental interactions” as a re-organized and extended version of the original text written 2018 as an article and a section of a chapter of the book already mentioned. i added several detailed examples about the application of tgd inspired theory of quantum biology so solve basic problems of quantum biology. it seemed however appropriate to collect some specific applications as particularly interesting applications discussed also in the chapter [?]. the examples to be discussed represent new results related to bio-catalysis with application to dna replication, to the selection of bio-molecules, and genetic code. metabolism is second topic i have included also a universal purely thermodynamical model of remote metabolism relying on zero energy ontology. also a discussion of replication is included. 1correspondence: matti pitkänen http://tgdtheory.com/. address: rinnekatu 2-4 a8, 03620, karkkila, finland. email: matpitka6@gamail.com. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.com/ mailto:matpitka6@gmail.com dna decipher journal | october 2019 | volume 9 | issue 2 | pp. 71-80 72 pitkänen, m., some applications of tgd inspired quantum biology: biochemistry, metabolism & replication i have not included the vision about pre-biotic evolution. the first key idea in the model of prebiotic evolution is that in tgd universe the magnetic body of water makes it an excellent candidate for a pre-biotic life form in itself [30, 15]: even genetic code would be realized non-chemically in two manners. in tgd universe bio-chemical life could have evolved inside planetary interiors [25]. for this the recent findings from mars challenging the maxwellian view about magnetic fields and characterized as ”magnetic madness” provide support [?] (see http://tinyurl.com/yxzye6xu). quite generally, it seems that the maxwellian notion of magnetic field is encountering grave difficulties: the stability of the earth’s magnetic field is still not understood, and the existence of magnetic fields in cosmological scales is also a mystery. the existence of monopole flux tubes predicted by tgd solves all these problems and serves as a cornerstone of tgd inspired quantum biology. my expectation is that this will be one of the reasons eventually forcing to accept tgd. 2 questions related to bio-chemistry 2.1 biocatalysis as already mentioned, bio-catalysis remains a total mystery in bio-chemical approach. magnetic body carrying dark matter could provide the needed mechanisms. actually these mechanism would be also basic mechanisms behind water memory and dare i say it aloud? homeopathy [4]. according to tgd view about catalysis, reactants find each other by cyclotron resonance for dark cyclotron radiation assignable to massless extremals (mes) possibly associated with u-shaped flux tubes. the u-shaped flux tubes of the molecules reconnect to a pair of flux tubes connecting the molecules. this occurs only if the flux tubes have same strength of magnetic field and therefore same thickness by flux quantization. the same value of heff guarantees resonance. the next step is the shortening of the flux tubes by a reduction of heff and liberating the energy kicking the reactants over the potential wall making the process extremely slow otherwise. dna replication, transcription to rna, and translation of rna to amino-acids are the fundamental processes in biology and tgd should provide a general model for them. consider dna replication as an example. 1. the standard model assumes that dna opens and nucleotides build up the dna codons in ordered manner. nucleotides would be caught one-by-one from the environment by u-shaped flux tubes from dna reconnecting with similar flux tubes from nucleotides. in the proposed model however dark codons are the fundamental units and expected to induce the process at the level of chemistry. dark codons do not allow a decomposition to letters. therefore ordinary codons rather than nucleotides should serve as basic units in energy resonance binding them to dark codons (triple resonance or ordinary resonance with respect to the sum of resonance energies). this looks like a problem for both replication and transcription. translation in which rna codons are paired with amino-acids suggests a solution of the problem. 2. suppose that dark codons are the basic units also in the environment, and are connected by long flux tubes with rather large heff to ordinary nucleotides forming thus loose but actually strongly correlated triplets. nucleotides would serve as basic units only apparently: the entities in question would be analogous to trna codons. in the replication and transcription the dark codons of opening dna sequences would form flux tube contacts with dark codons in the environment coupled to ordinary loose codons by dark triple resonance. after that the planck constant heff associated with the connecting flux tubes would be reduced, the flux tubes would shorten and the complementary dark codon would be drawn near the the dark codon associated with dna. also the flux tubes connecting the dark codon to the nucleotides would shorten and the codon and complementary codon would form 3 base pairs. shortening by issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/yxzye6xu dna decipher journal | october 2019 | volume 9 | issue 2 | pp. 71-80 73 pitkänen, m., some applications of tgd inspired quantum biology: biochemistry, metabolism & replication a reduction of heff would provide the energy making the process fast enough. the loose codon property would allow to store the energy needed to make the reaction fast. 3. this model can explain also the claim of montagnier et al [2] about remote dna replication [13, 23]. gariaev et al have reported the same process much earlier [3] and together with peter gariaev we have developed a model for the process [12]. the situation is as follows. one has two vessels a and b: a contains genes and b only nucleotides. the vessels are connected by channels so narrow that the genes cannot leak through them. the system is irradiated at 7 hz frequency, which is near the lowest schumann frequency. the generation of the copies of genes in b is reported. the proposed model suggest that the flux tubes emanating from the dark dna codons associated with the opening dna extend to the other side possibly through the channels so that there is a strong correlation between the directions of flux tubes and their endpoints are close to each other. if they have same value of heff they would have same length. they would reconnect with dark codons at the other side connected to nucleotide triplets by long flux tubes and the process would continue in the same manner as in the ordinary replication. 2.2 what selected the biomolecules? why only very few candidates for relevant biomolecules are actually selected? who/what selected and how? this leads to very unpleasant questions circumvented by deciding that the emergence of life was nothing but a thermodynamical fluctuation. it has however become clear that complex organic molecules are present even in interstellar and intergalactic space. the miraculous thermodynamical fluctuation explaining evolution without real evolution would have been really huge. more philosophically minded tends to conclude that we simply have no clue about what selection at the bio-molecular level really is and continue that some new physics is involved so that it is time to think giving up the reductionistic narrative. the selection problem appears also at the level of biochemical reaction pathways. one can imagine endless variety of ”reaction vertices”. if one assumes that only very few basic ”reaction vertices” are allowed but the rest not, one can construct a limited number of reaction pathways. but this is an ad hoc assumption: this selection of allowed reaction pathways certainly occurs but we do not have a slightest idea about the physics behind it. there is also an analogy with computer science. one can construct endless variety of linguistically correct computer programs: why only very few of them would be selected. and with neuroscience: from a huge array of behavioral patters only some are selected. here one can of course try a loophole: darwinian selection. but there is no selection in the universe of physicalist. this would require free will and intentionality. the trick does not work. but what about this network in which biomolecules are connected by this something already mentioned?, asks philosopher. could this something connect only biomolecules if they are in the same relationship as sender and receiver of radio signal. could these somethings connect stably only systems possessing common resonance frequencies? could this criterion could select both the preferred biomolecules and the ”reaction vertices” and thus also reaction pathways. one can develop this idea further. 1. the resonance between systems with the same value of heff would be both frequency and energy resonance. the resonance between systems with different values of heff requires change of heff of either system so that heff is same for the systems. energy is conserved, which means that the frequency of the photon would change to satisfy e = heff,1f1 = heff,2f2. one would have only energy resonance. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2019 | volume 9 | issue 2 | pp. 71-80 74 pitkänen, m., some applications of tgd inspired quantum biology: biochemistry, metabolism & replication the resonance of dark matter states with bio-molecules would be energy resonance and make it possible for long scales to control short scales by inducing molecular transitions. the transformed photons could have interpretation as bio-photons [10, 11]. 2. one can however argue that mere resonance is not enough to select bio-molecules. magnetic flux tubes containing dark particles can vary their thickness and by the conservation of the monopole flux also magnetic field and cyclotron frequency so that they can get in resonance with any bio-molecule. a stronger condition is required. the obvious idea is that also biomolecules can be in resonance and surviving bio-molecules are able to build networks. selection would not be selection of mere individuals but that of networks able to co-operate. there would be a choir singing resonantly in unisono rather than only resonating pairs. the biomolecules involved would have common transition energies which would poses extremely strong conditions on survivors. 2.3 genetic code genetic code definitely represents information. is it really an outcome of thermodynamical fluctuation? is there some deep mathematics associated with the genetic code?, asks the philosopher now. be patient! genome contains also intronic portion: most of it consists of introns and the intronic portion is the larger the higher the evolutionary level is. the prevailing interpretation has been as ”junk”. is it really junk?, wonders philosopher. luckily, the attitude that trash bin represents the highest level of evolution has begun to slowly change to more rational one. could there be a beautiful mathematics behind genetic code? could it be something similar to codes in computer science and have not only one representation the chemical one but numerous representations? if computer science would have developed before genetics this question would have been completely natural and we would probably know a lot about these representations. could this dark matter with large planck constant at these mysterious somethings identified by our philosopher tentatively as magnetic flux tubes realize the really fundamental representation of the genetic code and also of of dna, rna, trna, and amino-acids (aas) in information theoretic sense? and could also radiation provide realization of genetic code necessary for communications? this is what the philosopher claims [16, 22, 21, 14, 26]. the most plausible vision at this moment is that since magnetic body is the boss, chemical code should be incomplete secondary representation of more fundamental genetic code realized at the level of magnetic body controlling bio-matter. the realizations based on 3-proton triplets and dark light 3-chords defining icosa-tetrahedral representation of the genetic code in terms of hamiltonian cycles [28] would be the deeper realizations. there would be several hamiltonian cycles distinguishing assignable to the same chemical representation of the genetic code. the analogy with music suggests that the realization in terms of 3-chords defining bio-harmony gives rise to quantum correlates of emotions assignable to magnetic body as kind of higher level sensory perceptions. genetic codon as 6-bit unit would correspond to the ”bitty” aspects of intelligence and harmony would correspond to emotional intelligence as the holistic aspect of intelligence [28, 14]. emotions would be realized already at the level of magnetic body[24, 33, ?]. the recent findings that the rna of a conditioned sea snail scattered over neurons of second sea snail in petri dish generate neuronal correlates of conditioning supports the view that the magnetic body of the rna of sea snail infects the emotion/mood related to the conditioning. the emotional state, mood, of dna and rna would affect gene expression. epigenesis is a poorly understood in standard biology and could be based on emotional states lasting for several generations. this is natural in zeo [14, ?]. how different representations of the genetic code relate to each other? 1. the natural hypothesis is that given dark codon generates corresponding light 3-chord in communications and control. alike likes alike rule of homeopathy suggests that triple resonance between identical codons is the basic mechanism of communications between various representations. similar issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2019 | volume 9 | issue 2 | pp. 71-80 75 pitkänen, m., some applications of tgd inspired quantum biology: biochemistry, metabolism & replication codons of dna sequences would be in resonance if the mood defined by bio-harmony is same for them. for the same value of heff one would have both energy and frequency resonance for different values only energy resonance. 2. the condition that all possible or at least some moods coded by hamiltonian cycles are realized, poses additional conditions on ordinary dna codons since given codon should be able to respond to several 3-chords resonantly. an open question is whether ordinary codons responds via triple resonance or to the energy associated with the sum of the three frequencies in which case one can consider the possibility that the sum of frequencies does not depend of bio-harmony. 3. since dark protons are entangled and do not allow a decomposition to letters, it is not possible to realize the correspondence with ordinary codons by assigning a frequency separately to each nucleotide: the chemical codon reacts as a holistic entity [28]. this gives highly non-trivial conditions on transcription and dna replication: dna and rna nucleotides must form loose codons connected to dark codon by long flux tubes and in transcription/replication these flux tubes shorten. this allows to understand [13] also the remote replication of dna reported by montagnier et al [2]. the loose codons formed by nucleotides and dark codons would be very similar to trna codons except that the flux tubes connecting dark codon to nucleotide would be long. 3 metabolism metabolism is one of the key aspects of biology. we must eat and plants must busily photosynthesize in order to survive. but why metabolic energy feed is needed? again a mystery. 3.1 non-equilibrium thermodynamics non-equilibrium thermodynamics is one attempt to answer this question. thermodynamical equilibrium is completely uninteresting, entropy is maximal and in the case of local dynamics the state of system is completely determined by a small sample of it. however, if one has energy feed, situation changes since equilibrium becomes flow equilibrium. the energy feed guarantees that there is macroscopic dynamics rather than mere thermal motion at microscopic level. also in this case one has essentially the same situation everywhere unless one introduces macroscopic parameters also energy flow depending on time and position to get something more interesting. simple reaction kinematics determined by differential equations can be replaced with that determined by partial differential equations obtained by allowing diffusion. also temperature, pressure and other thermodynamical parameters can be allowed to depend on position and time. turing proposed a model for the coloring of zebra as outcome of this kind of dynamics. the model for neuronal membrane and nerve pulse generation is also a rough model trying to reproduce basic facts about nerve pulse generation using thermodynamics for neuronal membrane regarded as a capacitor. this is of course a mere parameterization of the situation. tgd leads to a quantum model for the situation [5]. also the interpretation about the role of nerve pulse patterns at neuronal level changes dramatically [17, 24]. in non-equilibrium thermodynamics one speaks of self-organization. one can generalize this notion to quantum self-organization and the crucial criticality associated to the transitions between different self-organization patterns generalizes to quantum criticality [7]. could these transitions correspond to spatio-temporal self organization patterns, behaviors, functions, programs. this in turn leads to deep connections with conformal symmetry (even its generalization in tgd), fractality, and universality of the dynamics. it is a pity that biologists do not seem to know much about these possibilities. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2019 | volume 9 | issue 2 | pp. 71-80 76 pitkänen, m., some applications of tgd inspired quantum biology: biochemistry, metabolism & replication 3.2 zeo based view about quantum self-organization could it be that 4-d deterministic time evolution between initial and final states could be more fundamental than the 3-d snapshot? could superpositions of these 4-d evolutions define quantum states. if so, the state function reductions would occur between these superpositions and their non-determinism would be consistent with the determinism of field equations. free will would not break laws of physics. it would be like starting new deterministic computer program. our philosopher calls this ontology zero energy ontology (zeo) and claims that it leads to a theory of consciousness as a generalization of quantum measurement theory [20] (see http://tinyurl.com/ycxm2tpd). irritating. zeo based quantum measurement theory predicts that in ordinary state function predicts that the arrow of time changes in ordinary state function reductions but is preserved in ”small” state function reductions identifiable as analogs of so called weak measurements. the recent strange findings of minev et al [1] provide direct evidence for the change of the arrow of time in state function reductions of atomic systems [29]. zeo predicts also the possibility of signals propagating backwards in time. this led to the vision that episodal memories involve communications with the brain of geometric past [6], to the idea that motor actions and sensory perception are time reversals of each other [27]: motor action would involve sending of negative energy control signals to the geometric past, and to the notion of remote metabolism based on quantum credit card mechanism. one can say that the system sends negative energy to a system able to receive it rather than receiving positive energy. the energy of system as a function of heff increases when other parameters are kept constant. it costs energy build intelligence. heff for a given sub-system tends also to reduce spontaneously. hence there must be continual energy feed to keep the level of conscious intelligence. a highly interesting possibility that this condition applies to all self-organizing systems. self-organization generates long range coherence and requires energy feed. could it be that dark matter makes itself visible by giving rise to long range correlations and coherence induced by dark matter at the magnetic body of the system [31]? just as life also self-organization involves generation of coherence in long scales and requires energy feed. in the model for living system relying on dark matter as heff = n × h0 phases at magnetic body of the system coherence is induced by quantum coherence of the dark matter, and metabolic energy feed is required to increase heff tending to reduce spontaneously. could self-organization be quite generally modelled in the same manner so that dark matter would make itself visible in everyday physics [31]? could the realizations of the genetic code in terms of dark nuclei and dark photon 3-chords be involved with the self-organization of water and be involved with morphogenesis? 3.3 does metabolic energy feed generate conscious information? the basic question about the role of metabolic energy remains, says the philosopher. what is its real role? energy feed generates structures and structural complexity means information. it seems that metabolic energy feed involves also a feed of information or generation of information. and because living systems are in question, philosopher cannot avoid the question whether this information is actually conscious information. is there any other kind of information than conscious information?! to this question standard physics has no answer: it can only describe entropy mathematically and identification of information as lack of entropy is the easy answer suggested in lack of anything better. the question about a possible measure for conscious information analogous to shannon entropy is one manner to end up with p-adic physics as a correlate of cognition and the necessary fusion of real and various p-adic physics leads to adelic physics [18, 19]. adelic physics in turn predicts surprisesurprise a hierarchy of phases of matter labelled by the value of planck constant heff/h0 = n defining the dimension of the extension of rationals defining the adele. these phases residing at these somethings defining the networks magnetic flux tubes make possible macroscopic quantum coherence inducing the coherence of living matter. quite generally, the energies of states as function of heff increase. for instance, atomic binding issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/ycxm2tpd dna decipher journal | october 2019 | volume 9 | issue 2 | pp. 71-80 77 pitkänen, m., some applications of tgd inspired quantum biology: biochemistry, metabolism & replication energy scales decreases like h2 eff and cyclotron energies scale like heff . in order to generate phases with non-standard value of heff energy feed is needed. this energy is identifiable as metabolic energy. in adelic physics [19, 18] heff serves as a measure for the iq of the living system in well-defined system. the higher its value, the better changes the system has for generating conscious information and also for destroying it. this leads to a rather concrete view about the origin of good and evil. the ethics and moral are simple: good deed increases the conscious information of the universe. conscious entity can choose whether to increase the conscious information of the universe or reduce it. evil deeds indeed lead to a reduction of conscious information of the universe since the doer cannot confess others or even himself what he did. also the members of community become secretive complex encryption schemes develop. the self-knowledge of the universe knows is reduced. luckily, evolution unavoidably occurs in statistical sense and resources of conscious information increase in long enough time scale. 3.4 remote metabolism as a purely thermodynamical universal mechanism in zeo quite recently (towards end of 2019) i found a more precice formulation for the intuitive notion of remote metabolism, which strongly suggests that energy is conserved in zeo. there is a decomposition to system and the energy energy source: call them a and b. intuitively, a receives energy from b by sending negative energy to b. what does this really mean? 1. a ”big” (ordinary) state function reduction reversing arrow of time takes place: this would correspond to sending negative energy signal to past. the energy of a+b in the final time reversed state at new passive boundary of cd would be shared in new manner such that one can say that a has received from b the metabolic energy. 2. energy would be conserved. i have also considered the interpretation that the total energy of the system associated with cd increases [8] [32]: since cd itself breaks poincare invariance, it seems that one cannot exclude this. however, the poincare invariance is realized at the level of moduli space for the positions of the either boundary of cd, and one can assume energy conservation. even the wave functions at the boundary of cd can be taken to be in the representations of lorentz group acting as its isometries. plane waves correspond to wave functions in the moduli space for the boundary of cd keeping second boundary fixed. 3. to make this more precise one must define metabolic energy more precisely by introducing the hierarchy of planck constants and the fact that the increase of heff of sub-system keeping other parameters constant increases it energy. second law means that a tends to loose energy due to the decrease of heff for its sub-systems. this is true also for the time-reversed state but in opposite direction of geometric time so that with respect to standard direction of time the energy increases. this would provide extremely general purely thermodynamical mechanism of remote metabolism. 4 the mystery of replication replication is one of the deepest mysteries of biology. it is really something totally counterintuitive if cell is seen as a sack of water plus some chemicals. we have a lot facts about what happens in the replication at dna level but how this miracle happens is a mystery. at cell level the situation gets even more complex. one might think that behind the chemistry there might lurk a much simpler quantum dynamics and that chemistry only makes its best to mimic this deeper dynamics. is biochemistry controlled by something? does this something provide a template for the dynamics at chemical level? the idea about the presence of this something popped up already in the mystery of eeg. what could this something issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2019 | volume 9 | issue 2 | pp. 71-80 78 pitkänen, m., some applications of tgd inspired quantum biology: biochemistry, metabolism & replication perhaps receiving sensory information from vertebrate brain and maybe providing feedback as control signals affecting also chemistry? one is forced to attack the length scale reductionism again. isn’t it quite too much to require that all these replications in different length scales would result as accidental ”emergence” due to thermodynamical fluctuations? could the dynamics be fractal with essentially same patterns for instance replication occurring in different scales. could this dynamics be induced by what happens on this something. philosopher also suggests a concrete model for the controlling level: dark matter with large value of planck constant heff/h0 = n at magnetic flux tubes and asks whether the conjectured dark realization of dna in various scales performs the fundamental replication inducing in turn the biological replication in various scales as a mimicry? this would simplify the situation enormously but in totally different manner than length scale reductionism. morphogenesis controlled by the hierarchy of dark realizations of genetic code would be the basic vision (see http://tinyurl.com/yalny39x). this would simplify the situation enormously but in totally different manner than length scale reductionism. tgd suggests also a purely topological element involved with replication. magnetic body (mb) could replicate [9]. replication would be like 3-vertex of feynman diagram representing the decay of a particle to two particles. mb or part of it regarded as particle like entity splits into two. the incoming 4-surface and two outgoing 4-surfaces meet along 3-d surface common to all three. after that various molecules would self-organize around the resulting templates. this could happen also for the mb of dark dna in replication and induce the bio-chemical part of replication. references [1] minev zk et al. to catch and reverse 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[2] montagnier l et al. dna waves and water. available at: http://arxiv.org/abs/1012.5166, 2010. [3] gariaev p. materialization of dna fragment and wave genetics in theory and practice. dnadj. available at: http://www.amazon.com/decipher-journal-volume-issue-materialization/dp/ 1500127493, 4(1), 2014. [4] pitkänen m. homeopathy in many-sheeted space-time. in bio-systems as conscious holograms. online book. available at: http://www.tgdtheory.fi/tgdhtml/holography.html#homeoc, 2006. [5] pitkänen m. quantum model for nerve pulse. in tgd and eeg. online book. available at: http://www.tgdtheory.fi/tgdhtml/tgdeeg.html#pulse, 2006. [6] pitkänen m. quantum model of memory. in tgd inspired theory of consciousness. online book. available at: http://www.tgdtheory.fi/tgdhtml/tgdconsc.html#memoryc, 2006. 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[10] pitkänen m. are dark photons behind biophotons? in tgd based view about living matter and remote mental interactions. online book. available at: http://www.tgdtheory.fi/tgdhtml/ tgdlian.html#biophotonslian, 2013. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/yalny39x https://arxiv.org/abs/1803.00545 http://arxiv.org/abs/1012.5166 http://www.amazon.com/decipher-journal-volume-issue-materialization/dp/1500127493 http://www.amazon.com/decipher-journal-volume-issue-materialization/dp/1500127493 http://www.tgdtheory.fi/tgdhtml/holography.html#homeoc http://www.tgdtheory.fi/tgdhtml/tgdeeg.html#pulse http://www.tgdtheory.fi/tgdhtml/tgdconsc.html#memoryc http://www.tgdtheory.fi/tgdhtml/bioselforg.html#selforgac http://www.tgdtheory.fi/tgdhtml/bioselforg.html#selforgac http://www.tgdtheory.fi/tgdhtml/tgdquantum.html#uandm http://www.tgdtheory.fi/tgdhtml/tgdlian.html#lianpb http://www.tgdtheory.fi/tgdhtml/tgdlian.html#lianpb http://www.tgdtheory.fi/tgdhtml/tgdlian.html#biophotonslian http://www.tgdtheory.fi/tgdhtml/tgdlian.html#biophotonslian dna decipher journal | october 2019 | volume 9 | issue 2 | pp. 71-80 79 pitkänen, m., some applications of tgd inspired quantum biology: biochemistry, metabolism & replication [11] pitkänen m. comments on the recent experiments by the group of michael persinger. in tgd based view about living matter and remote mental interactions. online book. available at: http: //www.tgdtheory.fi/tgdhtml/tgdlian.html#persconsc, 2013. [12] gariaev p pitkänen m. quantum model for remote replication. in genes and memes. online book. available at: http://www.tgdtheory.fi/tgdhtml/genememe.html#remotereplication, 2011. [13] pitkänen m. dna waves and water . available at: http://tgdtheory.fi/public_html/ articles/mont.pdf, 2011. [14] pitkänen m. geometric theory of harmony. available at: http://tgdtheory.fi/public_html/ articles/harmonytheory.pdf, 2014. [15] pitkänen m. more precise tgd based view about quantum biology and prebiotic evolution. available at: http://tgdtheory.fi/public_html/articles/geesink.pdf, 2015. [16] pitkänen m. about physical representations of genetic code in terms of dark nuclear strings. available at: http://tgdtheory.fi/public_html/articles/genecodemodels.pdf, 2016. [17] pitkänen m. dmt, pineal gland, and the new view about sensory perception. available at: http: //tgdtheory.fi/public_html/articles/dmtpineal.pdf, 2017. [18] pitkänen m. philosophy of adelic physics. in trends and mathematical methods in interdisciplinary mathematical sciences, pages 241–319. springer.available at: https://link.springer. com/chapter/10.1007/978-3-319-55612-3_11, 2017. [19] pitkänen m. philosophy of adelic physics. available at: http://tgdtheory.fi/public_html/ articles/adelephysics.pdf, 2017. [20] pitkänen m. re-examination of the basic notions of tgd inspired theory of consciousness. available at: http://tgdtheory.fi/public_html/articles/conscrit.pdf, 2017. [21] pitkänen m. about dark variants of dna, rna, and amino-acids. available at: http://tgdtheory. fi/public_html/articles/darkvariants.pdf, 2018. [22] pitkänen m. about the correspondence of dark nuclear genetic code and ordinary genetic code. available at: http://tgdtheory.fi/public_html/articles/codedarkcode.pdf, 2018. [23] pitkänen m. could cancer be a disease of magnetic body? available at: http://tgdtheory.fi/ public_html/articles/nanotesla.pdf, 2018. [24] pitkänen m. emotions as sensory percepts about the state of magnetic body? available at: http: //tgdtheory.fi/public_html/articles/emotions.pdf, 2018. [25] pitkänen m. expanding earth model and pre-cambrian evolution of continents, climate, and life. available at: http://tgdtheory.fi/public_html/articles/expearth.pdf, 2018. [26] pitkänen m. new results in the model of bio-harmony. available at: http://tgdtheory.fi/public_ html/articles/harmonynew.pdf, 2018. [27] pitkänen m. sensory perception and motor action as time reversals of each other: a royal road to the understanding of other minds? available at: http://tgdtheory.fi/public_html/articles/ timemirror.pdf, 2018. [28] pitkänen m. an overall view about models of genetic code and bio-harmony. available at: http: //tgdtheory.fi/public_html/articles/gcharm.pdf, 2019. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://www.tgdtheory.fi/tgdhtml/tgdlian.html#persconsc http://www.tgdtheory.fi/tgdhtml/tgdlian.html#persconsc http://www.tgdtheory.fi/tgdhtml/genememe.html#remotereplication http://tgdtheory.fi/public_html/articles/mont.pdf http://tgdtheory.fi/public_html/articles/mont.pdf http://tgdtheory.fi/public_html/articles/harmonytheory.pdf http://tgdtheory.fi/public_html/articles/harmonytheory.pdf http://tgdtheory.fi/public_html/articles/geesink.pdf http://tgdtheory.fi/public_html/articles/genecodemodels.pdf http://tgdtheory.fi/public_html/articles/dmtpineal.pdf http://tgdtheory.fi/public_html/articles/dmtpineal.pdf https://link.springer.com/chapter/10.1007/978-3-319-55612-3_11 https://link.springer.com/chapter/10.1007/978-3-319-55612-3_11 http://tgdtheory.fi/public_html/articles/adelephysics.pdf http://tgdtheory.fi/public_html/articles/adelephysics.pdf http://tgdtheory.fi/public_html/articles/conscrit.pdf http://tgdtheory.fi/public_html/articles/darkvariants.pdf http://tgdtheory.fi/public_html/articles/darkvariants.pdf http://tgdtheory.fi/public_html/articles/codedarkcode.pdf http://tgdtheory.fi/public_html/articles/nanotesla.pdf http://tgdtheory.fi/public_html/articles/nanotesla.pdf http://tgdtheory.fi/public_html/articles/emotions.pdf http://tgdtheory.fi/public_html/articles/emotions.pdf http://tgdtheory.fi/public_html/articles/expearth.pdf http://tgdtheory.fi/public_html/articles/harmonynew.pdf http://tgdtheory.fi/public_html/articles/harmonynew.pdf http://tgdtheory.fi/public_html/articles/timemirror.pdf http://tgdtheory.fi/public_html/articles/timemirror.pdf http://tgdtheory.fi/public_html/articles/gcharm.pdf http://tgdtheory.fi/public_html/articles/gcharm.pdf dna decipher journal | october 2019 | volume 9 | issue 2 | pp. 71-80 80 pitkänen, m., some applications of tgd inspired quantum biology: biochemistry, metabolism & replication [29] pitkänen m. copenhagen interpretation dead: long live zeo based quantum measurement theory! available at: http://tgdtheory.fi/public_html/articles/bohrdead.pdf, 2019. [30] pitkänen m. do hydrogels learn in presence of irradiation and heating? available at: http: //tgdtheory.fi/public_html/articles/gellearns.pdf, 2019. [31] pitkänen m. quantum self-organization by heff changing phase transitions. available at: http: //tgdtheory.fi/public_html/articles/heffselforg.pdf, 2019. [32] pitkänen m. tesla still inspires. available at: http://tgdtheory.fi/public_html/articles/ teslastill.pdf, 2019. [33] m. pitkänen. emotions & rna. dna decipher journal, 8(2), 2018. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.fi/public_html/articles/bohrdead.pdf http://tgdtheory.fi/public_html/articles/gellearns.pdf http://tgdtheory.fi/public_html/articles/gellearns.pdf http://tgdtheory.fi/public_html/articles/heffselforg.pdf http://tgdtheory.fi/public_html/articles/heffselforg.pdf http://tgdtheory.fi/public_html/articles/teslastill.pdf http://tgdtheory.fi/public_html/articles/teslastill.pdf introduction questions related to bio-chemistry biocatalysis what selected the biomolecules? genetic code metabolism non-equilibrium thermodynamics zeo based view about quantum self-organization does metabolic energy feed generate conscious information? remote metabolism as a purely thermodynamical universal mechanism in zeo the mystery of replication dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 235 article dawkins’ darwinism part i: evolution the greatest illusion on earth and the new quantum platonic paradigm graham p. smetham * abstract many of the claims of materialist ultra-darwinist (mud) worldview are desperately implausible, having about the same credibility as fairy stories. for example, if we accept dawkins claim that the development of new adaptations is very gradual, the ancestor with the pouch mutation would still at this initial point be giving birth via egg birth. however we are supposed to believe, according to the dud-mud account, that there is some subtle slight alteration in the direction of pouch birth. now in order for this slight new mutational ‘something’, indicating the possibility of the future development of pouch birth, to actually get ‘favoured’ it must be advantageous in some way at that point in time. but how could this possibly be true? what kind of environment could make the potentiality of pouch birth signaled by a non-noticeable mutation, significantly more advantageous than an egg one? the egg birth process was presumably working perfectly well otherwise these pouch-mutant mammals would have died out before they became fully pouch endowed. what kind of mutated mind could possibly believe such a desperately implausible scenario? the only way this scenario could possibly make sense is if there is some kind of quantum evolutionary ‘look-ahead’ mechanism as suggested by mensky. the only possible explanation which accords with current scientific knowledge is that there is a deep level of quantum interconnection between an environment and the ‘design’ of the species found in that environment. and such an interconnection has been shown to exist; it is called ‘quantum entanglement’. this can happen precisely because the ‘themes’ for all the possibilities of life, including organisms and environments, are potential within the platonic quantum fields of potentiality, and when they are expressed and manifested they do so in a manner which is, in the main, coherent and consistent, the inhabitants fitting, because of the patterning of the internal potentialities, the manifested environments. when the evidence is examined with precision it becomes clear that the mud worldview is incoherent and a new quantum platonic paradigm must supplant it. keywords: darwinism, dawkins, michael mensky, amit goswami, intelligent design, evolution, evo-devo, random mutation, natural selection, illusion, quantum platonism, quantum interconnection, environment, design. the more examples of the writings of materialist ‘ultra-darwinism’ (the ‘new darwinian synthesis’ is also called neo-darwinism), which emphasizes the role of ‘random mutation’ (rm) and ‘natural selection’ (ns) in its theory of evolution, i read the more astonished i am by the childish simple-mindedness of its practitioners. they are able to pen the most ridiculous nonsense and yet at the same time remain convinced that they are engaged in expounding serious ‘science’. one of the core practitioners of this pseudo-science is, of * correspondence: graham smetham, http://www.quantumbuddhism.com e-mail: graham.smetham@gmail.com http://www.quantumbuddhism.com/ mailto:graham.smetham@gmail.com dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 236 course richard dawkins so we can dub this form of extreme materialist account of the evolutionary process dawkinsian ultra-darwinism, for which we may employ the appropriate acronym ‘dud’. a fine example an absurd dud account is provided by dawkins’ account of how, in the dim mists of time, fish were supposedly forced by environmental circumstances to drag themselves with their fins, no doubt gasping for air with their gills if such were possible, from one pond, which was drying out, to another with deeper waters. here is the relevant passage from dawkins’ book the greatest show on earth: my undergraduate imagination at oxford was fired by the lectures of the prodigiously knowledgeable harold pusey who, despite his dry and prolonged delivery, had a gift for seeing beyond dry bones to the flesh-and-blood animals that had to make a living in some departed world. his evocation of what drove some lobe-finned fish to develop lungs and legs, which was derived from romer himself, made memorable sense to my student ears, and it still makes sense to me even though it is less fashionable among modern palaeontologists than it was in romer’s time. romer, and pusey, envisaged annual droughts during which lakes and ponds and streams dried up, only to flood again the following year. fishes that made their living in water could benefit from a temporary ability to survive on land, while they dragged themselves from a shallow lake or pond that was threatened with imminent desiccation to a deeper one in which they could survive until the next wet season. on this view, our ancestors didn't so much emerge on to the dry land as use the dry land as a temporary bridge to escape back into the water. many modern animals do the same. rather unfortunately, romer introduced his theory with a preamble whose purpose was to show that the devonian era was a time of drought. consequently, when more recent evidence undermined this assumption, it seemed to undermine the whole romer theory. he’d have done better to omit the preamble, which was, in any case, overkill. as i argued in the ancestor’s tale, the theory still works, even if the devonian was less drought-ridden than romer originally thought. 1 the devonian period, named after devon, england, where rocks from this period were first studied, is a geologic period of the paleozoic era, which literally translates as the “time of ancient life” and spans the time period between 544 and 245 million years ago. the devonian period spans from the end of the silurian period, about 416 million years ago, to about 360 million years ago. as dawkins points out, at the end of the devonian period there begins “one of the most famous gaps in the fossil record” which is given the name ‘romer’s gap’ (after the american palaeontologist alfred sherwood romer) which stretches from the end of the devonian period to the beginning of the carboniferous period about 340 million years ago. after this gap there appears “unequivocal amphibians crawling through the swamps” whereas prior to romer’s gap there is only evidence of lobe-finned fish (figure 1). at the start of the twentieth century fossils of carboniferous tetrapod (four legged) amphibians (figure 2) were found in strata corresponding to a time period after romer’s gap. the story concocted by romer was supposed to give an ‘explanation’ of how the transition from fully paid up aquatic fish to land-roaming amphibians came about. as we shall see, like many dud ‘explanations’ of this type, romer’s offering relies upon the reader or listener imputing a kind of subtle intentionality where there should be none, although this would be stridently resisted by committed dud’s for whom the story involves nothing beyond mindless and random mutations which produce flaws in the mutated offspring. as dawkins states in the preface to his book river out of eden: dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 237 … when the ricochets of atomic billiards chance to put together an object that has a certain, seemingly innocent property, something momentous happens in the universe. that property is an ability to self-replicate; that is the object is able to use the surrounding materials to make exact copies of itself, including replicas of such minor flaws in copying as may occasionally arise. 2 in the dud worldview, of course, it is asserted that such ‘flaws’ in the copying of genetic information randomly and adventitiously turn out to be remarkably advantageous in fitting into an environment. figure 1 (3) figure 2 (4) in order to follow the following discussion it is necessary to be quite clear on what the dud view of the central evolutionary mechanism of natural selection actually is. dud natural selection (ns) is a kind of filter theory wherein ‘good’ genes get passed on and ‘bad’ genes fall by the wayside: genes do not improve in the using, they are just passed on, unchanged except for very rare random errors. it is not success that makes good genes. it is good genes that make success, and nothing an individual does during its lifetime has any effect whatever upon its genes. those individuals born with good genes are the most likely to grow up to become successful ancestors; therefore good genes are more likely than bad to get passed on to the future. each generation is a filter, a sieve: good genes tend to fall through the sieve into the next generation; bad genes tend to end up in bodies that die young or without reproducing. bad genes may pass through the sieve for a generation or two, perhaps because they have the luck to share a body with good genes. but you need more than luck to navigate successfully through a thousand sieves in succession, one sieve under the other. after a thousand successive generations, the genes that have made it through are likely to be the good ones. 5 when “very rare random errors” occur most must lead to ‘bad’ genes. in fact, no one has ever seen a random mutation leading to ‘good’ genes, random mutations we do know about, such as those caused by radioactivity, inevitably lead to dreadful results. however according to the dud mythology ‘very very very rare random good errors’ sometimes occur which produce adaptations of organisms which are more suited to their environments. it is these ‘good’ genes that are passed on to future generations, having been filtered by the environment. according dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 238 to the dud worldview as these genes increasingly separate into difference species, they eventually give rise to the “long goodbye”: from a gene’s point of view, speciation, the origin of new species, is “the long goodbye.” after a brief period of partial separation, the two rivers go their separate ways forever, or until one or the other dries extinct into the sand. secure within the banks of either river, the water is mixed and remixed by sexual recombination. but water never leaps its banks to contaminate the other river. after a species has divided, the two sets of genes are no longer companions. they no longer meet in the same bodies and they are no longer required to get on well together. there is no longer any intercourse between them-and intercourse here means, literally, sexual intercourse between their temporary vehicles, their bodies. 6 lineages that are separating eventually, according to the dud account, become entirely different species that cannot interbreed. this notion of what a ‘species’ consists of was put in place by the ernst mayr, held to be one of the twentieth century’s leading evolutionary biologists, despite the fact that he made dogmatic claims, based on fantasy and no evidence, which turned out to be entirely wrong, just as dawkins has done in the past (and continues to do). dawkins assertion concerning the “long goodbye,” which asserts that the genes of different species become increasingly dissimilar, is derived from one of mayr’s dogmatic mistaken fantasies, a fantasy that the evo-devo (evolutionary development) revolution has shown to be entirely incorrect. the evo-devo perspective has discovered a remarkable identity of gene types underlying all organisms, dawkins’ notion of “long goodbye,” then, is out of date and mistaken. the american philosopher and cognitive scientist jerry fodor gives the following summary of the ns (natural selection) ‘adaptationist’ perspective: darwin’s theory of evolution has two parts. one is its familiar historical account of our phylogeny; the other is the theory of natural selection, which purports to characterise the mechanism not just of the formation of species, but of all evolutionary changes in the innate properties of organisms. according to selection theory, a creature’s ‘phenotype’ – the inventory of its heritable traits … is an adaptation to the demands of its ecological situation. adaptation is a name for the process by which environmental variables select among the creatures in a population the ones whose heritable properties are most fit for survival and reproduction. so environmental selection for fitness is (perhaps plus or minus a bit) the process par excellence that prunes the evolutionary tree. 7 in his book what darwin got wrong fodor (with massimo piattelli-palmarini ) refers to these two components as “the genealogy of the species (gs), which is the recognition of the historical development of species; and ‘natural selection’ (ns) which is the mechanism that dud asserts to be fundamental. he gives the diagram shown in figure 3 with the caption: a schematic representation of the standard neo-darwinian model of evolution by natural selection. the square on the left represents random genetic mutations, the arrow the expression of those mutations as manifest traits (phenotypes), and the filters the action of natural selection. 8 dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 239 figure 3 (9) this view is entirely in accord with that of dawkins, who, as we have seen, has also used the ‘sieving’ metaphor. a further important ingredient in the rm+ns dud worldview is the claim that the process takes place gradually, one mutation at a time endowing a tiny advantage over long time periods and, furthermore, these tiny gradual transitions occur at the material level of reality. this means that as fish took to the land and then began their slow, excruciating evolutionary transformation, through various forms on the way to other species, each tiny mutation produced an actual animal. a fish’s fins, then, must have extended and transformed into legs, millimeter by millimeter, each transformation giving rise to a new animal, an animal with a difference from its predecessor that is hardly noticeable. here is what dawkins writes about this in the greatest show on earth: … every animal is linked to every other animal, say rabbit to leopard, by a chain of intermediates, each so similar to the next that every link could in principle made with its neighbours in the chain and produce fertile offspring. … on the evolutionary view, there really is a series of intermediate animals connecting a rabbit to a leopard, every one of whom lived and breathed, every one of whom would have been placed in exactly the same species as its immediate neighbours on either side in the long, sliding continuum. indeed, every one of the series was the child of its neighbour on one side and the parent of its neighbour on the other. yet the whole series constitutes a continuous bridge from rabbit to leopard … there are similar bridges from rabbit to wombat, from leopard to lobster, from every animal or plant to every other. … take a rabbit, any female rabbit (arbitrarily stick to females, for convenience: it makes no difference to the argument). place her mother next to her. now place the grandmother next to the mother and so on back in time, back, back, back through the megayears, a seemingly endless line of female rabbits, each one sandwiched between her daughter and her mother. we walk along the line of rabbits, backwards in time, examining them carefully like an inspecting general. as we pace the line, we’ll eventually notice that the ancient rabbits we are passing are just a little bit different from the modern rabbits we are used to. but the rate of change will be so slow that we shan't notice the trend from generation to generation, just as we can’t see the motion of the hour hand dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 240 on our watches – and just as we can't see a child growing, we can only see later that she has become a teenager, and later still an adult. 10 we see, then, that the dud account of evolution asserts that it is a fully materialized phenomenon, each tiny gene mutation giving rise to a tiny difference in a subsequent ‘living, breathing’ animal that “swam in the sea, walked or slithered on land, or flew in the air.” this means, of course, that one would expect a plethora of evidence of many ‘intermediates’ or ‘transitional’ forms. the supposed transition from a lobe-finned fish to early amphibians is supposed to be an example of this, although there no evidence of other animals with fin-leg protrusions intermediate between the two. figure 4 (11) at the time romer was pondering his fishy story, transitional forms from fish to tetrapod were absent from the fossil record, but there were supposedly clues elsewhere. one feature of late devonian geology is the prevalence of red sediments in europe and north america and in 1916 joseph barrell suggested that these oxidized sediments were evidence of a harsh landscape subject to severe droughts. he also argued that this severe climate was a major driving force in the evolution of air-breathing vertebrates, including tetrapods. this led to further elaborations on the idea that devonian droughts were the driving force for the evolution of tetrapods that culminated in 1950s with the “drying pond” scenario proposed by romer. in this scenario, tetrapods evolved from lobe-finned fishes driven onto the land by drought. as one pool or stream dried out, the fishes ventured onto the parched earth in search of other bodies of water. over time, natural selection was supposed to ‘favour’ those fishes who had randomly acquired more limb-like fins, and of course the beginnings of a lung or lungs. in such a fashion tetrapods are supposed to have literally evolved from fish out of water (figure 4). if we leave aside the issue of the fact that the drought scenario is no longer accepted, there is one huge problem with this explanation, a problem that, in different guises, can be regularly found in dud explanations and accounts, but is never addressed by dud practitioners. even if we accept, for sake of argument, the claim that a fish randomly acquired fins which also had a bone structure anticipatory of tetrapod limbs, they would also at the same time have to had randomly developed breathing apparatus also capable of dealing with breathing both in and out of water. somewhat like the lungfish, although the lungfish curls up in mud to use its lung, it does not scamper about on the land using its lung. in this case, we would need two random mutations, occurring at the same time, both of which radically altered the morphology of the fish. this in itself seems implausible, and we should ask ourselves whether it is actually likely that one tiny random mutation could modify gills, or add the functionality to supplement gills, so that a fish suddenly can function in water and also take the odd gulp of air whilst the fish is dragging itself around on land with its fins. dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 241 how does a fish that is quite content using its fully efficient gills for breathing in water start the operation of acquiring, through the operation of rm+ns, breathing apparatus to suit it for land? according to the dud account, a random mutation occurs and subsequently confers an advantage within a particular environment. in this way, the lucky creature endowed with this lucky flaw gets favoured. but what possible advantage could a random mutation which confers upon a fully paid up aquatic fish the possibility of breathing on land (if we can accept such an absurdity) bestow upon a fish which is never going to go near the land at the time that it acquired the mutational transformation. its new capacity would confer no advantage so would not get selected by ns, unless, that is evolution ‘knew’ that fish would need to take to the land at some point, but any such look ahead mechanism is denied in the dud worldview. however, this is the kind of ridiculous ‘explanations’ we have to agree to if we accept the kind of picture suggested by romer. and of course, the same can be said of dawkins who modifies romer’s absurd notion to try and rescue it: unfortunately, romer quoted the prevailing belief of his day that the devonian was a time of drought, a belief that has more recently been called into question. but i don’t think romer needed his devonian desiccated. even at times of no drought, there will always be some ponds shallow enough to be in danger of becoming too shallow for some particular kind of fish. if ponds three feet deep would have been at risk under severe drought conditions, mild drought conditions will render ponds one foot deep at risk. it is sufficient for the romer hypothesis that there some ponds which dry up, and therefore some fish could save their lives by migrating. even if the world of the late devonian was positively waterlogged, one could say this simply increases the number of ponds available to dry up, thereby increasing opportunities for saving the life of walking fish and the romer theory… nevertheless it is my duty to record that the theory is now unfashionable. … to be sure, there are plenty of other good reasons for a fish to emerge, temporarily or permanently, onto land. streams and ponds can become unusable for reasons other than drying up. they can become choked with weeds, in which case, again, a fish that can migrate over land to deeper water might benefit. if, as has been suggested contra romer, we are talking devonian swamps rather than devonian droughts, swamps provide plenty of opportunities for a fish to benefit by walking, or slithering or flip-flopping or otherwise travelling through the marshy vegetation, in search of deep water or, indeed, food. this still retains the essential romer idea that our ancestors left the water, not at first to colonise land, but to return to water. 12 this reworking has retained romer’s vision that the fish were not making a dash for land, so to speak, but rather, “walking, or slithering or flip-flopping or otherwise” from pond to pond. not only this, it accomplishes this by entirely inverting romer’s speculation. rather than speculating that the fish were desperately slithering about on what would have been a very hot land, as their ponds were evaporating, looking for deeper ponds, dawkins, in order to fix the evidence that that undermines that speculation, adopts the contrary speculation that “we are talking devonian swamps rather than devonian drought.” welcome to the wonderful fantasy world of evolutionary theory, or should we not rather use the term ‘evolutionary speculation’. fantasy and speculation, not science, it is. how else would it be possible for exactly contrary explanations be made to fit the same facts of the fossil record? look at some of terminology used by dawkins: a fish that can migrate over land to deeper water might benefit”, “if, as has been suggested contra romer, we are talking…” we shall find that this kind of speculative language is employed liberally in what dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 242 is claimed to be a watertight ‘science’. dawkins’ attempted reworking of romer, like much dud theory, is nothing more than speculative fantasy in the cause of shoring up the leaks in a ridiculous worldview. at the outset of the blind watchmaker dawkins proclaims: …the darwinian worldview … is the only known theory that could, in principle, solve the mystery of our existence. 13 as we shall see, such a claim is utterly deluded. whether fleeing dried up ponds or seeking a more spacious residence in devonian swamps, there has to be a first batch of fish that make the evolutionary leap, and that, through the magic of natural selection, have ‘acquired’ both fins which operate, however clumsily, on land and also suitable breathing apparatus at least to get them to the nearest deeper pond. but, as has been previously pointed out, there is absolutely no possibility of ns ‘selecting’ a randomly mutated produced lung whilst a fish is in water, and they are hardly likely to take an anticipatory gill-full of oxygen and hold their gill-breath. the whole notion is ridiculous, absurd and beyond belief. and the fact that putatively intelligent people ever took, and still take, such notions seriously is also beyond belief. the way in which the dud worldview promotes its silliness, however, is simply to gloss over its incoherencies and absurdities. thus dawkins tells us that: on this view, our ancestors didn’t so much emerge on to the dry land as use the dry land as a temporary bridge to escape back into the water. many modern animals do the same. 14 this is the dud tactic of suggesting that the transition is not that remarkable. the pond with deeper water was probably not too far away. modern animals manage it so there is no reason so their ancestors not to have also done so. this argument is just silly. the fact that some modern animals have the capacity to achieve this feat has no bearing whatsoever on accounting for how fish that have never ventured on to land suddenly develop the ability to do so. in fact from the point of view of the dud account the issue is how these modern animals came to have the ability. so to claim that the fact that they do have the ability as evidence that arriving at the ability is simple, is absurdly circular and misleading. but this kind of invalid circular reasoning is often found in dud modes of unreasoning. no one in the dud camp seems to notice that for the dud account to work the unfortunate first fish to encounter the drying up scenario must have been randomly equipped by rm+ns for the encounter with land and air, although there is no possible scenario that can account for how a fish acquires the equipment for breathing air whilst its environment is water. the dud worldview is replete with such nonsense. at this point, the notion that lungfish might have something to add to the debate might be raised. however, although dawkins tells us that “we land animals are aberrant lungfish”, in fact: …we are not descended from lungfish or from coelacanths. we share an ancestor with lungfish, which looked more like a lungfish than it looked like us. 15 coelacanths are members of an order of fish that includes the oldest known living lineage of lobe-finned fish and tetrapods. the fact that we did not descend from lungfish would seem to suggest that the fish that, according to the dud account, we did descend from must have scrambled onto land lungless, which would have been a heroic feat in order to grow feet! dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 243 lungfish (dipnoi–figure 5) are a group of lobe-finned fish (sarcopterygii or sometimes crossopterygii). lungfish have a “lung” which is a modified swim bladder, which in most fish is used for buoyancy in swimming, but in the lungfish also absorbs oxygen and removes wastes. modern lungfish in africa and south america are able to survive when their pools dry up by burrowing into the mud and sealing themselves within a mucous-lined burrow. during this time, they breathe air through their swim bladder instead of through their gills, and dramatically reduce their metabolic rate. in this condition lungfish will drown if they are kept underwater and not allowed to breathe air! this fact should, one might have thought, alerted a moderately intelligent person to the implausibility of the development of the lung whilst the supposed ancestor of the lungfish was underwater primarily relying on its gills. as we shall see, however, such basic logical capacities seem strangely absent from the dud worldview. figure 5 (16) the existence of lungfish is made much of by some duds. in the introduction to the ancestor’s tale dawkins primes his readers by claiming that: …the emergence of our remote fish ancestors from water to land was a momentous step an evolutionary rite of passage. it was undertaken by lobe-finned fish a bit like lungfish. 17 the implication, of course, is that the lobe-fined fish somehow developed a lung, or protolung, whilst swimming around in the sea and, then in ponds, using its gills to oxygenate itself. however, as indicated above such a notion is entirely implausible simply because there is absolutely no way that ns would ‘select’ a proto-lung whilst a fish is entirely in water using its gills. most lungfish, like the south american lungfish, have gills that are poorly developed. they breathe air mostly with their swim bladders. if one of these lungfish couldn’t reach the water’s surface, it would drown. the australian lungfish, however, breathes mostly with its gills; it gulps air at the water’s surface only when the water doesn’t have much oxygen in it. this indicates that not only would the evolving south american lungfish need the lung to be developing although not being used whilst entirely within water, at the same time the gills would have to be un-developing, even though there is absolutely no reason for them to do so according to the dud worldview. the only dud explanation that a dud perspective can offer is that at some point when oxygen in the water was depleted ns produced a proto-lung. at the same time it also gave the proto-lungfish instinctual knowledge that this new appendage could be used to gulp air. presumably the dud perspective conceives of this process leading to the un-development of the gills, although there is no reason for this to occur, the australian lungfish is quite happy using its gills as long as there is enough oxygen dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 244 in the water. why would ns wither away the gills so that the lungfish is in danger of drowning? the dud worldview does not offer precise accounts of many of its claims but only speculative ‘just-so’ stories involving lots of speculative “imagination: imagine a set of mutations of increasing magnitude. at one extreme a mutation of zero magnitude is by definition exactly as good as the parent’s copy of the gene which … must have been as least as good to survive childhood and reproduce. now imagine a random mutation of small magnitude: the leg, say, gets one millimeter longer or one millimeter shorter. assuming that the parental gene is not perfect, a mutation that is infinitesimally different from the parental version has a 50 per cent chance of being better and 50 per cent chance of being worse …but a very large mutation will probably be worse, even if it is in the right direction, because it will overshoot. to push to the extreme, imagine an otherwise normal man with thighs two metres long. 18 pure, unadulterated speculative imagination with absolutely no evidential backing! rationalwiki is a forum for dud enthusiasts to indulge their lack of significant research by posting short diatribes against intelligent design and creationism (rarely distinguished). the level of analysis is generally dismal and mostly one finds regurgitation of the mistaken views of dawkins and friends. a rationalwiki entry on the subject of lungfish begins: the lungfish are an example of the kind of life forms that creationists are very quiet about. they rant and rave about a lack of intermediate forms between fish and land animals, sometimes with ridiculous statements like “i’ve never seen a half-fish halfcow”. lungfish are able to breathe with their lung and can live out of water for fairly long periods. they also use their lung to give a continuous oxygen supply while they sit out the dry period under exposed mudbanks. 19 the level of competence in analysis and reasoning is very limited on this forum. our dud enthusiast claims that: the australian lungfish (n. forsteri) lives in brackish rivers and lakes and still have functional gills which supplement their lungs. this shows creationists are wrong when they argue that a fish could not survive without gills while its lungs were evolving. fish did not lose their gills till their lungs were fully evolved. some lungfish are more adapted to water and others to land. 20 the existence of the australian lungfish, however, proves no such thing. it just means that there is an australian lungfish that have “functional gills which supplement their lungs.” the conclusion that this proves that fish developed lungs whilst still keeping their gills, and whilst living fully in water, is entirely spurious, it proves no such thing. this conclusion is a speculation adopted because of a prior commitment to the dud worldview. it should not take a great effort of intellectual insight to figure out that if a random mutation requires an advantageous environment in order for it to survive, then a proto-lung in a fish in water is not in an advantageous environment. the lung, even if we grant the ridiculous notion of a tiny random mutation producing a functioning lung within a fish happily living in water and using its gills, would never be “naturally selected” in a water environment. however, our dud rationalwiki blogger thinks he has proved his or her point: “they’re three fish. with lungs. accept it.” of course, there is no reason not to “accept it,” but it proves nothing concerning the truth of the absurd materialist dud account of the process of evolution. dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 245 in another rationalwiki entry, entitled fish that survive on land, the claim is made that lungfish “breathe through lungs like our lungs.” 21 however, this is not true. if one looks into the opinions expressed by dud followers one often finds that they do not bother to do any research to delve into the truth of issues, they simply accept the simplistic nonsense fed to them! lungfish are vertebrates and all vertebrates have a similar underlying plan with brains and livers, hearts, intestines and skeletons and so on, but this does not mean that lungfish have human-type organs. although lungfish are unusual among fish in having a kind of lung, it does not operate in the same way as a mammal’s lung. a lung in a mammal consists of billions of tiny cavities containing air, known as alveoli. in a lungfish, the lung has large air sacs and no minute alveoli. figure 6 shows: a scanning electron micrograph of the lung of a young lungfish. the air sacs are large, and there are no alveoli. the scale bar is equivalent to 0.2 of a millimetre, so the air scales are up to a millimetre wide. 22 figure 6 (23) the reason that such darwinian fairy tales are accepted unquestioningly by most dud enthusiasts is that they are already in the grip of an irrational belief in the materialist dud worldview. the obvious flaws in the arguments and presentations simply do not register. there are some duds, however, who do not have completely blinkered reasoning faculties. the following is a response to an incoherent post claiming that the evo-devo (evolutionarydevelopment) revolution and the existence of lungfish disproves intelligent design: 24 the mere thought that intelligent design could even be put forward in this day and age is mind boggling to most scientists. but with all due respect, merely citing that the transition from water to land was accompanied by the appearance of the aldosterone receptor does not explain how this may have occurred based on natural selection. without a mechanism for this process, the evolutionists are telling kipling “just so stories” that are no more credible than those of the intelligent design proponents, which is why the intelligent designers maintain credibility with the lay public. 25 this comment, by someone who is opposed to the intelligent design hypothesis, isolates the issue precisely. without a fully elucidated precise account of the mechanisms involved, the claims made by duds are specious. duds, of course, think they have a fully worked out mechanism, rm+ns. but they do not, it is a deluded fantasy, a kipling “just so story.” to reiterate, even if one accepts that a random mutation might produce the beginnings of a lung in a gill-breathing fish, in a water environment there is no advantage to having a lung so how could it possibly be “selected” by ns. duds, however, do not worry about plausibility or dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 246 rationality, despite their pugilistic claims to be the only rational people around, they love their ‘just so stories’: the fishes of the early and middle devonian found themselves forced to choose between the invading salt water marshes and the isolated fresh-water pools which periodically contracted into stagnant swamps or hard mud flats… the more advanced of the fishes, however, in order to survive in the stagnant waters of the continents, took to swallowing air and thus invented lungs and prepared the way for the evolution of the terrestrial vertebrates. 26 fish that are able to “invent” lungs! far from being an advantage for the dud case, however, the existence of the lungfish actually undermines it for the same reason that we have already discussed. life arose in the sea and the earliest method for obtaining oxygen was by means of gills. so the dud problem remains as to how a lungfish, which according to the dud worldview must have randomly evolved its lung through natural selection, in which the environment is supposed to select advantageous mutations through filtration of favorable ‘flaws’, managed to evolve its lung without an environment within which the lung was an advantage. dawkins writes on this that: short of rocketing into space, it is hard to imagine a bolder or more life-changing step than leaving the water for dry land. the two life-zones are different in so many ways that moving from one to the other demands a radical shift in almost all parts of the body. gills that are good at extracting oxygen from water are all but useless in air, and lungs are useless in water. methods of propulsion that are speedy, graceful and efficient in water are dangerously clumsy on land, and vice versa. no wonder ‘fish out of water’ and ‘like a drowning man’ have both become proverbial phrases. 27 indeed, no wonder, then, that the notion that rm+ns could do the job is blatantly absurd. after his speculative inversion of romer’s speculation dawkins continues his exposition with an overview of the fossil record of the fish’s supposed emergence onto land. first he introduces us to the eusthenopteron (see figure 7 which illustrates the supposed evolutionary sequence) which was discovered in a collection of fossils in 1881. this creature, dawkins tells us, seems: …to have been a surface-hunting fish and probably didn’t ever come on land, notwithstanding some early imaginative reconstructions. nevertheless it did have several anatomical similarities to the amphibians of 50 million years later, including its skull bones, its teeth and, above all, its fins. although they were probably used for swimming and not walking, the bones followed the typical pattern of a tetrapod (the name given to all land vertebrates). in the forelimb, a single humerus was joined to two bones, the radius and ulna, joined to lots of little bones, which we tetrapods would call carpals, metacarpals and fingers. and the hind limb shows a similar tetrapod-like pattern. 28 dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 247 figure 7 (29) figure 8 (30) he then outlines the discoveries of the fossils of the various ‘transitional forms’ indicated in figure 7. ichthyostega (figure 8) was discovered in 1932 in greenland. this was followed by acanthostega. these two were largely water dwellers and “had lungs and limbs which strongly suggest that [they] could cope on land as well as water.” 31 panderichthys, dawkins tells us, is an “amphibian like fish” and the final “missing link” was discovered by a team of scientists from the university of pennsylvania who: …deliberately thought about where might be the best place to look, and carefully chose a rocky area of exactly the right late devonian age in the canadian arctic. there they went and struck zoological gold. tiktaalik! 32 figure 9 shows an artist’s impression of tiktaalik. dawkins says concerning the discovery of tiktaalik: if you were to meet a real live tiktaalik, snout to snout, you might start back as if threatened by a crocodile, for that is what its face resembled. a crocodile's head on a salamander’s trunk, attached to a fish's rear end and tail. unlike any fish, tiktaalik had a neck. it could turn its head. in almost every particular, tiktaalik is the perfect missing link perfect, because it almost exactly splits the difference between fish and amphibian, and perfect because it is missing no longer. we have the fossil. you can see it, touch it, try to appreciate the age of it… 33 so now we are supposed to believe that this is the entire sequence that proves the dud account, a sequence which, according to the dud worldview, proves the dud style gradual, dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 248 incremental evolution through random gene mutations, each mutation producing advantageous ‘flaws’, that are filtered by ns in the direction of moving on to the land. dawkins says of this that “the move from water to land launched a major redesign of every aspect of life, from breathing to reproduction…” but, as we have seen, the redesign of breathing required in order for fish originally equipped with only gills to acquire landbreathing equipment could not have occurred in the manner that the dud worldview claims that it did. figure 9 (34) consider the first creature in the chain, eusthenopteron, which did not come near the land (and if dawkins were to be wrong about this we can consider the fish previous in the sequence which had not yet ventured landwards). this fish was presumably happy enough with the operation of its gills for extracting oxygen. now let’s humour the dud delusion and suppose that some kind of random mutational flaw occurred which produced in its offspring some kind of predisposition for breathing air with a lung; this new innovation would need to be filtered by the environment so it can be amplified through descendants. but the fish in question is happily living in water, does not go near land; so how could the land-breathing mutation possibly be ‘selected’ by the supposed natural selection of the water environment, where there is no free air. the entire account is nothing more than an absurd fantasy. however, it certainly looks as if there is a definite sequence which suggests this type of fantasy, which is why the fantasy has had such a devoted following of duds (‘dud’ can stand for ‘dawkinsian ultra-darwinism’ or ‘‘dawkinsian ultra-darwinist’, the context should indicate which is appropriate). the crucial issue, however, is how we interpret this sequence. the dud worldview is also a mud worldview, a materialist ultra-darwinian perspective wherein everything is thought to take place within a fully paid up material world. in such a mud perspective genes are thought of as ultimate material bits of self-enclosed independently existing units of stuff, all of which have a kind of informational token glued on to them. as these dna ‘units’ are passed on through the generations they do not change, nor does their glued on bits of information, unless that is, a “very rare random error” occurs. in river out of eden dawkins presents his dud-mud vision this way: it is tempting to think that when ancestors did successful things, the genes they passed on to their children were, as a result, upgraded relative to the genes they had received from their parents. something about their success had rubbed off on their dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 249 genes. … wrong, utterly wrong! genes do not improve in the using, they are just passed on, unchanged except for very rare random errors. 35 in other words according to the dud-mud worldview genes only change in the direction of becoming more advantageously flawed. but this perspective, apart from being unworkable as we have seen, also does not fit in with the evidence, unless, that is, one is already genetically predisposed and hard-wired into the dud-mud worldview. consider again the first creature in the chain, eusthenopteron, which did not come near the land. according to dawkins “it did have several anatomical similarities to the amphibians of 50 million years later, including its skull bones, its teeth and, above all, its fins.” in other words it seems to have an anatomical structure which anticipates future developments which will take place 50 million years in the future. dawkins and the dudmud brigade would no doubt ridicule such a notion, but the evidence that there is anticipatory structure underlying the process of evolution is now gathering force. an example of such an anticipatory morphological structure is given by simon conway morris, professor of evolutionary palaeobiology at the university of cambridge, in his excellent work life’s solution: inevitable humans in a lonely universe: to give one example: the central nervous system of amphioxus is really rather simple. it consists of an elongate nerve chord stretching back along the body, above the precursor of the vertebral column (our backbone, consisting of a row of vertebrae) and a so called brain. the brain can only be described as a disappointment. it is little more than an anterior swelling … and has no obvious sign in terms of its morphology of even the characteristic threefold division seen in the vertebrate brain of hind-, mid-, and fore-sections. yet the molecular evidence, which is also backed up by some exquisitely fine studies of microanatomy, suggests that, cryptically, the brain of amphioxus has regions equivalent to the tripartite division seen in the vertebrates. the clear implication of this is that folded within the simple brain of amphioxus is what can almost be described as a template for the equivalent organ of the vertebrates: in some sense amphioxus carries the inherent potential for intelligence. 36 this ‘molecular evidence’ indicates the tripartite division within the brain which emerges within evolution much later is somehow written into the molecular structures of the simplest organisms as a kind of template for future development. and this molecular anticipatory structuring must have a quantum origin, there is nowhere else it can come from, molecular arrangements are determined by quantum potentialities. conway morris provides convincing evidence that the spectacular convergences upon similar ‘solutions’ within evolution also suggest internal patterning templates. and such patterning templates, which have a quantum origin, can be also identified with rupert sheldrake’s notion of a ‘morphogenetic field’, which is a quantum probabilistic field of potentiality which underlies the development of any organism. dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 250 figure 10 – the amphioxus animal (37) having finished his exposition of the dud-mud absurdity of the supposed fully materialized, millimetre by millimetre, rm+ns transformation of fish into land animals, dawkins adds intellectual insult to intellectual injury by moving on to another dud-mud absurdity, the supposed trek back to the sea by a group of hippo-like land animals. he writes of this in his greatest show book: …with what seems almost wanton perversity, a good number of thorough-going land animals later turned around, abandoned their hard-earned terrestrial retooling, and trooped back into the water again. seals and sea lions have only gone part-way back. they show us what the intermediates might have been like, on the way to extreme cases such as whales and dugongs. whales (including the small whales we call dolphins), and dugongs with their close cousins the manatees, ceased to be land creatures altogether and reverted to the full marine habits of their remote ancestors. they don’t even come ashore to breed. they do, however, still breathe air, having never developed anything equivalent to the gills of their earlier marine progenitors. 38 of course, according to the dud-mud worldview there should be no reason why rm+ns could not have eventually equipped whales and dugongs with gills. and given the fact that it must be rather irritating for whales to have keep coming to the surface to get a gasp of air one can only wonder at the lack of concern for the full welfare of them on the part of rm-ns. but, then again there probably hasn’t been enough time, so the whale is stuck with having to come to the surface all the time for a gulp of air! dawkins continues: whales were long an enigma, but recently our knowledge of whale evolution has become rather rich. molecular genetic evidence … shows that the closest living cousins of whales are hippos, then pigs, then ruminants. even more surprisingly, the molecular evidence shows that hippos are more closely related to whales than they are to the cloven-hoofed animals (such as pigs and ruminants) which look much more like them. this is another example of the mismatch that can sometimes arise between closeness of cousinship and degree of physical resemblance. we noted it above in connection with fish that are closer cousins to us than they are to other fish. in that case, the anomaly arose because our lineage left the water for the land, and consequently surged away in evolution, leaving our close fish cousins, the lungfish and coelacanths, resembling our more distant fish cousins because they all stayed in the water. now we meet the same phenomenon again, but in reverse. hippos stayed, at least partly, on land, and so still resemble their more distant land-dwelling cousins, the ruminants, while their closer cousins, the whales, took off into the sea and changed so drastically that their affinities with hippos escaped all biologists except molecular geneticists. as when their remote fishy ancestors originally went in the other direction, it was a bit like taking off into space, or at least like launching a dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 251 balloon, as the ancestors of whales floated free of the constraining burden of gravity and severed their moorings to dry land. 39 there are two important and connected issues here. the first concerns the nature of the relationship between hippos and whales, is it necessarily a fully paid up material relationship, with a direct line of material descent, with vast numbers of intermediaries as a nose gradually becomes a blowhole, millimetre by millimetre. the second concerns the ‘drastic’ nature of the transformation required; could an intelligent person really believe that the extraordinary coordinated biological re-engineering could possibly be the result of rm+ns. with reference to the first issue we must ask: what are the watertight implications of the molecular evidence that “hippos are more closely related to whales than they are to the cloven-hoofed animals,” what kind of ‘relationship’ is suggested by the ‘molecular evidence.’ does it indicate that the ‘relationship’ must be one of a direct fully materialised descent involving the supposed hippo-like creature’s external breathing apparatus gradually moving back, millimetre by excruciating millimetre, over 50 million years or thereabouts, until it migrates to the position of a whale’s blowhole. the answer is that, whilst this molecular evidence is consistent with the unlikely notion, it in no way proves it, just as the fossil evidence does not prove it either. shortly we shall see that there is a much more coherent, and must less implausible, account which fits the evidence, including the evidence of quantum theory, much more coherently and plausible, if, that is, one is not blinded by a dogmatic metaphysical preference for a materialist explanation. as quantum physicist amit goswami points out: darwinists make a big case for another intermediate, this time a series of them that allegedly arose between land mammals and cetaceans-swimming mammals. in the late 1980s and early 1990s, the biologist phillip gingerich and collaborators uncovered this series. the animal at the midpoint of the series was named ambulocetus natans, “the swimming whale that walks.” the shape of the front and hind limbs of the fossil remnant make it quite plausible that the animal could both walk and swim. the darwinists assume that this new trait could come about continuously from gradual modification of the land mammal with walking limbs only. they forget that swimming requires many other internal modifications (including some involving the brain) all acting coherently as a whole, besides just the shape of the limbs! 40 goswami’s book creative evolution indicates in great detail that the only coherent account of evolution which accords with the discoveries of modern science, including quantum theory, requires that much of the organization underlying the evolutionary process must take place creatively at the quantum level of potentiality and primordial consciousness, which he terms the “supramental”: in the theory of creative evolution, we accept the new trait as the quantum leap to express a new biological function a new archetype that of swimming. the emergence of the “walking whales” is an instance of fundamental creativity, the leap into the supramental realm. the change from these creatures to the earliest cetaceans, the archeocetes, occurred through situational creativity working within established archetypes, a process of refinement. 41 according to the new insights of evolutionary developmental biology (evo-devo) and quantum, theory, the dud-mud worldview must be replaced with a new perspective which accepts the operation of quantum archetypes, which operate through a quantum ‘implicate’ dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 252 hierarchical organisation from subtle quantum levels to the material world, in the process of evolution. dawkins, however, remains dogmatically insistent upon his discredited dud-mud belief system. in his later section in greatest show discussing ‘molecular comparisons’ he writes that: just as the vertebrate skeleton is invariant across all vertebrates while the individual bones differ, and just as the crustacean exoskeleton is invariant across all crustaceans while the individual ‘tubes’ vary, so the dna code is invariant across all living creatures, while the individual genes themselves vary. this is a truly astounding fact, which shows more clearly than anything else that all living creatures are descended from a single ancestor. not just the genetic code itself, but the whole gene/protein system for running life is the same in all animals, plants, fungi, bacteria, archaea and viruses. what varies is what is written in the code, not the code itself. and when we look comparatively at what is written in the code the actual genetic sequences in all these different creatures we find the same kind of hierarchical tree of resemblance. we find the same family tree albeit much more thoroughly and convincingly laid out as we did with the vertebrate skeleton, the crustacean skeleton, and indeed the whole pattern of anatomical resemblances through all the living kingdoms. 42 here, again, dawkins leaps to the conclusion that the fact of this hierarchical structure that underlies the molecular and genetic structures which organise life means that this hierarchical structure must have been fully expressed on a completely material level. and he furthermore concludes that there must have been just a “single ancestor.” presumably he thinks of this as a kind of blob-like cell somehow eking out a precarious existence in a primeval under sea geezer, or some such. but this is not a watertight conclusion by any means, it is a conclusion reached on the basis of a prior commitment to the dud-mud worldview. proponents of this worldview, dawkins, coyne, dennett and many other dud-muds, claim that there are so many interlocking pieces of evidence: fossils, molecular structures, vestigial appendages, cladistics amongst them, that the entire picture put together is irresistible. but this is not the case. each separate area of evidence is evaluated on the basis of the dud-mud worldview in the first place, and, furthermore, the gaping scientific and philosophical problems and absurdities are routinely ignored. one of the core tenets of the dud-mud worldview was the belief, heartily embraced by dawkins in his early days, that the genes involved in the evolution of different species would themselves be different, different species would not have common gene structure. thus the evolutionary biologist ernst mayr wrote confidently in the 1960’s that: much that has been learned about gene physiology makes it evident that the search for homologous genes is quite futile except in very close relatives. if there is only one efficient solution for a certain functional demand, very different gene complexes will come up with the same solution, no matter how different the pathway by which it is achieved. the saying “many roads lead to rome” is as true in evolution as in daily affairs. 43 an excellent example of a pronouncement made on the basis of little evidence but a huge emotional, intellectual and career investment in the dud-mud worldview, an investment which can still be found in much ‘scientific’ writing in the dud-mud camp. however, this dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 253 dogmatic assumption has now been shown by the evolutionary development (evo-devo) revolution in biology to be completely false; as sean b. carroll writes in his book endless forms most beautiful: the first shots in the evo devo revolution revealed that despite their great differences in appearance and physiology, all complex animals flies and flycatchers, dinosaurs and trilobites, butterflies and zebras and humans share a common “tool kit” of “master” genes that govern the formation and patterning of their bodies and body parts. … the important point to appreciate from the outset is that this discovery shattered our previous notions of animal relationships and of what made animals different, and opened up a whole new way of looking at evolution. 44 this new evidence, evidence which does not support the darwinian worldview but counts against it, suggests a preformed body-plan, existing at the dawn of time, which is activated in a multitude of ways. the american cognitive scientist and philosopher jerry fodor, professor of philosophy at rutgers university, in an essay why pigs don’t fly, has questioned the neo-darwinian assumption of random ‘adaptationism:’ everybody thinks evo-devo must be at least part of the truth, since nobody thinks that phenotypes are shaped directly by environmental variables. even the hardest core darwinists agree that environmental effects on a creature’s phenotype are mediated by their effects on the creature’s genes: its ‘genome’. indeed, in the typical case, the environment selects a phenotype by selecting a genome that the phenotype expresses. once in place, this sort of reasoning spreads to other endogenous factors. phenotypic structure carries information about genetic structure. and genotypic structure carries information about the biochemistry of genes. and the biochemical structure of genes carries information about their physical structure. and so on down to quantum mechanics for all i know. 45 and, as we shall see, it is at the quantum level that body-plans and potentialities for various types of creatures and environments must ‘exist’ as potentialities. the second issue mentioned with regard to whale evolution is that of the plausibility and credibility of the notion that there was a long lineage of creatures, each of them differing to a tiny degree to the one before, wherein the two nostrils of the original land animal migrated back to become a blowhole whilst at the same time other drastic, dramatic and heroic biological transformations took place to enable whales to dive to bone-crushing depths of the sea. sperm whales are believed to be able to reach 3 kilometres (1.9 mi) and remain submerged for 90 minutes. the sperm whale has adapted to cope with drastic pressure changes when diving. a flexible ribcage allows lung collapse, reducing nitrogen intake, and metabolism can decrease to conserve oxygen. myoglobin, which stores oxygen in muscle tissue, is much more abundant than in terrestrial animals. the blood has a high red blood cell density, which contain oxygen-carrying haemoglobin. the oxygenated blood can be directed towards only the brain and other essential organs when oxygen levels deplete. 46 all of this reengineering would have had to have taken place in a co-ordinated manner, supposedly driven by rm+ns. this would mean that small mutations of genes would have to alter, in a tiny, tiny manner of course, the entire system of nose/blowhole, ribcage, blood chemistry and so on, each altering the entire system in just the right way to allow the animal to dive a millimetre, or metre or….(?) deeper! such a notion is massively implausible. dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 254 one of the main reasons for diving to the depths that sperm whales dive is to feed on squid, so why the hippo like creature decided to try and start diving is a mystery, did they know that the squid were down there? after all the primary reason offered for the supposed return to the sea is the abundance of food. when dud-mud just-so tales and fairy stories are subjected to rigorous analysis they simply fall apart. dawkins, however, in order to try and counter the obvious implausibility, has adopted the tactic of defending by attacking, appealing to his notion that ‘personal incredulity’ is inadmissible as a criticism of the dud-mud worldview: the general lesson we should learn is never use human judgment in assessing such matters. never say, and never take seriously anybody who says: “i cannot believe that so-and-so could have evolved by gradual selection.” have dubbed this kind of fallacy “the argument from personal incredulity.” time and time again, it has proved the prelude to an intellectual banana-skin experience. 47 this is a classic dawkinsian invalid, absurd and ridiculous statement, and for those capable of analysis and clear reasoning there are many such absurdities in the dawkins’ oeuvre. doesn’t science depend upon “human judgment,” might not someone examine the evidence in detail and decide on the basis of rigorous reasoning that: “i cannot believe that so-and-so could have evolved by gradual selection.” the context for this statement is an assertion by an opponent that the interrelationship between orchids and the wasps that pollinate them could not have evolved incrementally. the orchid mimics features of the female wasps that attract males, this includes the sheen of wings, colouring of hairs, “having an opening in the proper place” and also the emission of a pheromone. dawkins launches into a vitriolic irrelevant diatribe about how humans, animals and wasps are easy to fool and therefore the mimicry would not need to be “perfect” in order to work. in all this he entirely misses the point which is that the interdependency of orchid and wasp could not have evolved from a situation of nodependency. without the pollinating wasp the orchid would not have survived, so there could never have been a time when a non-wasp-attracting orchid had the good fortune to be provided by rm+ns with wasp paraphernalia including the emission of wasp pheromone. dawkins misses the point entirely: the argument i am attacking is the one that says: gradual evolution of so and so couldn’t have happened, because so-and-so “obviously” has to be perfect and complete if it is to work at all. 48 however, it is obvious that the interdependency between orchid and wasp must be in place at the outset, even if imperfectly, and therefore cannot evolve out of no-dependency. furthermore such interdependencies, wherein members of seemingly completely unrelated species are in fact bound within a network of survival dependencies are replete in nature. this was made stunningly clear in a recent bbc documentary series secrets of the living planet presented by chris packham: ten million species live on planet earth, each one is incredible, yet none can live by itself. in this series, naturalist chris packham reveals the natural world in a way that you’ve never seen it before. for him, what is really beautiful about nature is not the amazing animals and plants that we share the planet with but the hidden relationships between them. these relationships may sound bizarre but without them, no life would be possible. chris reveals: why a crab in the swamps of bangladesh needs a tiger, why the mighty brazil nut tree needs a rare orchid and a small rodent, why a small gecko in kenya needs a giraffe, why the north american lynx needs a tiny moth caterpillar. 49 dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 255 analysis indicates that none of these interrelationships could have evolved gradually and incrementally from a state of no-interrelationship, no-dependency. the natural world must have always been characterized by complex interdependency, and such an interdependency and fine-tuned interrelationship does not chime well with the notion of a continuous mechanism of accumulations of “flaws” in non-interdependent, self-enclosed bits of matter. dud-muds, however, are blinded to certain clear facts because of a chronic state of ‘personal credulity’ which leads them to accept desperately implausible dud-mud claims. figure 11 (50) in his greatest show chapter ‘the tree of cousinship’ dawkins waxes lyrically on the subject of the underlying homology, or essential sameness of pattern underlying the skeletons of all creatures. the details, of course can be very different but at the base of it all there is a fundamental prototype skeleton-blueprint or body-plan. figure 11 shows the famous example of pierre belon noting the agreement between the skeleton of a pigeon and a human in 1555. dawkins also gives an example of two more closely related animals, the giraffe and okapi and he writes that: …the pattern of resemblances among the skeletons of modern animals is exactly the pattern we should expect if they are all descended from a common ancestor, some of them more recently than others. the ancestral skeleton has been gradually modified down the ages. some pairs of animals, for example giraffes and okapis, share a recent ancestor. it is not strictly correct to describe a giraffe as a vertically stretched okapi for both are modern animals. but it would be a good guess … that the shared ancestor looked more like the okapi than the giraffe. 51 dawkins also gives the examples of a pterodactyl and ‘flying lizard’ (figure 12). according to dawkins this guess is supported by the fossil evidence. this means that he is claiming that there is a sequence fossils, starting with the ‘common ancestor’, indicating a sequence of giraffe ancestors with a neck getting progressively longer; this claim, however, seems to be false. dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 256 figure 12 (52) in 2006 researcher wolf-ekkehard lönnig, an expert on mutation genetics having been a researcher for over thirty years, published a long carefully researched paper entitled ‘the evolution of the long-necked giraffe – what do we really know’. the opening summary section of this remarkable document begins: 1. ulrich kutschera made the following statement regarding the origin of the giraffe, … “...the evolution of the long-necked giraffe can be reconstructed from fossils.” according to today’s best giraffe researchers, all fossil links that could show us the gradual evolution of the long-necked giraffe from the short-necked giraffe are missing, apart from the insufficiently answered question of causes. some paleontologists postulate a “neck elongation macromutation” to explain the origin of the long-necked giraffe. 2. richard dawkins likewise considers in a striking exception to his usual theoretical framework the origin of the long-necked giraffe through a macromutation. this exception would, of course, be entirely superfluous if the gradual evolution of the long-necked giraffe could really be reconstructed from fossils, especially since he much prefers the gradualist view. dawkins draws the okapi, in relation to the giraffe, nearly twice as large as it really is. in this way, the problem of its evolution (the gap between the two forms) appears only about half as large. one may well ask if this technique is really useful in the search for truth. 53 the italics in the above quote are due to lönnig. this quote indicates that dawkins, who rants about the necessity for scientific rigor, is at the same time not averse to falsifying the evidence, stretching a neck in order to promote the fallacies of the dud-mud just so story. this may seem shocking but it is par for the course in dud-mud polemics. i actually came across lönnig’s work after i had scanned and pasted in figure 13a from the greatest show i was taken aback when i saw his claim and thought i should immediately check it out. i therefore found a photo of the giraffe and okapi skeletons which was independent of dawkins’ influence which is shown in figure 13b and it does seem to be the case that dawkins has an elongated view of the okapi’s neck. the comparison is shown in figures 14a and 14b. lönnig’s paper was published in 2006 and the source for his example of dawkins’ giraffe-okapi was dawkins’ book climbing mount improbable which was published in 1996 and the diagram that dawkins uses in this book is shown in figure 15. this means that dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 257 dawkins has continued the use of this deception for well over fifteen years. notice how dawkins’ okapi (figure 15) seems to be actually stretching its neck in order to elongate it! lönnig also points out that the correct relative sizes is shown in the silhouettes on the left of the man in figure 16. these are taken from the book animals of the world (1988), bertelsmann lexikothek. lönnig writes that: on the left side i have placed dawkins’ illustration for comparison, but with the okapi placed on the same level as the giraffe (cf. dawkins illustration above). in between, i have repeated the drawing of the okapi with its real relative size shown (silhouette). from dawkins’ portrayal one gets the impression that the step from okapi to long-necked giraffe is slight, and the text reinforces this impression. 54 as lönnig points out, if proponents of intelligent design (id) were to engage in this kind of practice dud-muds would be up in arms, no one in their ranks seems to be bothered by dawkins, and others, resorting to these underhand methods. figure 13a (55) figure 13b (56) figure 14a – dawkins’ okapi figure 14b – correct proportions dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 258 figure 15 (57) figure 16 (58) after a detailed and exhaustive examination of the claims, counter-claims and the evidence lönnig concludes that: if, however, the general lineages for almost all modern groups of vertebrates are as uncertain as in the case of giraffes, then we are dealing with only suggestive evolutionary interpretations in most other groups as well, yet without solid scientific proof. 59 in my article the giraffe reveals the evolutionary tall tale i look into lönnig’s work in detail. in his discussion of the ‘tree of cousinhood’ dawkins indicates that any two creatures whatsoever, such as the giraffe and okapi, can trace their ancestry back to a ‘common ancestor’. at the start of his greatest show book dawkins calls this the “hairpin thought experiment.” take any two species, the rabbit and the leopard for example. now start with the rabbit, a female one, and start tracing its lineage backwards in time: …back in time, back, back, back through the megayears, a seemingly endless line of female rabbits, each one sandwiched between her daughter and her mother. we walk along the line of rabbits, backwards in time, examining them carefully like an inspecting general. as we pace the line, we’ll eventually notice that the ancient dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 259 rabbits we are passing are just a little bit different from the modern rabbits we are used to. but the rate of change will be so slow that we shan’t notice the trend from generation to generation, just as we can't see the motion of the hour hand on our watches – and just as we can’t see a child growing, we can only see later that she has become a teenager, and later still an adult. an additional reason why we don’t notice the change in rabbits from one generation to another is that, in any one century the variation within the current population will normally be greater than the variation between mothers and daughters. … nevertheless, steadily and imperceptibly, as we retreat through time, we shall reach ancestors that look less and less like a rabbit and more and more like a shrew (and not very like either). one of these creatures i’ll call the hairpin bend … this animal is the most recent common ancestor (in the female line, but that is not important) that rabbits share with leopards. we don't know exactly what it looked like, but it follows from the evolutionary view that it definitely had to exist. 60 however, if we take into account the latest quantum discoveries made by science, then dawkins’ claim that this common ancestor of a rabbit and leopard “definitely had to exist” as a fully paid up material organic creature can be shown to be wrong. this assertion may raise a few eyebrows; how else could it possibly exist? the answer to this central question is that many of the ‘common ancestors’ which dawkins thinks must definitely have actually roamed the planet as fully materialized flesh and blood creatures certainly did not. they were, and still are, ‘implicate’ quantum templates of potentiality. in his discussion of the ‘tree of cousinship’ dawkins asks whether there are any alternative explanations for the patterns of the evolutionary ‘tree of resemblances’ and refers, in heavily disparaging terms, to the pre-darwinian view that these hierarchical patterns and interrelations reflect “themes in the mind of the designer”: he had various ideas for how to make animals. his thoughts ran along a mammal theme, and, independently, they ran along an insect theme. within the mammal theme, the designer’s ideas were neatly and hierarchically bisected into sub-themes (say, the cloven-hoofed theme) and sub-sub-themes (say, the pig theme). there is a strong element of special pleading and wishful thinking about this, and nowadays creationists seldom resort to it. 61 dawkins continues by lampooning this proposal in his usual piranha style, using unsubtle parody and crude misunderstanding. in greatest show he refers to this view as “the dead hand of plato.” plato, of course, considered that the phenomena of the manifested world were merely shadows of the perfect archetypes which resided in an immaterial realm of ideas. dawkins writes of this: biology, according to mayr, is plagued by its own version of essentialism. … the rabbits that we see are wan shadows of the perfect ‘idea’ of rabbit. the ideal essential platonic rabbit, hanging somewhere in conceptual space … flesh and blood rabbits may vary, but their variations are always as flawed deviations from the ideal essence of rabbit. 62 however, we shall see that, when we replace the notion of a platonic realm of conceptual archetypes with that of the quantum realm of potentiality, the idea that there are animal archetypes that are manifested at the material level is close to the truth. the shocking fact, given that dawkins constantly rants about the need to conform to the findings of science, is that this notion, when formulated in less archaic form, is far more consistent with modern physics that the crude materialism embraced by dawkins. dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 260 a further startling fact is that this kind of platonic ‘theme’ perspective, wherein an infinite fecund immaterial source of the manifested world manifests a vast variety of plant and animal forms based on ‘templates’ which are contained as potential within it, was proposed by darwin’s intellectual opponent, the nineteenth century geologist, glaciologist, and zoologist jean louis rodolphe agassiz (fig. 6) who correctly criticized darwin’s (fig. 7) ideas: perhaps one of the most interesting criticisms of evolution by natural selection in darwin’s era came from the swiss american geologist, glaciologist, and zoologist louis agassiz, agassiz didn’t deny that evolution occurs in nature but his idea of evolution was that it entailed the preordained unfolding of a plan. 63 this means, of course, that agassiz’s view was actually closer to the truth, as now revealed by the evo-devo discoveries, than darwin’s. in a remarkable piece of prescience agassiz wrote: it is not that i hold darwin himself responsible for these troublesome consequences. … it is his henchmen who took hold of his theories… 64 an insight still very true today! agassiz wrote that: however much likeness there is among the animals or plants of the same species, there always is in all individuals, even externally, some … differences, more or less pronounced, of an individual’s features through which it’s individuality shows up clearly. however, as large as these differences may be … the differences don’t exceed this that i called, on another occasion, the boundaries of the flexibility, of the pliability of the species. finally, never in the succession of these individuals has one been born entirely similar to its parents, nor later have they become one of another species ,… the school of darwin goes beyond facts when it states that these individual differences constitute the transitions from one species to another. 65 in other words, although darwin, and dawkins following him, claimed and claim that selective breeding is crucial evidence for evolution by rm+ns, an example of selective breeding creating an entirely new species has never been demonstrated. all that has been demonstrated is the latitude of malleability and variability within the ‘template’ of a species. it was because of this fact that agassiz considered that the species were in some sense ‘created’ as ‘fixed’ elements of life. agassiz was a staunch creationist who saw a divine plan everywhere in nature, and he could not reconcile himself to a theory that did not invoke design. he defined a species as “a thought of god.” thus he wrote in his essay on classification: the combination in time and space of all these thoughtful conceptions exhibits not only thought, it shows also premeditation, power, wisdom, greatness, prescience, omniscience, providence. in one word, all these facts in their natural connection proclaim aloud the one god, whom man may know, adore, and love; and natural history must in good time become the analysis of the thoughts of the creator of the universe … 66 . dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 261 figure 17 (67) figure 18 (68) in agassiz’s time of course the notion of a creator god was for many a natural explanation. today, however, it is not necessary to invoke a ‘creator’, although some may still wish to. however, if we wish to stick to the implications of physics then the source of all phenomena would seem to be quantum fields: quantum field theory, the tool with which we study particles, is based upon eternal, omnipresent objects that can create and destroy those particles. these objects are the “fields” of quantum field theory. … quantum fields are objects that permeate spacetime … they create or absorb elementary particles … particles can be produced or destroyed anywhere at any time. 69 these “eternal” quantum fields provide the quantum potentialities for all manifestation. in this context it is worth briefly examining a controversy which was prompted by the claim by lawrence krauss, a theoretical physicist and director of the origins institute at arizona state university, in his book a universe from nothing: why there is something rather than nothing, that the entire universe could have emerged from ‘nothing.’ by ‘nothing’ what krauss is referring to is quantum field theory. the physicist and philosopher of science david albert rightly took krauss to task for claiming that quantum fields are ‘nothing’. albert wrote in a new york times review of the book: dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 262 the particular, eternally persisting, elementary physical stuff of the world, according to the standard presentations of relativistic quantum field theories, consists (unsurprisingly) of relativistic quantum fields. and the fundamental laws of this theory take the form of rules concerning which arrangements of those fields are physically possible and which aren’t, and rules connecting the arrangements of those fields at later times to their arrangements at earlier times, and so on — and they have nothing whatsoever to say on the subject of where those fields came from, or of why the world should have consisted of the particular kinds of fields it does, or of why it should have consisted of fields at all, or of why there should have been a world in the first place. period. case closed. end of story. … relativistic-quantum-fieldtheoretical vacuum states — no less than giraffes or refrigerators or solar systems — are particular arrangements of elementary physical stuff. the true relativisticquantum-field-theoretical equivalent to there not being any physical stuff at all isn’t this or that particular arrangement of the fields — what it is (obviously, and ineluctably, and on the contrary) is the simple absence of the fields! 70 in other words albert is pointing out that it is not the case that the universe emerged from ‘nothing’ because quantum fields are a kind of ‘physical’ stuff, although quantum field ‘physical’ stuff is actually immaterial and consists of quantum potentiality. physicist wojciech zurek refers to quantum field ‘stuff’ as ‘dream stuff’. krauss, wants to use physics to undermine the possibility of any religious or mystical perspective. albert, however, points out that krauss: …complains that “some philosophers and many theologians define and redefine ‘nothing’ as not being any of the versions of nothing that scientists currently describe,” and that “now, i am told by religious critics that i cannot refer to empty space as ‘nothing,’ but rather as a ‘quantum vacuum,’ to distinguish it from the philosopher’s or theologian’s idealized ‘nothing,’” and he does a good deal of railing about “the intellectual bankruptcy of much of theology and some of modern philosophy.” but all there is to say about this, as far as i can see, is that krauss is dead wrong and his religious and philosophical critics are absolutely right. 71 ‘eternal’ quantum fields are quite clearly not ‘nothings’ but are fields of potentiality for universes containing sentient beings to come into a derived ‘existence.’ furthermore, there is no reason to rigidly distinguish between theological and philosophical notions and quantum vacuums or fields of potentiality, the two can coexist and interpenetrate harmoniously. that is to say quantum field theory can have theological significance. in his recent book from quantum to cosmos: the universe within neil turok, director of the perimeter institute for theoretical physics, writes concerning krauss and dawkins: as an example from my own field of cosmology, let me cite lawrence krauss’s recent book, a universe from nothing. in it, he claims that recent observations showing that the universe has simple, flat geometry imply that it could have been created out of nothing. his argument is, in my view, based upon a technical gaffe, but that is not my point here. through a misrepresentation of the physics, he leaps to the conclusion that a creator was not needed. the book includes an afterword by richard dawkins, hailing krauss’s argument as the final nail in the coffin for religion. dawkins closes with, “if on the origin of species was biology’s deadliest blow to supernaturalism [which is what dawkins calls religion], we may come to see a universe from nothing as the equivalent from cosmology. the title means exactly what it says. and what it dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 263 says is devastating.” the rhetoric is impressive, but the arguments are shallow. the philosopher david albert one of today’s deepest thinkers on quantum theory – framed his response at the right level, in his recent review of krauss’s book in the new york times, lamenting that “all that gets offered to us now, by guys like these, in books like this, is the pale, small, silly, nerdy accusation that religion is, i don’t know, dumb. in comparing krauss’s and dawkins’s arguments with the care and respectfulness of those presented by hume in his dialogues concerning natural religion, all the way back in the eighteenth century, one can’t help feeling the debate has gone backwards. 72 albert is correct, books like krauss’s and those of dawkins are “silly” in their crude embracement of an unscientific materialism in their quest to debunk spiritual perspectives. many of their claims are clearly out of step with the modern discoveries of quantum theory. turok also writes: great mysteries remain. why did the universe emerge from the big bang with a set of physical laws that gave rise to heavy elements and allowed complex chemistry? why did these laws allow for planets to form around stars, with water, organic molecules, an atmosphere, and the other requirements for life? why did the dna-protein machinery, developed and selected for in the evolution of primitive single-cell organisms, turn out to be able to code for complex creatures like ourselves? how and why did consciousness emerge? at every stage in the history of the universe, there was the potential for vastly more than what had been required to reach that stage. today, this is more true than ever. our understanding of the universe has grown faster than anyone could have imagined a century ago, way beyond anything that could be explained in terms of past evolutionary advantage. … might we be the means for the universe to gain a consciousness of itself? 73 physicist sean carroll also tells us that: we are part of the universe which has developed a remarkable ability: we can hold an image of the world in our minds. we are matter contemplating itself. 74 here carroll betrays a materialist leaning in his mistaken notion that it is “matter contemplating itself”. if the “world is made of fields”, as he himself says, then ultimately it is the immaterial quantum fields which organize themselves in order to manifest and contemplate their own internal qualities. quantum fields, then, must contain the potentialities for the appearance of the material world as well as the potential for the arising of conscious awareness. the notion that mute and completely unaware ‘matter’ could end up contemplating itself is internally contradictory. the emerging perspective, then, requires that we understand that consciousness is primary and matter derivative, a view which planck eventually came to: all matter originates and exists only by virtue of a force... we must assume behind this force the existence of a conscious and intelligent mind. this mind is the matrix of all matter. 75 as did schrödinger: mind has erected the objective outside world … out of its own stuff. 76 goswami describes the new quantum paradigm which embraces consciousness: dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 264 …in the beginning consciousness includes all possibilities. ponder what that means. among other things, “all possibilities” must include literally all possibilities, past, present, and future. in other words, when every possibility is included, there is no scope for the passage of time. to bring time into the equation of the manifest universe, consciousness must limit what is possible. the imposition of progressive limitation on what is possible is seen as an involution of consciousness. in this way, when evolution is viewed from the context of the primacy of consciousness, involution must precede it. from a primacy-of-consciousness point of view it is also possible to ask, what is the purpose of evolution? why evolution at all? the answer is easy: evolution is needed for experiencing the possibilities of consciousness in manifestation. when consciousness is inseparable from its possibilities, there is only one thing, and no experience is possible. as the mathematician g. spencer brown (1977) pointed out, “we cannot escape the fact that the world we know is constructed in order (and in such way as to be able) to see itself, but in order to do so it must cut itself up into at least one state that sees, and at least one other state that is seen. 77 in other words the first step in the manifestation of the universe as a self-exploring, selforganising system is the division into a subject-field and an object-field. the subject-field is the pole of manifestation which later divides into to multitude of species of sentient beings, and the object-field is the pole which will become the environments which are inhabited by the various type of sentient beings. according to russian quantum physicist michael mensky, consciousness is an interior aspect or quality of the quantum field which reflexively operates upon quantum potentialities in order to manifest subject-object embodied experiential awarenesses of a multitude of types. for individuated consciousness itself to become manifest from the fundamental quantum field as explicit experiential aspects of reality it must bring an experienced world into being. such a world is manifested through the actualisation of the potentialities within the universal quantum wavefunction of potentiality and the subsequent selection of primary experiential pathways. according to mensky a crucial question which requires explication is why the alternatives which naturally arise are classical. mensky gives the following account: if the picture of the world as it appears in consciousness were far from classical, then, due to quantum non-locality, this would be a picture of a world with ‘locally unpredictable’ behaviour. the future of a restricted region in such a world could depend on events even in very distant regions. no strategy of surviving could be elaborated in such a world for a localised living being. life (of the form we know) would be impossible. on the contrary, a (close to) classical state of the world is ‘locally predictable’. the evolution of a restricted region of such a world essentially depends only on the events in this region or not too far from it. influence of distant regions is negligible. strategy of surviving can be elaborated in such a world for a localised living being. 78 entangled quantum phenomena can instantaneously affect each other over vast cosmic distances, a quantum feature called ‘non-locality’. in fact distance does not seem to be an issue for this kind of entangled mutual interrelationship. it follows, therefore, that in a nonclassical, quantum-entangled scenario there would be no environments wherein environmental functioning was determined purely by local events. such environments would not be locally coherent and predictable and consequently they could not support coherent life. dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 265 quantum theory indicates that an entangled interconnected field of potentiality unravels its own possibilities through an internal mechanism of unfoldment involving consciousness. the manifested classical lineaments of a life-supporting manifested reality is fashioned by consciousness itself for its own manifestation within embodied sentient beings. in quantum field theory there is a non-substantial quantum field of potentiality and, within the process that mensky envisages, a primitive level of quantum consciousness operates upon this entangled and interdependent field, and through this mechanism the field is localised through the quantum evolution of the ‘classical’ world of individualised sentience and materiality. mensky indicates that the level of consciousness at which the process begins is: …the most primitive, or the most deep, level of consciousness, differing perceiving from not perceiving. 79 the quantum physicist wojciech zurek echoes this emphasis on the primacy of an internal quantum ‘epiontic’ perceiving function: measurement – perception – is the place where physics gets personal, where our role and our capabilities as observers and agents of change in the universe (and our limitations as entities subject to the laws of physics) are tested or, rather, where we get put in our place. … the virtue of the focus on quantum measurement is that it puts issues connected with information and existence at the very center. this is where they should be.’ 80 however, many physicists are still having a tough time coming to terms with the notion that at its heart the universe is immaterial. such views are, of course, ‘anthropic’ to various degrees, the universe must give rise to sentient beings in order to “contemplate itself.” physicist paul davies, following john wheeler, speaks of ‘teleology without teleology’ 81 we may perhaps, admittedly tongue in cheek, speak of a ‘god without god!’ the platonic ‘theme’ theory, wherein all organic forms which come into manifestation derive from a deep level of potentialities within a mind-like field of energy-consciousness, is consistent with the theory of everything outlined by stephen hawking and leonard mlodinow (henceforth ‘h&m’) in their book the grand design: new answers to the ultimate questions of life (henceforth ‘gd’) and several other important modern quantum perspectives. according to h&m: quantum physics tells us that no matter how thorough our observation of the present, the (unobserved) past, like the future, is indefinite and exists only as a spectrum of possibilities. the universe, according to quantum physics, has no single past, or history. the fact that the past takes no definite form means that observations you make on a system in the present affect its past. 82 furthermore: …the universe doesn’t have just a single history, but every possible history, each with its own probability; and our observations of its current state affect its past and determine the different histories of the universe, just as the observations of the particles in the double-slit experiment affect the particles’ past. 83 what h&m are saying here is that all potentialities exist as potentialities at the dawn of time and, dramatically, observations made by all sentient beings in the present moment affect those potentialities backwards in time. dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 266 and so we come to the astonishing proposal required by modern quantum theory. from the timeless point of creation a spontaneous universal quantum creative act projects all possible futures into a universal possibility or potentiality space. at the point of creation everything that possibly can happen becomes potential, so at the point of creation all possible future histories of the universe come into being as potentialities, although not yet experienced realities: in this view, the universe appeared spontaneously, starting off in every possible way. most of these correspond to other universes …. some people make a great mystery of this idea, sometimes called the multiverse concept, but these are just different expressions of the feynman sum over histories. 84 sentient beings, through acts of observation involving consciousness collectively create the history of the universe: we create history by our observations, rather than history creating us. 85 in other words the observers, or what the famous twentieth century physicist john wheeler called ‘observer-participants,’ are able to weed out possible universes, and thereby select those which remain in the possibility mix, even backwards in time. wheeler expressed this: directly opposite to the concept of universe as machine built on law is the vision of a world self-synthesized. on this view, the notes struck out on a piano by the observer participants of all times and all places, bits though they are in and by themselves, constitute the great wide world of space and time and things. 86 h&m support this dramatic metaphysical perspective in what is perhaps the central chapter in the grand design entitled ‘choosing our universe’: the idea that the universe does not have a unique observer-independent history might seem to conflict with certain facts that we know. there might be one history in which the moon is made of roquefort cheese. but we have observed that the moon is not made of cheese, which is bad news for mice. hence histories in which the moon is not made of cheese do not contribute to the current state of our universe, though they might contribute to others. this might sound like science fiction but it isn’t. 87 figure 19 dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 267 figure 19 provides graphic presentation of this quantum platonic metaphysical view of the evolution of the universe. the process operates over long time scales ‘unconsciously’ (although guided by primordial consciousness) before there are sentient beings, or observerparticipants, extant within the universe to take part in the process of universal selection and solidification. once there is a community of sentient organisms inhabiting the universe then their perceptions, which have influence at the quantum level, affect the probabilities which have been projected at the moment of the big bang. if we accept the cosmic quantummetaphysical story presented by h&m, wheeler and other significant physicists then at the point of creation all possible ‘alternative histories’ are projected into a kind of cosmic possibility space, but none of these possibilities are ‘actualized’ as yet. for actualization to take place requires the presence of sentient beings to perceive and experience. in this model we can visualize all the ‘observer-participants’ moving, being born and dying but also leaving descendants to maintain the process, through the vast cosmic pool of potentialities and as they do so their perceptions alter the probabilities of potentialities both backwards and forwards in time. for instance, at the moment of creation there is a possibility (according to h&m) that the moon might end up being made of roquefort cheese and also a possibility that it may end up comprised of moon-rock, as it is in our current universe. when sentient beings get on the job of filtering through the probabilities through their perceptive activities, they somehow ‘choose’ to have a moon-rock moon rather than a roquefort cheese moon. thus the possibility of a roquefort cheese moon is filtered out of the cosmic mix of potentialities whilst the possibility of a moon-rock moon is solidified into actuality. goswami refers to the ‘backwards in time’ quantum effect wherein consciousness can determine which quantum potentialities become actual at a past point in time. on a collective and cosmic scale this backwards in time effect may operate back into the dim recesses of time and thereby provides a mechanism which brings a universe into actuality from a past quantum superposition of potentialities ( a ‘superposition’ is the quantum state of multiple quantum possibilities which obtains prior to observation). goswami writes concerning this: the lesson of the delayed choice experiment is profound. it solves the measurement problem of quantum cosmology how the universe of possibility can be actualized even though no sentient being was present to observe the big bang. the universe remains as a superposition of baby universes that evolves in possibility until, in one of the possible universes, the possibility of sentience arises; then quantum consciousness/god collapses the possibilities and the evolved first sentient being observes itself as separate from its environment, whereupon simultaneously the universe manifests retroactively, going backward in time from the moment of collapse all the way to the big bang. so it is true that we are here because of the universe and its purposive design, but it is also true that the universe is here because of us, our power of downward causation in our godness. there is circularity here, a breakdown of logic-quantum collapse manifests not only the observed, but also the observer. 88 it is important to note here that goswami’s notion of god is not that of an independent designer/creator but, rather, the field of potentialities and the collective consciousness acting upon them. this view is entirely consistent with the h&m perspective. this quantum platonic vision is also contained within the work of several other significant physicists, both current and recent. one example is the work of david bohm which is being dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 268 carried forward by paavo pylkkänen and basil hiley. bohm calls the cosmic possibility soup the ‘implicate order’ and the actualized experienced world the ‘explicate order’: bohm calls the implicate order the primary reality, this reality exists ‘folded up’ in nature and gradually unfolds as the universe evolves, enabling organization to emerge, in this way, the implicate becomes explicate over time. 89 in his important book wholeness and the implicate order bohm gives an overview of his perspective as follows: our overall approach has thus brought together questions of the nature of the cosmos, of matter in general, of life, and of consciousness. all of these have been considered to be projections of a common ground. this we may call the ground of all that is, at least in so far as this may be sensed and known by us, in our present phase of unfoldment of consciousness. although we may have no detailed perception or knowledge of this ground it is still in a certain sense enfolded in our consciousness… 90 all such quantum platonic viewpoints, including h&m’s, require consciousness to be a primary internal feature of the process of the evolution of the universe and the sentient beings within it. according to basil hiley: the world is basically organic. the mechanistic part is just an aspect of the deeper organic part. that’s not denying mechanism, it’s putting mechanism in its place. … physics is biology at the small scale. maybe one can be outrageous and say that an electron has a proto-consciousness. 91 and the notion that physics is small scale biology derives directly from bohm: we can say that human meanings make a contribution to the cosmos, but we can also say that the cosmos may be ordered according to a kind of ‘objective’ meaning. new meanings may emerge in this over all order. that is we may say that meaning penetrates the cosmos, or even what is beyond the cosmos. for example there are current theories in physics that imply that the universe emerged from the ‘big bang’. in the earliest phase there were no electrons, protons, neutrons, or other basic structures. none of the laws that we know would have had any meaning. even space and time in their present well-defined form would have had no meaning. all of this emerged from a very different state of affairs. the proposal is that, as happens with human beings, this emergence included the creative unfoldment of generalized meaning. later, with the evolution of new forms of life, fundamentally new steps may have evolved in the creative unfoldment of further meanings. that is, we may say that some evolutionary processes occur which could be traced physically, but we cannot really understand them without looking at some deeper meaning which was responsible for the changes. the present view of the changes is that they are random, with selection of those traits that were suited for survival, but that does not explain the complex, subtle structures that actually occurred. 92 it is meaning, awareness, and consciousness that organizes the evolution of sentient beings into the hierarchical vast variety of organic forms with various degrees of consciousness. as f. david peat, another researcher developing the ideas of bohm, points out with reference to bohm’s notion of ‘active information’, which resides at the quantum level: …information is that which gives form to energy. (it is the “subtle” energy spoken of in eastern science.) information would have an objective nature. it would play an active role in giving “form” to energy and be responsible for quantum processes. as a dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 269 “field” of active information it provided a collective, global form for a superconductor or superfluid. information would be copresent as an aspect of physical law, but also through what appear to be more subjective elements such as meaning and significance. it particular, information may be responsible for global processes in the brain and have a role to play in the nature of consciousness. and it is within the quantum fields of ‘active information’ that the quantum ‘templates’ of potentiality, which drive the evolutionary process, reside. such quantum templates can be identified with rupert sheldrake’s suggestion that organic development is organized by quantum ‘morphogenetic fields’: …morphogenetic fields are not precisely defined but are probability structures that depend on the statistical distribution of previous similar forms. the probability distributions of electronic orbitals described by solutions of the schrödinger equation are examples of such probability structures, and are similar in kind to the probability structures of the morphogenetic fields of morphogenetic units at higher levels. 93 the morphogenetic field which molds any particular morphogenetic unit provides a ‘virtual form’ which directs, through some natural mechanism (the inverse quantum zeno effect) the way in which the physical ‘stuff’ is organized. organic morphogenesis takes place through a hierarchy of levels of developmental pathways, each pathway is called a ‘chreode’. these levels correspond to bohm’s nested ‘implicate orders’, each succeeding order-level being more materialized out of quantum potentiality. the development of an organism takes place through the operation of a succession of nested morphogenetic fields. morphogenetic fields are established over time through a process of “morphogenetic resonance” which depends on “patterns and structures of vibration.” 94 once the morphogenetic structure is established there is a continued action of morphogenetic resonance which stabilizes the unit and, furthermore, the stability of the morphogenetic field itself depends on the repeated manifestation of the morphogenetic unit it gives rise to, so there is an interdependent relationship between the morphogenetic field and its morphogenetic unit. this means that “phenomena become more probable the more often they occur.” 95 this is an important aspect of the evolutionary process, the more often a quantum potentiality is materialized the more likely its future materialization becomes. it is this repeated actualization and materialization of quantum potentialities which underlies the appearance of evolution. in the early stages only very simple organisms can be actualized, but they pave the way for more complex creatures to subsequently emerge from quantum potentiality. this new quantum platonic evolutionary perspective concords precisely with h&m’s metaphysical perspective. in their penultimate chapter h&m tell us that their view is a form of the strong anthropic principle (sap). before their discussion of the sap they briefly discuss the wap (weak anthropic principle). this, they say, is not controversial; the very fact that sentient beings exist in this universe clearly means that this universe must be finetuned for sentient life. if this were not the case then obviously sentient life would not inhabit this particular universe. but, according to the h&m quantum platonic model requires the strong version which: …suggests that the fact that we exist imposes constraints not just on our environment but on the possible form and contents of the laws of nature themselves. the idea arose because it is not only the peculiar characteristics of our solar system dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 270 that seem oddly conducive to the development of human life but also the entire characteristics of the entire universe, and that is much more difficult to explain. 96 and another conclusion which must be drawn from this quantum platonic account of the evolution of the universe, which is driven by the collective consciousness, either explicit or implicit, of the sentient beings who eventually end up inhabiting the universe as apparently fully paid-up ‘material’ organisms, is that all possible forms of organic creature must be potential at the moment of the big bang. this conclusion is reached by the biologist adrian woolfson in his book life without genes: in the beginning there was mathematical possibility. at the very inception of the universe fifteen billion years ago, a deep infinite-dimensional sea emerged from nothingness. its colourless waters, green and turquoise blue, glistened in the nonexistent light of the non-existent sun … a strange sea though, this information sea. strange because it was devoid of location … 97 ignoring the apparently endemic misguided notion that a vast realm of experience can magically arise from complete absence, woolfson’s, strangely haunting, suggestion is that there must have been some kind of field of potentiality at the inception of the universe. although there was not a fully manifested and experienced reality there was, according to his picture, which clearly echoes aspects of the h&m quantum metaphysics, what he calls a ‘mathematical possibility’. this field is the quantum ‘wavefunction’ of the universe, a universal quantum field of potentiality that contains: …all possible histories … through which the universe could have evolved to its present state… 98 in the beginning, of course, the quantum ‘wavefunction’ of the universe would contain all the future evolutionary possibilities: the information sea is thus a quantum mechanical sea, composed from infinite repertoires of entangled quantum descriptions. 99 within this all-encompassing field of potentiality all possibilities for evolutionary manifestation are encoded. from out of the vast entangled web of infinite possibilities for manifestation only certain privileged members will actually make it into reality, so to speak: an information space of this sort would furnish a complete description of all potentially living and unrealizable creatures… 100 it therefore follows that there is a sort of design woven into the potentialities for evolution; it is a vast complex design of all possible manifestations written into the quantum field of potentiality of the universe standing on the very edge of time. in such a quantum platonic universe the dud-mud account of evolution cannot be true, it is pure illusion. such is the power of the illusion that dawkins and other dud-muds are still mesmerized and held in its material thrall, so much so they stretch the necks of drawings of okapi, or engage in various materialist obfuscations in order to avoid, cover over and dismiss the huge absurdities, such as hippo-like creatures walking back into the sea and materially transforming into whales, rather than see the illusion for what it is, an illusion generated by interactions of immaterial quantum fields of potentiality, a fact which has been established by recent events at the large hadron collider (lhc). the science writer jim baggott in his recent book higgs: the invention and discovery of the ‘god particle’ writes: dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 271 in the standard model the concept of mass, as an intrinsic property or measure of an amount of substance, has gone. mass is instead constructed from the energy of the interactions that occur between elementary quantum fields and their particles. the higgs boson is part of the mechanism that explains how all the mass of all the particles in the universe is constructed. all the matter in the world might consist of quarks and leptons, but it owes its very substance to the energy gained through interactions with the higgs field and the exchange of gluons. without these interactions, matter would be as ephemeral and insubstantial as light itself, and nothing would be. 101 this makes the entire apparently ‘material’ world an illusion so it certainly renders the dudmud worldview an illusion. as baggott further points out: it seems logical that there should be some ultimate constituents, some undeniable reality that underpins the world we see around us and which lends it form and shape. if matter is endlessly divisible, then we would reach a point where the constituents themselves become rather ephemeral to the point of non-existence. then there would be no building blocks, and all we would be left with are interactions between indefinable, insubstantial phantoms which give rise to the appearance of substance. unpalatable it may be but, to a large extent, this is precisely what modern physics has shown to be true. mass, we now believe, is not an inherent property or ‘primary’ quality of the ultimate building blocks of nature. in fact, there is no such thing as mass. mass is constructed entirely from the energy of interactions involving naturally massless elementary particles. the physicists kept dividing, and in the end found nothing at all. 102 quantum fields are entirely insubstantial: now, from a philosophical point of view, this is rather big stuff. our whole manner of speech … rather naturally makes us think that there is some stuff or substance on which properties can, in a sense, be glued. it encourages us to imagine taking a particle and removing its properties one by one until we are left with a featureless ‘thing’ devoid of properties, made from the essential material that had the properties in the first place. philosophers have been debating the correctness of such arguments for a long time. now, it seems, experimental science has come along and shown that, at least at the quantum level, the objects we study have no substance to them independent of their properties. 103 the weight of modern quantum evidence, then, entirely supports a quantum platonism wherein all organic forms are latent, awaiting unfoldment from quantum potentiality, within the quantum fields existing eternally as fields of insubstantial potentiality. dud-muds, however, breezily assume that none of this affects their theories, thinking that they can mistakenly and materialistically theorize away to their hearts content, pretending that a non-quantum fully paid up ‘material’ world can still be assumed to exist. however, this is not the case. as stapp points out: we live in an idealike world, not a matterlike world.’ the material aspects are exhausted in certain mathematical properties, and these mathematical features can be understood just as well (and in fact better) as characteristics of an evolving idealike structure. there is, in fact, in the quantum universe no natural place for matter. this conclusion, curiously, is the exact reverse of the circumstances that in the classical physical universe there was no natural place for mind. 104 dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 272 a point of view required by quantum theory which, again, supports a quantum platonic worldview. but, even if it were the case that it was appropriate to treat ‘matter’ as ultimate type ‘stuff’, we have already seen that dud-mud accounts have serious absurdities lying at their heart. it is these absurdities which can be avoided by taking the profound implications of modern quantum discoveries, as well as the dramatic evidence of evo-devo paradigm, into account. as biologist and evo-devo enthusiast sean b. carroll has indicated concerning the situation prior to the beginning of the evolution of life: …we know for certain that the full genetic tool kit for body-building was in place, but its potential was largely untapped for a considerable length of time. … the potential of the tool kit was realized largely through the evolution of switches and gene networks and the shifting of hox zones, in the cambrian and more recent periods. 105 the evo-devo revolution, which completely rocked the world of evolutionary biology and undermined hallowed dogmas of the dud-mud worldview, even though many evolutionary biologists are desperately trying to contain it within the darwinian worldview, confirms the quantum platonic perspective in a profound way, for it indicated that the “potential” fundamental “full genetic tool kit for body-building” of all potential organisms was in place long before organic evolution actually began. this extraordinary discovery fits precisely with the quantum evidence that the potentialities for all life were latent in the quantum fields of reality. this is not to say that there is a fully determinate human, lion, giraffe or kangaroo templates, all waiting to be expressed or manifested as is, so to speak, but, rather, all possible basic body-plans along with various possibilities for modifications of that fundamental body-plan in terms of limbs, organs and sense organs and so on are potential within levels of quantum possibility. these are expressed through quantum implicate orders through a mechanism of “quantum morphic resonance” within quantum implicate morphogenetic fields. bohm indicated this hierarchical system of implicate orders, from subtle to fully materialized, with his notion of a “super-implicate order’: … which is a … higher field (the implicate order would be a wavefunction) [which] would be a function of the wavefunction, a higher order, a super-wavefunction. the super-implicate order makes the implicate order non-linear and organises it into relatively stable forms with complex structures. 106 these quantum implicate orders can also be identified as shedrakian “morphogenetic fields”: the development of multicellular organisms takes place through a series of stages controlled by a succession of morphogenetic fields. at first the embryonic tissues develop under the control of primary embryonic fields. then … different regions come under the influence of secondary fields, in animals those of limbs, eyes, ears etc. … generally speaking, the morphogenesis brought about by the primary fields is not spectacular, because it establishes the characteristic differences between cells in different regions that enable them to act as the morphogenetic germs of the organ fields. then in the tissues developing under their influence, germs of subsidiary fields, fields which control the morphogenesis of structures within the organ as a whole… 107 dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 273 thus the development of the embryo is controlled by a nested hierarchy of morphogenetic fields, which are, according to sheldrake, ‘quantum probability fields’ 108 akin to bohm’s implicate orders. this process which underlies the development of an embryo also apples at a deeper level to the evolutionary development of a species within quantum implicate levels of reality. goswami has pointed out that the fact that much of the evolutionary processing of potentialities takes place at quantum implicate immaterial levels explains the lack of intermediaries which the dud-mud worldview takes great pains to conceal. as the ‘testing out’ of possibilities is quantum in nature it follows that a new species can suddenly appear during certain creative periods of the history of life, such as the cambrian ‘explosion’: we also need to remember that the radically new, manifest form is not in fact arrived at by itself; the corresponding vital blueprint is also available to the unconscious processor that is quantum consciousness/god. that blueprint offers a rough guideline of what needs to be sought through unconscious processing. … when does consciousness choose? well, before any choice can be made, consciousness needs microlevel possibilities to be amplified into macrolevel possibilities. therefore, collapse does not take place at the micro genetic level. an amplification of the micro genotype to the macro phenotype first takes place in possibility. i think that this amplification involves … chaos dynamics … when there is a match between the possibilities for macrophysical form and the morphogeneric blueprint of form, a match that rupert sheldrake (1981) calls morphic resonance, collapse of the possibility waves precipitates, a quantum leap takes place all at once, and consciousness has succeeded in making a physical representation (the physical trait or organ, the form) of the morphogenetic blueprint and, along with it, a new species or even higher taxon. there are no fossil records for the intermediate stages, because there are no manifest intermediate stages! it is as simple as that. 109 the term ‘collapse’ here refers to the point at which the multitude of possibilities which are potential at the quantum level are ‘collapsed’ by the quantum resonant ‘choice’ of the most efficient and appropriate one. this kind of quantum ‘look-ahead’ mechanism is employed by the mechanism of photosynthesis where in all possible ‘paths’ for energy transfer are ‘tested’ within a quantum superposition and the most efficient one is ‘chosen’: electronic spectroscopy measurements made on a femtosecond (millionths of a billionth of a second) time-scale showed these oscillations meeting and interfering constructively, forming wavelike motions of energy (superposition states) that can explore all potential energy pathways simultaneously and reversibly, meaning they can retreat from wrong pathways with no penalty. this finding contradicts the classical description of the photosynthetic energy transfer process as one in which excitation energy hops from light-capturing pigment molecules to reaction center molecules step-by-step down the molecular energy ladder. 110 this shows that one of the fundamental mechanisms uses a quantum mechanism in order to test, or ‘look ahead’, to find the most efficient pathway. there is an interesting remark by one of the team of researchers which indicates the remarkable lack of philosophical insight, or even perhaps common sense, in certain areas of discourse, especially evolution, on the part of otherwise intelligent people: “nature has had about 2.7 billion years to perfect photosynthesis, so there are huge lessons that remain for us to learn,” engel said. “the results we’re reporting in this dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 274 latest paper, however, at least give us a new way to think about the design of future artificial photosynthesis systems.” there is absolutely no evidence that nature has been “perfecting” photosynthesis. furthermore, it is highly unlikely that life would have got going if this mechanism had not been functioning effectively when it emerged as part of the process of the development of life. it is far more likely that quantum photosynthesis is a mechanism which is part of the inner ‘intelligence’ of the process of life and the quantum look-ahead mechanism is fundamental. this is the view of michael mensky who has proposed his extended everett concept (eec), which is an extension of everett’s ‘many worlds’ wherein consciousness can choose which is the most advantageous pathway amongst quantum alternatives: there is one more unsolved problem in biology that also could obtain its explanation in eec. this is the problem of morphogenesis. how an embryo is constructed starting from a single cell? where is a plan of the process of constructing it, step by step, or how constructing is controlled and directed? …consciousness (the primitivelevel consciousness, or ability to somehow perceive, which is connected with a living being from the very beginning) periodically addresses to the quantum world as a whole, compare various scenarios of constructing embryo (various 'building plans') and then, returning to the usual state, increase probabilities of those scenarios that lead to the right construction, of course, this is only a sketch of a possible explanation of the phenomenon, its main idea. 111 this is a stunning insight into how the process of life generates itself from quantum potentiality using a mechanism like the quantum ‘look ahead’ mechanism demonstrated within photosynthesis. the excitatory intelligence which is organizing the quantum potentialities into structures which are capable of channelling the ground energy-awareness into the individual individuated consciousnesses of embodied sentient beings is able to ‘feel’ its way ahead by addressing the “quantum world as a whole”. the morphogenetic structures are already within the quantum ground as potentialities, they need to be actualised through repetition into more ‘explicate’, ‘solidified’ or materialised versions. it should be immediately apparent that this insight is entirely consistent and amplificatory with all the other versions the quantum platonic perspective (which is a general term for the notion that archetypes reside as potentialities within the quantum realm) covered so far. the quantum physicist h. dieter zeh has lyrically characterised the emergence, or emanation, of the realms of apparent materiality and experience from the quantum realm by quoting the greek philosopher anaxagoras: the things that are in a single world are not parted from one another, not cut away with an axe, neither the warm from the cold nor the cold from the warm. when mind began to set things in motion, separation took place from each thing that was being moved, and all that mind moved was separated. 112 the world of separation which is generated by the interactions of quantum fields and the movement of mind within quantum fields does not produce an ultimate separation but, rather, produces an appearance of a process of experienced reality by unfolding the potentialities which are latent within the realm of the ultimate unity of the ultimate field of potentiality. as the h&m quantum platonism indicates, the movement, or observational activities, of a kind of universal collective consciousness unfolds the process of ‘reality’ from the potentialities, or ‘themes’, which are hidden within the “eternal” quantum fields. it is within these immaterial fields of potentiality that the potentialities for all manifestation, including organic creatures, are held. and, as h&m say: “this might sound like science fiction but it isn’t.” 113 dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 275 we can understand how this applies to the elucidation of the proper understanding of the apparent phenomenon of evolution by contrasting it with dawkins’ discussion of ‘the tree of cousinship’. according to dawkins: every species is a cousin of every other. any two species are descended from an ancestral species, which split in two. for example, the common ancestor of people and budgerigars lived about 310 million years ago. the ancestral species split in two, and the two strands went their separate ways for the rest of time. i chose human and budgie to make it vivid, but that same ancestral species is shared by all mammals on one side of that early divide, and all reptiles (zoologically speaking birds are reptiles…) on the other side. in the unlikely event that a fossil of this ancestral species was ever found it would need a name. let’s call it protamnio darwinii. we do not know any details about it, and the details don’t matter at all for the argument, but we won't go far wrong if we imagine it as a sprawling lizard-like creature, scurrying about catching insects. 114 he then proceeds to tell the speculative dud-mud story, or myth is probably a more appropriate word, of how the common ancestor of mammals and reptiles (figure 17 shows an artist’s impression of this, figure 18 is an artist’s impression of the putative fact of direct line of descent of birds from dinosaurs which is alluded to by dawkins) divided into two subpopulations, although at this point you would not be able to tell them apart and they would be able to interbreed. later as the two populations diverge from each other the ability to interbreed is supposed to be lost because the genes, according to the dud-mud worldview, have diverged too much. this is what dawkins has called the gene’s “long goodbye”. the dud-mud evolutionary just-so story offered by dawkins is that some kind of geographical barrier divides the two populations, and then subsequently the differences in the environment and natural selection, or genetic drift alone, cause the two populations to drift further and further apart. this process is termed ‘speciation’. how various terrestrial animals have become separated onto different land masses has been a controversial topic since the turn of the century, earthquakes opening impassable gorges, change in river courses and overwater transport were some suggestions. many thought that over-water transport which requires rafting across large expanses of sea on floating debris would be a highly improbable means of dispersal for animals larger than insects. however, dramatically, the event has been seen: figure 20 (115) dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 276 figure 21 (116) raft-riding green iguanas that reached the caribbean island of anguilla in the wake of a hurricane have provided ecologists with rare proof of one of the most debated theories of animal colonization of islands. as ellen j. censky from the carnegie museum of natural history in pittsburgh, pennsylvania and colleagues report in the 8 october edition of nature, at least 15 green iguanas (iguana iguana) arrived on the eastern beaches of anguilla on a large mat of logs and uprooted trees, shortly after autumn hurricanes in 1995. 117 so it would certainly appear that this kind of division of populations can occur. whether the division could, however, separate the two populations into one lot on one side of the sea without the putative mutant gene, whilst the hapless seafaring group just happened to all have the mutant genes is, however, a moot point. we are ourselves floating in a sea of speculation here. dawkins tells us that “the point about such freak dispersal events that they must be common enough to account for speciation, but not too common.” 118 dawkins then proceeds to claim that such a geographic division between evolving branches of the common ancestor of sauropsid reptiles and mammals must have occurred: the evidence from modern animals gives us every reason to think that something like the story i have just told is what happened in the past, for every one of the divergences between the ancestry of any animal and any other. 119 the evidence from modern animals is, of course, primarily that of selective breeding within a species. he then goes on to claim that even with identical environments animals will drift apart from each other, “whether by random drift alone, or with the aid of differential natural selection” 120 and because of this, according to dawkins, our mammal-reptile ancestor lineage “drifts” and splits into a mammal lineage and a sauropsid lineage. dawkins also tells his readers that the “details of his little story are pure fiction.” there is reason to think, however, that fictional aspect may permeate the entire scenario. for in his scenario dawkins seems to go as far has to suggest that undirected “random drift” alone, without “the aid of differential natural selection” could achieve this remarkable feat. this event is supposed to have taken place about 310 mya (million years ago) so mammals were around at the time of the dinosaurs (230 mya to about 65 mya), although until the demise of the dinosaurs they were restricted to being “small shrew like animals.” about 180 dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 277 mya the lineage of the monotremes, the egg-laying mammals which consist of the duckbilled platypus and echidna, split off. then, according to the dud-mud fairy tale, about 140 million years ago 121 the remaining mammals diverged into two distinct groups, the placental mammals (a group that includes humans and most modern mammals) and the marsupial mammals (a group that now includes koalas, kangaroos, wombats, and pouched mice). these two groups are then supposed to have evolved over millions of years in two increasingly different directions. the major divergence, of course, is in their reproductive methods. placental mammals develop inside their mother's womb for an extended period of time and their young are born quite alert and are often able to move about within just a few hours of birth. marsupial mammals, on the other hand, give birth to less developed young that must crawl up the mother's abdomen to the safety of her pouch. once inside the pouch, they continue their development until ready to move about on their own. the fact that there are three very different methods of mammal reproduction which have supposed to have evolved gradually, the earliest being the amniotic egg, clearly poses a significant issue of just how such a supposedly gradual transition could possibly have taken place. it is the modus operandi of dud-mud enthusiasts, however, to assume and assert that such a gradual transition must have happened because dud-mud type evolution must have happened. before about one hundred and fifty million years ago, south america, africa, india, antarctica and australia were all part of the landmass called gondwana (the southern major landmass at the time, the northern was laurasia, both of these supposedly split apart from the previous landmass called ‘pangaea’ which they made up) which subsequently broke apart to form the various continents. according to the received mud wisdom as conveyed by dawkins: it is generally agreed that marsupials came to australinea [dawkins’ term for australia, tasmania and new guinea] from south america, via antarctica. … it is not unlikely that all of australia’s marsupials stem from a single introduction of an opossum-like founder animal from south america, via antarctica. we don’t know exactly when, but it can’t have been much later than 55 million years ago, which is approximately when australia … pulled far enough away from antarctica to be inaccessible to island-hopping mammals. it could have been much earlier… marsupials, then, did not originate in australia, but america. according to one source: about 120 million years ago, the mammalian line ceased laying eggs and began bearing live young. these forms of mammals were the first marsupials, who bore their young at a very early stage in their development and transferred them to a pouch where modified sweat glands secreted milk. it is generally accepted that the first marsupials arose in north america and spread to south america, then to antarctica and australia some time before the breakup of pangaea near the end of the cretaceous period, some 70 million years ago. others argue that a southern continental origin is more probable. 122 if we accept the sequence of evolution of mammalian reproduction was egg, then marsupial and finally placental birth (although the same argument applies to any sequence), then we may ask how we can possibly conceive of such an evolution taking place gradually. can we really conceive of such a radical transformation happening gradually “by random drift alone, or with the aid of differential natural selection” 123 . what are the intermediate stages? there are no fossil records to help us out regarding significant stages. dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 278 at some point we have to imagine an egg-laying mammal suddenly being endowed with a mutant ‘pouch-predisposing’ gene, or set of genes, by random mutation. apparently this mutant pouch gene (or set) was extraordinary potent and eventually and cumulatively with other random mutations completely transformed the manner in which this group of mammals gave birth to their young. according to the wikipedia entry for marsupials: marsupials’ reproductive systems differ markedly from those of placental mammals…. females have two lateral vaginas, which lead to separate uteri but both open externally through the same orifice. a third canal, the median vagina, is used for birth. … the males generally have a two-pronged penis, which corresponds to the females’ two vaginas. … pregnant females develop something similar to a yolk sac in their wombs, which delivers nutrients to the embryo. marsupials give birth at a very early stage of development (about 4–5 weeks); after birth, newborn marsupials crawl up the bodies of their mothers and attach themselves to a nipple, which is located on the underside of the mother either inside a pouch called the marsupium or open to the environment. to crawl to the nipple and attach to it, the marsupial must have well developed forelimbs and facial structures. this is accomplished by accelerating forelimb and facial development in marsupials compared to placental mammals. as a result, there is decelerated development of such structures as the hindlimb and brain. there they remain for a number of weeks, attached to the nipple. the offspring are eventually able to leave the marsupium for short periods, returning to it for warmth, protection and nourishment. 124 but, just as in the case of the hippo to whale fantasy scenario, the complexity of the coordinated transformations required, all the while allowing the intermediate forms to reproduce, defy imagination. what kind of reproductive process would be exhibited by the mid-point intermediate form? how many mutated genes would be needed to transform an egg-laying mammal into a marsupial? one gene? a few? a lot of them? how could such a radical transformation in one of the central processes of life, the means of its very replication, take place via a sequence of small mutations? it is beyond ‘beyond belief’. in this context, and in the light of all the blatant incoherencies in the dud-mud worldview, “personal incredulity”, a response that dawkins claims should not be applied to the mud worldview, is a mark of sanity. evolution is meant to be a gradual, in fact very gradual, affair. but can one really imagine a gradual transformation from egg to marsupial reproduction, or marsupial to placental. what are the intermediate steps? dud-muds regularly deride those who ask about the usefulness of half an eye, but half a pouch! or what about a hundredth of a pouch; it would hardly be worth being born; only to find one’s allotted residence not ready for occupation! furthermore, according to the theory of natural selection it is not just the gene mutation which is responsible for the development of an adaptation, the filtering effect of the environment is crucial. but both marsupial and placental modes of birth arose on the american continent, within a similar environment. marsupial reproduction really took hold in australia, but is the environment in australia radically different to other continents, different enough to ‘favour’ getting out of the womb quickly and taking up residence in a pouch. just what kind of environment would ‘favour’ such a radical adjustment of mode of reproduction? is the environment in australia that different? presumably, if we accept dawkins claim that the development of new adaptations is very gradual, then the ancestor with the pouch mutation would still at this initial point be giving dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 279 birth via egg birth. however we are supposed to believe, according to the dud-mud account, that there is some subtle slight alteration in the direction of pouch birth. now in order for this slight new mutational ‘something’, indicating the possibility of the future development of pouch birth, to actually get ‘favoured’ it must be advantageous in some way at that point in time. but how could this possibly be true? what kind of environment could make the potentiality of pouch birth signaled by a non-noticeable mutation, significantly more advantageous than an egg one? the egg birth process was presumably working perfectly well otherwise these pouch-mutant mammals would have died out before they became fully pouch endowed. what kind of mutated mind could possibly believe such a desperately implausible scenario? the only way this scenario could possibly make sense is if there is some kind of quantum evolutionary ‘look-ahead’ mechanism as suggested by mensky. in this context it is intriguing to examine some results of a google search with the question “evolutionary environmental advantages of pouch reproduction.” someone in the google list asks: can someone please explain the benefits of raising babies in a pouch rather than carrying them full-term? and the following answer is offered: well, the way of reproduction of the marsupials … is not necessarily better, it is an alternative evolution to the placental animals and we have diverged in our mode of reproduction about 110 millions ago. obviously the placenta is much better mode of connecting with the baby but there are certain advantages to giving birth to an underdeveloped baby and raising it further. this is an excerpt from a very useful article in marsupial evolution which i think will be helpful: although the advantages of marsupial vs. placental birth may not be obvious, upon further examination several trade-offs become apparent. the placenta is extremely beneficial for many reasons, and allows the organism enough advantage to replace its marsupial counterpart if introduced into the same area. however, for everything there is a trade-off, and the gestation length may represent a direct exchange between what’s advantageous for the child as opposed to the mother. in particular circumstances or levels of stress, the marsupial reproductive mode may be more beneficial in reducing the deaths specifically related to the child-mother union. carrying a child internally for longer periods can have its consequences: principally the death of one frequently remains concomitant to that of the other. if one dies the other dies also if carried internally, but that is less frequently the case with pouched babies. if the mother is killed, a pouched baby can survive whereas birth subsequent to the mother's death never occurs regardless of the level of maturity of the fetus. likewise, if the baby dies during gestation, a pouched baby will not sacrifice the life of the mother. giving birth to offspring more fully developed can also have obvious disadvantages. basically, the larger the child at birth; the more difficult the delivery is for the mother. breech positions and such are not an issue for marsupials, but only become problematic for mammals with longer gestation periods. at times when survival has become difficult and the death rates of mothers and children are high, the marsupial mode of reproduction may prevent high mortality rates from affecting the death of the other. under severe environmental stress when giving birth earlier becomes advantageous for the success of the population, then the marsupial reproductive mode may be selectable from the natural variation that exists within the timing and developmental rates of these events. 125 dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 280 now this may seem plausible to some degree. but these considerations are not the kind of advantages that can be blindly selected by an environment which is supposedly filtering immediately a small increment in ‘fitness’ due to a small change in the structure and function of an organism. even if the female egg-laying pouch mutants had small glimmers of pouches, two uteruses etc. etc. (which is nonsense) … need i go on – it’s nonsense. in fact, if you think about it carefully, the above account is the kind of reasoning an intelligent designer would ponder in the process of his or her designing process; the notion that the ‘blind’ processes hypothesized by dud-mud pundits could achieve this ‘fine-tuning’ is, well, blind! another attempt to explain the advantages claims that: this is an adaptation that enhances the survival prospects of the kangaroo in australia’s harsh climate. the kangaroo has something called embryonic diapause: the mother kangaroo spends most of her adult life pregnant, but in drought times, she has the ability to indefinitely “freeze” the development of the young embryo until food sources are replenished. having two vaginas enables the embryo, when ready, to pass to the birth canal, or the median vagina while another embryo waits in suspended development. 126 again, this is not an adaptation which could possibly occur through the dud-mud gradual process of ‘blind’ natural selection. what possible sequence of tiny, tiny random changes could, even with the help of natural selection, possibly change egg reproduction to the radically, very radically, different mode of marsupial reproduction with two vaginas and so on. furthermore, how could the ‘selecting’ environment possibly ‘notice’ a tiny, hardly noticeable, mutation in the direction of pouch-birth a quantum ‘look-ahead’ mechanism which triggers quantum potentialities, on the other hand, can coherently account for such an interconnection between organism and environment. in many cases, placental and marsupial mammals physically resemble each other, except for the pouch. dawkins provides the picture shown in figure 19 to illustrate this. examples are the pouched marsupial mouse and the harvest mouse, the marsupial mole and the common mole, the marsupial wombat and the marmot, the tasmanian wolf and the wolf. dawkins says of this: i have already mentioned the magnificent marsupial mammal fauna of australia … the relevant point … is the repeated convergences between these marsupials and a great variety of opposite numbers among the ‘eutherian’ (i.e. non-marsupial) mammals, which dominate the rest of the world. though far from identical, even in superficial characteristics, each marsupial in the illustration … is sufficiently similar to its eutherian equivalent – that is the eutherian that most closely practices the same ‘trade’ – to impress us, but certainly not sufficient to suggest ‘borrowing’ by a creator. 127 dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 281 figure 22 (128) why dawkins thinks he can be “certain” that such convergences do not indicate ‘borrowing’ by a creator he does not elucidate. however, contrary to dawkins’ blind prejudice that evolution is ‘blind’, the fact of convergences does indicate the appropriateness of the quantum platonic perspective. because dawkins is committed to the dud-mud worldview he must resist the evidence. his assertion that, whilst the remarkable convergences between species might “impress us”, they are “certainty not sufficient to suggest ‘borrowing’ by a creator” is aimed at the notion that the repeated patterns with the diversity of life are indicative of “themes in the mind of the designer”. in true dawkins style he perversely parodies the suggestion by misrepresenting it: to emphasize how odd the idea of a creator sticking rigidly to ‘themes’ is, reflect that any sensible human designer is quite happy to borrow an idea from one of his inventions, if it would benefit another. maybe there is a ‘theme’ of aircraft design, dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 282 which is separate from the ‘theme’ of train design. but a component of a plane, say an improved design for the reading lights above the seats, might as well be borrowed for use in trains. why should it not, if it serves the same purpose in both? … if feathers are a good idea within a bird ‘theme’, such that every single bird, without exception, has them whether it flies or not, why do literally no mammals have them? why would the designer not borrow that ingenious invention, the feather, for at least one bat? the evolutionist’s answer is clear. all birds have inherited feather from their distant ancestor, which had feathers. no mammal is descended from that ancestor. it’s as simple as that. 129 dawkins remains committed to a dogmatic insistence on a direct line of fully materialized animals passing on genes from generation to generation. in contrast to this dud-mud view he parodies the ‘design’ view by implying the need for a fully conscious designer putting animals together with conscious intent. this, however, is a blatant and silly misrepresentation the quantum platonic perspective, which is that there must be ‘ideal forms’, or ‘templates’, existing as potentialities at a subtle quantum transcendent level of the process of reality. these forms are activated within deep quantum, ‘unconscious’, levels by a process of ‘morphic resonance’ and part of this resonance includes the environment. but there is no claim that every possible configuration of forms will be activated in the quantum platonic perspective, only a subset need be manifested. so dawkins’ criticism is entirely irrelevant. at the outset of the greatest show on earth dawkins appeals to the flawed authority of the evolutionary biologist ernst mayr (who actually opposed dawkins’ radical gene-centered viewpoint), whose work contributed to the conceptual revolution that led to the modern evolutionary synthesis of genetics and darwinian evolution, and to the development of the species concept. mayr was another biologist given to making wildly incorrect sweeping assertions on the basis of flimsy evidence. mayr, like dawkins following him, proclaimed as a matter of incontrovertible certainty that genes in diverse species must also be completely different. evo-devo showed that he did not have a clue what he was talking about. the same can be said about mayr’s view that: biology according to mayr, is plagued by its own version of essentialism. biological essentialism treats tapirs and rabbits, pangolins and dromedaries, as though they were triangles, rhombuses, parabolas or dodecahedrons. the rabbits that we see are wan shadows of the perfect ‘idea’ of rabbit, the ideal, essential, platonic rabbit, hanging somewhere out in conceptual space along with all the perfect forms of geometry. flesh-and-blood rabbits may vary, but their variations are always to be seen as flawed deviations from the ideal essence of rabbit. 130 quantum platonism indicates that there was, and is, much truth in plato’s viewpoint, and the remarkable convergences clearly indicate the necessary ‘existence’, as potentiality, for quantum ‘morphogenetic’ templates underlying all organic life forms. the quantum platonic perspective can be elucidated by considering the ‘object-oriented’ paradigm within computer modeling which constitutes the initial phase of computer systems development. the object of this approach is to be able to design a computer software system in a hierarchical modular fashion in which the system starts at the base as a highly abstract module and then descends through levels of ‘object-classes’ of increasing complexity; each level adds functionality to the level above. thus in figure 20 we see that at the top of a bank account class tree there is the most ‘abstract’ class which is just a base level bank account. within this class only the information which is common to all bank accounts can be placed, dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 283 information which is specific to various types of bank account are contained in the classes on lower levels of the tree. from the quantum platonic perspective the first movement within the deepest quantum implicate order is that between a potential perceiving being and a potential perceived environment. as mensky says the process begins at: …the most primitive, or the most deep, level of consciousness, differing perceiving from not perceiving. 131 the ‘epiontic’ internal ‘pressure’ of the life-operator operates upon the infinite quantum potentialities and begins to organise a coherent world of perceivers and perceived environments within the implicate quantum levels of potentiality. in this context it is worth noting that the dud-mud view takes for granted the fact that organisms have a desire to survive but has no means for accounting for the origin and internal pressure to produce sentient organisms. from the quantum platonic perspective the pressure is internal to the quantum realm as the ‘life-operator’ which operates to unfold sentient organisms in order to produce a world of perception through which, as neil turok says, “the universe gains a consciousness of itself.” at this primordial point there is only the mere quantum glimmer, so to speak, of a perceiving ‘pole’ and a perceived ‘pole’, there is no content. however quantum potentiality hold an infinite world of potentiality for producing all possible modes of perception and sensing, all possible modes of organic being. returning to the ‘object-oriented’ computer analogy, a further refinement of this hierarchical structure which is a vital part of the object-orientation paradigm is the idea of ‘virtual members’. these are members of a class which form part of the overall structure but cannot be fully specified within the class because the exact form of the member depends upon the implementation of members at a lower level of the hierarchy. so the top level ‘bank account’ class might look as shown in figure 20. the personal details of the account holder can be ‘implemented’ within this level but the ‘virtual’ members will be fully specified at a lower level of the object hierarchy. thus the ‘virtual’ members specify an ‘abstract’ structure which can be implemented in different ways at a later point depending upon the paths taken through the lower levels of the hierarchy. dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 284 figure 19 figure 20 dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 285 figure 21 dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 286 the findings of the evo-devo revolution now indicate that a similar hierarchical modular development is fundamental within the evolutionary development of species. figure 21 gives a flavor of this perspective in a very crude and reduced form (obviously), indicating the principle rather than detail. the essential point is that, whereas the previous view of divergent ‘random’ mutation of material gene units asserted the lack of common structure between divergent species it now turns out that in fact there is a common structure, which is clearly apparent within the genetic structure underlying all species. from the quantum platonic perspective the ‘family resemblances’ between marsupials and placentals, for instance, is due to the fact that the quantum morphogenetic templates of the various animals are prepared within the quantum implicate orders before they are expressed materially. as the various ‘template’ animals are organized through ‘morphic resonance’ through the increasingly more ‘explicate’ quantum levels, they take on ever more detailed ‘appearance’ within the quantum implicate realms. thus at the point indicated by the box ‘pre-eutherian/marsupial prototypes’ we can imagine the animal has been quantum-virtually ‘assembled’ to the point where ‘virtual’ features of sensing and locomotion have been put in place (not indicated on the diagram – see figure 22) but a method of reproduction has not yet been implemented. there are two methods available within quantum potentiality – marsupial and placental – and so the same template animal is ‘expressed’ in two varieties, one with the marsupial reproductive method and the other with the placental. the convergences illustrated within the comparison between placental and marsupial animals is exactly what one would expect from the quantum platonic perspective. in fact the quantum platonic perspective accounts for all the remarkable biological convergences found in nature. furthermore, through this quantum implicate layered mechanism, together with the quantum ‘look-ahead’ mechanism, each ‘template’ animal and plant eventually gets equipped with features ‘fitted’ to its target environment. figure 22 (rcg illustration/paula c. rondeau132) it would be remiss to leave out a brief discussion of one of the most bizarre creatures extant today, the duck bill platypus (figure 22), which is one of the two types of monotreme, the earliest split off mammalian lineage. this creature poses significant problems for the dudmud perspective, despite attempts dud-mud to explain away the problems. however, as we shall see, this remarkable creature beautifully illustrates the power and appropriateness of the quantum platonic paradigm. dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 287 the platypus has a bizarre physiology, it appears to be a hybrid blend of a bird, beaver, reptile and otter, with additional features not found in any of these four. when the naturalist george shaw, keeper of the department of natural history at the british museum, received a specimen from captain john hunter at the end of the eighteenth century he remarked that it was “impossible not to entertain some doubts as to the genuine nature of the animal, and to surmise that there might have been practiced some arts of deception in its structure.” 133 the two most remarkable features are the, on first appearance, duck-like bill, which is actually a highly sensitive electro-location sensor, detecting miniscule electrical impulses generated by its food source of small crustaceans and worms, and, secondly, the fact that it is the only mammal which lays eggs. the platypus has webbed feet, similar to those found on otters. unlike an otter, however, the webbing is far more pronounced on the front feet of the platypus, which it uses like paddles for swimming. while in the water, the back feet are tucked into its body and hardly used at all. it has a beaver-like tail, but whereas a beaver’s tail is covered in scales, is flattened, and propels the rodent through the water when swimming, the tail of the platypus is covered in fur and is used more in the way a rudder might guide a boat. the platypus has two sharp heel spurs behind its hind feet which can pierce skin. male platypuses are able to inject a protein-based extremely potent toxin. platypuses hunt underwater, where they swim gracefully by paddling with their front webbed feet and steering with their hind feet and beaver-like tail. folds of skin cover their eyes and ears to prevent water from entering, and the nostrils close with a watertight seal. in this posture, a platypus can remain submerged for a minute or two and employ its electrosensitive bill to find food. in his book the ancestor’s tale is full of admiration for the construction and functioning of the platypus’ bill’s electrosensitivity, comparing it to the “extra nose grafted onto a nimrod reconnaissance aircraft” which is the american equivalent to awacs system. the platypus’ bill, he says, “a reconnaissance device, an awacs organ”: platypuses have about 40,000 electrical sensors distributed in longitudinal stripes over both surfaces of the bill. … a large proportion of the brain is given over to processing the data from these 40,000 sensors. but the plot thickens. in addition to the 40,000 electrical sensors, there are about 60,000 mechanical sensors called push rods, scattered over the surface of the bill. pettigrew and his co-workers have found nerve cells in the brain that receive inputs from mechanical sensors. and they have found other brain cells that respond to both electrical and mechanical sensors (so far they have found no brain cells that respond to electrical sensors only). both kinds of cell occupy their correct position on the spatial map of the bill, and they are layered in a way that is reminiscent of the human visual brain, where layering assists binocular vision. just as our layered brain combines information from the two eyes to construct a stereo percept, the pettigrew group suggests that the platypus might be combining the information from electrical and mechanical sensors in some similarly useful way. 134 a truly remarkable piece of bio-engineering which, dawkins tells us, “has evolved far, even if other parts of the platypus have not.” 135 the significant issue, however, is that of whether this kind of bio-technology could have ‘evolved’ through the mechanism of rm+ns. anyone who believes this must also believe that a random mutation can produce a fully functioning electrosensitive bill along with the appropriate brain ‘wiring’ interconnections to process the information gathered by the dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 288 complex system of the electrosensitive bill. even if this ‘original’ bill was not as complex as that possessed by today’s platypuses, the random-mutatedly produced bill would need to be complex enough to function as an electrosensitive device capable of indicating location. given the fact that we know that all possible types of sense organ must be potential within the primordial quantum ground, such a desperately implausible account seems beyond the absurd. dawkins points out that other animals have ‘evolved’ similar electrosensitive organs, which is supposed to indicate dud-mud ‘convergent evolution’. such convergences, however, are much more coherently explained form the quantum platonic perspective. as animals are ‘assembled’ within the implicate levels of quantum potentiality through the mechanism of ‘morphic resonance’ they can avail themselves (metaphorically) of organs appropriate to the target environment. the quantum ‘look-ahead’ mechanism allows this mechanism of ‘fitting’ to function. this also gives an indication of how the platypus has such a diverse and seemingly peculiar set of features which defy dud-mud explanation. its features are absolutely well-suited to its environment and mode of life. recently the platypus’ genome was sequenced and the results caused some surprise: the creature, considered one of the strangest mammals in the world, has become the latest to have its genetic code sequenced, revealing it to be a bizarre mix of mammal, bird and reptile, with very complex sexuality. while humans have two sex chromosomes, the x and y, the platypus has 10, with five of each kind. 136 this kind of “bizarre mix” is not easily accounted for from a dud-mud worldview. however, it is entirely to be expected within with the viewpoint of the quantum platonic paradigm. the only possible explanation which accords with recent scientific knowledge for all of the above, as well as the remarkable interconnected bio-diverse interdependency found in nature in general, is that there is a deep level of quantum interconnection between an environment and the ‘design’ of the species found in that environment. and such an interconnection has been shown to exist; it is called ‘quantum entanglement’. this can happen precisely because the ‘themes’ for all the possibilities of life, including organisms and environments, are potential within the platonic quantum fields of potentiality, and when they are expressed and manifested they do so in a manner which is, in the main, coherent and consistent, the inhabitants fitting, because of the patterning of the internal potentialities, the manifested environments. this is a result of an internal quantum ‘entangled’ interconnection between manifested creatures and their containing environments. dawkins, of course, scoffs at such ideas and dogmatically proclaims their erroneous nature: zoologists … are tempted to think of the divide between major groups as a momentous event. the reason zoologists may be so misled is that they have been brought up in the almost reverential belief that each of the great divisions of the animal kingdom is furnished with something deeply unique, often called by the german word bauplan. although this word just means “blueprint”, it has become a recognized technical term … in its technical sense, bauplan is often translated as “fundamental body plan.” the use of the word “fundamental” (or, equivalently, the self-conscious dropping into german to indicate profundity) is what causes the damage. it can lead zoologists to make serious errors. 137 dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 289 the quantum evidence and the evo-devo revolution, however, indicate that it is dawkins, with his stubborn adherence to a discredited materialist metaphysics, who is in the dudmud grip of “serious errors.” both these areas of enquiry suggest the deep importance of the quantum ‘existence’ of such body plans as quantum potentialities. and, because of this, it now looks entirely likely that each species has its own quantum ‘template,’ or set of templates underlying manifestation, which is manifested through the operation of an internal quantum ‘pressure’ which drives the process of quantum evolution into the manifested ‘material’ world. the dud-mud worldview is now revealed as nothing more than an illusion created by dogmatic adherence to a thoroughly unscientific materialist metaphysics. 1 dawkins, r. (2010), 165-166 2 dawkins, r. (1995), xi 3 http://gareths-biology-assignment.weebly.com/ 4 http://gareths-biology-assignment.weebly.com/ 5 dawkins, r. (1995), 3 6 dawkins, r. (1995), 6-7 7 fodor, jerry – ‘why pigs don’t fly’, new york review of books 8 fodor, j. & piattelli-palmarini, m. (2011), 23 9 fodor, j. & piattelli-palmarini, m. (2011) 10 dawkins, r. (2010), 24 11 http://www.devoniantimes.org/order/old-order.html 12 dawkins, r. (2010) 13 dawkins (2006a) 14 dawkins, r. (2010), 165 15 dawkins, r. (2010), 164 16 http://users.tamuk.edu/kfjab02/biology/vertebrate%20zoology/b3405_ch08.htm 17 dawkins, r. (2005), 5 18 dawkins, r. (2005), 458 19 http://rationalwiki.org/wiki/lungfish#in_a_nutshell 20 ibid. 21 http://rationalwiki.org/wiki/fish_that_survive_on_land#creationist_responses 22 http://www.annekempslungfish.com/what_is_a_lungfish.html 23 http://www.annekempslungfish.com/what_is_a_lungfish.html 24 http://www.fasebj.org/content/21/8/1623.full 25 http://www.fasebj.org/content/21/11/2640.2.full 26 smith, h. (1965) the evolution of the kidney. chasis, herbert goldring, william eds. homer william smith: his scientific and literary achievements, 81 new york university press new york. 27 dawkins, r. (2010), 161 28 dawkins, r. (2010), 166 29 http://www.earthhistory.org.uk/transitional-fossils/fish-to-amphibian 30 http://www.devoniantimes.org/order/re-ichthyostega.html 31 dawkins, r. (2010), 168 32 ibid. 33 dawkins, r. (2010), 169 34 http://gareths-biology-assignment.weebly.com/ 35 dawkins, r. (1995) 2-3 36 conway morris, simon (2003), 6 37 conway morris, simon (2003) 38 dawkins, r. (2010), 169-170 dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 290 39 dawkins, r. (2010), 170 40 goswami, a. (2008), 190-191 41 goswami, a. (2008), p 191 42 dawkins, r. (2010), 315 43 carroll, sean b. (2006), 72 44 carroll, sean b. (2006), 9 45 fodor, jerry – ‘why pigs don’t fly’, new york review of books 46 http://en.wikipedia.org/wiki/sperm_whale#respiration_and_diving 47 dawkins, r. (1995), 81 48 dawkins, r. (1995), 81-82 49 http://www.chrispackham.co.uk/television/major-new-series/secrets-of-our-living-planet 50 http://en.wikipedia.org/wiki/pierre_belon 51 dawkins, r. (2010) 295-296 52 dawkins, r. (2010) 53 wolf-ekkehard lönnig (2006) ‘the evolution of the long-necked giraffe – what do we really know’ part 1, 1 54 wolf-ekkehard lönnig (2006) ‘the evolution of the long-necked giraffe – what do we really know’ part 1, 7 55 dawkins, r. (2010), 295 56 http://unrealnature.wordpress.com/2009/08/18/dining-and-dancing/ 57 dawins climbing mount improbable (1996) 58 animals of the world (1988) 59 wolf-ekkehard lönnig (2006) ‘the evolution of the long-necked giraffe – what do we really know’ part 1, 21 60 dawkins, r. (2010), 24-25 61 dawkins, r. (2010), 296-297 62 dawkins, r. (2010), 22 63 randall, l. ‘designing words’ in brockman, j. (ed.) (2006), 194 64 http://www.athro.com/general/atrans.html 65 http://www.athro.com/general/atrans.html 66 http://www.ucmp.berkeley.edu/history/agassiz.html 67 http://www.nceas.ucsb.edu/~alroy/lefa/lagassiz.html 68 http://urbantimes.co/magazine/2011/07/a-darwinian-victory-teaching-of-evolution-accepted-intexas/ 69 randall, l. (2006) p158 70 http://www.nytimes.com/2012/03/25/books/review/a-universe-from-nothing-by-lawrence-mkrauss.html 71 ibid. 72 turok, n. (2013), 247 73 turok, n. (2013), 201 74 carroll, s. (2012), 280-281 75 das wesen der materie” (the nature of matter), speech at florence, italy, 1944 (from archiv zur geschichte der max-planck-gesellschaft, abt. va, rep. 11 planck, nr. 1797) 76 schrödinger, e. (1944), what is life, (13th printing, 2013) cambridge university press, 121. 77 goswami, a. (2008), 72-73 78 rosenblum, bruce and kuttner, fred (2006), 179 79 mensky, michael: ‘reality in quantum mechanics, extended everett concept, and consciousness’, 6 80 schlosshauer, m. (ed.) (2011), 159 81 http://www.counterbalance.org/ctns-vo/davie-body.html 82 hawking, stephen & mlodinow, leonard (2010) 82 83 hawking, stephen & mlodinow, leonard (2010) 83 dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 291 84 hawking, stephen & mlodinow, leonard (2010) 136 85 hawking, stephen & mlodinow, leonard (2010) 140 86 barrow, john d., davies, paul c. w., harper, charles l. (eds.) (2004) p577 – wheeler, j a (1999) ‘information, physics, quantum: the search for links.’ in feynman and computation: exploring the limits of computers, ed. a. j. g. hey, p309 (314). cambridge, ma: perseus books. 87 hawking, stephen & mlodinow, leonard (2010), 140 88 goswami, a. (2008), p119 89 michele caponigro, xiaojiang jiang, ravi prakesh, ram lakhan pandey vimal; ‘entanglement: can we ‘see’ the implicate order? philosophical speculations’ in neuroquantology – september 2010, vol 8, issue 3, 382. 90 bohm, david (2003), 119 91 http://www.seekeraftertruth.com/basil-hiley-quantum-physics-and-the-holistic-universe/ 92 bohm, david (2003), 180 93 sheldrake, rupert (2009), 145 94 sheldrake, rupert (2009), 144 95 sheldrake, rupert (2009), back cover blurb 96 hawking, stephen & mlodinow, leonard (2010), 155 97 woolfson, adrian (2000), 74 98 barrow, john, d. & tipler, frank j. (1986), 105 99 woolfson, adrian (2000), 83 100 woolfson, adrian (2000), 76 101 baggott, j. (2012), 221 102 baggott, j. (2012), 2-3 103 allday, jonathan (2009) p493 104 stapp, henry (2004) p223 105 carroll, sean b. (2006) p164 106 bohm, david (2003) p140 107 sheldrake, rupert (2009) p136 108 sheldrake, rupert (2009) p104 109 goswami, a. (2008), p182 110 http://www.lbl.gov/science-articles/archive/pbd-quantum-secrets.html 111 mensky, michael: ‘reality in quantum mechanics, extended everett concept, and consciousness’ p12 112 barrow, john d., davies, paul c. w., harper, charles l. (eds) (2004) p114 – h. dieter zeh: ‘the wave function: it or bit?’ 113 hawking, stephen & mlodinow, leonard (2010) p140 114 dawkins, r. (2010) p254 115 http://rhamphotheca.tumblr.com/post/16652899559/deuterosaurus-a-genus-of-the-therapsids-one-of 116 http://news.discovery.com/animals/dinosaurs/birds-dinosaurs-120530.htm 117 http://www.nature.com/news/1998/981015/full/news981015-3.html 118 dawkins, r. (2010), 258 119 dawkins, r. (2010), 255 120 dawkins, r. (2010), 256 121 dawkins, r. (2005), 230 122 http://www.bobpickett.org/evolution_of_mammals.htm 123 dawkins, r. (2010), 256 124 http://en.wikipedia.org/wiki/marsupial 125 http://au.answers.yahoo.com/question/index?qid=20110603230046aaj3r0k dna decipher journal | july 2013 | volume 3 | issue 3 | pp. 235-292 – issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 292 126 http://wiki.answers.com/q/why_do_female_kangaroos_have_two_vaginas 127 dawkins, r. (2010) 300-301 128 dawkins, r. (2010) 129 dawkins, r. (2010) 297-298 130 dawkins, r. (2010) 22 131 mensky, michael: ‘reality in quantum mechanics, extended everett concept, and consciousness’ p6 132 http://realtruth.org/articles/110819-005.html 133 http://www.museumofhoaxes.com/hoax/hoaxipedia/duckbilled_platypus/ 134 dawkins, r. (2005), 245 135 dawkins, r. (2005), 242 136 http://www.guardian.co.uk/science/2008/may/08/genetics.wildlife 137 dawkins, r. (1995), 12 login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x dna decipher journal | may 2014 | vol. 4 | issue 1 | pp. 01-02 gariaev, p. p. et. al., materialization of dna fragment in water through modulated electromagnetic irradiation issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 1 preliminary report materialization of dna fragment in water through modulated electromagnetic irradiation peter p. gariaev * et al. abstract we present a preliminary report on the materialization of dna fragment in pure water in the presence of its phantom delivered by modulated wide-spectrum electromagnetic irradiation. a full article with details will be presented later. key words: dna synthesis, dna fragment, phantom, wave genetics, modulation, electromagnetic irradiation. figure 1. left to right: (1) the top bands in 1st, 4th and 6th strips are dna synthesized in water; (2) the band in 11th strip is the sample dna (268bp) which was received by mshei spectrum and the latter was then served on the water; (3) the higher 4 bands in the 12th strip shows markers 139, 268, 394 and 613 (base pairs of dna); (4) the bottom bands in the strips are from schmier primers; and (5) the 9th strip is control. the herein author first discovered the phenomenon of dna phantom in 1984 and subsequently *correspondence: peter gariaev, ph.d., quantum genetics institue, maliy tishinskiy per. 11/12 25, moscow 123056, russia. email: gariaev@mail.ru mailto:gariaev@mail.ru dna decipher journal | may 2014 | vol. 4 | issue 1 | pp. 01-02 gariaev, p. p. et. al., materialization of dna fragment in water through modulated electromagnetic irradiation issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 2 did numerous related research. the first publications in the wave transfer of genetic information came in 2003 [p.p. garyaev, 2003, cloning, aids, cancer, diabetes and wave genetics. consciousness and physical reality. vol. 8, № 2, pp. 52-60; p.p. gariaev, 2003, der wellengenetische code. tattva viveka, № 20, pp. 68-73 (in german); p. p. garyaev, e. a. leonova, 2003, strange world of wave genetics. consciousness and physical reality, vol.8, № 6, pp. 27-40]. more recently, there was an article on the same subject by luc montagnier’s group in “dna waves and water” http://arxiv.org/pdf/1012.5166.pdf. this paper provides experimental evidence of remote (high) wave transmission of dna information directly into water. here we give a preliminary report on the results from one of our latest experiments on the synthesis of dna fragment in water in the presence of its phantom through modulated widespectrum electromagnetic irradiation. a full article with details will be presented later. figure 1 shows one of our experiments on the synthesis of dna fragment by pcr (polymer chain reaction) in the presence of the phantom mwei (modulated wide-spectra electromagnetic irradiation) of the said dna fragment. from left to right, figure 1 shows: (1) the top bands in 1st, 4th and 6th strips are dna synthesized in water; (2) the band in 11th strip is the sample dna (268bp) which was received by mshei spectrum and the latter was then served on the water; (3) the higher 4 bands in 12th strip shows markers 139, 268, 394 and 613 (base pairs of dna); (4) the bottom bands in the strips are from schmier primers; and (5) the 9th strip is control. prospects of broadcasting working genes based on this technology are potentially vast. for example, it may be used to program stem cells for regenerating the retina, teeth and all other organs and tissues such as damaged endocrine glands, the spinal cord and the brain (we have done case studies). further, it may be sued to repair chromosomal damage such as cystic fibrosis and reduce excess chromosome in down's syndrome and treat the terminal cancer (we have done case studies). further work in this direction will give a powerful impetus to new development of biology, bio-computation, medicine, agriculture, bio-internet and deep space communications, etc. http://arxiv.org/pdf/1012.5166.pdf login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x dna decipher journal | july 2017 | volume 7 | issue 1 | pp. 01-05 1 pitkänen, m., steps towards understanding of the origins of life article steps towards understanding of the origins of life matti pitkänen 1 abstract two highly interesting findings providing insights about the origins of life have emerged. the group led by thomas carell has made an important step in the understanding the origins of life. they have identified a mechanism leading to the generation of purines a and g which besides pyrimidines a,t (u) are the basic building bricks of dna and rna. the crucial step is to make the solution involved slightly acidic by adding protons. for year later i learned that a variant of urey-miller experiment with simulation of shock waves perhaps generated by extraterrestrial impacts using laser pulses generates formamide and this in turn leads to the generation of all 4 rna bases. there is however problem: the early atmosphere was assumed to be reductive and this probably not true. these findings, in particular the problem due to the reductivity, represent a fascinating challenge for tgd inspired quantum biology. the proposal is that in formamide is the unique amide, which can form stable bound states with dark protons and crucial for the development of life as dark mattervisible matter symbiosis. local reductivity could be due to the formation of electron rich exclusions zones due to pollack effect generating also dark protons at magnetic flux tubes. dark protons would bind stably with unique amine leading to generation of purines and the 4 rna bases. this would be starting point of life as symbiosis of ordinary matter and dark matter as large heff/h = n phases of ordinary matter generated at quantum criticality induced by say extraterrestrial impacts. 1 introduction two highly interesting findings providing insights about the origins of life have emerged and it is interesting to see how they fit to the tgd inspired vision. the group led by thomas carell has made an important step in the understanding the origins of life. they have identified a mechanism leading to the generation of purines a and g which besides pyrimidines a,t (u) are the basic building bricks of dna and rna. the crucial step is to make the solution involved slightly acidic by adding protons. for year later i learned that a variant of urey-miller experiment with simulation of shock waves perhaps generated by extraterrestrial impacts using laser pulses generates formamide and this in turn leads to the generation of all 4 rna bases. these findings represent a fascinating challenge for tgd inspired quantum biology. the proposal is that formamide is the unique amide, which can form stable bound states with dark protons and crucial for the development of life as dark matter-visible matter symbiosis. pollack effect would generate electron rich exclusions zones and dark protons at magnetic flux tubes. dark protons would bind stably with unique amine leaving its chemical properties intact. this would lead to the generation of purines and the 4 rna bases. this would be starting point of life as symbiosis of ordinary matter and dark matter as large heff/h = n phases of ordinary matter generated at quantum criticality induced by say extraterrestrial impacts. the tgd based model for cold fusion and the recent results about superdense phase of hydrogen identifiable in tgd framework as dark proton sequences giving rise to dark nuclear strings provides support for this picture. there is however a problem: a reductive environment (with ability to donate electrons) is needed in these experiments: it seems that early atmosphere was not reductive. in tgd framework one can imagine two not mutually exclusive solutions of the problem. either life evolved in underground oceans, where oxygen concentration was small or pollack effect gave rise to negatively charged and thus 1correspondence: matti pitkänen http://tgdtheory.com/. address: karkinkatu 3 d 3, 03600, karkkila, finland. email: matpitka6@gamail.com. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.com/ mailto:matpitka6@gmail.com dna decipher journal | july 2017 | volume 7 | issue 1 | pp. 01-05 2 pitkänen, m., steps towards understanding of the origins of life reductive exclusion zones (ezs) as protons were transferred to dark protons at magnetic flux tubes. the function of uv radiation, catalytic action, and of shock waves would be generation of quantum criticality inducing the creation of ezs making possible dark heff/h = n phases. 2 the first step: binding of dark protons to formamido-pyrimidine i learned about very interesting discovery related to the problem of understanding how the basic building bricks of life might have emerged. rna (dna) has nucleotides a,g,c,u (t) as basic building bricks. the first deep question is how the nucleotides a,g,c,u, and t emerged. 1. there are two types of nucleotides. pyrimidines c and t/u (see http://tinyurl.com/k3vxl9b) have single carbon 6-cycle. purines a and g (see http://tinyurl.com/odvqw2p) in turn have single 6-single and 5-cycle fused attached together along one side. purines are clearly more complex than pyrimidines. 2. u.k. chemist john sutherland demonstrated a plausible sequence of steps leading to the emergence of pyrimidines. purines turned out to be more problematic. leslie orgel and colleagues suggested a possible pathway but it produces purines in too tiny amounts. now a group led by thomas carell in ludwig maximilian university have found a more plausible mechanism [3] (see http://tinyurl.com/z65kpyo). 1. carell and colleagues studied the interaction of biomolecule formamido-pyrimidine (fapy) with dna and found that it also reacts to produce purines. could fapys have served as predecessors of purines? (for formamide see http://preview.tinyurl.com/lwqyqnu and for the class of chemical compounds known as amines see http://tinyurl.com/mad6c2u). 2. the first step would have been a copious production of amino-pyrimidines containing several chemical groups known as amines. the problem is that the are so many amines and they normally react indiscriminantly to produce many different compounds. one wants mostly purines so that only one critical amine is wanted. 3. when carell and his team added some acid to the solution to decrease its ph, a miracle happened. the extra protons from acid attached to the amines of the amino-pyrimidine and made them nonreactive. there was however one exception: just the amine giving rise to purine in its reactions! the reactive amine also readily bonded with formic acid acid (see http://tinyurl.com/lmstt7n) or formamide. hence it seems that one big problem has been solved. the second challenge is to understand how the building bricks of rna and dna combined to form longer polymers and began to replicate. 1. one prevailing vision is that so called rna world preceded the recent biology dominated by dna. the goal has been to achieve generation of rna sequence in laboratory. unlike dna rna sequences are not stable and long sequences are difficult to generate. dna in turn replicates only inside cell and the presence of what is known as ordered water seems to be essential for this. 2. this step might involve new physics and chemistry and i have considered the possibility that the new physics involves magnetic bodies and dark proton sequences as a representation of the genetic code at the level of dark nuclear physics. there is no need to add that the fact that dark proton states provide representations for rna, dna, trna, and amino-acids [6, 7] looks like a miracle and i find still difficult to believe that it is true and for genetic code. also the representation of vertebrate code emerges in terms of correspondences of dark proton states. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/k3vxl9b http://tinyurl.com/odvqw2p http://tinyurl.com/z65kpyo http://preview.tinyurl.com/lwqyqnu http://tinyurl.com/mad6c2u http://tinyurl.com/lmstt7n dna decipher journal | july 2017 | volume 7 | issue 1 | pp. 01-05 3 pitkänen, m., steps towards understanding of the origins of life this suggests that the replication of dna and takes place at the level of dark proton sequencies dark nuclear strings serving as a dynamical template for the biological replication. also transcription and translation would be induced by dark process. actually all biochemical processes could have as template the dynamics of molecular magnetic bodies and biochemistry would be kind of shadow of deeper dynamics. 3. there is actually support for dark proton sequences. quite recently i learned about the article of leif holmlid and bernhard kotzias [1] (see http://tinyurl.com/hxbvfc7) about the superdense phase of hydrogen. in tgd superdense phase has interpretation as dark proton sequences at magnetic flux tubes with the compton length of dark proton coded by heff/h ' 211 to electron’s compton length [8]. remarkably, it is reported that the superdense hydrogen is super-conductor and super-fluid at room temperatures and even above: this is just what tgd predicts. the dark protons in tgd inspired quantum biology [9] should have much longer compton length of order of the distance between nucleotides in dna sequences in order to serve as templates for chemical dna. this gives a dark compton length of order ' 3.3 angstroms from the fact that there are 10 codons per 10 nm. this gives heff/h ' 218. one can return back to the first step in the genesis of dna and rna. the addition of protons to the solution used to model prebiotic environment to make it slightly acidic was the key step. why? 1. here cold fusion might help. cold fusion is claimed to take place in electrolysis involving ionization and charge separation. the electric fields used in electrolysis induce ionization and thus charge separation. for me it has however remained a mystery how electric fields, which are extremely tiny using the typical strength of molecular electric field as standard are able to induce a charge separation. of course, every chemist worth of his salt regards this as totally trivial problem. i am however foolish enough to consider the possibility that some new physics might be involved. 2. the mechanism causing charge separation could be analogous to or that discovered by pollack as he irradiated water bounded by a gel phase [2] [9]: in the recent case the electric field would take the role of irradiation as a feeder of energy. negatively charged exclusion zones (ezs) were formed and 1/4 of protons went somewhere. the tgd proposal is that part of protons went to magnetic flux tubes and formed dark proton sequences identifiable as dark nuclear strings. the scaled down nuclear binding energy favours the formation of dark nuclear strings perhaps proceeding as analog of nuclear chain reaction. this picture allows to ask whether dark proton sequences giving rise to a fundamental representation of the genetic code could have been present already in water [9]! 3. how dna/rna could have then formed? could the protons making the solution acidic be dark so that the proton attaching to the amine would be dark? could it be that for all amines except the right one the proton transforms to ordinary proton and destroys the chemical reactivity. could the attached dark proton remain dark just for the correct amine so that the amine would remain reactive and give rise to purine in further reactions? could a,g,c,t and u be those purines and pyrimidines or even more general biomolecules for which the attachment to dark proton does not transform it to ordinary proton and in this manner affect dramatically the chemical properties of the molecule? what is the condition for the preservation of the darkness of the proton? 3 second step: could shock waves due to extraterrestrial impacts have produced rna bases? about year later i learned about a further interesting finding related to the prebiotic evolution (see the popular article at http://tinyurl.com/m8npeor). the conclusion of the research article (see [4]) is that issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/hxbvfc7 http://tinyurl.com/m8npeor dna decipher journal | july 2017 | volume 7 | issue 1 | pp. 01-05 4 pitkänen, m., steps towards understanding of the origins of life that the extraterrestrial impacts on earth’s early atmosphere might have generated all 4 rna bases (see http://tinyurl.com/kxxc7db). also now the formamide is involved and my layman guess is that the motivation for this comes from the experiment of carell et al [3] (see http://tinyurl.com/z65kpyo) discussed above. if formamide is generated then it becomes possible to generate formamido-pyridine and from this the rna bases can be generated. the experiment was a modern version of urey-miller experiment originally intended to simulate the situation at the surface of the early atmosphere modelled as a mixture a water h2o, carbon-monoxide co, and ammonium nh3. the shock waves generated by the impacts were modelled in the experiment using terawatt laser pulses. in the original urey-miller experiment amino-acids were generated. in the modern version of the experiment it was found that also formamide conh3 is formed, whose presence under suitable circumstances can lead to the generation of all 4 rna bases. the presence of uv radiation, shock waves caused by extraterrestrial collisions, or of catalyst is the necessary condition. in tgd universe the additional condition could guarantee quantum criticality accompanied by dark heff/h = n phases leading to the generation of dark protons and their stable binding with formamidopyrimidine. the stable binding would not be possible for other amido-pyrimidines since dark protons would transform to ordinar protons for them. all 4 rna bases would emerge from formamido-pyrimidine. all basic molecules of life could be produced in the reductive atmosphere. the atmosphere was assumed to be reductive and this is a problem: the best that one can hope is that the early atmosphere was weakly reductive. chemical compound is reductive (see http://tinyurl.com/ m9cqnob) if it tends to donate electron. reduction means receiving electron and in chemistry hydrogen atom. to obtain a reducing atmosphere (see http://tinyurl.com/lx4tat2) one should remove oxygen from it. it however seems that the early atmosphere has contained oxygen and was oxidative rather than reductive. how could one overcome the problem? 1. in the experiment of carell et al protons were added to reduce the ph of water. the basic experimental rule is that this makes the environment more reductive. the tgd proposal is that it led to a formation of dark proton-amine pair for the amine leading to the formation of purine. charge separation by pollack effect [2] [9] leading to the generation of dark proton sequences (dark nuclei) at magnetic flux tubes could have been due to the ir radiation, and maybe also by uv radiation, catalytic action, or by shock waves. the presence of electrons in the exclusion zones (ezs) could have made them electron donors and therefore reductive. the addition of protons in the experiment of carell reducing the ph of water could have induced a transformation of dark protons at magnetic flux tube to ordinary protons. dark protons bound to the amines would have transformed to ordinary protons and inducing their chemical inactivity. only for the amine formamide serving as a precursor of purine the dark proton-amine bound state was stable and remained chemically reactive since dark proton did not affect the properties of visible matter part of the compound. symbiosis between dark and ordinary matter began. this view conforms also with the vision about the pairing of dna/rna and dark dna/rna formed by sequences of proton triplets representing dna/rna codons [10]. dna is indeed negatively charged and dark proton could neutralize it but allow it to remain chemically active. 2. second possibility is suggested by the conjecture that prebiotic life evolved in the crust of earth, perhaps in the underground oceans or regions related to volcanoes [5, 9]. the content of oxygen of this environment could have been much lower than at the surface making it reductive: it would not be possible to even talk about atmosphere. but where did the metabolic energy come from? could volcanic energy emitted as dark long wave photons with energies in the range of bio-photon energies help here? there are indeed a theories assuming that first life forms emerged from volcanoes. these problems are discussed in [5, 9] from tgd viewpoint. note that these two explanations do not exclude each other. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/kxxc7db http://tinyurl.com/z65kpyo http://tinyurl.com/m9cqnob http://tinyurl.com/m9cqnob http://tinyurl.com/lx4tat2 dna decipher journal | july 2017 | volume 7 | issue 1 | pp. 01-05 5 pitkänen, m., steps towards understanding of the origins of life references [1] holmlid l and kotzias b. phase transition temperatures of 405-725 k in superfluid ultra-dense hydrogen clusters on metal surfaces. aip advances. available at: http://tinyurl.com/hxbvfc7, 6(4), 2016. [2] the fourth phase of water : dr. gerald pollack at tedxguelphu. available at: https://www. youtube.com/watch?v=i-t7tcmudxu, 2014. [3] carell t et al. a high-yielding, strictly regioselective prebiotic purine nucleoside formation pathway. science. available at:http://science.sciencemag.org/content/352/6287/833, 352(6287):833– 836, 2016. [4] ferus m et al. formation of nucleobases in a millerurey reducing atmosphere. pnas.available at: http://tinyurl.com/kxxc7db, 2017. [5] pitkänen m. expanding earth model and pre-cambrian evolution of continents, climate, and life. in genes and memes. in online book. available at: http://tgdtheory.fi/public_html/ genememe/genememe.html#expearth, 2006. [6] pitkänen m. homeopathy in many-sheeted space-time. in bio-systems as conscious holograms. in online book. available at: http://tgdtheory.fi/public_html/hologram/hologram. html#homeoc, 2006. [7] pitkänen m. nuclear string hypothesis. in hyper-finite factors and dark matter hierarchy. in online book. available at: http://tgdtheory.fi/public_html/neuplanck/neuplanck.html# nuclstring, 2006. [8] pitkänen m. cold fusion again . available at: http://tgdtheory.fi/public_html/articles/ cfagain.pdf, 2015. [9] pitkänen m. more precise tgd based view about quantum biology and prebiotic evolution. available at: http://tgdtheory.fi/public_html/articles/geesink.pdf, 2015. [10] pitkänen m. about physical representations of genetic code in terms of dark nuclear strings. available at: http://tgdtheory.fi/public_html/articles/genecodemodels.pdf, 2016. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/hxbvfc7 https://www.youtube.com/watch?v=i-t7tcmudxu https://www.youtube.com/watch?v=i-t7tcmudxu http://science.sciencemag.org/content/352/6287/833 http://tinyurl.com/kxxc7db http://tgdtheory.fi/public_html/genememe/genememe.html#expearth http://tgdtheory.fi/public_html/genememe/genememe.html#expearth http://tgdtheory.fi/public_html/hologram/hologram.html#homeoc http://tgdtheory.fi/public_html/hologram/hologram.html#homeoc http://tgdtheory.fi/public_html/neuplanck/neuplanck.html#nuclstring http://tgdtheory.fi/public_html/neuplanck/neuplanck.html#nuclstring http://tgdtheory.fi/public_html/articles/cfagain.pdf http://tgdtheory.fi/public_html/articles/cfagain.pdf http://tgdtheory.fi/public_html/articles/geesink.pdf http://tgdtheory.fi/public_html/articles/genecodemodels.pdf introduction the first step: binding of dark protons to formamido-pyrimidine second step: could shock waves due to extraterrestrial impacts have produced rna bases? dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 01-21 1 pitkänen, m., homonymy of the genetic code from tgd point of view article homonymy of the genetic code from tgd point of view matti pitkänen 1 abstract peter gariaev and colleagues have applied the linguistic notions of synonymy and homonymy to genetic code. also the notion of syhomy fusing these concepts is introduced. homonymy is visible in mrna-trna pairing and induced by the 1-to-many pairing of the third mrna nucleotide with trna nucleotide. the homonymy in mrna-aa (aa for amino-acid) pairing is also present albeit rare. the codons for the standard code can be divided to two classes. for 32 codons the first two letters fix aa completely. for the remaining 32 codons this is not the case. there is however almost unbroken symmetry in that u and c resp. a and g code for the same aa. the breaking of this symmetry is minimal appearing only for 3 4-columns of the code table and present for a-g only. the deviations from the standard code as a rule break a-g or t-c symmetry or re-establish it. the notion of homonymy is highly interesting from tgd point of view. tgd leads to two basic proposals for non-chemical realization of genetic code predicting the numbers of dna codons coding for aa rather successfully. the first proposal relies on tgd based view about dark matter as heff/h = n phases of ordinary matter and identifies counterparts of dna, rna, tnra, and aas as entangled dark proton triplets. second proposal emerged from the model of music-harmony based on fusion of icosahedral and tetrahedral geometries. codons are represented as photon triplets (dark or ordinary) defining the allowed 3-chords of given harmony defined by hamilton cycle at icosahedron extended to hamilton cycle to the fusion of icosahedron with tetrahedron along common face. photon triplets give rise to resonant coupling giving rise to physical pairing of biomolecule and its dark counterpart. remarkably, there are 3 different realizations of trna in terms of 3-chords. there is large number of bio-harmonies corresponding to hamiltonian cycles. since music expresses and creates emotions, the proposal is that a realization of emotions at molecular level adding additional degrees of freedom not visible at the level of chemistry is in question. this might give rise to a context dependence of the code. the proposal is that genetic code at dark level extends to a sequence ddna → dmrna → dtrna → daa of horizontal pairings analogous to projections is fundamental one. codon-codon pairings are realized via dark photon triplet resonance and mrna-aa pairing by resonant coupling to the sum fxy z = f1 + f2 + f3 of 3-chord frequencies: the codons coding same aa would have frequencies fxy z differing only by a multiple of octave. one might perhaps say that aa sequence defines melody and mrna sequence the accompaniment. there is context dependence and homonymies already in dmrna-dtrna pairing and due the fact that dtrna corresponds to a 2-harmony which is subharmony of 3-harmony and can be chosen in 3 different manners. the vertical pairings ddna → dna, dmrna → mrna, etc. also mediated by frequency couplings induce ordinary genetic code and horizontal pairings in dna → mrna → trna → aa. daa → aa pairing dictates mrna → aa pairing and mrna → trna homonymy does not matter and actually makes the translation safer by increasing the number of trnas performing the same task. the rather rare homonymies in dna-aa pairing can be understood as accidental degeneracies. aa couples resonantly to the sum fxy z = f1 + f2 + f2 of frequencies associated with codon xyz and it can occur that the sum frequencies can be identical for two codons. keywords: genetic code, dna, rna, synonymy, homonymy, tgd. 1 introduction this article was motivated by the article of peter gariaev [7] about the linguistic notions of synonymy and homonymy applied to genetic code (for other works of gariaev and collaborators on the linguistic aspects 1correspondence: matti pitkänen http://tgdtheory.com/. address: rinnekatu 2-4 a8, 03620, karkkila, finland. email: matpitka6@gamail.com. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.com/ mailto:matpitka6@gmail.com dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 01-21 2 pitkänen, m., homonymy of the genetic code from tgd point of view of dna see [5, 4]). in another article by peter gariaev and ekaterina leonova-gariaeva to be published in open journal of genetics the notion of syhomy fusing these concepts is introduced. homonymy is visible in mrna-trna pairing and induced by the 1-to-many pairing of the third mrna nucleotide with trna nucleotide. the homonymy in mrna-aa (aa for amino-acid) pairing is also present albeit rare and might be explainable in terms of context dependence of this pairing. the article summarizes much what is known about the theoretically poorly understood role of the third nucleotide of mrna in the translation of mrna to aas. that many trnas correspond to same mrna synonymy is not surprising since the number of trnas is smaller than that of mrnas. there is however also homonymy present the third nucleotide of mrna can correspond to several trnas. if the aas associated with homonymous trnas are same, the is no homonymy in mrna-aa pairing. this is not quite always the case but the deviations are surprisingly small. the article emphasizes the fact that the codons for the standard code can be divided to two classes. for 32 codons the first two letters fix aa completely. for the remaining 32 codons there is almost unbroken symmetry in that u and c resp. a and g code for the same aa. this symmetry is broken only for the the three 4-columns of the code table containing stop codon or start codon coding also for met: this symmetry breaking is unavoidable given that the number of both start and stop codons is odd. this symmetry breaking is minimal and applies only to a-g whereas t-c symmetry is exact. for the deviations of the code from the standard code the deviation as a rule breaks a-g or t-c symmetry or re-establishes it. the notion of homonymy is extremely interesting from tgd point of view. tgd leads to two basic proposals predicting the numbers of dna codons coding for aa rather successfully. 1. the first proposal [15] relies on tgd view about dark matter as heff/h = n phases of ordinary matter [9, 11, 12][16, 17] motivated by adelic physics extending physics to include also the correlates of cognition [16] [17]. the empirical motivation comes from several sources, in particular from the findings of pollack [1] discussed in [14]. one can understand the formation of negatively charged regions exclusion zones (ezs) as being due to the transformation of part of protons to dark protons residing at magnetic flux tubes. dark genetic code would be realized in ters of dark proton sequences to be denoted by ddna, dmrna, dtrna, and daa would provide dark analogs of dna, mrna, trna, and aa. biochemistry would emerge as a shadow of the much simpler dynamics of dark matter at flux tubes and genetic code would be induced by dark code code. the dark code would be sequence ddna → dmrna → dtrna→ daa of pairings. 2. second model of genetic code emerged accidentally from a geometric model of music harmony [13] (see http://tinyurl.com/yad4tqwl) involving icosahedral (12 vertices-12-note scale and 20 facesnumber of aas) and tetrahedral geometries leading to the proposal that dna codons and possibly also aas correspond to 3-chords defining the harmony and obtained as unions of 20+20+20 3-chords associated with icosahedral 20-chord harmonies with symmetries z6, z4, z2 plus tetrahedral 4-chord harmony. there is large number of these harmonies bringing in additional degrees of freedom. remark: this model has obviously analogies with the notion of wave genome introduced by peter gariaev [2, 3, 6]. since music both expresses and creates emotions the proposal is that these harmonies assigning additional hidden degrees of freedom to the magnetic bodies of ddna, drna, etc... serve as correlates of emotions also at the molecular level. this emotional context could also give rise to context dependence of the code if several harmonies are realizable chemically. taking seriously tgd inspired theory of consciousness [18] and model of emotions [19] (see http://tinyurl.com/ ydhxen4g), one might say that the details of the code might depend slightly on the ”emotional” state of dna, rna, and possibly other molecules. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/yad4tqwl http://tinyurl.com/ydhxen4g http://tinyurl.com/ydhxen4g dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 01-21 3 pitkänen, m., homonymy of the genetic code from tgd point of view in the sequel i will consider the following proposal for the various pairings of dark dna and ordinary dna visualizable as a 2 × 4-matrix with two rows representing ddna, dmrna, dtrna, daa resp. dna, mrna, trna, aa. 1. the proposal is that genetic code at dark level extends to a sequence ddna→ dmrna→ dtrna → daa of horizontal pairings analogous to projections is the fundamental one, and realized via dark photon triplet resonance expect for the coupling to daa for which coupling is based on the sum fxy z = f1 + f2 + f3 of 3-chord frequencies. one might perhaps say that aa sequence defines melody and mrna sequence the accompaniment. the frequencies fxy z for codons coding same aa would be same modulo octave multiple. there is context dependence and homonymies already in dmrna-dtrna pairing and due the fact that dtrna corresponds to a 2-harmony as subharmony of 3-harmony and can be chosen in 3 different manners. also this choice perhaps by state function reduction could correlate with emotional state. 2. there are also vertical mappings ddna → dna, dmrna → mrna, dtrna → trna and daa → aa. these pairings would induce the horizontal pairings dna→ mrna→ trna→ aa at the chemical level. the homonymy at mrna-trna level would have no effects on dna-aa pairing. 3. apart from mrna-aa pairing all these pairings would be realized dynamically in terms of 3chords (f1, f2, f3) and giving rise to a resonant coupling between members of the pair connected by magnetic flux tubes to single dynamical unit carrying the dark photon triplets at the frequencies characterized by the 3-chord. the model for musical harmony [13] leading also to a realization of genetic code suggests the existence of a large number of harmonies. it is not however obvious whether these harmonies can be realized bio-chemically since the 3-chords must be resonance 3-chords for bio-molecules. for dna-aa and mrna-aa correspondence the constraints are the slightest ones since they couple to fxy z = f1 +f2 +f3: aas could have emerged in rather early stages of the prebiotic evolution. one cannot even exclude the possibility fxy z are same for different harmonies. slight chemical modifications of dna and mrna and aa analogous to wobbling for trna might allow to realize the slightly different collections of 3-chords defining the harmonies. 4. the model leads to an explanation for the homonymy of mrna → trna pairing as being induced by the mrna-trna homonymy realized already at dark level. the rather rare homonymies in dna-aa pairing can be understood as accidental degeneracies. aa couples resonantly to the sum fxy z = f1+f2+f3 of frequencies associated with codon xyz, and one can have fx1y1z1 = fx2y2z2 modulo octave multiple for two codons. daa coded by ddna codes for aa and trna serves only in the role of transferring daa-aa pairs and attaching them to dmrna-mrna pairs: the mrnaaa pairing would be determined completely by dark molecules. it is actually advantageous to have trna homonymy since it can happen that the concentration of particular certain kind of trna is low. 5. what distinguishes between dna and rna and between codons and anti-codons is not obvious in the harmonic model. the most plausible identification for the map mapping codons to anti-codons is reflection symmetry of the icosahedron permuting opposite faces. an internal reflection changing the orientation of the scale could map dna to rna: this makes sense if the chords can be regarded as arpeggios. 6. the vision of biological evolution as chemical evolution in which dark variants of genetic code gradually find biological representations suggests a concrete model for rna era. at that era aas would have catalyzed mrna replication possibly as non-faithful process. this era might have preceded trna era with mrna replaced with trna analog corresponding to to the fusion of two 20-chord representations. the era before this could have been era with single 20-chord representation and corresponding trnas and amino-acids. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 01-21 4 pitkänen, m., homonymy of the genetic code from tgd point of view 2 some background in the following i will discuss briefly the basic facts about genetic code at wikipedia level with emphasis on the poorly understood aspects of the code. 2.1 variations of the genetic code there exists also as many as 31 genetic codes (see http://tinyurl.com/ydeeyhjl) and an interesting question is whether this relates to the context dependence. mitochondrial codes differs from the nuclear code and there are several of them. the codes for viruses, prokaryotes, mitochondria and chloroplasts deviate from the standard code. as a rule, the non-standard codes break u-c or a-g symmetries for the third code letter. some examples are in order (see http://tinyurl.com/puw82x8). 1. uuu can code leu instead of phe and cug can code ser rather than leu. in bacteria the gug and uug coding for val and leu normally can serve as start codons. 2. uga can code to trp rather than stop: in this case the broken symmetry is restored since also ugg codes for trp. 3. there is variation even in human mitochondrial code (see http://tinyurl.com/puw82x8). in 2016, researchers studying the translation of malate dehydrogenase found that in about 4 per cent of the mrnas encoding this enzyme the uag stop codon is naturally used to encode the aas trp and arg. this phenomenon is known as stop codon readthrough (see https://www.ncbi.nlm.nih. gov/pmc/articles/pmc5133446/). 4. there is also a variant of genetic code in which there are 21st and 22nd aas sec and pyl coded by stop codons. uga can code for sec and stop in the same organism. uag can code for pyl instead of stop and introduces additional breaking of a-g symmetry for the third letter (uaa to stop and uag to pyl). 2.2 wobble base pairing wobble base pairing (see http://tinyurl.com/y73se8vs) emerges from the observation that the number of trnas pairing with mrnas is smaller than 45 and considerably smaller than that of mrnas. the needed minimum number of trnas is 32. therefore the rna-trna pairing cannot be 1-1 and some mrna codons must correspond to several trna codons. remark: one could ask whether mrnas code for trnas just like dnas code for aas. homonymy for mrna-trna pairing implies that the pairing can be many-to-1 only in given context. 1. according to the standard code, the first two bases of mrna codon corresponds to two last bases of trna anti-codon and obey standard code. wobble base pairing hypothesis applies to the pairing of the 3rd mrna base to the 1st base in trna anticodon. at the level of chemistry the hypothesis is that the position of the first trna anticodon base pairing with the third mrna base is variable and allows it to pair with several bases appearing as 3rd base in mrna. this homonymy would be due to ”wobbling” of the position of the first trna anticodon. 2. in the original model for wobble base pairing trna bases contain besides standard a, c, g, u also inosine i as a modification of g obtained by dropping nh2 from the 6-cycle of g. it has turned out that there are actually variants of c and 5 variants of u (see http://tinyurl.com/y73se8vs). the large amount of homonymy for trnas forces to ask whether chemistry alone really dictates the genetic code. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/ydeeyhjl http://tinyurl.com/puw82x8 http://tinyurl.com/puw82x8 https://www.ncbi.nlm.nih.gov/pmc/articles/pmc5133446/ https://www.ncbi.nlm.nih.gov/pmc/articles/pmc5133446/ http://tinyurl.com/y73se8vs http://tinyurl.com/y73se8vs dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 01-21 5 pitkänen, m., homonymy of the genetic code from tgd point of view 3. the first trna letter is assumed to be spatially wobbling so that the association of trna with rna is not unique and mrna-trna pairing involves both synonymy and homonymy as the two tables for the pairing of the 1st 5’ anticodon base of trna and 3rd 3’ codon base of mrna show. in the second column bold letters for mrn bases allow to read the standard pairing with trna codons in the first column and non-bold letters allow to deduce the non-standard behavior. 4. the first table (see http://tinyurl.com/y73se8vs) represents the original watson-crick proposal. (a) the pairings of the 3rd letter of mrna codon to the 1st letter of trna anti-codon are following. • u → g. • g → u • {a, c or u} → i. the 2nd and 3rd trna letters a and c are paired with the 1st and 2nd mrna letters in the canonical manner. there are only 3 trna letters, which implies that the number of trnas is smaller than maximal. (b) there is single 1-to-many pairing: u→ {g, i} giving rise to 2-fold homonymy. 5. revised pairing rules (see http://tinyurl.com/y73se8vs) are more complex since the number of trna bases is larger (u has 5 variants and c has 2 variants). all mrna letters have 1-to-many pairing. even if one counts the variants of u as single u there is 4-fold homonymy for u and homonymies for other codons. for a one has 9-fold homonymy. these variations do not induce variation in dna → aa pairing if the aa associated with the homonyms of trna are identical. this seems to be the case almost always since the variation of the genetic code is surprisingly small. this raises the question whether there is some mechanism eliminating to high degree the expected effects of homonymy in mrna→ trna pairing. 3 two tgd based realizations of genetic code during years i have considered several visions about genetic code. two of them have allowed to build concrete contacts with the empirical reality. they are realized in terms of dark protons sequences [15] and in terms of 3-chords of bio-harmony [13]. 3.1 dark realization of genetic code the first tgd view about this is based on the dark realization of the genetic code [15] (see http: //tinyurl.com/jgfjlbe). this relies on general vision that dark matter and magnetic flux tubes magnetic body (mb) controls the biochemistry and that biochemical realization need not be complete. 1. tgd proposal is that dark proton sequences dark nuclei at magnetic flux tubes parallel to dna strands provide the fundamental realization of the genetic code. dark proton triplets would represent the analogs of dna, mrna, trna, and aas. there would be 64 ddnas, 64 dmrnas, 40 dtrnas and 20 daas. dark codon cannot be separated to a product of letters but is an entangled state of 3 dark protons. there is a linguistic analogy: in primitive languages entire words are holistic basic units having no decomposition to letters. 2. ddna, dmrna, dtrna, and daa would control their biochemical variants and would be associated flux tubes carrying dark proton sequences. dark code would dictate what happens at the chemical level. chemistry would be a shadow of dark dynamics. transcription and translation would take place at dark level. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/y73se8vs http://tinyurl.com/y73se8vs http://tinyurl.com/jgfjlbe http://tinyurl.com/jgfjlbe dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 01-21 6 pitkänen, m., homonymy of the genetic code from tgd point of view one can argue that this assumption is too strong. it requires that also the stop codon codes for daa and this in turn requires at the level of chemistry to an analog of trna attaching to the stop codon. for standard realization of the genetic code there are indeed 2 release factors rf1, rf2 which are proteins not involving rna (see http://tinyurl.com/ydcgnlb3) attaching to stop codons and stopping the translation. rf1 recognizes uaa and uag. rf2 recognizes uaa and uga. there is also release factor rf3 binding to gtp (not appearing in rna) and leading to a dissociation of rf1/rf2 after peptide release. therefore rf3 does not play a role of trna. note that both release factors recognize uaa so that the map from rna codon to release factor is 1-to-2. the 1-to-many character of mrna-aa association requires hidden degrees of freedom for ddna affecting the genetic code by changing daa → ordinary aa pairingat the level of chemistry. 3. if there is no homonymy at the dark level, one would have the following picture to start with. remark: one could of course ask whether the dark variants of the 3 codes unique are there several dialects possible already at this level. the degeneracies of dark codons coding for dark codon at lower levels down the ladder dna-mrna-trnaa-as are unique but how many codes satisfying this condition are possible? in the sequence dark code is however assumed to be universal. (a) dark genetic code decomposes to a sequence of three many-to-one codes without context dependence/homonymy: ddna → dmrna, which is 1-to-1, dmrna → dtrna, which is 64-to-40 and dtrna → aa, which is 40→ 20. (b) chemical representation of dark variants of biomolecules is induced by the dark-chemical pairing, which can be context dependent to some degree. this in turn would induce context dependence of mrna-trna pairing and possibly trnaa-a pairing and as a consequence also that of mrnaa-a pairing. it is important to notice that the dx-x pairing involves transformation of dark photons to ordinary photons. the proposal is that the ordinary photons are bio-photons with much higher frequencies. the transition reducing the value of heff/h = n would allow energy preserving transformation of extremely low frequency photons with large n and to bio-photons inducing molecular transitions. remark: mrna-aa correspondence is basically induced by daa → aa correspondence. (c) one could say that there are several dialects each free of homonymies in their own context. even the genes or the two strands of dna might speak different dialects. what could be the quantum physics behind these dialects? at which level one can find the contexts causing the dialects? in tgd framework magnetic body (mb) carrying dark matter suggest itself. one can ask whether ddna and drna, and maybe dtrna and daa could have a context defined by internal degrees of freedom, which varies in the situation when same dna/rna codes for 2 different aas or aa and stopping sign. magnetic body (mb) would naturally give rise to these new integral degrees of freedom. 3.2 the notion of magnetic body carrying dark matter and resonance as a mechanism of pairing pairing is the basic mechanism of molecular biology appearing in dna replication, translation, and transcription. pairing could be based on resonance coupling by dark photons propagating along magnetic flux tubes connecting the pairing systems. the pairing between ddna and dmrna and ddna and ordinary dna would rely on resonance. more generally both dark and ordinary variants of the basic biomolecules would be characterized by collections of frequencies and if the frequencies are same the objects pair with each other. the 3-letter structure of the genetic codon suggests that resonance coupling occurs simultaneously for 3 frequencies defining the 3-chord. the pairing objects able to pair must be characterized by same the 3-chord. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/ydcgnlb3 dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 01-21 7 pitkänen, m., homonymy of the genetic code from tgd point of view 1. ddna, mrna, trna, and aas would pair horizontally. these horizontal pairings together with vertical pairings of dark molecules to their ordinary counterparts (ddna →dna, dmrna → mrnadtrna → trna, daa → aa would induce the horizontal pairings of dna, mrna, trna, and aas. 2. all these pairings would rely on resonant coupling and the structure of codons suggests that 3-chords of frequencies are involved. 3. the first idea was that there is no context dependence at the level of horizontal pairings. it turned out that there are naturally 3 different dmrna-dtrna pairings for a given harmony for mrna. this induces context dependence at the level of chemistry and would due to variation of the collection of 3-chords characterizing dtrna. 3.3 the geometric model for music harmony and genetic code for some years ago i developed a model of music harmony [13] (see http://tinyurl.com/yad4tqwl), which should define map of dark codons to 3-chords represented as dark photon triplets and defining allowed 3-chords of music harmony (music of light and perhaps also of sound). the appendix provides the tables describing the details of the harmonies. 1. the model of music harmony is separate from the model of genetic code based on dark proton triplets and one of the challenges has been to demonstrate that they are equivalent. the model relies on the geometries of icosahedron and tetrahedron and representation of 12-note scale as so called hamiltonian cycle at icosahedron going through all 12 vertices of icosahedron. the 20 faces correspond to allowed 3-chords for harmony defined by given hamiltonian cycle. this brings in mind 20 aas. single step of hamiltonian cycle connecting vertices of a face of icosahedron (triangle) is assume to correspond to a scaling of the frequency by factor 3/2. this leads to a problem since 12 scalings of this kind does not quite given 7 octaves which reduced octave equivalence to the basic octave would give 12-note scale. the solution is to add single notice slightly differing from 7 octaves and represented as vertex p of a tetrahedron glued to icosahedron along face. the hamilton cycles are deformed so that they begin and end from this vertex. this also gives the missing 4 dna codons realized as 3-chords and also defines unique ground note for the scales. 2. it turns out that has three basic types of harmonies depending on whether the symmetries of icosahedron leaving the shape of the hamiltonian cycle is z6, z4 or z2. for z2 there are two options: z2,rot is generated by rotation of π and z2,refl by reflection with respect to a median of equilateral triangle. combining together one harmony from each type one obtains union of 3 harmonies and if there are no common chords between the harmonies, one has 20+20+20 3-chords and a strong resemblance with the code table. to given aa one assigns the orbit of given face under icosahedral isometries so that codons correspond to the points of the orbit and orbit to the corresponding aa. 4 chords are however missing from 64. these one obtains by adding tetrahedron. one can glue it to icosahedron along chosen face or keep is disjoint. the model predicts a highly unique and realistic model for numbers of dna codons coding for a given aa. the model in its original form predicts two codes and also explains the fact that there are two additional aas pyl and sec that appear as end-products. 3. the model in its original form predicts 256 different harmonies with 64 3-chords defining the harmony. dna codon sequences would be analogous to sequences of chords, pieces of music. same applies to mrna. since music expresses emotions and produces them, the proposal is that these issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/yad4tqwl dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 01-21 8 pitkänen, m., homonymy of the genetic code from tgd point of view harmonies correspond to different molecular emotional states. the fundamental realization could be in terms of dark photon triplets replacing phonon triplets for ordinary music. geometrically the two codes can be described as attachment of tetrahedron to icosahedron along face or as union of the two. icosahedron corresponds to 60 dnas and tetrahedron to 4 dnas. during writing of this article i learned that the number of harmonies could be different, probably larger. there is however the question of the chemical realizability of the harmony: it is not at all clear whether there exist biomolecules to which the 3-chords of several harmonies could couple resonantly. 4. as i developed the model of bio-harmony [13] (see http://tinyurl.com/yad4tqwl) it did not occur to me that also the trna part of the dark code should have counterpart in the icosahedral model. aas correspond to single 20-codon code, dna and rna to union of 3 20-codon codes with symmetries z6, z4 or z2: here z2 would correspond to z2,rot or z2,refl and this would give to two two different codes. could trna correspond to a union of 2 20-codon codes? combining only 2 20-codon codes with 40 codons and tetrahedral code with 4 codons would give maximally 44-letter code and the upper bound for trnas is according to wikipedia 45! dark proton model predicts 40 dtrnas suggesting that only the 40 isosahedral codons contribute to dtrna code. the additional trnas could result from homonymy. the code sequences could be seen as a hierarchical sequence 3 → 2 → 1 in this framework. an important implication is that there are many realizations of dtrna and trna harmony: (z6, z4), (z6, z2), (z4, z2) and z2 could be either z2,rot or z2,refl. this could explain the homonymy of mrna-trna pairing via difference in the chords in turn affecting biochemical counterparts. note however that the chords for trna must be a subset of chords for mrna so that rna harmony determines trna harmony apart from the three choices (z6, z4), (z6, z2) or (z4, z2) giving rise to 3 different contexts. if daas code by 3-chords the aas then this choice does not affect aas. 3.3.1 what conditions pairings pose on the frequency triplets? the realization of ddna-dtrna and ddna-daa pairings in terms of frequencies must involve a loss of information since the correspondence is many-to-one. 1. for dna-mrna pairing information is not lost and the pairing must be of form (f1, f2, f3) → (f1, f2, f3). note that the frequencies cannot be associated with the letters. it is however possible to consider the assignment of (f1, f2) to the first letter pair xy as a whole and f3 to the third letter z. 2. for ddna-daa and dmrna-daa pairing the natural hypothesis is (f1, f2, f3)→ f1+f2+f3. aa couples to the sum of the frequencies of the triplet. the simplest possibility is that the f1 + f2 + f3 is same for all codons coding for given aa. one might say that aa sequence defines melody and mrna sequence the accompaniment. if the sums for codons coding given aa are different they must couple resonantly to it. if there are several harmonies the sum must same for all realizable 3-harmonies or all chords of 3-chord harmonies coding for same aa couple to it resonantly. since one has linear 1-d structures one might ask whether frequency differences coming as multiples of lattice frequencies are allowed. second natural possibility is octave equivalence. mrna-aa pairing would take place directly rather than with the mediation of of trna. 3. in the case of dmrna-dtrna pairing one one does not lose so much information since the number of dark dnas is 40 (as also the 3-chords if tetrahedron does not contribute). one must remember that trnas are pairs of rna like codons call them rnat, and aas. therefore there pairing issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/yad4tqwl dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 01-21 9 pitkänen, m., homonymy of the genetic code from tgd point of view involves also the pairing mrna-aa give by (f1, f2, f3) → f1 + f2 + f3 and guaranteeing that the code is realized by this pairing alone irrespective of mrna-rnat pairing. at chemical level the first to mrna codons pair with trna anticodons according to the standard rules. could rnat have completely passive role in carrying the aa? this cannot be the case since the last two letters of rnat couple in standard manner to the first two letters of mrna. remark: trna is analogous to melody + accompaniment using one of the 3 possible 2-harmonies for a given 3-harmony. suppose that mrna-rnat pairing corresponds to 3 possible choices of 2-harmonies as sub-harmonies of 3-harmony. this would suggest these different sub-harmonies define maps (f1, f2, f3)→ (f1, f2, f3) such that rnat pairs only with two sub-harmonies. for each choice rnat would correspond effectively to 40 sub-codons of the entire code (forgetting the tetrahedral part giving 4 additional codons). the three different realizations of the projection would give rise to the homonymy. also the aa-trna coupling would come out correctly. daas would be different in the sense that they couple only to the sum of the frequencies. this is in accordance with bio-harmony in which aas correspond to orbits of 3-chords for dna under isometries rather than single 20-chord harmony. the coupling to the sum of frequencies is in accordance with the quantal interpretation as 3-dark-photon state whose energy is e = heff (f1 + f2 + f3) and couples to aa chemically via the transition to ordinary photons with the same energy. this leaves some questions. 1. could one consider the possibility that the chords of one of the 20-chord harmonies corresponds to aas? there would be 3 basic types of aas. this does not look plausible and the association of aas with the orbits of 20-note chords is more natural and fits nicely with f = fxy z picture. 2. it would be nice to assign notes to the individual letters of codons. this is not possible since codons with 2 or 3 identical letters would reduce to 2-chords or 1-chords. it is also impossible to assign frequencies with letters at dark level since letter decomposition does not exist. thus the 3-chord has resonant interaction with the entire codon. 3. the symmetries of the genetic code however suggest that it might make sense to treat the first two letters xy of the codon as a single unit and the third letter as separate single unit. could one assign to xy a 2-chord not reducible to frequencies for the letters x and y, and to letter z its own frequency. the frequencies of a,g, t,c as third letter must be different. four 32 codons of standard code the aa would not be sensitive to the frequency of z: this is possible if these frequencies are resonance frequencies of the same aa. for the remaining 32 codons the aa would not distinguish between frequencies of t and c resp. a and g so that the two frequencies would be both resonance frequencies of the corresponding aa. 3.3.2 probabilistic estimates for single 20-chord harmony one can make first some naive probabilistic estimates about single 20-chord harmony. 1. given 20-chord harmony makes 20/220 = 1/11 ' 9 per cent about al possible 3-chords. three 20 chord harmonies would make 3×9 = 27 per cent about all possible 3-chords if there are no common chords so that the optimistic expectation might make sense. of course, one cannot exclude the possibility that there are also triplets of 20-codon codes which gives smaller number of codons. 2. the total number of chords with different notes is 12× 11× /3! = 220. bio-harmony has 64 chords corresponding to faces of icosahedron: this is about 64/220 making 29 per cent of all possible 3chords with different notes. given bio-harmony thus throws out roughly 2/3 of all possible codons. this should be easy to test. for instance, does given gene correspond to a fixed bioharmony? or issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 01-21 10 pitkänen, m., homonymy of the genetic code from tgd point of view does even entire genome do so. if bio-harmony is realized for non-nuclear genomes, it must satisfy rather strong constraints. 3. given 20-chord harmony corresponds to 12 edges. each edge is shared by two adjacent triangles. if all 20 triangles would contain just single face, there would be 24 triangles altogether. therefore there must be triangles containing two subsequent edges of the cycle. each triangle of this kind reduces the number of 24 neighbours by 2 units. hence it seems that one must have at least 2 triangles with 2 edges at the cycle (two quints in the 3-chord). if there are more than 2 triangles of this kind, there must be triangles having no edges along the path. each vertex of icosahedron is shared by 5 triangles and there are 5 edges starting from it. 4. the notion of hamilton cycle generalizes to any graph and magnetic flux tube networks define such graphs as tensor networks. why only icosahedron? could one consider the possibility that any tensor network is characterized by harmonies characterize by hamiltonian cycles and that one could assign some kind of codes with the combinations of these cycles? in the general case symmetries would be absent so that the notion of code in the proposed sense would fail: one could not identified codons as points at orbits of symmetry group. rather, one can imagine that the notion of code could be defined quite generally in terms of orbits as aas and points at them as dnas coding them. for regular polygons in any dimension the symmetries are present and one could define the notion of code and also fuse the codes. for arbitrary tensor network the faces need not be symmetry related and one can also have faces that can be interpreted as higher-dimensional polytopes. one can also ask whether the icosahedron is realized physically. icosahedral geometry is indeed very common in biology. could the fusion of icosahedral and tetrahedral geometries have some concrete realization at molecular level? 3.3.3 is the maximal number of codons for the fusion of 3 20-codon codes possible? it has not earlier occurred to me to wonder whether the chords associated with the 3-different icosahedral harmonies giving 20 codons each correspond to 20+20+20=60 different chords as assumed. could there be common 3-chords? this question could be answered by studying the hamiltonian cycles at icosahedron. remark: perhaps more important constraint than absence of common chords is the chemical realizability of the codes. if same mrnas and dnas realized different bio-harmonies then they must be able to respond resonantly to several 3-chords. one can make naive probability estimates for a pair of codes to allow the maximal number of 60 codons. it seems natural to assume that the isometries of icosahedron (or their subgroup) can be applied separately and only the isometries acting on both in similar manner are symmetries. the situation would be the same as in the case of many-particle system: only the translations acting on all particles simultaneously remain symmetries and relative translations cease to be symmetries. with this assumption the icosahedral group gives a large number of code pairs. for the fusion of 3 20-codon codes giving dna/rna the number is even higher. by choosing suitably the relative isometries it might be possible to obtain the maximal number of 60 different codons for the icosahedral genetic code. on the other hand, by a suitably choice of relative isometries one might have undesired common 3-chords. in any case, the earlier estimate 256 for the number of bio-harmonies [13] suggested to correlate with ”emotional” states of the basic biomolecules is expected to change. before going to estimates one must consider some delicacies related to the notion of 12-note scale as hamiltonian cycle. 1. one can regard the cycles as purely geometric objects without orientation or assign to them orientation. for two different orientations the scales would run in opposite directions as scalings by 3/2 along single edge of the cycle. if two codes have common edge, the scaling must be same along it. if the orientation of the second cycle is changed, the common edge ceases to be common. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 01-21 11 pitkänen, m., homonymy of the genetic code from tgd point of view 2. the basic note of the 12-note scale at cycle can be chosen arbitrarily: this corresponds to the choice of the key in music (one could of course argue that the key does not make sense in 12-note scale if one has tempered scale with notes comes as powers of 21/2 scaling of ground note rather than pythagorean scale with rational ratios of notes). the fusion of tetrahedron to icosahedron selects one particular triangular face and brings in one additional vertex outside the icosahedron, call it p . it would be natural to assign the ground note as p . the isometries not affecting p would correspond to those of icosahedron leaving the common face invariant and isometries of tetrahedron leaving p un-affected and continuable to icosahedral isometries. one would have subgroup of icosahedral group as allowed isometries acting on the cycles to be fused. 3. if one assigns note sequences to the cycle by quint rule, cycles c1 and c2 can have common triangle in geometric sense but if the distances of the vertices a,b,c of the triangles from p measured as the number of edges of cycle portion connecting them are not same along c1 and c2, the triangles correspond to different chords and are thus orthogonal in the proposed description as many-fermion states. 4. to sum up, the states associated with triangles would be characterize by the position of triangle (20 values), by the notes of the triangle characterized by the distances from p , and the number 0, 1, 2 of the edges belonging to the cycle and should make easier to find ortogonal basis. again one can make probabilistic estimates: cycles are treated as purely geometric entities without orientation and without assignment of notes to the triangles. 1. given cycles c1 and c2 what is the probability that they have at least one common edge as purely geometric entities without the sequence of notes? there are 30 edges so that given edge is shared with probability 1/30. if the edges of cycles were chosen randomly (certainly not true), the probability of having a common edge for two cycles would be p (1) = 12/30. the assumption of note sequence reduces this probability dramatically. 2. by the above estimate each cycle contains at least two triangles with 2 edges at the cycle with minimal angle between them. one can call these these edge pairs v-corners. assume that for cycle c1 one has v-corner abc at vertex a, call it v1,a. what is the probability that one one of the v-corners of c2 is located at a co-incides with abc. the probability of v-corner of c2 to locate at a is 1/12 and the probability that the edge of c2 from b is bc is is 1/4 so that the probability of having common v-corner is 1/48. if c2 contains n v-edges the probability is naively n/48. this estimate takes into account only geometry. the situation changes if one assumes that the cycles are oriented. in this case one can have common v-corner if the local orientations of c1 and c2 are opposite at the v-corner. if one assumes that the external vertex p of the tetrahedron defines the ground note then the number of edges connecting p to a defining distance d(p,a) must be same for c1 and c2. 3. given c1 and c2 (and vertices a with same distance d(p,a)) it might be possible to perform suitable isometry for c2 that there is common v-corner. therefore not all possible combinations of three code types allowing relative isometries need not maximal number of 3-chords. remark: an interesting question is whether these can be allowed meaning that some codons are missing in the chemical realization of the dark codons in terms of ordinary dna codons. also the 1-1 pairing between dark dna and and dark rna would not be 1-1 if mediated by 3-chord resonance and one would have homonymy. this suggests that only codes without common chords can be allowed. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 01-21 12 pitkänen, m., homonymy of the genetic code from tgd point of view 4. what about chords having 1 edge at cycle for two cycles c1 and c2? let the edge be ab. as found, the naive probability for this is p (1) = 12/30. both cycles must go through the third vertex c of the triangular face. the subsequent notes along cycle differ by a quint that is scaling of the frequency by factor 3/2. notes are same if the numbers of the needed quints are same for c1 and c2 for c1 the number nb > 1 of quints is known. in the approximation that possible portions of c1 represent n-step non-self-intersecting random walks from b to c, one must estimate the number of all non-self-intersecting n-step-paths from b to c and find what is the number of the paths leading to c. one can go from a to c with na steps and similar estimate applies. 5. the third possibility is that the one has 3 common vertices a, b, c forming a triangular face such that neither cycle contains any of its edges. the cautious conclusion is that it is plausible that one can find 3 cycles having no common chords if one allows relative rotations of the cycles and that this condition is necessary for realizing the absence of homonymies at dark level. the automatic orthogonality of the hamiltonian cycles cannot be excluded but would allow also codes with codons containing more than 3 letters so that one could have kind of superdna. whether they can be realized chemically depends on whether there are biomolecules resonating with the the n frequency triplets involved. octave equivalence for frequencies might give hopes about chemical realization of several harmonies. therefore the evolution might be seen as gradual emergence of molecules able to pair with ddna and one can even imagine artificial evolution by tailoring the frequencies involved (maybe cyclotron frequencies). 3.3.4 could harmonies form a hilbert space the condition that there are no common 3-chords brings in mind orthogonality and suggests that harmonies as hamiltonian cycles could be defined as quantum states in suitable hilbert space. 1. one could define inner product for hamiltonian cycles as the number of common chords suitably normalized so that the norm of cycle of cycle equals to one. the number of common chords in the norm squared is 20 in the icosahedral case and 24 for the fusion of icosahedral and tetrahedral codes. could hilbert space picture for cycles make sense? the fusion of 2 (trna) or 3 (dna) codes does not however naturally correspond to quantum superposition but rather tensor product. 2. could one think that each cycle correspond to a 20-fermion product state with 3-chord characterizing the state of given triangle created by fermionic oscillator operator so that product p of 20 fermionic oscillators assignable to the triangles would create the harmony? the fusion of cycles c1 and c2 would be obtained by product p1p2. by fermionic statistics the resut would be zero if there are common cycles. these considerations are purely formal and have no implications for what follows. 3.4 how the symmetries of the model of harmony could relate to those of the genetic code? genetic code has surprisingly strong symmetries. i have discussed a possible interpretation of these symmetries using analogies with particle physics and considered also a mechanism explaining their emergence earlier [8, 10]. the proposal was that 3-letter code emerged as a fusion of 2-letter code with 16 codons and 1-letter coded with 4 codons. in the recent framework, a more natural option is that the third codon of 3-letter code was originally passive and became active via symmetry breaking distinguishing first between uc and ag pairs and later between u and c resp. a and g. note that for the standard code the breaking is minimal and caused by odd number of start and stop codons. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 01-21 13 pitkänen, m., homonymy of the genetic code from tgd point of view 1. for vertebrate code one half of codons has very high symmetry in the sense that the two first letters dictate the aa for 32 cases. exception is uuu, which codes for phe or leu for some modifications of the standard code. uuu → leu means breaking of maximal symmetry. 2. there is also a second symmetry, which i have referred to as isospin symmetry. it is only slightly broken. for general codons xyu and xyc code for same aa as also xya and ad xyg. for the standard code this symmetry is broken only in columns containing initiation codon or stop. the start codon aug codes also for met. uga and ugg code for stop and trp. for the remaining codons one has slightly broken”isospin symmetry”. the breaking of isospin symmetry is minimal for vertebrate code. the modifications of the code tend to break the isospin symmetry and even the maximal symmetry of 32 codons. this must be important. if the model of genetic code based on music harmony [13] is correct, the symmetries for the model of music harmony must relate to those of genetic code. 1. how the symmetries of the genetic code relate to the symmetries of icosahedron (60-element group) and tetrahedron (permutation group s4 with 24 elements) in the model of bio-harmony? icosahedral symmetry group has 60 elements and has sub-groups z2, z4, z5, z6 = z2z3. note that there are two z2:s having rotation by π and reflection as generators. the gluing of tetrahedron to icosahedral along single face reduces its group of symmetries to s3 leaving the point p not belonging to icosahedron invariant. s3 has as subgroups reflection group z2,refl and z4 consisting of rotations. 2. what is the counterpart for maximal symmetry in icosahedral and tetrahedral groups? do the 3-chords for codon xyz decompose to two-chord characterizing xy and a note characteriing z= a,u,c,g, which can depend on xy. the symmetry relating uc pair and ac pair could correspond to z2,refl reflection symmetry, which is shared by icosahedral and tetrahedral groups. for 32 icosahedral codons the action of z2,refl × z2,rot would be trivial so that aa would not depend on the third letter at all. for most of the remaining codons the action of the symmetry group on icosahedral codons would reduce to z2,rot permuting the third letters u and c resp. a and g. at the level of frequencies the sums of frequencies for codons coding for the same aa sould be same modulo octave equivalence. the addition of tetrahedron brings in 4 tetrahedral codons with one of them shared with icosahedron. icosahedral z2,rot does not make sense for these codons. intriguingly, there are 4 codons in vertebrate code which break isospin symmetry aua and aug coding for i and met/start and uga and ugg coding for stop and trp. if these codons correspond to the tetrahedral codons which cannot have z2,rot as isospin symmetry, the breaking of z2,rot would follow from the breaking of symmetry induced by the attachment of tetrahedron to icosahedron. 3.5 what distinguishes between codons and anti-codons and between dna and rna? the icosahedral model should provide answer to several questions not considered yet. 1. the model for the genetic code in terms of dark proton sequences both dna and rna are predicted. this should be the case also in the icosahedral model. the 3-chords for dna and rna should be the same but there should be some inherent distinction between the two realizations. 2. besides the active dna strand there is also the inactive dna strand (no transcription to mrna) consisting of anti-codons. what does anti-strand correspond in the representation consisting of 3-chords? the chords assignable to the anti-strand should exist but there should be some difference between chords and anti-chords. why this strand is inactive? mrna is produced only via the issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 01-21 14 pitkänen, m., homonymy of the genetic code from tgd point of view pairing of rna codons with active dna strand. could rnat as part of trna and counterpart of anti-rna be unable to form stable strands in the recent biological environment and could lonely rnat codons fail to exist stably so that the transcription of dna anti-strand to rnat strands would be impossible. 3. what does anti-dna anti-rna and anti-trna mean at the level of dark proton sequences? i have approached these problems from particle physics point of view by using analogies and they might be helpful in the attempts to answer these questions [10]. there are two mirror symmetries in the icosahedral harmony: 3-d reflection with respect to origin and change of the direction of the 12-note scale. could these reflection symmetries help to understand the situation? 1. the symmetry mapping letters to antiletters (t ↔ a, g ↔ c) is mirror symmetry like chargeparity symmetry cp of particle physics equivalent with time reversal t by cpt theorem. cp is mysteriously broken: we have matter but where is the antimatter? the biological analogy with matter-antimatter asymmetry is that strand is active but anti-strand is passive no transcription to mrna. this would be the case if anti-rna does snot exist as stable sequences. this would also explain why rna does not replicate and does not form stable double helices. 2. codons and conjugate letters for dna are related by the cp like transformation (t ↔ a, g ↔ c). there should exist an icosahedral symmetry realizing this symmetry. icosahedron allows also 3-d reflection through the origin as a symmetry (see http://tinyurl.com/y8capjz7). it permutes the opposite faces of icosahedron and extends the icosahedral rotation group with 60 elements to a group with 120 elements. the extended symmetry should preserve the set of 3-chords: they should be identical for dna codon and anticodon. harmony and anti-harmony for dna would differ in that the attached tetrahedron would be at opposite face for the anti-codon representation since the reflection maps the tetrahedron to the opposite face. could one see this as an analog of matter antimatter asymmetry? for double dna strand anti-codons would correspond to icosahedron with tetrahedron attached to the opposite face. this symmetry should map the codons to their anticodons and there should be no fixed codon this is indeed the case since there are no fixed faces. icosahedral reflection should however leave the chords invariant apart from transponation by some power of 3/2 in order to leave the harmony invariant: codons and anticodons would be in different key in order to resonate. icosahedral reflection would be an additional symmetry of the hamiltonian cycles. the tetrahedron attached to the opposite face in reflection would be shifted back in transponation. mrna should have icosahedral realization with same 3-chords. what distinguishes mrna from dna at icosahedral level? could only mrna exists as stable sequences and anti-mrna fails to exist in this manner? this would be analog of cp breaking and the codons rnat in trna would correspond to anti-rnat existing only as single codon attached to aa. could also the 4 tetrahedral anticodons for rnat (anti-trna) fail to exist (this would give 40 trna codons as also dark proton model predicts). otherwise one would have 44 rnat codons. dna and mrna differ only in single aspect: the letter t is replaced with letter u. how the replacement of u→ t (and the replacement of riboses with de-oxy-riboses) is visible in the icosahedral harmony if the set of chords remained the same? why rnas would have resonant 3-chord coupling with the dark variant of rna but not with that of dark variant of rna if the chords are same. could the order of notes along the hamiltonian cycle distinguish between dna and rna? the chords would remain the same but the order of notes in the chord would change. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/y8capjz7 dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 01-21 15 pitkänen, m., homonymy of the genetic code from tgd point of view 1. if the reversed scale proceeded downwards in quarts (quint backwards, say c-g to c-g), the 3-chords would be same for the scales and the two scales are identical. could one imagine that 3-chords are ”played” as arpeggios! the order of arpeggio (upwards downwards in scale) would be opposite for up-chord and down-chord. rnat would define down-chords for mrna up-chords but they would not form stable sequences and 4 anti-chords might be even missing. 2. if it proceeds in quints, the chords for the harmonies would not be same in general (for instance c-g upwards quint is replaced with c-f downwards quint). the scalings (3/2)k are replaced by scalings (3/2)12−k and the cycle becomes mirror image retaining its shape so that it is still a cycle and since the shape is preserved the symmetries are preserved too. chords are in reflected positions and related by the map (k1, k2, k3)→ (12− k1, 12− k2, 12− k3). the chords are obviously different so that dna and mrna cannot differ in this manner. the scale and its quint-reversed counterpart differ much like major and quint scales as one easily finds (consider only the upwards scale cmajor scale cdefg... in c major and the downwards cminor scale cb[a[g...). they could therefore correspond to two different moods rather than mrna-rna. 3. tgd and tgd inspired theory of consciousness bringing observer part of physical system relies on zero energy ontology (zeo). in zeo the scale and its quint reversal could correspond to two different arrows of time for zero energy states. as self dies in state function reduction to the opposite boundary of causal diamond (cd), it is predicted to reincarnate with reversed arrow of time [18]. death is a sad event: could it be that the death of sub-self representing mental image is experienced by self as sad event and that in bio-harmony time reversal would change joy to sadness? this relates in an interesting manner to the earlier speculations in tgd inspired view about pre-biotic life. 1. the proposal made in [10] is that during rna era preceding dna era rna replicated and aas associated with pre-trna served as catalyst and later stole the stage so that rna replication became translation. the greatest betrayal in the history of life! at this moment also dna had to emerge. otherwise rna and life would have disappeared. amusingly, also in cosmology cp symmetry was broken, when antimatter and matter annihilated and what remained was matter (there was slight imbalance originally). 2. could one think that before the breaking of the analog of cp symmetry the tetrahedral part of the code was not present and the number of mrna codons was 60. mrna and anti-mrna realized as mrnat had common chords related by icosahedral reflection symmetry. also the 1st letter of mrnat was just like the other letters. in the transition a and c as 1st letters disappeared and were replaced with g,u and i (in watsoncrick scenario). the 4 tetrahedral codons containing start and stop codons emerged in the transition. in the symmetry breaking dna with opposite direction of the scale (the reversed scale proceeded downwards as quarts rather than quints) and arpeggios emerged. perhaps this required the replacement of u with t and perhaps also of riboses with de-oxy-riboses. 3. was the letter mrna letter u replaced with dna letter t in this transition. did this make possible the existence dna as double strands but not stable as single strands but only in presence of cell membrane. did the 4 additional tetrahedral codons responsible for the breaking of the analog of isospin symmetry (a ↔ g and t ↔ c) associated with the stop and start codons emerge in this transition. before the transition the entire mrna strand was able to replicate. mrna-aa pairing was present and aa served as a catalyst for replication. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 01-21 16 pitkänen, m., homonymy of the genetic code from tgd point of view 4. did the 4 additional tetrahedral codons responsible for the breaking of the analog of isospin symmetry (a ↔ g and t ↔ c) associated with the stop and start codons emerge in this event so that 60-codon realization of the code was replaced with 64 codon realization. if start and stop emerged in this event the entire mrna strand replicated before it. 5. was the letter mrna letter u replaced with dna letter t in this transition. did this make possible the existence dna as double strands stable in the presence of nuclear or cell membrane but not stable as single strand. did the 4 additional tetrahedral codons responsible for the breaking of the analog of isospin symmetry (a↔ g and t↔ c) associated with the stop and start codons emerge in this transition. before the transition the entire mrna strand would have been able to replicate. mrna-aa pairing was present and aa would have catalysed the replication. 6. was the homonymy present in mrna replication before the transition. the updated scenerio for mrna-trna correspondence allows the replication albeit not in 1-1 manner (see http://tinyurl. com/y73se8vs). was the letter i present at that period: was it part of both mrna and rnat or of only rnat giving therefore rise to a leakage? if rna era in the proposed sense was realized, what happened before it? 1. one imagine that before rna era the rnat not necessary identical with its recent form as a realization of 2-harmony (or perhaps of all 3 different types of 2-harmonies) with 40 codons was realized and was able to replicate with aas serving as catalysts attached to rnat. only the complementary rnat was able to appear as sequences: tetrahedral codons were absent. in the transition from 2-harmony to 3-harmony both dna and full rna emerged. replication of rnat transformed to translation of aas. this vision would be more in spirit with the idea about the gradual emergence of biological representations of the dark variants of biomolecules. 2. one could go even further and ask whether this period was preceded by a period during which pre-trna identifiable as single 20-codon representation choosable in 3 manners. pre-trna ↔ aa correspondence would have been 1-1. aas would have decomposed to three types corresponding to these 3 choices. for instance for the code with z6 symmetry only 4 aas would have been present. for the details of harmonies see the appendix of [13] (see http://tinyurl.com/yad4tqwl). 4 context dependence from tgd point of view the original idea was that context dependence and homonymy are absent at the level of dark variants of various codons and aas and would result from the pairing with chemical counterparts of dark codons. more precisely: the horizontal dark dx-dy pairings would be context independent and would not depend on emotional state whereas the vertical dx-x pairings are induced by dx-dy pairings and induce x-y pairings. this is obviously something new from the point of biology as chemistry paradigm. it however turned out that the context dependence appears very naturally at the dark level. dtrna bio-harmony allows naturally 3 different representations as 2-harmonies realized as sub-harmonies of 3-harmony associated with dna and mrna. one would have 3 basic context already at this level. one can imagine at least 3-sources of context dependence and expression of emotions by gene expression. 1. several bio-harmonies are possible and dx and x would couple by different resonant 3-chords for each harmony. it is of course possible that very few of these bioharmonies perhaps only one are realized at the level of dna and mrna. this would explain the uniqueness of dna and mrna codons in biological sense. if several bioharmonies are realized for dna then both mrna, rnat and aa must have resonance couplings to all these bioharmonies. for aa this is satisfied if fxy z = f1 +f2 +f3 is same (perhaps issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/y73se8vs http://tinyurl.com/y73se8vs http://tinyurl.com/yad4tqwl dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 01-21 17 pitkänen, m., homonymy of the genetic code from tgd point of view modulo octave equivalence) for all harmonies involved or if aa has all all the frequencies fxy z as resonance frequencies. for mrna (f1, f2, f3) → (f1, f2, f3) pairing would require even larger spectrum of resonant 3-chords at the level of chemistry. hence it is quite possible that only single 3-harmony is realized for ddna, dmrna, and daa. if several harmonies are present, the evolution would have gradually invented the biomolecules having the needed spectrum and would still be in progress. 2. the situation with dtrna is different. the dmrna-dtrna pairings would involve 3 different unions of 2 20-chord harmonies. this choice implies context dependence already at dark dna level and could be the fundamental reason for mrna-trna homonymy. what is however important that the decomposing of trna to (rnat,aa) pairs guarantees automatically genetic code via fxy z = f1 + f2 + f3 coupling. aa dictates the pairing unlike usually thought. 3. if the frequencies are cyclotron frequencies determined by the magnetic fields at flux tubes, the variation of magnetic field strength due to the variation of flux tube thickness changes the frequency scale. this could be also seen as emotional expression (in analogy with membrane potential in biology inducing variation of josephson frequencies and varying the degree of alertness in neurons). the gradual variation of magnetic fields strengths during evolution could explain the slight differences in the genetic code. evolution would be clearly in question in the sense that the symmetries of the code are maximal for the nuclear code. it will be found that also this mechanism is needed in order to understand all deviations of the code. 4.1 context dependence as ”emotional expression” at molecular level? using the attribute ”emotional” certainly raises eyebrows and i will drop even the quotation marks in the following. reader can freely add them. 4.1.1 basic guide lines consider first the basic guidelines 1. one plausible possibility is that genetic code as dna-aa pairing is unique in given context whatever it is physically but there exist what one might call dialects just like slight modifications of vertebrate genetic code. there is homonymy, which however disappears when context is taken into account: same mrna can correspond to two aas or aa and stop. the homonymy is associated with mrna-trna pairing for the third mrna letter which is many-to-one and 1-to-many. which the actual choice depends on context as in ordinary language. 2. wobble base pairing is the model explaining both the many-to-1 and 1-to-many pairings. an interesting finding is that for 32 codons the pairing does not depend on third letter at all. i have proposed long time ago a model in which 2-letter code emerged first and then fused with 1-letter code to give 3-letter code. a more plausible interpretation is as activation of the 3rd letter in 3-letter code. the wobble base pairing and homonymy would have emerged in this fusion of codes. 3. from the tables of wikipedia at article (see http://tinyurl.com/y73se8vs) for standard code one can read when the pairing of the third letter is many-to-one and 1-to-many. if it is 1-to-many and unless the resulting trna anticodons correspond to the same aa, the outcome can be several aas. this does not lead to 1-to-many mrna → aa if the rnas associated with trnas in mrna → trna pairing couple with the same aa. the pairing between mrna and aas is 1-to-many rather rarely and could be accidental. it seems that there is a principle taking care that the deviations from the standard code get minimized. 4. the homonymy for mrna-aa pairings is very rare. this suggests that it is accidental and disappeared during the evolution. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/y73se8vs dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 01-21 18 pitkänen, m., homonymy of the genetic code from tgd point of view 4.1.2 the origin of mrna-trna homonymy and mrna-aa homonymy mrna-trna homonymy is clearly exceptional and the proposal that trna bio-harmony corresponds to a fusion of 2 20-chord codes together with the fact that there are 3 basic types of these codes could explain this. 1. suppose that dtrna harmony corresponds to a sub-harmony of full bio-harmony for ddna and drna as a fusion of two sub-cycles from the union of 3 cycles defining ddna and drna harmony. one can make this choice in 3 manners corresponding to the choices (z6, z4), (z6, z2) and z4, z2. these 3 basic choices would naturally explain the dtrna-trna homonymy without the dependence on emotional state. this would not however explain the deviations from the standard code. in the case dtrnatrna pairing it is enough that trna couples resonantly only to the 3-chord representatives associated with one 2-harmony appearing as sub-harmony of 3-harmony that is selected and defines the context. this obviously allows larger number of trnas satisfying the resonance conditions. this could relate to the homonymy. the function of trna as an agent transferring daa-aa pair and attaching it to dmrna-mrna pair. hence trna homonymy is desirable it can happen that the concentration of particular certain kind of trna is low so that second kind of trna coupling to same mrna can handle the job. 2. trna homonyms for the first anticodon of trna would reflect the emotional state of ddna/mrna. why only the third? this might relate to the idea about fusion of 2-letter codes and 1-letter codes. for 2-letter code there would be no ”emotional expression” and no context dependence. the emergence or perhaps better, the activation of additional letter at the level of chemical expression, would have brought in the chemical emotional expression. consider now mrna-aa homonymy. this homonymy is rather rare and could be accidental. 1. if aa couples to the sum fxy z = f1+f2+f3 of the frequencies characterizing the codon x1y1z1, it can happen that one has fx1y1z1 = fx2y2z2 modulo octave multiple so that besides codon x1y1z1 also the wrong codon x2y2z2 codes for the same aa. of course, this condition might hold true only approximately. this could explain mrna-aa homonymies as accidental. 2. there is however an objection against the proposal. if the frequencies fxy z are identical in octave equivalence for all codons coding for aa, the accidental degeneracy would suggests that the entire mrna multiplet containing x2y2z2 codes for aa. typically however only one member of the mra multiplet codes for wrong aa. should one give up the idea that the members of mrna multiplet satisfy fx1y1z1 = fx2y2z2 . if so, aa would have the frequencies fxy z of mrna multiplet as distinct resonance frequencies. for instance, could one think that the a-g and t-c breakings at the level of frequencies are present although they are not large enough to make themselves visible in the mrna-aa correspondence (say for the mrna 4-plets coding for same aa). this is the case if aa has all these frequencies as resonance frequencies. also the number of octaves distinguishing between x1y1z1 and x2y2z2 matters somewhat. in this case the accidental resonance condition for wrong aa could be satisfied for single member of mrna multiplet only. 4.1.3 a concrete objection against the model one can try to understand the possible dependence of code on the emotional state by looking the numbers of 3-harmonies obtained as fusion of z6, z4 and z2 symmetries. one can find explicit tables for the codes in the appendix of [13] (see http://tinyurl.com/yad4tqwl). issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/yad4tqwl dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 01-21 19 pitkänen, m., homonymy of the genetic code from tgd point of view 1. a crucially important thing to notice is that z6 harmony is unique. this harmony allows 3 6-plets for which 6 dnas code for single aa. there is also one doublet. therefore the codons associated 3 6-plets and doublet should always code the same aa unless the magnetic fields at flux tubes determining the cyclotron frequencies van vary. it is easy to verify that this prediction is correct for the nuclear code. for non-nuclear codes the situation is different. there are 3 6-plets and they code for leu, ser, and arg. these 6-plets should be stable under the modifications of the standard code. this rule is however broken in at least two cases: (a) for cug coding for ser instead of leu. ser is coded usually by ucg. both daa and aa couple to the sum fxy z = f1 + f2 + f3 of the 3-chord frequencies. the simplest explanation already discussed is that dser and dleu have accidentally fcug = fucg modulo octave multiple. t (b) uug coding for stop rather than leu. stop is coded usually by ugg. accidental degeneracy would be the explanation also now. stop identified as release factor fr1 or fr2 playing the role of aa and possibly having also dark aa counterpart would have fugg = fuug. 2. all deviations from the standard code could be determined solely by the accidental degeneracies for the frequencies fxy z associated with two codons coding for different aas or aa and stop. for standard code they would have been eliminated almost completely by evolution: as noticed earlier, even in human mitochondrial code there is this kind of homonymy. 3. for 3-chords with z4 as isometry group one has 2 different harmonies, which means non-trivial conditions on dna and mrna since the 3-chords of all these harmonies must act as resonance chords. in principle homonymy becomes possible for ddna → dna and dmrna → mrna pairings but is not realized. either coupling to both harmonies is possible or there are no dnas or mrnas coupling resonantly to all 3-chords of either harmonies so that only 1 harmony is realized completely. this is important if one requires uniqueness of the genetic code. 4. for 3-chords having zrot isometries there are 3 harmonies and for zrefl 5 harmonies. this gives increasingly stronger conditions on resonant couplings. the uniqueness of the code suggests that only a subset of possible harmonies is possible. also the probability of homonymy for daa-aa pairing increases and might explain 21st and 22nd aas pyl and sec coupling to non-standard representation. deviations typically occur for the doublets as indeed found. what is interesting that if one loosens the conditions and allows different couplings and allows several 3-harmonies, it is in principle possible to have larger number of dna and mrna codons than usually. also analogs of aas can be considered. frequency coding relates interestingly to extended genetic codes with 4 or 5 codons (see http://tinyurl.com/ycsfgu7n) and nucleic acid analogues (see http://tinyurl. com/y8tj8hsm). 4.2 is the notion of reading frame consistent with the proposed realizations of the genetic code? reading frame (see http://tinyurl.com/yb6wr3d7) represents also a context dependence of the code. reading frame begins with the start codon and new reading frame can begin at second or third letter of codon. there must be also stop after 3× n letters also in the new reading frame. shifting of reading frame by 1 or 2 units can take place for viral, prokaryote, and mitochondrial genomes but for some reason not in nuclear genome. shift makes sense if the first codon is start codon. for human genome mt-aot8 and mt-atp6 are examples of reading frames for mitochondrial genes coding for different proteins. the interesting question is why the shift occurs only at the level of viruses, prokaryotes, and mitochondria and chloroplasts. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/ycsfgu7n http://tinyurl.com/y8tj8hsm http://tinyurl.com/y8tj8hsm http://tinyurl.com/yb6wr3d7 dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 01-21 20 pitkänen, m., homonymy of the genetic code from tgd point of view does the notion of reading frame make sense for the two models of genetic code? consider first the representation of 64 codons as 3-chords. if all 64 codons are are realized as chords, shift does not produce chords not belonging to the harmony. since the notes of chords cannot correspond to the letters the shift is highly non-trivial since it is not only shifted decomposition of notes to triplets but change also the notes. is this possible at the level of dmrna? at the dark level code words do not have decomposition to letters. dark proton triplets should re-organize in a new manner into triplets. if the dark protons inside proton triplet are connected by colored bonds to form color singlet, the shift would produce colored 3-proton states unless also the color structure of the states is re-organized so that it is consistent with the shift at the level of codons. kind of phase transition would take place and induce the change of the reading frame. references biology [1] the fourth phase of water : dr. gerald pollack at tedxguelphu. available at: https://www. youtube.com/watch?v=i-t7tcmudxu, 2014. [2] gariaev pp et al. holographic associative memory of biological systems. proceedings spie the international soc for opt eng . optical memory and neural networks, pages 280–291, 1991. [3] gariaev pp et al. the spectroscopy of bio-photons in non-local genetic regulation. j non-locality and remote mental interactions. available at: http://www.emergentmind.org/gariaevi3.htm, (3), 2002. [4] bludorf f fozar g. scientists prove dna can be reprogrammed by words and frequencies, 2014. [5] maslow mu gariaev pp. fractal presentation of natural language texts and genetic code, 2nd international conference on quantitative linguistics. qualico ’94, pages 193–194, 1994. [6] tovmash av gariaev pp, tertishni gg. experimental investigation in vitro of holographic mapping and holographic transposition of dna in conjuction with the information pool encircling dna. new medical technologies, 9:42–53, 2007. [7] gariaev pp. another understanding of the model of genetic code theoretical analysis. open journal of genetics. available at: http://file.scirp.org/html/5-1370212_57601.htm, 5:92–109, 20158. books related to tgd [8] pitkänen m. dna as topological quantum computer. in genes and memes. online book. available at: http://tgdtheory.fi/public_html/genememe/genememe.html#dnatqc, 2006. [9] pitkänen m. does tgd predict the spectrum of planck constants? in hyper-finite factors and dark matter hierarchy. online book. available at: http://tgdtheory.fi/public_html/neuplanck/ neuplanck.html#planck, 2006. [10] pitkänen m. evolution in many-sheeted space-time. in genes and memes. online book. available at: http://tgdtheory.fi/public_html/genememe/genememe.html#prebio, 2006. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://www.youtube.com/watch?v=i-t7tcmudxu https://www.youtube.com/watch?v=i-t7tcmudxu http://www.emergentmind.org/gariaevi3.htm http://file.scirp.org/html/5-1370212_57601.htm http://tgdtheory.fi/public_html/genememe/genememe.html#dnatqc http://tgdtheory.fi/public_html/neuplanck/neuplanck.html#planck http://tgdtheory.fi/public_html/neuplanck/neuplanck.html#planck http://tgdtheory.fi/public_html/genememe/genememe.html#prebio dna decipher journal | may 2018 | volume 8 | issue 1 | pp. 01-21 21 pitkänen, m., homonymy of the genetic code from tgd point of view [11] pitkänen m. criticality and dark matter. in hyper-finite factors and dark matter hierarchy. online book. available at: http://tgdtheory.fi/public_html/neuplanck/neuplanck.html#qcritdark, 2014. [12] pitkänen m. quantum gravity, dark matter, and prebiotic evolution. in genes and memes. online book. available at: http://tgdtheory.fi/public_html/genememe/genememe.html#hgrprebio, 2014. articles related to tgd [13] pitkänen m. geometric theory of harmony. available at: http://tgdtheory.fi/public_html/ articles/harmonytheory.pdf, 2014. [14] pitkänen m. pollack’s findings about fourth phase of water : tgd view. available at: http: //tgdtheory.fi/public_html/articles/pollackyoutube.pdf, 2014. [15] pitkänen m. about physical representations of genetic code in terms of dark nuclear strings. available at: http://tgdtheory.fi/public_html/articles/genecodemodels.pdf, 2016. [16] pitkänen m. philosophy of adelic physics. available at: http://tgdtheory.fi/public_html/ articles/adelephysics.pdf, 2017. [17] pitkänen m. philosophy of adelic physics. in trends and mathematical methods in interdisciplinary mathematical sciences, pages 241–319. springer.available at: https://link.springer. com/chapter/10.1007/978-3-319-55612-3_11, 2017. [18] pitkänen m. re-examination of the basic notions of tgd inspired theory of consciousness. available at: http://tgdtheory.fi/public_html/articles/conscrit.pdf, 2017. [19] pitkänen m. emotions as sensory percepts about the state of magnetic body? available at: http: //tgdtheory.fi/public_html/articles/emotions.pdf, 2018. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.fi/public_html/neuplanck/neuplanck.html#qcritdark http://tgdtheory.fi/public_html/genememe/genememe.html#hgrprebio http://tgdtheory.fi/public_html/articles/harmonytheory.pdf http://tgdtheory.fi/public_html/articles/harmonytheory.pdf http://tgdtheory.fi/public_html/articles/pollackyoutube.pdf http://tgdtheory.fi/public_html/articles/pollackyoutube.pdf http://tgdtheory.fi/public_html/articles/genecodemodels.pdf http://tgdtheory.fi/public_html/articles/adelephysics.pdf http://tgdtheory.fi/public_html/articles/adelephysics.pdf https://link.springer.com/chapter/10.1007/978-3-319-55612-3_11 https://link.springer.com/chapter/10.1007/978-3-319-55612-3_11 http://tgdtheory.fi/public_html/articles/conscrit.pdf http://tgdtheory.fi/public_html/articles/emotions.pdf http://tgdtheory.fi/public_html/articles/emotions.pdf introduction some background variations of the genetic code wobble base pairing two tgd based realizations of genetic code dark realization of genetic code the notion of magnetic body carrying dark matter and resonance as a mechanism of pairing the geometric model for music harmony and genetic code what conditions pairings pose on the frequency triplets? probabilistic estimates for single 20-chord harmony is the maximal number of codons for the fusion of 3 20-codon codes possible? could harmonies form a hilbert space how the symmetries of the model of harmony could relate to those of the genetic code? what distinguishes between codons and anti-codons and between dna and rna? context dependence from tgd point of view context dependence as "emotional expression" at molecular level? basic guide lines the origin of mrna-trna homonymy and mrna-aa homonymy a concrete objection against the model is the notion of reading frame consistent with the proposed realizations of the genetic code? dna decipher journal | september 2018 | volume 8 | issue 2 | pp. 74-89 74 pitkänen, m., getting philosophical: on the problems in physics, neuroscience & biology article getting philosophical: on the problems in physics, neuroscience & biology matti pitkänen 1 abstract in this article, i summarize what i see as the basic philosophical problems of the recent conceptual framework of biology and neuroscience and discuss how tgd can resolve these problems. since one cannot actually avoid the problems of fundamental physics and of consciousness theory , so these are discussed to some degree. keywords: philosophy, physics, neuroscience, biology, tgd framework. 1 introduction this article was inspired by an fb discussion and is an attempt to summarize basic philosophical problems of biology and neuroscience and the tgd based solution of them. one cannot actually bypass basic philosophica problems of recent day theoretical physics so that the discussion begins with these. 1.1 importance of philosophical thinking the fb discussion that motivated this article once again made manifest both the extreme importance and regrettable lack of philosophical thinking not only biology but in natural sciences in general. i do not mean with philosophical thinking academic philosophy, which i have found mostly deadly boring. rather, for me good philosophical thinking means posing critical questions. what we really know and what we do not know? what do we believe and what part of this is just beliefs? are there facts challenging these beliefs? what is consciousness: is it really a property of something as ”-ness” suggests? what is free will? how it manifests itself? is it an essential aspect of consciousness so that ai hype could be forgotten? are free will and non-determinism really in conflict with physics as physicalist has decided to believe? concerning consciousness, what guidelines come from modern, physics, biology, and neuroscience? in physics critical thinking would have allowed to avoid the numerous fads and fashions that have plagued us during last 4 decades: guts that led to the wrong track, inflation theory, various ad hoc models of dark matter postulating some exotic strong ai, supersymmetry in its gut form, superstring models, loop gravity,... critical thinking would have challenged various ”interpretations” of quantum theory and we could have continued immediately the work of the fathers of quantum theory rather than waiting for almost a century. critical thinking would have also inspired the question whether the non-determinism of state function reduction has something to do with free will and how one should generalize the ontology of physics (copenhagen ontology gives is it up altogether) to build a logically consistent framework. unfortunately critical thinking tends to lengthen the time spent in academic assembly line so that it is strongly discouraged. thinkers tend also to become isolated from their social groups since everyone of us wants desperately to belong to some group and this requires sharing of its beliefs. it is easier to believe what professor and text book tell and get the research position and funding. people are also very lazy. ai scientist decides that consciousness is running computer program or a property of the network structure or something equally ad hoc: no need to learn huge amount of 1correspondence: matti pitkänen http://tgdtheory.com/. address: rinnekatu 2-4 a8, 03620, karkkila, finland. email: matpitka6@gamail.com. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.com/ mailto:matpitka6@gmail.com dna decipher journal | september 2018 | volume 8 | issue 2 | pp. 74-89 75 pitkänen, m., getting philosophical: on the problems in physics, neuroscience & biology physics, biology, neuroscience. biologist decides that biology is nothing but schrdinger equation and electromagnetism (or mere chemistry as in the older variant of the belief still prevailing). neuroscientist desides that physicalism is correct and brain is the seat of the consciousness module. brain as a computer paradigm makes the situation even easier. physicist decides to believe in physicalism stating in its modern version that all physics reduces to planck length scale: one can safely forget all other branches of sciences as a kind of taxonomy and specialize to apply one particular algorith to build cv. 1.2 basic dogmatics the key dogmas common to all branches of natural science are physicalism and reductionism. physicalism states that matter is all that matters and consciousness is mere epiphenomenon and that world is deterministic in the quantum version of the dogma it obeys statistical determinism. reductionist sees natural sciences are a victorious march towards shorter and shorter space and time scales. science is an imperium that grows conquest by conquest. we are told that super string theorists have taken the last step to planck scale by building the only possible theory of everything. this step is really gigantic: from electroweak length scale there are 16 orders of magnitude to planck length scale. before this every order of magnitude has contained a lot of su4prises but now the situation would be different as already gut theorists revealed to us. the surprise was however that the theory in planck length scale does not allow to predict anything in long length scales: situation is like trying to predict the behavior of initial value sensitive system. the question of philosopher would be obvious: could something have gone wrong? this question has been made by some theoreticians. the decision of elite however seems to be that physics has reached its end. nothing can be predicted and we should be happy about this marvellous feature of the only possible theory. this series of conquests is marked by transitions. from biology to biochemistry, from biochemistry in vivo to organic chemistry in vitro, from chemistry to molecular physics, from molecular physics to atomic physics. then follows a transition from atomic physics to nuclear physics: the assumption is that these two physics have practically nothing to do with each other. there are numerous experimental anomalies found during the last century challenging this belief. ”cold fusion” people were labelled next to criminals for their scandalous claims. luckily the situation has now changed. but people talking about water memory belong still to the pariah of science. after this jump we jump from nuclear physics to hadron physics to physics at quark-gluon level and then comes the really really big planck jump. so simple. there is however a little problem. every successful conqueror must build a lot of bridges, without them the maintenance fails. reductionistic conquerors were so hasty that they did not have time to to build the bridges between these different physics. we do not understand how nuclear physics emerges from hadron physics emerges from quark physics. we do not understand how biochemistry emerges from organic chemistry emerges from molecular physics emerges from atomic physics. but we can decide that this is only a technical difficulty: if we had enough computational power we could fill these gaps. 2 restricting the attention to biology and neuroscience in the following the attention is restricted mostly to the philosophical problems of biology and neuroscience. it however turns that these problems are actually also problems of physics. 2.1 nothing but biochemistry and electromagnetism the basic dogmatics says that life is nothing but chemistry plus a little bit of electromagnetism needed to model cell membrane and neuronal membrane. there is also eeg but this is taken as noise due to neural circuits so that there is no need to waste time with it. luckily, not all experimentalists know or issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | september 2018 | volume 8 | issue 2 | pp. 74-89 76 pitkänen, m., getting philosophical: on the problems in physics, neuroscience & biology care about dogmatics and have found correlations of eeg with behavior and physiology and they are used as a diagnostic tool. most of them however refuse to consider seriously the possibility that eeg might possibly communicate something from brain somewhere. where would this somewhere could reside: outside brain? no! philosopher must be producing totally weird fairy tale now! says the mainstreamer inside me with such a friendly but delicate tone that it becomes clear that he regards the poor philosopher as a screwball. but philosopher continues asking. didn’t libet discover that our sensory data is fraction of second old? could it take fraction of second of this data to propagate as eeg signals from brain to this something. as a matter fact, libet discovered also that the conscious decision to raise finger is preceded by neural activity starting for a fraction of second earlier. one cannot understand this unless one decides that it supports the absence of free will. philosopher asks also whether our decision that experienced time and the time of physicist are one and the same thing is be wrong. they are indeed different in many respects as any first year physics student understands. should we trust facts instead of textbook wisdom? and what about libet’s second finding: could we give up our firm decision that signals propagate in only single direction of geometric time? there is also a second strange electromagnetic phenomenon in biology: bio-photons. already discovered almost century ago, they are still taken as pseudoscience by many biologists. they appear in visible and uv range but it seems that they are not produced in molecular reactions (this would mean peaks in the distribution). what is their origin? 2.2 why vivo-vitro difference? even the basic dogmatist must admit that one must speak about organic chemistry in vivo and in vitro. in vitro one can build models for reactions, deduce estimates for the excitation energies of molecules, construct thermodynamical models for reactions in terms of thermodynamics involving parameters like activation energies and chemical potentials, one can develop complex networks of reaction pathways. the typical assumption of these models is that everything is homogenous and isotropic: one has spatially constant concentrations of various reactions obeying differential equations determined by the kinetics. one can however construct more complex structure by allowing diffusion making possible spatial gradients. the problem is that this dynamics has very little to do with what happens in living cell. the in vitro estimates for the rates of reactions are many many orders of magnitudes too low as compared to those in living matter. we do not understand anything about bio-catalysis. we know that enzymes and ribozymes somehow make the miracle but that’s all. we do not have slightest clue about how reactants manage to find each other in the molecular soup full of different molecules. we have no idea wherefrom the reactants get the energy to jump over potential wall making the reaction quite too slow. philosopher would say that here is an excellent opportunity for new physics to enter in biology. how can reactants find each other? could they possibly be connected by something, which shortens as the reactants meet? could the notion of tensor network involving quantum entanglement be essential element of biology and entire physics. particles would not be lonely riders but could be connected by something at least temporarily. could this something liberate energy quanta allowing to get over the potential wall making reaction so slow? could these networks have dynamical topology and make living systems what they are. unfortunately, standard space-time picture does not allow this something. also planck constant is quite too small. should we conclude that the philosopher is weirdly fairytaling again? issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | september 2018 | volume 8 | issue 2 | pp. 74-89 77 pitkänen, m., getting philosophical: on the problems in physics, neuroscience & biology 2.3 what selected the biomolecules? philosopher also asks why only very few candidates for relevant biomolecules are actually selected. who/what selected and how? this leads to very unpleasant questions circumvented by deciding that the emergence of life was nothing but a thermodynamical fluctuation. it has however become clear that complex organic molecules are present even in interstellar and intergalactic space. the miraculous thermodynamical fluctuation explaining evolution without real evolution would have been really huge. philosopher tends to conclude that we simply have no clue about what selection at the bio-molecular level really is and continue that some new physics is involved so that it is time to think giving up the reductionistic narrative. the selection problem appears also at the level of biochemical reaction pathways. one can imagine endless variety of ”reaction vertices”. if one assumes that only very few basic ”reaction vertices” are allowed but the rest not, one can construct a limited number of reaction pathways. but this is an ad hoc assumption: this selection of allowed reaction pathways certainly occurs but we do not have a slightest idea about the physics behind it. there is also an analogy with computer science. one can construct endless variety of linguistically correct computer programs: why only very few of them would be selected. and with neuroscience: from a huge array of behavioral patters only some are selected. here one can of course try a loophole: darwinian selection. but there is no selection in the universe of physicalist. this would require free will and intentionality. the trick does not work. but what about this network in which biomolecules are connected by this something already mentioned?, asks philosopher. could this something connect only biomolecules if they are in the same relationship as sender and receiver of radio signal. could these somethings connect stably only systems possessing common resonance frequencies? could this criterion could select both the preferred biomolecules and the ”reaction vertices” and thus also reaction pathways? it is easy to guess the reaction of mainstreamer: fairy-taling again. 2.4 where does the coherence come from? a further mystery is how the biochemical reactions can occur coherently in length scales longer than atomic scale. without this coherence i could not write this article, play piano, or even raise my hand. if we were just sacks of water containing some chemicals we would be doing science and arts. we would be indeed just sacks of water containing some chemicals in chemical and thermodynamical equilibrium and microscopic sample from this water would characterize us completely. mysteriously, the coherence of biodynamics in scales up to the size of the organism emerges somehow. the required coherence need not be quantum coherence and probably it is not but it could be induced by quantum coherence. quantum coherence of what? there is also the problem due to quite too small value of planck constant. we have learned about the effects supporting the vision about quantum biology. it is now however becoming clear that these effects would however require large value of planck constant. here the philosopher remembers the findings of blackman and other pioneers of bio-electromagnetism. they found that the irradiation of vertebrate brain by elf radiation at eeg frequencies scale had effects on both behavior and physiology and these effects look quantal occurring at harmonics of endogenous magnetic field of .2 gauss. e = h× f makes these effects extremely small and totally masked by thermal noise. what if the value of planck constant were so large that the energies were above thermal energy? now the mainstream physicist inside us is getting really angry: is this recklessly speculating philosopher really suggesting that our cherished quantum theory might not be the final word of science? 2.5 morphogenesis the problem of structure formation in biology morphogenesis was put under the rug by most biologists after the emergence of genetics. sheldrake [4, 5] is one of those who have taken it seriously and has been issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | september 2018 | volume 8 | issue 2 | pp. 74-89 78 pitkänen, m., getting philosophical: on the problems in physics, neuroscience & biology labelled as a crackpot by mainstreamers (i have discussed sheldrake’s views from tgd point of view in [4, 23]). one just assumes that the structures are there and performs chemistry around these structures. this approach is very practical and has given an enormous amount of data but very little understanding. in standard physics the description of spatial structures would be in terms of enhanced densities of biomolecules or of their gradients in some space-time region. this is the only possibility because the space-time of standard physics is topologically and geometrically utterly trivial. empty minkowski space is an excellent approximation for it. what philosopher has to say about this? if space-time topology were topologically non-trivial, situation would change dramatically. already wheeler saw this possibility and in the biology inspired by tgd (for which wheeler suggested its name) all structures correspond to structures of topologically non-trivial space-time identified as surface in certain 8-d space-time: space-time sheets, magnetic flux tubes, etc... the entire tgd inspired quantum biology relies on this vision. the structures that we see around us would represent the non-trivial topology of space-time surface. all structures including bio-molecules, membrane like structures, organelles, organs, ... would be 4-d space-time surfaces. again philosopher gets excited since this would reduce the notion of shape in biology to a precisely defined and testable geometrodynamics coupling to em fields. 2.5.1 the dynamics of space-time surfaces this dynamics predicts two kinds of space-time regions [21] (see http://tinyurl.com/yboog5sr. 1. the regions of first kind are locally minimal surfaces. these minimal surfaces are as 4-d analogs of geodesic lines analogs of asymptotic states of particle physics for which interactions are not on. they also satisfy non-linear geometrization of massless field equations so that both particle and wave aspects are present. what is especially important is that static minimal surfaces have vanishing mean curvature and look like saddles locally. they cannot be closed surface if stationary. 2. second type of regions are not minimal surfaces: there is a non-trivial coupling of the minimal surface term to 4-force density analogous to the divergence of maxwellian energy momentum tensor. this is a generalization of the dynamics of a point-like charged particle in maxwell field. these regions are identified as interaction regions: in particle physics these two regions correspond to external free particles and the interaction region. magnetic flux tubes play fundamental role in tgd based quantum biology are deformations of string like objects, which represent simplest 4-d minimal surfaces. essential is the coupling between induced kähler form (mathematically like maxwell field) and the geometry of the surface: the divergence of energy momentum current assignable to the analog of cosmological term (4-volume) equals to the divergence of that assignable to kähler action: this expresses local conservation of four-momentum. one could also speak about coupling between kähler field and gravitational field: penrose’s intuition about the the role of gravitation in biology would be correct. when the coupling is absent, minimal surface property implies the separate vanishing of both divergences and separate conservation of corresponding energy-momenta. all the known extremals of kähler action are minimal surfaces: this is due to their very simple algebraic properties making easy to discover them. physically this correspond to quantum criticality: dynamics is universal and does not depend on coupling parameters. 2.5.2 general view about morphogenesis these observations lead to a rather general view about morphogenesis. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/yboog5sr dna decipher journal | september 2018 | volume 8 | issue 2 | pp. 74-89 79 pitkänen, m., getting philosophical: on the problems in physics, neuroscience & biology 1. the presence of the kähler field (em field is sum of kähler field and second term) makes possible flow equilibria such as cell membrane, which are not minimal surfaces. these surfaces can be closed and stationary making possible isolation from environment crucial for living organisms. spherical soap bubble is a good analogy: it is not minimal surface as the soap films spanned by frames are. they look locally like saddle surfaces with opposite external curvatures in two orthogonal directions, this implies that they cannot be closed surfaces. bubble is not possible without a pressure difference ∆p between the interior and exterior of the bubble: the blowing of the soap bubble generates ∆p, and means external energy feed analogous to metabolic energy feed. ∆p is analogous to a non-vanishing voltage v over cell membrane. the electric field of cell membrane and the energy feed providing the energy of electric field as metabolic energy are essential for the stability. more generally, v would generalize to non-vanishing of energy momentum tensor of kähler field with non-vanishing divergence serving as a correlate for the energy transfer between kähler and volume (gravitational) degrees of freedom. this generalises to all morphologies, which correspond to closed surfaces. they necessarily involve both kähler electric and magnetic fields coupling to the geometry to stabilize the morphology. this statement would give some content for the exaggerated claim that biology is nothing but electricity + schrödinger equation that i heard during my first student year. 2. for instance, the presence of kähler electric field can correspond to electric fields of cell membrane or along a part of body. if it is too weak, things go wrong in development. as was found decades ago, consciousness is lost if the electric field between frontal lobes and hindbrain gets too weak or has wrong direction [8]. cell dies if the membrane potential becomes zero and eeg disappears in death. also microtubules have electric field along their axes essential for their existence. michael levin and his collaborators [1, 2, 6] have discovered further fascinating connections between electric fields and morphogenesis. one of the discoveries is that the electric fields of the embryo are controlled by neurons of the still developing brain (see http://tinyurl.com/y77fcc7r). this conforms with the view that neurons and their mbs correspond to a higher level in the hierarchy than ordinary cells and there take care of control in longer scales. the mb of the developing brain would be the controller. 3. a non-trivial coupling (four-momentum transfer) between the volume and kähler degrees of freedom requires that the energy momentum currents have opposite and non-vanishing divergences. for the energy momentum tensor of ordinary maxwell field the divergence is proportional to the contraction of maxwell current and maxwell field so that the current must be non-non-vanishing. in tgd the energy momentum tensor is replaced with energy momentum current allowing to have well-defined notion of energy momentum and corresponding conservation laws. now the divergence contains two terms. the first one is the contraction tr(tkhk) of energy momentum tensor tk of kähler action with the second fundamental form hk: this term proportional to tk is new. second term is proportional to the contraction jkj∇hk of the induced kähler form j with kähler current jk and gradients ∇hk of imbedding space coordinates analogous the divergence of energymomentum tensor jβfαβ in the case of ordinary maxwell action. one expects both terms to be non-vanishing. for the mere kähler action, which i believed for decades to determine the preferred extremals, jk is either vanishing or light-like. in presence of coupling it can be both non-vanishing and timelike. the realization that cosmological term is present was forced by the twistor lift of tgd whose existence is possible only for h = m4 × cp2 [14, 18]. 4. the predicted stabilizing kähler (and em) currents would naturally correspond to the dc currents flowing along the body in various scales discovered already by becker [10, 8] and found to be essential for the survival of the organism. in particular, becker’s dc currents are essential for the healing of issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/y77fcc7r dna decipher journal | september 2018 | volume 8 | issue 2 | pp. 74-89 80 pitkänen, m., getting philosophical: on the problems in physics, neuroscience & biology wounds and in the regeneration of organs. in the first first aid stage of the healing dc currents are generated locally and after than central nervous system (cns) takes care of the generation of the current (for tgd based discussion of becker currents see [15] (see http://tinyurl.com/ydg6okkk) or [11]). also this is easy to understand from the proposed stability criterion. this picture is discussed quantitatively in the framework of the twistor lift tgd in [17] [32]. 2.6 metabolism metabolism is one of the key aspects of biology. we must eat and plants must busily photosynthesize in order to survive. but why metabolic energy feed is needed? again a mystery. non-equilibrium thermodynamics is one attempt to answer this question. thermodynamical equilibrium is completely uninteresting, entropy is maximal and in the case of local dynamics the state of system is completely determined by a small sample of it. however, if one has energy feed, situation changes since equilibrium becomes flow equilibrium. the energy feed guarantees that there is macroscopic dynamics rather than mere thermal motion at microscopic level. also in this case one has essentially the same situation everywhere unless one introduces macroscopic parameters also energy flow depending on time and position to get something more interesting. simple reaction kinematics determined by differential equations can be replaced with that determined by partial differential equations obtained by allowing diffusion. also temperature, pressure and other thermodynamical parameters can be allowed to depend on position and time. turing proposed a model for the coloring of zebra as outcome of this kind of dynamics. the model for neuronal membrane and nerve pulse generation is also a rough model trying to reproduce basic facts about nerve pulse generation using thermodynamics for neuronal membrane regarded as a capacitor. this is of course a mere parametrization of the situtation. tgd leads to a quantum model for the situtation [12]. also the interpretation about the role of nerve pulse patterns at neuronal level changes dramatically [24, 30]. in non-equilibrium thermodynamics one speaks of self-organization. one can generalize this notion to quantum self-organization and the crucial criticality associated to the transitions between different self-organization patterns generalizes to quantum criticality [13]. could these transitions correspond to spatio-temporal self organization patterns, behaviors, functions, programs. this in turn leads to deep connections with conformal symmetry (even its generalization in tgd), fractality, and universality of the dynamics. it is a pity that biologists do not seem to know much about these possibilities. now the philosopher starts to talk about ontology. in standard physics the 3-d time= constant snapshot defines the state. this belief has led to weird proposals: in quantized general relativity one ends up with a proposal that there is no time at all. could it be that 4-d deterministic time evolution between initial and final states could be more fundamental than the 3-d snapshot? could superpositions of these 4-d evolutions define quantum states. if so, the state function reductions would occur between these superpositions and their non-determinism would be consistent with the determinism of field equations. free will would not break laws of physics. it would be like starting new deterministic computer program. our philosopher calls this ontology zero energy ontology and claims that it leads to a theory of consciousness as a generalization of quantum measurement theory [27] (see http://tinyurl.com/ycxm2tpd). irritating. 2.7 does metabolic energy feed generate conscious information? the basic question about the role of metabolic energy remains, says the philosopher. what is its real role? energy feed generates structures and structural complexity means information. it seems that metabolic energy feed involves also a feed of information or generation of information. and because living systems are in question, philosopher cannot avoid the question whether this information is actually conscious information. is there any other kind of information than conscious information?! issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/ydg6okkk http://tinyurl.com/ycxm2tpd dna decipher journal | september 2018 | volume 8 | issue 2 | pp. 74-89 81 pitkänen, m., getting philosophical: on the problems in physics, neuroscience & biology to this question standard physics has no answer: it can only describe entropy mathematically and identification of information as lack of entropy is the easy answer suggested in lack of anything better. the question about a possible measure for conscious information analogous to shannon entropy is one manner to end up with p-adic physics as a correlate of cognition and the necessary fusion of real and various p-adic physics leads to adelic physics [25, 26]. adelic physics in turn predicts surprisesurprise a hierarchy of phases of matter labelled by the value of planck constant. these phases residing at these somethings defining the networks magnetic flux tubes make possible macroscopic quantum coherence inducing the coherence of living matter. 2.8 genetic code genetic code definitely represents information. is it really an outcome of thermodynamical fluctuation? is there some deep mathematics associated with the genetic code?, asks the philosopher now. genome contains also intronic portion: most of it consists of introns and the intronic portion is the larger the higher the evolutionary level is. the prevailing interpretation has been as ”junk”. is it really junk?, wonders philosopher. luckily, the attitude that trash bin represents the highest level of evolution has begun to slowly change to more rational one. could there be a beautiful mathematics behind genetic code? could it be something similar to codes in computer science and have not only one representation the chemical one but numerous representations? if computer science would have developed before genetics this question would have been completely natural and we would probably know a lot about these representations. could this dark matter with large planck constant at these mysterious somethings identified by our philosopher tentatively as magnetic flux tubes realize the really fundamental representation of the genetic code and also of of dna, rna, trna, and amino-acids in information theoretic sense? and could also radiation provide realization of genetic code necessary for communications? this is what the philosopher claims [22, 29, 28, 19, 34]. 2.9 hen-or-egg questions of biology standard biology suffers from several hen-or-egg problems as philosopher reminds. which came first: genes or metabolism? the problem is that genes require metabolism and metabolism requires genes! genes-first leads to the vision about rna world and metabolism-first to lipids world idea. the emergence of basic biomolecules is the second problem. what selected these relatively few basic molecules from huge multitude of molecules? again hen-or-egg problems emerge. which came first: proteins or the translation machinery producing them from rna? did rna arrive before proteins or did proteins and rnas necessary for their transcription and translation machinery emerge first. one can argue that ribozymes served as catalysts for rna replication but how rnas managed to emerge without replication machinery involving ribozymes? what about dna: did it emerge before rna or could it have emerged from rna? it seems that something extremely important is missing from the picture. tgd predicts the existence of dark variants of basic biomolecules dna, rna, trna, and aminoacids (aas). one can ask whether something very simple could be imagined by utilizing the potential provided by dark variants of bio-molecules present already from beginning and providing both genes and metabolism simultaneously. one can start from a couple of observations which forced myself to clarify myself some aspects of tgd view and also to develop an alternative vision about prebiotic period. 1. viruses are probable predecessors of cellular life. so called positive sense single stranded rna (ssrna) associated with viruses can form temporarily double strands and in this state replicate just like dna (see http://tinyurl.com/yc5f8b3t). the resulting single stranded rna can in turn be translated to proteins by using ribosomal machinery. rna replication takes place in so called issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/yc5f8b3t dna decipher journal | september 2018 | volume 8 | issue 2 | pp. 74-89 82 pitkänen, m., getting philosophical: on the problems in physics, neuroscience & biology viral replication complexes associated with internal cell membranes, and is catalyzed by proteins produced by both virus and host cell. could ribozyme molecules have catalyzed rna replication during rna era? for this option aa translation would have emerged later and the storage of genetic information to dna only after that. there is however the question about the emergence of aas and of course, dna and rna. which selected just them from enormous variety of options. 2. lipid membranes are formed by self-organization process from lipids and emerge spontaneously without the help of genetic machinery. it would be surprising if prebiotic life would not have utilized this possibility. this idea leads to the notion of lipid life as a predecessor of rna life. in this scenario metabolism would have preceded genes (see http://tinyurl.com/y7ehv8cq and http://tinyurl.com/y8nltb9e). the basic objection against both genes-first and metabolism-first options is that they need each other! consider now the situation in tgd. 1. in tgd framework the dark variants of dna, rna, aa, and trna would provide the analogs of genes and all basic biomolecules. they would also provide a mechanism of metabolism in which energy feed by (say) solar radiation creates so called exclusion zones (ezs) of pollack [7] in water bounded by a hydrophilic substance. ezs are negatively charged regions of water giving rise to a potential gradient (analog of battery) storing chemically the energy provided by sunlight and the formation of these regions gives rise to dark nuclei at magnetic flux tubes with scaled down binding energy. when the p-adic length scale of these dark nuclei is liberated binding energy is liberated as metabolic energy so that metabolic energy feed giving basically rise to states with non-standard value heff/h = n of planck constant is possible. for instance, processes like protein folding and muscle contraction could correspond to this kind of reduction of heff liberating energy and also a transformation of dark protons to ordinary protons and disappearance of ezs. the cell interiors are negatively charged and this is presumably true for the interiors of lipid membranes in general and they would therefore correspond to ezs with part of protons at magnetic flux tubes as dark nuclei representing dark variants of basic biomolecules. already this could have made possible metabolism, the chemical storage of metabolic energy to a potential gradient over the lipid membrane, and also the storing of the genetic information to dark variants of biomolecules at the magnetic flux tubes formed in pollack effect. 2. in tgd framework biochemistry would have gradually learned to mimic dark variants of basic processes as a kind of shadow dynamics. lipid membranes could have formed spontaneously in water already during prebiotic phase when only dark variants of dna, rna, aas and trna, water, and lipids and some simple bio-molecules could have been present. the dark variants of replication, transcription and translation would have been present from the beginning and would still provide the templates for these processes at the level of biochemistry. dark-dark pairing would rely on resonant frequency pairing by dark photons and dark-ordinary pairing to resonant energy pairing involving transformation of dark photon to ordinary photon. the direct pairing of basic biomolecules with their dark variants by resonance mechanism could have led to their selection explaining the puzzle of why so few biomolecules survived. this is in contrast with the usual view in which the emergence of proteins would have required the emergence of translation machinery in turn requiring enzymes as catalyzers so that one ends up with hen-or-egg question: which came first, the translation machinery or proteins. in rna life option similar problem emerges since rna replication must be catalyzed by ribozymes. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/y7ehv8cq http://tinyurl.com/y8nltb9e dna decipher journal | september 2018 | volume 8 | issue 2 | pp. 74-89 83 pitkänen, m., getting philosophical: on the problems in physics, neuroscience & biology 3. gradually dna, rna, trna, and aa would have emerged by pairing with their dark variants by resonance mechanism. the presence of lipid membranes could have been crucial in catalyzing this pairing. later ribozymes could have catalyzed rna replication by the above mentioned mechanism during rna era: note however that the process could be only a shadow of much simpler replication for dark dna. one can even imagine membrane rnas as analogs of membrane proteins serving as receptors giving rise to ionic channels. note however that in tgd framework membrane proteins could have emerged very early via their pairing with dark aa associated with the membrane. these membrane proteins and their rna counterparts could have evolved into transcription and translation machineries. dna molecules would have emerged through pairing with dark dna molecules. the difference between deoxi-ribose and ribose would correspond to the difference between dark rna and dark dna manifesting as different cyclotron frequencies and energies making possible the resonant pairing for frequencies and energies. proteins would have emerged as those proteins able to pair resonantly with dark variants of amino-acid sequences without any pre-existing translational machinery. it is difficult to say in which order the basic biomolecules would have emerged. they could have emerged even simultaneously by resonant pairing with their dark variants. 2.10 how life began? the central question of biology is ”how life began?” and philosopher certainly agrees with this. the dark variants of biomolecules suggest not only a solution to various paradoxes but also a concrete answer to this question. the transcription machinery for rrna including ribozymes and mrna coding for the proteins associated with ribosomes is central for the translation. the dna coding for rrna is associated with nucleolus (see http://tinyurl.com/yavahwzt) in the center of the nucleus. 1. after the emergence of the first ribosome the ribosomes of the already existing nucleus can take care of the translation of the ribosomal proteins. but how could the first ribosome emerge? this question leads to a paradox bringing in mind self-reference the basic theme of gödel-escher-bach of douglas hofstadter, perhaps the most fascinating and inspiring book i have ever read. the ribosomal proteins associated with the first ribosomes should have been translated using ribosome, which did not yet exist! 2. could the translation of the first ribosomal proteins directly from the dark variants of these proteins solve the paradox? the idea of shadow dynamics induced by the pairing of basic biomolecules with their dark variants even allows to ask whether the replication, transcription, and translation could occur at dark level so that dark genes for ribosomes would be transcribed to dark ribosomal rna and dark mrna translated to dark aa associated with the ribosomes. these in turn would pair with ordinary ribosomal rna and aa. 3. but what about dark variants of ribosomes? one can encounter the same paradox with them if they are needed for the translation. could it be that dark variants of the ribosomes are not needed at all for the translation but would only give rise to ordinary ribosomes by the pairings basic biomolecules and their dark variants. dark dna would pair with dark mrna, which pairs spontaneously with dark trna. once the ordinary ribosomes are generated from the dark ribosomes by pairing, they could make the translation much faster. 4. there is however a problem. both dark rna and aa correspond to dark nuclear strings. dark trna realized as nuclear string in the proposed manner does not have a decomposition to dark aa and dark rna as ordinary trna has. the pairing of dark trna and dark mrna should rise to dark aa and dark nuclear string call it x serving as the analog for the pairing of mrna sequence with ”rnas” of trnas in the ordinary translation. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/yavahwzt dna decipher journal | september 2018 | volume 8 | issue 2 | pp. 74-89 84 pitkänen, m., getting philosophical: on the problems in physics, neuroscience & biology 5. how to identify x? could the translation be analogous to a reaction vertex in which dark mrna and dark trna meet and give rise to dark aa and x? x cannot be completely trivial. could x correspond to the dark dna?! if so, the process would transcribe from dark dna dark rna and translate from dark rna and dark trna aa and dark dna. this would lead to an exponential growth of dark dna and other dark variants of bio-molecules. this exponential growth would induce exponential growth of the basic bio-molecules by pairing. life would have emerged! no rna era or lipid era might be needed. all basic biomolecules or their precursors could emerge even simultaneously presumably in presence of lipids but this is not the only possibility. one can take a more precise look at the situation and try to understand the emergence of bio-molecules and their basic reactions as shadows of the dark variants of bio-molecules appearing in dark particle reactions. the basic idea is that same dark reaction can give rise to several reactions of biomolecules if varying number of the external dark particles are paired with corresponding bio-molecules. under what conditions this pairing could occur, is left an open question. consider now the dark 2→ 2 reactions and possible reactions obtained by pairing of some particles. 1. the reaction dmrna+dtrna→ daa + ddna gives rise to translation mrna+trna → aa if ddna-dna pairing does not occur in the final state but other dark particles are paired with the their ordinary variants. if only dmrna-mrna and ddna-dna pairings occur, the reaction gives the reversal mrna → dna of transription. it should be easy to check whether this is allowed by the tensor product decomposition for the group representations associated with dark proton triplets [22]. same applies to other reactions considered below. if this reaction is possible then also the reversal daa + ddna → dmrna+dtrna. can occur. if only ddna-dna and dmrna-mrna pairings occur this gives rise to transcription of dna→ mrna. also reverse translation aa → mrna is possible. 2. one can consider also the reaction dmrna+dtrna → daa + dmrna . if all pairings except daa-aa pairing are present, the outcome is instead of translation the replication of mrna such that the amino-acid in trna serves the role of catalyzer. i have considered the possibility that this process preceded the ordinary translation: in a phase transition increasing heff the roles of aa and rna in trna would have changed [34]. if this reaction is possible then also its reversal daa + dmrna → dmrna+dtrna is allowed. if all pairing except dmrna-mrna occur, this gives rise to aa +rna → trna allowing to generate trna from aa and rna (not quite rna). 3. the replication of dna strand would correspond at dark level to a formation of bound states by the reaction ddna+ddna→ ddna +bound ddna in which all particles are paired. the opening of dna double strand would correspond to the reverse of this bound state formation. these dark particle reactions behind the shadow dynamics of life should be describable by s-matrices, which one might call the s-matrix of life. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | september 2018 | volume 8 | issue 2 | pp. 74-89 85 pitkänen, m., getting philosophical: on the problems in physics, neuroscience & biology 1. for instance for dmrna+dtrna→ x, where x can be dmrna+dtrna (nothing happens forward scattering) or daa + ddna and perhaps even daa+dmrna, one would have unitary s-matrix satisfying ssdagger = id giving probability conservation as ∑ n pm,n = |smn|2 = 1 as a special case. writing s = 1 + it unitarity gives i(t − t †) + tt dagger = 0 giving additional constraints besides probability conservation. for dmrna+dtrna→ daa + ddna the non-vanishing elements of t are only between pairs [(dmrna,dtrna), (daa,ddna)] for which mrna pairs with trna and dna codes for aa. unitary matrix would be coded by amplitudes t(aa,dnai(a)) satisfying ∑ i pi(daa) = p(ddna+daa), pi(aa) = |t(daa,ddnai(a)|2. p(ddna+daa) equals to p(ddna+daa) = (1− p)br(ddna+daa), where p is the probability that nothing happens (forward scattering) and br(ddna + daa) is the branching ratio to ddna+daa channel smaller than 1 if br(ddna + dmrna) is non-vanishing. the natural interpretation for pi(aa) would be as probability that dnai codes for it. 2. for the reverse reaction daa + ddna rightarrow dmrna+dtrna it is natural to assume that dtrna corresponds to any trna, which pairs with rna. the aa associated with this trna is always the same but the counterpart of rna can vary (wobbling). one can speak of the decomposition of dark genetic code to dmrna → dtrna → daa to a pair of codes mapping dmrna to dtnra and dtrna to daa [31]. there is a set trnai(mrna) of trnas coding for given mrna, and the probabilities pi(dmrna) sum up to p = ∑ i pi(dmrna) = (1 − p)br(dmrna + dtrna), where p is the probability for forward scattering and br(dmrna + dtrna) is the branching fraction. the natural identification of pi(dmrna) is as the probability that mrna pairs with trnai. a possible weak point of the proposal is pairing: what are the conditions under which it occurs and are different pairing patterns possible. possible second weak point is purely group theoretic: one should check whether which reactions are allowed by the tensor product decompositions for the states of dark proton triplets. 2.11 the mystery of replication replication is one of the deepest mysteries of biology. it is really something totally counterintuitive if cell is seen as a sack of water plus some chemicals. we have a lot facts about what happens in the replication at dna level but how this miracle happens is a mystery. at cell level the situation gets even more complex. philosopher thinks that behind the chemistry there might lurk a much simpler quantum dynamics and that chemistry only makes its best to mimic this deeper dynamics. is biochemistry controlled by something? does this something provide a template for the dynamics at chemical level? the idea about the presence of this something popped up already in the mystery of eeg. what could this something perhaps receiving sensory information from vertebrate brain and maybe providing feedback as control signals affecting also chemistry? now our brave philosopher attacks the length scale reductionism again. isn’t it quite too much to require that all these replications in different length scales would result as accidental ”emergence” due to thermodynamical fluctuations? could the dynamics be fractal with essentially same patterns for instance replication occurring in different scales. could this dynamics be induced by what happens on this something. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | september 2018 | volume 8 | issue 2 | pp. 74-89 86 pitkänen, m., getting philosophical: on the problems in physics, neuroscience & biology philosopher also suggests a concrete model for the controlling level: dark matter with large value of planck constant heff/h0 = n at magnetic flux tubes and asks whether the conjectured dark realization of dna in various scales performs the fundamental replication inducing in turn the biological replication in various scales as a mimicry? this would simplify the situation enormously but in totally different manner than length scale reductionism. morphogenesis controlled by the hierarchy of dark realizations of genetic code would be the basic vision (see http://tinyurl.com/yalny39x). this would simplify the situation enormously but in totally different manner than length scale reductionism. tgd suggests also a purely topological element involved with replication. magnetic body (mb) could replicate [15]. replication would be like 3-vertex of feynman diagram representing the decay of a particle to two particles. mb or part of it regarded as particle like entity splits into two. the incoming 4-surface and two outgoing 4-surfaces meet along 3-d surface common to all three. after that various molecules would self-organize around the resulting templates. this could happen also for the mb of dark dna in replication and induce the bio-chemical part of replication. 2.12 homeostasis homeostasis means that system is able to preserve its flow equilibrium under changing conditions. this involves many-layered hierarchies of pairs of control signals with opposite effects so that the system stays in equilibrium. for instance, we could not stand without this control system as one can easily check by using non-living test body! for instance, in bio-chemical homeostasis the ratios of concentrations remain constant. for the philosopher it is not at all obvious whether ordinary chemistry can explain homeostasis. in zero energy ontology (zeo) one can imagine very fundamental mechanism of homeostasis. 1. zero energy states are pairs of ordinary 3-d states with members located at opposite boundaries of causal diamond (cd). their total quantum numbers are opposite, which is only a manner to say that conservation laws hold true. the space-time surfaces connecting the 3-surfaces are preferred extremals of the action principle. in quantum field theory this picture can be seen only as a book keeping trick and one assumes that space-time continues beyond causal diamond. there is however no need for this in tgd framework although it is natural to assume that there is some largest cd beyond which space-time surfaces do not continue. cds form a hierarchy and sub-cds of this cd can be connected by minimal surfaces, which are analogs of external particles. one obtains networks analogs to twistor grassmannian diagrams. 2. conscious entities (selves) correspond in zeo to a sequences of state function reductions having interpretation as weak measurements, ”small” state function reductions [27]. in given weak measurement the members of the zero energy state at the passive boundary of cd are not affected: this is essentially zeno effect associated with repeated measurements in ordinary quantum theory. the members of the state pairs at the active boundary of cd change and also the temporal distance between the tips of cd increases: this assigns a clock time to the experienced flow of time as sequence of state function reductions. eventually it becomes impossible to find observables, whose measurement would leave the passive parts of the zero energy state invariant. first ”big” state function reduction changing the roles of active and passive boundaries of cd takes place and time begins to run in opposite direction since the formerly passive boundary recedes away from the formerly active boundary which is now stationary. self dies and re-incarnates with an opposite arrow of time. in tgd biology these two time-reversed selves are proposed to correspond to motor actions and sensory perceptions. already fantappie [9] realized that two arrows of time seem to be present in living matter (consider only spontaneous assembly of bio-molecules as decay in opposite direction) and introduced the notion of syntropy as time-reversed entropy. for an observer with given arrow of time, a system issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/yalny39x dna decipher journal | september 2018 | volume 8 | issue 2 | pp. 74-89 87 pitkänen, m., getting philosophical: on the problems in physics, neuroscience & biology with opposite arrow of time seems to break the second law. temperature and concentrations gradients develop, system self-organizes. 3. these two quantal time evolutions with opposite arrows of time look very much like competing control signals in homeostasis. the 4-d conscious entities corresponding to control signals would have finite lifetime so that in their ensemble the effects of the signals with opposite arrows of time tend to compensate. this would give rise to homeostasis. 2.13 evolution philosopher cannot avoid the question ”what is evolution?” in standard biology evolution is mystery. if one believes on standard thermodynamics, evolution is impossible by second law and the eventual heat death is unavoidable. evolution means generation of structures and second law indeed states that all gradients die so that the finals state is totally uninteresting homogenous stuff. the weird proposal that biology is just an enormous thermodynamical fluctuation has been already mentioned. boltzmann brain was indeed a kind of fad of pop physicists for some years ago. the idea if you want to call it such was that boltzmann brains and also ours popped up from the multiverse by a complete accident. one could even argue that this occurred only at planet earth to make the claim more plausible. to my opinion this is however not science anymore. philosopher asks questions and now the most obvious questions are following. is evolution something much more general than biological evolution? is evolution a basic aspect of physics as already cosmological evolution suggests? is evolution ”must”, something completely unavoidable? what could force it? the universe governed by second law certainly does not allow evolution: just the contrary. could the increase of entropy and increase of conscious information and development of cognition relate somehow? it has been argued by jeremy england [3] (see http://tinyurl.com/o64rd7o) that biological evolution involves increase of the rate of entropy production as any-one can see by just looking around. these two things are not the same but are they somehow related [20] (see http://tinyurl.com/zjp3bp6). philosopher already mentioned that p-adic physics as physics of cognition not only leads to a measure for conscious information something very non-trivial but to adelic physics fusing physics in various number fields [25, 26]. adeles form a hierarchy labelled by the dimension of the extension of rationals inducing the extension of p-adic number fields labelled by primes. this dimension corresponds to the effective value of planck constant and the larger it is, the larger the scale of quantum coherence is. this has been already said but now comes the basic point. since the number of extensions of rationals with dimension larger than given integer n is finite and the number of those with dimension larger than n is infinite, this dimension is bound to increase in statistical sense in the sequence of state function reductions recreating the quantum universe again and again. evolution is unavoidable! this is like random work from origin upwards. the height from the origin unavoidably increases. even more, the total negentropy coming from various p-adic sectors turns out to be larger than the entropy coming from the real sector. the bad news not actually a news is that increase of this negentropy is accompanied by the increase of entropy: civilizations indeed have the bad habit of polluting their environments. the good news is that negentropy increases faster than entropy: for a trivial extension of rationals from which everything would have started, negentropy equals to entropy. but for more complex extensions it is larger. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/o64rd7o http://tinyurl.com/zjp3bp6 dna decipher journal | september 2018 | volume 8 | issue 2 | pp. 74-89 88 pitkänen, m., getting philosophical: on the problems in physics, neuroscience & biology references [1] levin m. the wisdom of the body: future techniques and approaches to morphogenetic fields in regenerative medicine, developmental biology and cancer. regen med . available at: http: //www.futuremedicine.com/doi/pdf/10.2217/rme.11.69, 6(6):667–673, 2011. 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[19] pitkänen m. geometric theory of harmony. available at: http://tgdtheory.fi/public_html/ articles/harmonytheory.pdf, 2014. [20] pitkänen m. jeremy england’s vision about life and evolution: comparison with tgd approach . available at: http://tgdtheory.fi/public_html/articles/englandtgd.pdf, 2015. [21] pitkänen m. about minimal surface extremals of kähler action. available at: http://tgdtheory. fi/public_html/articles/minimalkahler.pdf, 2016. [22] pitkänen m. about physical representations of genetic code in terms of dark nuclear strings. available at: http://tgdtheory.fi/public_html/articles/genecodemodels.pdf, 2016. [23] pitkänen m. comments about the representations in sse-2016 conference about consciousness, biology, and paranormal phenomena. available at: http://tgdtheory.fi/public_html/articles/ sse.pdf, 2016. [24] pitkänen m. dmt, pineal gland, and the new view about sensory perception. available at: http: //tgdtheory.fi/public_html/articles/dmtpineal.pdf, 2017. [25] pitkänen m. philosophy of adelic physics. in trends and mathematical methods in interdisciplinary mathematical sciences, pages 241–319. springer.available at: https://link.springer. com/chapter/10.1007/978-3-319-55612-3_11, 2017. [26] pitkänen m. philosophy of adelic physics. available at: http://tgdtheory.fi/public_html/ articles/adelephysics.pdf, 2017. [27] pitkänen m. re-examination of the basic notions of tgd inspired theory of consciousness. available at: http://tgdtheory.fi/public_html/articles/conscrit.pdf, 2017. [28] pitkänen m. about dark variants of dna, rna, and amino-acids. available at: http://tgdtheory. fi/public_html/articles/darkvariants.pdf, 2018. [29] pitkänen m. about the correspondence of dark nuclear genetic code and ordinary genetic code. available at: http://tgdtheory.fi/public_html/articles/codedarkcode.pdf, 2018. [30] pitkänen m. emotions as sensory percepts about the state of magnetic body? available at: http: //tgdtheory.fi/public_html/articles/emotions.pdf, 2018. [31] pitkänen m. homonymy of the genetic code from tgd point of view. available at: http:// tgdtheory.fi/public_html/articles/homonymy.pdf, 2018. [32] pitkänen m. morphogenesis in tgd universe. available at: http://tgdtheory.fi/public_html/ articles/morphotgd.pdf, 2018. [33] pitkänen m. new insights about quantum criticality for twistor lift inspired by analogy with ordinary criticality. available at: http://tgdtheory.fi/public_html/articles/zeocriticality.pdf, 2018. [34] pitkänen m. new results in the model of bio-harmony. available at: http://tgdtheory.fi/public_ html/articles/harmonynew.pdf, 2018. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://www.tgdtheory.fi/public_html/tgdquantum/tgdquantum.html#twistquestions http://www.tgdtheory.fi/public_html/tgdquantum/tgdquantum.html#twistquestions http://tgdtheory.fi/public_html/articles/harmonytheory.pdf http://tgdtheory.fi/public_html/articles/harmonytheory.pdf http://tgdtheory.fi/public_html/articles/englandtgd.pdf http://tgdtheory.fi/public_html/articles/minimalkahler.pdf http://tgdtheory.fi/public_html/articles/minimalkahler.pdf http://tgdtheory.fi/public_html/articles/genecodemodels.pdf http://tgdtheory.fi/public_html/articles/sse.pdf http://tgdtheory.fi/public_html/articles/sse.pdf http://tgdtheory.fi/public_html/articles/dmtpineal.pdf http://tgdtheory.fi/public_html/articles/dmtpineal.pdf https://link.springer.com/chapter/10.1007/978-3-319-55612-3_11 https://link.springer.com/chapter/10.1007/978-3-319-55612-3_11 http://tgdtheory.fi/public_html/articles/adelephysics.pdf http://tgdtheory.fi/public_html/articles/adelephysics.pdf http://tgdtheory.fi/public_html/articles/conscrit.pdf http://tgdtheory.fi/public_html/articles/darkvariants.pdf http://tgdtheory.fi/public_html/articles/darkvariants.pdf http://tgdtheory.fi/public_html/articles/codedarkcode.pdf http://tgdtheory.fi/public_html/articles/emotions.pdf http://tgdtheory.fi/public_html/articles/emotions.pdf http://tgdtheory.fi/public_html/articles/homonymy.pdf http://tgdtheory.fi/public_html/articles/homonymy.pdf http://tgdtheory.fi/public_html/articles/morphotgd.pdf http://tgdtheory.fi/public_html/articles/morphotgd.pdf http://tgdtheory.fi/public_html/articles/zeocriticality.pdf http://tgdtheory.fi/public_html/articles/harmonynew.pdf http://tgdtheory.fi/public_html/articles/harmonynew.pdf introduction importance of philosophical thinking basic dogmatics restricting the attention to biology and neuroscience nothing but biochemistry and electromagnetism why vivo-vitro difference? what selected the biomolecules? where does the coherence come from? morphogenesis the dynamics of space-time surfaces general view about morphogenesis metabolism does metabolic energy feed generate conscious information? genetic code hen-or-egg questions of biology how life began? the mystery of replication homeostasis evolution login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x retrieval – dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 104-129 miller, i., novel approaches to genomic science: retrieval & curation issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 104 guest editorial novel approaches to genomic science: retrieval & curation iona miller * abstract from 2000-2006 emergent mind published the open-source, nonprofit and peer-reviewed journal of nonlocality and remote mental interactions. this journal was founded by lian sidorov, phd, who served as the executive editor, with iona miller and leane roffey line serving as assistant editors. it mapped the frontiers of consciousness and mind-matter interaction. sidorov is a physicist and put together a superb global team of researchers. the aim was to create a road map for the future of mind-body research and energy medicine, genetic architecture and regulation, studies in consciousness-related anomalies, and experiments in a comprehensive academic psi research program to provide critical references. dr. sidorov continues working under the international consciousness research laboratories (icrl) umbrella, which proposes the establishment of a world-wide, cross-disciplinary network of researchers, technical experts and volunteers committed to a sustained, active participation in this exploratory effort. they propose the creation of an open, searchable database of article preprints (including experimental proposals and reports, case studies and testable hypotheses). both the icrl and quantum dream, inc. projects support conceptual and infrastructural platforms of open-source scientific inclusion, among novel approaches for the representation and assessment of scientific knowledge in modeling, experimentation and education. key words: genomic science, novel approach, retrieval, curation, jnrm, icrl, heuristics, consciousness, hermeneutics, mind-body mapping, meta-narrative, pandisciplinary, epigenetics, wave genetics, meta-genetics, biophysics, paradigm shift, archetypes, gene expression. heuristic passion is ...the mainspring of originality --the force which impels us to abandon an accepted framework of interpretation and commit ourselves, by the crossing of a logical gap, to the use of a new framework. . . . having made a discovery, i shall never see the world again as before. my eyes have become different; i have made myself into a person seeing and thinking differently. i have crossed a gap, the heuristic gap, which lies between problem and discovery. -(polyani, 1962, cited in moustakis, 1990) * correspondence: iona miller e-mail: iona_m@yahoo.com mailto:iona_m@yahoo.com dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 104-129 miller, i., novel approaches to genomic science: retrieval & curation issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 105 introduction owing to the lack of conclusive evidence, this editorial proposes likely hypotheses, not definitive solutions. heuristic inquiry requires that we remain open, receptive, attuned to all facets of experience of a phenomenon. intuition facilitates perception of wholes, an essential characteristic of seeking knowledge. all heuristic inquiry begins with the internal search to discover, a passionate desire to know, a devotion and commitment to pursue a well-posed question. six phases of heuristic research guide unfolding investigations, comprising the basic research design. they include: the initial engagement, immersion into the topic and question, incubation, illumination, explication, and culmination of the research in a creative synthesis. (moustakis) over a hundred years have passed since quantum physics proved that consciousness cannot be separated from a complete view of reality. such pioneering efforts require archiving and curation, much as takes place in the arts. mcniff (1998) points out that “art-based research expands heuristic research by introducing the materials of creative expression to the experimental process”. all maps of reality are filtering systems. research is problem solving that also awakens self-knowledge. to correlate data accumulating within the field, many extraordinary theorists were included in jnlrmi, some of whom have unfortunately passed since that time, while others continue to inspire the mind-body sphere of research, genetics and complementary medicine. the forum included an archive of innovative papers by recognized experts in physics, biology, parapsychology, cognitive science, and noetics: bohm, penrose, laszlo, sarfatti, popp, goswami, pitkanin, sedlak, varela, hameroff, stapp, freeman, oschman, rubik, grof, chouinard, beichler, beal, tiller, targ, and more. jnlrmi published eight issues, featuring sidorov, pitkanin, kaivarainen, gariaev, miller, miller & webb, benford, and more, with interviews of parapsychology pioneers joseph mcmoneagle, roger nelson, stanley krippner, fred alan wolf, jim tucker, gerry zeitlin, chris king, mark germine, etc. the dormant jnlrmi can still be found at emergentmind.com. the journal of nonlocality looks forward to a re-launch as a purely experimental publication (only experimental proposals and reports). in an open letter on their “mind-matter mapping project”, sidorov, et al (2012) from the international consciousness research laboratories summarize the current research climate: (appendix a) bending an existing paradigm to accommodate new facts has always been a process fraught with inertia, higher-than-justified resistance and violent rebounds. to say that the study of nonlocal, consciousness-related phenomena faces a similar challenge today is an understatement. although many prominent scientists would agree that simple reductionism has failed to produce an adequate explanation for some of our most important questions, such as the hard problem of consciousness or the foundations of quantum mechanics, few of these scientists are ready to dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 104-129 miller, i., novel approaches to genomic science: retrieval & curation issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 106 accept a change in our set of axioms, particularly the possibility that consciousness may be an elemental, rather than emergent component of reality. as a result, researchers in the field of mind-matter interactions find that they not only need to struggle with the limitations of our current scientific tools to make sense of their data, but also to fight for the legitimization of this data with a mainstream science community that is unwilling to accept its conceptual challenges. and yet, as daunting as this position seems at the moment, it is also an exhilarating one – for rarely in the history of science have we been faced with such unknowns. from ever-expanding entangled systems to remote perception and fieldreg effects, the evidence for nonlocality and mind-matter interactions keeps flooding in; but if this data cannot be plotted within our current system of coordinates, how do we begin to find our way toward a new one? among other remedies, they recommend the following, which is very much within the research goals of the quantum dream, inc. research group: we propose the establishment of a world-wide, cross-disciplinary network of researchers, technical experts and volunteers committed to a sustained, active participation in this exploratory effort. the goal of this collaborative project would be to index relevant questions and research leads; create a searchable roster listing each member’s background, interests, technical expertise and access to laboratory resources; to develop new experimental models; share expertise and equipment resources; mentor on and critique study methodology; make inroads into mainstream applications; and publish all such developments in one centralized, searchable database which would be highly visible and readily accessible online. given the scarcity of funding and resources available for mind-matter projects, we must try to do less with more. the ability to capture ideas, connect experimental proposals to available resources and create a formal venue for the publication of such proposals would ensure that no good ideas remain stillborn for lack of opportunity and that proposed studies can be critiqued and methodologically strengthened at the earliest possible stage. outreach to mainstream science is another goal of the project. however, academia is often accused of stunting creativity and progress in the name of the status quo: creativity enhances life. it enables the great thinkers, artists, and leaders of our world to continually push forward new concepts, new forms of expression and new ways to improve every facet of our existence. the creative impulse is of particular importance to scientific research. without it, the same obstacles, ailments, and solutions would occur repeatedly because no one stepped back and reflected to gain a new perspective. unfortunately, in the academic world—where much of today’s scientific innovation takes place— researchers are encouraged to maintain the status quo and not “rock the boat.” this mentality is pervasive, affecting all aspects of scientific research from idea generation to funding to the training of the next generation of scientists. (southwick, 2012) dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 104-129 miller, i., novel approaches to genomic science: retrieval & curation issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 107 digital curation the collection and re-contextualization of the artifacts and pioneering articles of any scientific field is as important as art curation. both art-based research and science involve the use of systematic experimentation with the goal of gaining knowledge about life. digital curation is the selection, preservation, maintenance, collection and archiving of digital and print assets. the web is a user-curated platform but subject to link-rot and site-rot. curation of meaningful works helps those new to any interdisciplinary field retain a sense of the whole field and its arc of development. in art, a more naïve rendering is rarely considered less valuable than the latest style or approach. to the contrary, it may be seen as foundational; proto is not confounded with pseudoanything. the joy of research and discovery is an inherent part of the creative process. content curation selects what will be remembered in the history of any discipline. some important notions arise in unrelated and even esoteric worldviews. that is, metaphysical concepts often precede solid scientific modeling. armchair theoretics aside, even self-described “scientific papers” by recognized experts may sound uncritical in retrospect. still such works introduce fundamental issues, such as ‘resonance’, ‘intentionality’, ‘holism’, and a host of ideas once thought irrelevant to the core science of physics. so, whether such papers read as “dated” or of their own era, the best deserve to be retained in the literature. each field must preserve such archives or lose the developmental thread from courageous colleagues. because of its exclusion from conventional reportage, frontier science is often relegated to a disjointed series of small journals and obscure publications that limit its exposure in the arena of ideas and inspirations. curation is further compounded by cyberculture, and the scattered online musings of self-styled and genuinely worthy independent scholars. we generally resolve this cognitive dissonance by doubling-down on our own prejudices in opposition to those with whom we disagree. we tend to pathologize and demonize the other. we frame these conflicts as zero-sum and negative-sum competitions. yet, if we take a more artful approach to science, we can maintain an open attitude as well as the rigor demanded by best practice. theoretics uses creative thought, disciplined logic, and the current knowledge base to develop credible scientific theory. experimental support emerges from such approaches, distinguishing concept from reality. when we experience new events, the brain encodes a memory of it by altering the connections between neurons. this requires turning on many genes in those neurons. neuroscientists at mit’s mcgovern institute for brain research identified a master gene -npas4 -that controls this complex process in the hippocampus, a brain structure known to be critical in forming longterm memories. (kurzweil, 2011) dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 104-129 miller, i., novel approaches to genomic science: retrieval & curation issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 108 ideas advance, in part, because of their popularity among stakeholders in the theories of by-gone eras. conversely, some ideas are actively suppressed for security and financial interests. it holds true from cosmology to micro-physics and micro-biology. competing metanarratives shape our theories, lives and identities. the philosophy of interpretation can help us dig our way out of this relativistic mess, an entangled web of worldviews. yet, science is rooted in prediction and a keen eye for the future of technology. in art, the visionary is rewarded; in science, often spurned, even when the motivation is to inspire others to greater heights of human experience and understanding. even in nature, growth occurs at the very edge of creativity. speculation is an inherent part of the process in which we argue many sides of the nature of reality. too frequently, such “blue sky” speculation is withheld from the academic or pandisciplinary arena where its relative value can be more accurately assessed, literally or metaphorically. pierre teilhard de chardin saw an emerging sphere of consciousness encircling the planet. in his view, recognizing this new reality and living in that awareness was essential to solving the major problems of humanity. a cultural retrieval is undoubtedly a fundamental aspect of the process of cultural transformation. marshall mcluhan created a cultural geography where "space" is the master trope. he introduced the tetrad concept, a notion of process that includes enhancement, obsolescence, retrieval, and reversal. this tetrad of the effects of technologies is not sequential, but rather simultaneous. all four aspects are inherent from the start, and all four aspects are complementary. even while technology extends or enhances our sensory perception, it numbs or diminishes other areas of experience. every form pushed to its limits reverses its characteristics. retrieval implies that older notions may contain important overlooked information. thus, we find that the nature of “nothing”, the vacuum of absolute space, once spurned as irrelevant to the explication of force and form is arguably the most important aspect of 21 st century physics. the void of space has become a plenum. rather than an artifact of obsolete thinking, it has become one of the potentially most fruitful areas of investigation, more fundamental than the minute building blocks of particle physics, even though it remains a perennial mystery. hermeneutics developments in micro-biology at the threshold of molecular biology and wave-genetics imply a necessary retrieval of “hermeneutics”. if dna can be read as a “text”, as gariaev and others suggest, then that text necessarily requires decoding, translation and interpretation, compounding our exploration. dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 104-129 miller, i., novel approaches to genomic science: retrieval & curation issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 109 our attitude toward the text is shaped by whether we approach it skeptically or sympathetically. we all have a finite amount of time and attention, so these pre-filters are not insignificant. the text itself is not disconnected from the historical as well as biological context. perhaps, in some metaphorical sense, we are moving so fast, time is just the holographic blur of superpositions we cannot “read” or see with our multi-sensory sampling. if we have no place for certain notions in our maps of reality, they can be prematurely discarded as irrelevant. only the curating of such heterodox ideas, including them in the acceptable literature, keeps them relevant. naturally, this does not mean every old idea will bear new fruit, but often we firm up our own ideas by disagreeing with unproven notions which inspire through the gaps in such theories. critical theory applies psychological, sociological, philological, literary, historical, and philosophical theories to the text. critical frameworks are like lenses through which we discover new insights. a new interpretation can emerge, based on a close, critical reading of the text, with a deeper understanding. reading the text again, our understanding can be enriched by previous readings. the challenge, then, is to imagine the prospect of standing outside a tradition or ideology as an objective observer of the text using multiple methodologies and critical theories. the suspension of judgment, experimental reconfiguration, and shifting of standpoint are the keys to turning interpretation into a dynamic hermeneutical spiral. naturally, not all retrievals will yield scientific gold from the alchemical ore of literature and experimentation. yet, virtually any discourse or theory has the potential to stimulate original thought, experiments and vision. both literally and figuratively, hermeneutics can reverse the relationship between text and reader. instead of reading a "passive" text, we should allow an "active" text to read us, informing and transforming our world with new insights and understandings. in this sense, dna is arguably the best “read” currently available. there may be many correct readings of the intra-textual “information”, more or less available to “truth seekers” within the limited field of possible constructions. genomics genomics is the study of all the genes of a cell, or tissue, at the dna (genotype), mrna (transcriptome), or protein (proteome) levels, dna sequencing and fine-scale genetic mapping. even though great progress has been made in biology and medicine, when it comes to such areas as genetic genealogy results remain wide open to interpretation, often requiring other disciplines dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 104-129 miller, i., novel approaches to genomic science: retrieval & curation issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 110 to read meaningful findings. meta-genomics has revealed that the vast majority of microbial biodiversity was missed by cultivation-based methods. in its relatively short history, the unfolding science of dna deciphering has already produced surprises and revisions in the forms of epiand meta-genetics, strongly suggesting we need a socio-scientific dark-adapted eye for our explorations of the nature of ourselves and reality. as epigeneticist bruce lipton explains in the biology of belief, dr. temin, who was “originally ridiculed for his ‘heresy’,” subsequently “won a nobel prize for describing reverse transcriptase, the molecular mechanism by which rna can rewrite the genetic code.” dr. lipton hypothesizes that proteins also must have the ability, despite the prevailing genetic theory, to “buck the predicted flow of information.” logically, this must be the case, “since protein antibodies in immune cells are involved with changing the dna in the cells that synthesize them.” there are, however, “tight restrictions on the reverse flow of information, a design that would prevent radical changes in the cell’s genome.” similarly, lipton describes epigenetics as the science of how genes can be modified “without changing their basic blueprint.” these two quotes provide clues as to what lies beyond the reach of epigenetics and nurture. the latter function with “tight restrictions” on the way our own localized consciousness, in response to environmental signals, can flow in reverse and rescript our “basic blueprint”. specific epigenetic processes include paramutation, bookmarking, imprinting, gene silencing, x chromosome inactivation, position effect, reprogramming, transvection, maternal effects, the progress of carcinogenesis, many effects of teratogens, regulation of histone modifications and heterochromatin, and technical limitations affecting parthenogenesis and cloning. epigenetics is incapable of explaining evolution because it provides no mechanism allowing dna to be rewritten, spontaneously, sufficiently to create “radical changes in the cell’s genome” that transform a species into a new one. transcending both genetics and epigenetics, metagenetics concludes that the origin and evolution of species are driven neither by coding dna nor by regulatory proteins in cell membranes. rather, meta-genetics establishes that these two basically similar phenomena are controlled, via potential dna, by what might be called a lifewave, or wave genetics. today, meta-genetics encompasses a group of related fields including quantum bioholography, genetic linguistics, and wave-genetics. the discovery of gene-expression transcended the nature/nurture dichotomy. the life-wave is described as a potentially infinite series of waves, much as an ocean has an endless number of waves but remains a single body of water. the ocean is analogous to the “torsion,” source field, vacuum potential, or hyperdimensional sound domain of absolute space, where individual waves act as sonic carrier waves for the genetic blueprints of past, present and future species. dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 104-129 miller, i., novel approaches to genomic science: retrieval & curation issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 111 potential dna serves as the principal connection point between manifest and unmanifest form. in other words, potential dna, far from being inactive, constitutes the hyperdimensional interface between the sound and light domains. the existence of the genetic sound-light translation mechanism indicates that the flow of information, or conscious bioenergy, through dna is a two-way street. light becomes sound, and sound becomes light. biophotonic light is stored in the cells of the organism more precisely, in the dna molecules of their nuclei. a dynamic web of light is constantly released and absorbed by the dna and may connect cell organelles, cells, tissues, and organs within the body and serve as the organism's main communication network and as the principal regulator for all life processes. dna acts as a holographic projector of acoustic and em information which contains the informational quintessence of the biohologram. in the meta-genetic model, potential dna is both a form and function of the life-wave. in both cases, potential dna can be theorized to exist as a consciousness blueprint. fundamentally, we are not in any way separate from our environment, locally and cosmically. fractal science has shown that nature is self-similar at all scales, including those which escape observation at any given time. dna is an expressive potential. a unified understanding of science and history requires that many facts of science from diverse disciplines be organized by level of observation, chronology of emergence, the scale of size, and thresholds of complexity realized. the challenge is to use the book of nature as a common reality-based reference in our debates. genomics has psycho-social dimensions. ernest rossi, m.d. reveals his jungian approach, stating, “nothing, it seems turns on gene expression and brain plasticity as much as the presence of others of the same species!” jung suggested that "individual consciousness is only the flower and the fruit of a season, sprung from the perennial rhizome beneath the earth; and it would find itself in better accord with the truth if it took the existence of the rhizome into its calculations. for the root matter is the mother of all things." the nature of consciousness consciousness remains the “hard problem” of frontier science and the elusive target of consciousness studies – though many experts admit we are no closer to solutions than we were some forty years ago. neurology has made some tantalizing suggestions, but often fails to separate ‘consciousness’ from simple ‘awareness’ or self-direction. the nature of consciousness is recursive, self-similar, self-referential, and self-reflexive. it is as weird as the quantum world. meta-genetics recognizes the primacy of consciousness over environment and molecular biology. consciousness is connected with one unity. findings from new sciences provide external validation for the new biopsychosocial perspective and offer important insights into the dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 104-129 miller, i., novel approaches to genomic science: retrieval & curation issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 112 manifold means by which socioenvironmental experiences influence neurobiological structure and function across the life course. according to csíkszentmihályi, flow is completely focused motivation. it is a single-minded immersion and represents perhaps the ultimate in harnessing the emotions in the service of performing and learning. in flow, the emotions are not just contained and channeled, but positive, energized, and aligned with the task at hand. openness is essential. from ancient times, people have described an ecstatic experience of the connectedness of all things as the pinnacle of human emotions. different religious traditions have different words for this state: "enlightenment" -"ecstasy" -"being one with the tao", vision quest, -"religious transport." in the language of contemporary science, self-actualization is famously at the top of maslow's hierarchy of needs. in process therapy, flow means parareception: "access" to the depths of the psyche with the doors of perception wide open. areas of extrasensory perception or anomalous cognition include (1) telepathy; (2) clairvoyance; and (3) retrocognition/precognition. recent research by xiao-song ma, et al suggests the entanglement of two intimately-connected particles implies a future decision can affect the past states of the particles. (moskowitz) dna is the universal information transducer, the hidden intelligence or "hidden fire" within us. this vast archive of information is passed along through a replicating process that involves the copying and encoding of genetic information from dna to rna (ribonucleic acid). the original dna that is housed within the nucleus of our cells programs instructions for the production of enzymes and proteins. these dna instructions are not directly converted into proteins, but are copied into rna. this ensures that the information contained in the dna does not become tainted, thus preserving the archive. rna polymerase attaches to the dna at a specific area called the promoter region. the dna strand opens and allows rna polymerase to transcribe only a single strand of dna into a single stranded rna polymer called messenger rna. the messenger rna carries the information to the sites of protein synthesis (ribosome), thereby creating a replica of the original dna. in this manner the genetic code is passed from cell to cell, mother to child. vision (future memory) relates to precognition; healing is a form of creativity, and gnosis is an access state – self-realization. self realization demands unlocking knowledge by direct experience. the greek word "gnosis" means direct experiential knowledge. stories of distance healing, a form of pk or psychokinesis (mind over matter), require another article of their own to do them justice. it may be easier to model virtual information transfer than mind over matter. "spooky action at a distance" requires even stronger evidence than sensing at a distance. but is "distance" here really a factor or an illusion in a holographic simply-connected or nonlocal universe? the paradox of spacetime and relativity presents itself in psi as psychoretrocognition, or time-reversed pk. dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 104-129 miller, i., novel approaches to genomic science: retrieval & curation issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 113 though these experiences of knowing at a distance are called "extra-sensory," they often appear "as if" received by conventional sensory or mental means, for how else can we "know what we know"? it is a holistic psychophysical experience, affecting the whole self, physically, emotionally, mentally and often spiritually. the impediments of distance and time seem to dissolve; the barriers of spacetime are mysteriously overcome. the information is 'just there' in one form or another, whether spontaneous or facilitated. however it occurs, information becomes available to consciousness through imagery, sensation and awareness. cellular and soul memory might also include some ancestral dread. gnosis is an immediate experience -a psychosensory gestalt, ranging from the "a-ha!" experience to peaking in the cognitive orgasm of illumination. the blueprint for our future memory as a species may be encoded in our seemingly dormant dna material. perhaps the evolutionary instructions for humanity’s future development contained within the dna material rest in a dormant state, waiting to be activated. information gleaned not only from our genetic past, but our environment's collective past -earth's cumulative organic database -is available on a cellular level to all species within the biosystem. a planetary intelligence, the universally consistent dna coding system is potentially capable of passing information throughout the biosphere. quantum coherence & entanglement our biophysics is bioelectronic, electrochemical, biomagnetic, biophotonic and quantum. the energy body or field body is linked directly to the creative plenum. we refresh ourselves from it in the gaps between our breaths. dr. mae-wan ho is a world renowned geneticist & biophysicist. she is a life-long critic of neodarwinism and genetic engineering and pioneer of a physics of organisms. she proposes that quantum coherence is the basis of living organization and can also account for key features of conscious experience. they include the "unity of intentionality", our inner identity of the singular "i", the simultaneous binding and segmentation of features in the perceptive act, the distributed, holographic nature of memory, and the distinctive quality of each experienced occasion. further, a thoroughly organicist way of thinking transcends both conventional thermodynamics and quantum theory. quantum coherence and nonlocal intercommunication are the expression of the radical wholeness of the organism, where global and local are mutually entangled, and every part is as much in control as it is sensitive and responsive. the life cycle, with its complex of coupled cyclic processes, forms a heterogeneous, multidimensional and entangled space-time which structures experience. in the ideal, it is a quantum superposition of coherent space-time modes, constituting a pure state that maximizes both local freedom and global cohesion in accordance with the factorizability of the quantum coherent state. dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 104-129 miller, i., novel approaches to genomic science: retrieval & curation issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 114 quantum coherence gives rise to correlations between subsystems which resolves neatly into products of the self-correlations so that the sub-systems behave as though they are independent of one another. one can also picture the organism as a coherent quantum electrodynamical field of many modes, with an uncertainty relationship between energy and phase. if quantum coherence is characteristic of the organism as conscious being, then the conscious being will possess something like a macroscopic wave-function. this wave function is ever evolving, entangling its environment, transforming and creating itself anew. in bohm and hiley's ontological interpretation of quantum theory there is no collapse of the wave function. with quantum potential playing the role of active information to guide the trajectories of particles, the wave function simply changes after interaction to become a new one. the possibility remains that there is no resolution of the wave functions of the quantum objects after interacting. so one may remain entangled and indeed, delocalized over past experiences (i.e., in lazlo's ambient field). some interactions may have time scales that are extremely long, so that the wave function of interacting parties may take a correspondingly long time to become resolved, and large scale nonlocal connectivity may be maintained. the wave function may look like an intricate supramolecular orbital of multidimensional standing waves of complex quantum amplitudes. it would be rather like a beautiful, exotic flower, flickering in and out of many dimensions simultaneously. that would constitute our quantum holographic self, created from the entanglements of past and future experiences, the memory of all we have suffered and celebrated -the totality of our anxieties and fears, our hopes and dreams. (ho, 1997)). gene-expression gene expression is the cellular process that decodes the genetic information in dna and converts it into proteins. it is regulated at many levels: when messenger rna is transcribed from dna; when mrna is translated into proteins; and at the epigenetic level, when the structure of chromatin, coils of dna wound around histone proteins, is altered. although most discussion of gene expression focuses on the regulation of transcription, the other components of the process are also crucial. yet little is known about how they are integrated. (rossi, 2010) work by tom misteli at the national cancer institute in bethesda, maryland, and his team provides a striking example of the integration of seemingly disparate components in geneexpression regulation (luco et al., 2010). they describe how patterns of alternative splicing of newly made rna, a key regulatory mechanism, can themselves be regulated by specific chemical modifications in the chromatin. they also found that a given set of modifications to histones predicts patterns of rna splicing. the authors conservatively estimate that this mechanism occurs in dozens to hundreds of genes in the human genome. dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 104-129 miller, i., novel approaches to genomic science: retrieval & curation issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 115 this remarkable study makes a connection between a quintessential transcription-regulation mechanism, histone modification, and a post-transcriptional process, alternative splicing. it shows that chromatin can regulate not only how much of a protein, but also which protein, is made in a cell. we have seen a surge of intriguing studies suggesting that molecules that were thought to regulate transcription also direct epigenetic modifications, modify alternative-splicing patterns and participate in the intracellular transport of rna. synaptic connections underlie associative learning. psychological, social, and cultural signals modulate gene expression. psychosocial genomics measures changes in the deep psychobiological process of “activity or experience-dependent gene expression and brain plasticity” associated with creativity and healing. psychosocial genomics produces long-term changes in behavior, vision and worldview, through learning and morphological changes in gene expression that alter the strength of synaptic connections. structural changes alter the anatomical pattern of interconnections between nerve cells of the brain. stated simply, the regulation of gene expression by social factors makes all bodily functions, including all functions of the brain, susceptible to social influences. (rossi) neuro-gnosis neurognostic structures organize experience and cognition, and correspond somewhat to carl jung's archetypes. jung was ambiguous about the ontological status of the archetypes and the collective unconscious, because of the inadequacy of the science of his day. modern developments in the neurosciences and quantum physics especially the new physics of the vacuum allow us to develop jung's understanding of the archetypes further. direct neurophysiological-quantum coupling suggests how neural processing and quantum events may interpenetrate. he insisted that the archetype is not merely another word for the physiology of the image or thought. while it included the physiological basis of knowledge, the concept was intended to run deeper deep into the instincts and beyond, outward into the universal ground of existence. archetypes form the total ground the collective unconscious – upon which conscious cultural and personal experience develops. these structures are the products of natural selection, and are the impressions left by recurrent experiences of the species upon the nervous systems of individuals. they generate (or "cause") an endless variety of transformations that are experienced as images and ideas had in dreams, fantasies and visions. these images and ideas bear the mark of personal and cultural conditioning, and the archetypes themselves are involved in the development of consciousness. the archetypes produce all of the universal material in myth and ritual drama. archetypal experiences tend to be numinous and transpersonal in their impact upon personal development, for they are the eruption of archaic and timeless meaning into the personal world of the ego. dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 104-129 miller, i., novel approaches to genomic science: retrieval & curation issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 116 the archetype exists as the intersection of spirit and matter. we are now beginning to understand in a scientific way how this intersection might be possible, if by "spirit" we mean the order of the quantum sea. human experience becomes the localized instantiation of the universal the transcendental through the medium of neurognosis. and neurognosis is precisely the local embodiment of the structure of the sea, and at the same time the structures mediating consciousness. when michael persinger suggests in his book, neuropsychological bases of god beliefs (1987), that certain experiences of unity with the godhead may be mediated by structures in the temporal lobes, such an analysis need not imply a reduction of transpersonal experiences to neurophysiology. among other things, to reduce these experiences to their neurophysiological foundations begs such questions as the profundity of insight, or the causation-at-a-distance that may accompany such experiences. neurognostic or archetypal structures in the brain may transduce insights pertaining to the universal structure of the quantum sea. each human brain may indeed prove to be a microcosm that contains, like the proverbial mustard seed, or the more modem hologram all the wisdom of the ages, requiring only the optimal conditions of development for each person to individuate into a sage. (miller, 2008). rossi reports that neurogenesis can occur in the motor cortex simply through the act of imagining playing the piano (pascual-leone, amedi, fregni, & merabet, 2005). similarly, taxicab drivers develop the areas of their brains involved in spatial relationships by memorizing the labyrinthine streets and avenues of the cities in which they work (maguire et al., 2000). although the underlying mechanisms are different, neuroplasticity research suggests that challenging learning experiences can lead to the development of brain tissue in a manner analogous to the ways that physical exercise can lead to the development of muscle tissue. one area of research that has found significant evidence of mental training leading to neuroplastic modifications in brain activity focuses on the study of meditation. meditation, although greatly varying in technique and purpose across the diverse spiritual and cultural traditions in which it is used, may be generally defined as the intentional practice whereby one grasps "the handle of cognition" to cultivate a competent use of one's own mental capacities, gaining agency over thought and emotion (depraz, várela, & vermersch, 2003). such intentional mental training has been shown to induce functional neurobiological changes. jung's reference to the essential unknowability of the archetypes-in-themselves also applies to neurognostic structures. neurognosis may also refer to the functioning of these neural structures in producing either experience or some other activity unconscious to the individual. this usage is similar to jung's reference to archetypal imagery, ideas, and activities that emerge into and are active in consciousness. this includes ancestral / genetic memory. in the inward experience the connection between the psyche and the outward image or creed is first revealed as a resonance, relationship or correspondence. dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 104-129 miller, i., novel approaches to genomic science: retrieval & curation issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 117 jung's genius was in holding the tension of opposites of mind-body dualism that is, between experiential relativism on the one hand and physical reductionism on the other. it was clear to jung that an individual's experience is both structured by processes universal to the human psyche, and the manifestation of individuation. holding the tension of the opposites, one transcends them. holding a divine "tension" allows a new consciousness to unfold. as hybrid "spirit-matter" beings, we must realize it is appropriate for us to be living in two worlds at once -the world of the ego and the world of the soul. we do not become one watered-down nondescript composite: we each bring forth our entire way of being -as a very rich and inviting way to live. you can't wait to discover something without knowing how it is going to happen. expectancy and surprise in the neuro-psycho-physiology generate detectable changes in the dynamics of gene expression and neurotransmission. regulation of the priming step of the neurotransmitter release has important consequences for memory, learning, problem solving, and behavior change at the synaptic level. a synaptic protein called rim, among others, is involved in a key regulatory step of synaptic plasticity facilitated by priming the synaptic vesicles between neurons to release their neurotransmitters. the molecular messengers generated by stress, injury, and disease can activate immediate early genes within stem cells so that they then signal the target genes required to synthesize the proteins that will transform (differentiate) stem cells into mature well-functioning tissues. such activity-dependent gene expression and its consequent activity-dependent neurogenesis and stem cell healing is proposed as the molecular-genomic-cellular basis of rehabilitative medicine, physical, and occupational therapy as well as the many alternative and complementary approaches to mind-body healing. the therapeutic replaying of enriching life experiences that evoke the novelty-numinosumneurogenesis effect during creative moments of art, music, dance, drama, humor, literature, poetry, and spirituality, as well as cultural rituals of life transitions (birth, puberty, marriage, illness, healing, and death) can optimize consciousness, personal relationships, and healing in a manner that has much in common with the psychogenomic foundations of naturalistic and complementary medicine. the entire history of alternative and complementary approaches to healing is consistent with this new neuroscience world view about the role of psychological arousal and fascination in modulating gene expression, neurogenesis, and healing via the psychosocial and cultural rites of human societies. (rossi, 2003). a single genotype, the genetic blueprint of an organism, can be expressed in a multiplicity of distinct physiological and behavioral forms, known as phenotypes. the mechanisms by which such different phenotypes are expressed are just beginning to be understood, but they appear to involve the regulatory effect of internal and external environmental signals on stress hormones, which in turn modify gene transcription processes (rossi, 2004). dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 104-129 miller, i., novel approaches to genomic science: retrieval & curation issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 118 experiences modulate gene expression. in turn, experience-dependent modifications to neural tissue may be driven by epigenetic processes (that is, changes in gene expression produced by environmental determinants) .the human environment is constantly conditioned by social experiences, which, when transduced by the nervous system into electrochemical signals, may modulate protein synthesis in the nuclei of nerve cells, ultimately leading to changes in the replication and growth of neurons. social experience can change gene expression, leading to the restructuring of the brain through neuroplasticity. thought, emotion, and action trigger neural activity, which can lead to a reorganization of the brain, shaping future psychosocial experience. from this perspective, we are not the passive products of neurophysiology and heredity; rather, through our behavior in the social environment, we become active agents in the construction of our own neurobiology and, ultimately, our own lives. we have the power to transcend and transform their limitations into opportunities for growth and well-being. paradigm shift novel approaches to genomic as well as other sciences take place in the context of three primary paradigms of separation, connection and wholeness, reflected in genomics as molecular, epi and meta-genetics (wave genetics): a) the hierarchical paradigm: searching for connection and wholeness b) the transformation paradigm: inner wisdom and relational understanding c) the synthesis paradigm: integration orthodox vs. heterodox models the hierarchical paradigm exerts control to impose a form of limitation to define and understand, manipulating the status quo of science and belief systems with a containing and controlling effect of relative truths on culture. it represents diverse interests, perceptions of reality, and motives of action, containing intuitive abilities, and perhaps emphasizing preservation of the conventional over creativity. arguably, hierarchy has trapped itself in vested specialization and in the limiting aspects of diversity that prevent it from evolving from an arduous ladder of evolution to a joyous pursuit. fragmented science focuses on the part not the whole. it might be served better by removing rigid boundaries and barriers to exploration in a way that recognizes consciousness rather than detours from the road to expanded consciousness. externally oriented, it supports subgroups linking energies of independent branches. transdisciplinary models dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 104-129 miller, i., novel approaches to genomic science: retrieval & curation issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 119 transformative and integrative paradigms express novel approaches to the collective potential of all life in the universe and a grand connective vision, while maintaining scientific rigor. our awareness is directly connected to the very borders of discovery. the roots of the hierarchical tree are bound in the soil of genetic memory, subconscious instincts, and orthodox beliefs and institutions. evolution shifts positions within the hierarchy. the transformation paradigm initiates accelerated, independent pathways that bypass the hierarchy and expand creativity, accessed through direct experience, including transformation and novel access to authentic information and healing of fragmentation. pandisciplinary models synthesis is integration of the dominant paradigm of the hierarchy with the transformation paradigm – recognizing the integral manifestation of the wholeness. the next step is to integrate the time-based incremental model of evolutionary progress with the realization-based model of the transformation paradigm and recognition of the multidimensional universe. the process goal is to transmit this future experience into communication symbols and life principles that facilitate the bridging of the two paradigms. such catalysts focus on developing new communication symbols through various art and science forms that facilitate detachment from the controlling aspects of the hierarchy. these people also demonstrate the natural ease of interweaving the two primary strands of existence into a synthesis paradigm. the foundational plan of life's original source and ultimate destiny reintegrates itself into timelessness by following it back into the very foundation from which all things arise and return. novel approaches to genomics are part of this integrative process of energy and patterns of information and relationship. bioinformatics was applied in the creation and maintenance of a database to store biological information at the beginning of the "genomic revolution", such as nucleotide sequences and amino acid sequences. development of this type of database involved not only design issues but the development of complex interfaces whereby researchers could access existing data as well as submit new or revised data. the primary goal of bioinformatics remains to increase the understanding, analysis and interpretation of biological processes. discussion there is a lack of exposition on interdisciplinary and innovative methods of data mining, visualization and multiscale modeling for biodata and mind-matter mapping. an interdisciplinary set of novel pandisciplinary techniques from pure science and engineering, pattern recognition, and ontological data mining fields are applicable to genomics and consciousness studies. dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 104-129 miller, i., novel approaches to genomic science: retrieval & curation issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 120 consciousness is a reciprocal function of resilience and energy transducing tensegrity structures (southwick & miller). full and unqualified interest informs determination to extend our understanding and knowledge of experience. we are not separate from that, and need only hark back to the injunction of the ancient oracle of delphi to “know thyself”. the phenomenological heuristic research mode outlined by moustakas is a way of knowing that involves self-search, self dialogue and self-discovery by focusing on experience and trusting one’s self awareness and understanding. the primary task of heuristic research is acknowledging the fundamental awareness that exists in the researcher’s consciousness -“to receive and accept it, and then to dwell on its nature and the possible meanings” (p. 11). the researcher adheres to the strict six phase methodology: 1) initial engagement: the researcher formulates a question from engagement with a topic of deep personal significance or interest. 2) immersion: the process of becoming one with the question or study topic – all aspects of the researcher’s life are addressed within the context of the question. 3) incubation: removal of oneself from the intense involvement of the immersion phase in order to provide room for unconscious understanding. 4) illumination: new meaning is discovered or old understandings corrected or modified. 5) explication: the researcher’s understanding is sharpened through concentrated attention. 6) creative synthesis: the culmination of the process, in which themes are discerned and connections made; the researcher is open to receiving a better understanding of the question through intuition and tacit knowing. while it has been suggested (lau) that “[tyrannical] peer review may stifle novel approaches” to developmental methodologies, it remains a valuable part of scientific discourse. alternative or complementary approaches to traditional peer review can be included in research evaluation (birukau et al), since no single system can suit all stakeholders in various communities. the problem becomes not one of how to know something radically new, but how to learn something radically new. how can we know or describe anything about the changes we have not yet experienced, change that by universal consensus takes us beyond the realm of everyday reality, for which our words and concepts have been fashioned? in the holographic paradigm, weber says that, "psychological death occurs when consciousness keeps step with the ever-moving and self-renewing present, allowing no part of itself to become caught or fixated as residual energy. it is residual energy that furnishes the framework for what will become the thinker, who consists of undigested experience, memory, habit-patterns, identification, desire, aversion, projection and image-making. this is not a purely personal process but the energy of aeons of such processes sclerosed through time, persisting on both personal and collective levels. ego-death dismantles this superstructure...” as zukav's (1979) virtual energy-exchanges show, during all of these transactions new particlewave patterns are being re-created as virtual-energy "vapor-trails", instantaneously recycled into other energy fields -the eventual material manifestations of which our entire observable and experiential universe is composed. dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 104-129 miller, i., novel approaches to genomic science: retrieval & curation issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 121 bohm suggested that we transform as eternity unfolds in us, but that eternity may also transform, as it returns to itself enriched by our participation. in this theory, knowledge consists of the process of tuning in on the manifestation (phenomenon) of the nonmanifest in order to make it accessible, through a state of consciousness which lies outside the barriers of the finite senses. bohm maintains that this capacity exists in the universe, not in us strictly speaking. conclusion spinoza called our greatest pleasure the union of the mind with nature. nick herbert poetically wonders, "when will physicists expand their craft by daring to suppose a more creative kind of measurement -the "greatest pleasure" of spinoza?” david bohm suggested psychological "atom-smashing" as a way of radically destructuring the ego, opening it to wider experience of the undivided whole. references birukou, aliaksandr et al, alternatives to peer review: novel approaches for research evaluation, http://www.frontiersin.org/computational_neuroscience/10.3389/fncom.2011.00056/abstract bohm, david, wholeness and the implicate order, routledge; reissue edition (may 13, 1996) charrier, cécile et al., inhibition of srgap2 function by its human-specific paralogs induces neoteny during spine maturation, cell, 2012, doi: 10.1016/j.cell.2012.03.034 csíkszentmihályi, mihály (1990), flow: the psychology of optimal experience, new york: harper and row, isbn 0-06-092043-2 dennis, megan y. et al., evolution of human-specific neural srgap2 genes by incomplete segmental duplication, cell, 2012, doi: 10.1016/j.cell.2012.03.033 depraz, natalie , francisco j. varela & pierre vermersch (2003). on becoming aware: a pragmatics of experiencing. advances in consciousness research. phenomenology and consciousness in philosophy of cognitive science. garland, eric l. and matthew owen howard. an introduction to psychosocial genomics: how the body speaks to us about the effects of non-invasive processes such as therapeutic hypnosis; hill, r. 2010 . australian journal of clinical hypnotherapy and hypnosis 31 (1), pp. 5-16 http://integralsocialwork.com/documents/neuroplasticity.pdf ho, mae-wan, kybernetes 26, 265-276, 1997. "quantum coherence and conscious experience"; http://www.i-sis.org.uk/brainde.php kurzweil, ray, 2011, neuroscientists identify a master controller of memory http://www.frontiersin.org/computational_neuroscience/10.3389/fncom.2011.00056/abstract dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 104-129 miller, i., novel approaches to genomic science: retrieval & curation issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 122 http://www.kurzweilai.net/neuroscientists-identify-a-master-controller-of-memory kurzweil, ray, 2012, how a gene copy helped our brains become ‘human’ http://www.kurzweilai.net/how-a-gene-copy-helped-our-brains-becomehuman?utm_source=kurzweilai+daily+newsletter&utm_campaign=5113d1c38b-ua-9467421&utm_medium=email lau, thomas. 2006, peer review 'may stifle novel approaches’, concludes international conference. http://www.esf.org/media-centre/ext-single-news/article/peer-review-may-stifle-novel-approachesconcludes-international-conference-101.html laughlin, charles d., archetypes, neurognosis and the quantum sea http://www.scientificexploration.org/journal/jse_10_3_laughlin.pdf lipton, bruce, the biology of belief: unleashing the power of consciousness, matter and miracles, mountain of love (march 2005). maguire et al. (2000) navigation-related structural changes in the hippocampi of taxi drivers. mcniff, shaun, 1998, art-based research, jessica kingsley pub. miller, iona, 2008, “neurotheology”, http://neurotheology.50megs.com/ mcniff, s. (1998). art-based research. philadelphia, pa: jessica kingsley. moskowitz, clara, 2012, quantum entanglement experiment shows how future can affect past in quantum world http://www.huffingtonpost.com/2012/04/30/quantum-entanglement-experiment-futurepast_n_1465517.html moustakas, clark, 1990, heuristic research: design, methodology, and applications. newbury park, ca: sage. pascual-leone, alvaro , amir amedi, felipe fregni, and lotfi b. merabet, the plastic human brain cortex, annual review of neuroscience, vol. 28: 377-401 (volume publication date july 2005) rossi, ernest, 2002, psychosocial genomics: gene expression, neurogenesis, and human experience in mind-body medicine. rossi, ernest, 2003, the bioinformatics of psychosocial genomics in alternative and complementary medicine. rossi, ernest, 2004, the psychosocial genomics of therapeutic hypnosis, psychotherapy, and rehabilitation http://www.asch.net/portals/0/journallibrary/articles/ajch-51/51-3/rossi51-3.pdf sidorov, lian (2012). liam gray, erik schultes, zachary jones, adam curry, the mind-matter mapping project, international consciousness research laboratories, princeton, nj. http://www.scientificexploration.org/journal/jse_10_3_laughlin.pdf dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 104-129 miller, i., novel approaches to genomic science: retrieval & curation issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 123 southwick, fred, 2012, opinion: academia suppresses creativity: by discouraging change, universities are stunting scientific innovation, leadership, and growth. http://the-scientist.com/2012/05/09/opinion-academia-suppresses-creativity/ southwick, peggy & iona miller, chaosophy 2002: tao of resilience, asklepia press. http://tao-of-resilience.iwarp.com/index.html weber, renee, the holographic paradigm and other paradoxes, shambhala (september 12, 1982) winkelman, michael, shamanism: a biopsychosocial paradigm of consciousness and healing. zukov, gary, 1979, the dancing wu li masters: an overview of the new physics, bantam; reissue edition (september 1, 1984) appendix a the mind-matter mapping project lian sidorov, liam gray, erik schultes, zachary jones, adam curry international consciousness research laboratories 211 n. harrison st., ste. c, princeton, nj 08540 usa open letter bending an existing paradigm to accommodate new facts has always been a process fraught with inertia, higher-than-justified resistance and violent rebounds. to say that the study of nonlocal, consciousness-related phenomena faces a similar challenge today is an understatement. although many prominent scientists would agree that simple reductionism has failed to produce an adequate explanation for some of our most important questions, such as the hard problem of consciousness or the foundations of quantum mechanics, few of these scientists are ready to accept a change in our set of axioms, particularly the possibility that consciousness may be an elemental, rather than emergent component of reality. as a result, researchers in the field of mind-matter interactions find that they not only need to struggle with the limitations of our current scientific tools to make sense of their data, but also to fight for the legitimization of this data with a mainstream science community that is unwilling to accept its conceptual challenges. and yet, as daunting as this position seems at the moment, it is also an exhilarating one – for rarely in the history of science have we been faced with such unknowns. from ever-expanding entangled systems to remote perception and fieldreg effects, the evidence for nonlocality and mind-matter interactions keeps flooding in; but if this data dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 104-129 miller, i., novel approaches to genomic science: retrieval & curation issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 124 cannot be plotted within our current system of coordinates, how do we begin to find our way toward a new one? current problems faced by experimental parapsychology 1. lack of visibility in the mainstream scientific community, which results in a limited expertise field funneling ideas and resources into our research program 2. severely curtailed financial and technical resources 3. a significant credibility issue, which is reinforced by publication bias, institutional politics and social and scientific conceptual frameworks which are too narrow to accommodate these empirical findings. it is easier to sweep the data under a proverbial rug of pseudo-skepticism than to deal with the conceptual upheavals that it its acceptance would require. 4. fear. the psychological, social and intellectual repercussions of accepting these empirical facts are overwhelming for vast numbers of people, which means that an experiential, rather than a purely intellectual approach may be necessary in order to cross this barrier and modify the existing paradigm. proposed approaches 1. connect ideas with technical resources and experimental volunteer pools (research network). identify most promising research directions based on idea futures market (see http://hanson.gmu.edu/ideafutures.html) and help to funnel funding toward these projects through membership dues or other pools set aside for such purposes on a voluntary basis. 2. a mind-matter arxiv-like database of experimental proposals and pre-prints extending the typical spectrum of parapsychology literature to include developments in areas such as biophoton research, genetic regulatory systems, qigong and other intent-based healing techniques, placebo effects, entanglement and foundations of physics research. 3. using semantic web analytical techniques and smart search engines to automatically identify patterns and correlations across related subfields. indexing existing mind-matter literature to generate standardized vocabularies and databases of nano-citations that integrate seamlessly with new mainstream search engines, eliminating previous publication filters and increasing the visibility of this research. http://www.google.com/url?q=http%3a%2f%2fhanson.gmu.edu%2fideafutures.html&sa=d&sntz=1&usg=afrqezemkqtiug1jntafih8bdg06zbhi-a dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 104-129 miller, i., novel approaches to genomic science: retrieval & curation issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 125 4. a sustained outreach effort to engage the broader science community based on research and applications that resonate with mainstream interests project components 1. research network we propose the establishment of a world-wide, cross-disciplinary network of researchers, technical experts and volunteers committed to a sustained, active participation in this exploratory effort. the goal of this collaborative project would be to index relevant questions and research leads; create a searchable roster listing each member’s background, interests, technical expertise and access to laboratory resources; to develop new experimental models; share expertise and equipment resources; mentor on and critique study methodology; make inroads into mainstream applications; and publish all such developments in one centralized, searchable database which would be highly visible and readily accessible online. given the scarcity of funding and resources available for mind-matter projects, we must try to do less with more. the ability to capture ideas, connect experimental proposals to available resources and create a formal venue for the publication of such proposals would ensure that no good ideas remain stillborn for lack of opportunity and that proposed studies can be critiqued and methodologically strengthened at the earliest possible stage. advantages: 1. faster, nimbler, task-oriented working groups sifting through empirical data to identify potential patterns across various mind-matter phenomena and design new testable hypotheses, experimental models or applications. 2. establishment of skills/expertise networks so that proposed experiments can be carried out by those with the capability to do so. 3. allow interested mainstream scientists to participate under pseudonym, without fear of professional consequences. 4. team members will be known to each other, develop ideas in password-secured “virtual labs” and publish their proposals collectively in the journal of nonlocality and other icrl technical bulletins, which will be posted regularly. dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 104-129 miller, i., novel approaches to genomic science: retrieval & curation issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 126 as an additional incentive, we have created the mind-matter mapping prize, to be awarded yearly to the best experimental proposal, as voted by our project members. membership structure membership will be by invitation or application review (to demonstrate relevant background and level of interest). member profiles including publications, interests, technical expertise and equipment access will be searchable on our website in order to facilitate collaborative efforts, mentorship and peer feedback. teams will be organized to develop semantic web vocabularies in order to enable smart search and data mining algorithms (nano-publication model); collect and index relevant literature according to these new semantic web criteria; develop new exploratory directions and experimental models; and establish working contacts with mainstream groups sharing possible interests in this research all members must commit to active participation in the project and sign on to one of several teams. teams will be anchored by coordinators whose job is to collect and post submitted references and ideas, moderate their group forum section and steer new proposals/experiments toward publication in the icrl bulletin. multiple coordinators may anchor any given group, in order to minimize the individual burden but maximize the expertise. to maintain membership one must contribute a minimum of four indexed literature references per month. this is a minimum degree of involvement designed to keep the information flow and discussion active within the group, and to keep members in touch with their project. in addition, members are encouraged to participate as volunteers when needed for online or other proposed experiments, so that we can generate data promptly and efficiently. we suggest that the mind matter mapping project should maintain a multi-platform web presence, possibly structured in the following way: 1. a cloud-based project website with open access to the journal of nonlocality, existing research resources, member profiles and announcements. 2. password-restricted working forums where smaller units of researchers can develop their experimental proposals in private, prior to publication (the equivalent of virtual labs). dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 104-129 miller, i., novel approaches to genomic science: retrieval & curation issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 127 3. an open access groups forum, where the general mandate and organization of the project are presented, with an opportunity for anyone to post ideas, questions and references. this would allow the broadest funneling of input and potential membership without diluting the searchable field of information on the project website. valuable contributions can be filtered by group moderators onto the appropriate project website pages and participants who show promise/expertise could be invited to become members. 2. new publication and data mining models we propose the creation of an open, searchable database of article pre-prints (including experimental proposals and reports, case studies and testable hypotheses) modeled on the existing arxiv.org but dedicated to nonlocality, mind-matter interactions and relevant mainstream fields. examples of such mainstream topics include (but are not limited to) work in quantum entanglement and computation, foundations of physics, biophysics, genetic regulatory mechanisms, placebo effects, intent-based complementary and alternative medicine, neuroimaging and scientific studies of internally-deployed attention states such as meditation. in addition, an open repository of planned experiments, their methodology and results could be created as proposed by jonathan schooler (ny times, jan 7, 2011) to increase transparency and the ease of replication. as with arxiv, there would be no peer-review assumption – only open critique. however, this would allow researchers anywhere in the world to post their proposals and data rapidly, in a visible and centralized forum, allowing us to expand the current empirical funnel to a much broader spectrum of research sources. since it typically takes years between the inception of an experimental idea and the completion of the study (with most ideas likely abandoned due to lack of time, training, funding or opportunity), we feel that being able to claim authorship of an experimental model despite other practical limitations would encourage scientists to develop and discuss new approaches thus enhancing transparency and the rapid dissemination of new empirical data and concepts, accelerating the pace of development far beyond the current peer-review system. one final but critical question remains, which is of course assigning validity to the citations included in our database. in the absence of peer review and adequate replications, the benefits of such an approach may be obscured by its inherent limitations. to circumvent this objection we recommend implementing a ranking system where each citation is assigned a validity code based on its source – from peer reviewed specialty journals to individual, anecdotal and case study reports, even “community confidence level” that can be voted on/earned after a certain number of forum contributions. in this manner, a search query return could easily be filtered according to the strength of evidence desired. dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 104-129 miller, i., novel approaches to genomic science: retrieval & curation issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 128 3. reaching out to mainstream science we will make a sustained effort to reach out to the broader science community through projects that resonate with mainstream research questions and applications, that may assist with providing answers to these questions and that will hopefully stimulate individual scientists to learn more about the techniques and theoretical frameworks we are proposing. examples remote viewing: develop specialized training /vocabularies geared to particular fields of research in order to sensitize viewers to the perception of processes and features particular to their area of investigation create a pool of intractable questions in science assign these as targets to a group of expert remote viewers then openly post the rv data. the hope is that enough currently verifiable information will be produced to generate an interest among those mainstream scientists focused on these questions to persuade them that there may be an “insight advantage” to learning rv. placebo/ healing effects: look into biophysical models of genetic regulation, correlations between subject eeg/physiological markers of meditative states and the biophoton profiles of in-vitro targets; explore long-term physiological changes with qigong and meditation; use in-vitro sample biofeedback to test the effectiveness of different visualization techniques on biological targets and find ways to technologically enhance these effects. working groups will be assembled around a number of basic cross-disciplinary questions, as follows (more research directions to be defined later): 1. probing the role of meaning in mind-matter interactions (target id in remote viewing; issues of displacement; strength of pk effect). use the tools of parapsychology to probe the foundations of quantum mechanics (measurement problem). dna decipher journal | may 2012 | vol. 2 | issue 2 | pp. 104-129 miller, i., novel approaches to genomic science: retrieval & curation issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 129 2. becoming proficient in the language of the interface (creating applications-specific abstract vocabularies; data integration: context, meme complexes and tasking intent; other tools of rv navigation) 3. intersecting minds: multiple observers and consensus reality. how does the intent of multiple participants align to create a target identity in remote perception or skew probabilistic processes in remote perturbation? the effect of bonding, weighted influence (i.e. are some participants more heavily invested and how does that compute in the overall effect); expectation; decline; sheep and goats; data fingerprinting; error propagation; which way does the information flow? 4. physiological and psychological remodeling (strengthening psi long term effects of meditation, belief filters, biofeedback technologies, types of visualization etc) 5. possible signatures of entanglement (biophotons/em pulses; physiologic and metabolic markers) 6. the genetic interface: organism coherence, biophotons and their role in genetic/physiologic regulation; biological transducers of remote intent; cracking the placebo code 7. positioning intent in time: synchronicity, expectation, delayed effects and causal flow. is psi always goal-oriented? finding the best fulcrum point to apply intent 8. analytical methods in remote perception data processing: multiple operators, fuzzy set theory and other approaches 9. mass threshold effects (see rupert sheldrake's studies and the global consciousness project); designing large scale experiments 10. methodological mine fields: causal loops, blindness, expectation and other rabbit holes. if interested in becoming a member, volunteering for administrative positions (including it projects) or submitting material for publication in the journal of nonlocality, please contact lian sidorov (liansidorov@gmail.com). your feedback is critical to the success of this effort, so we look forward to all your suggestions. login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x quantum karma: bohm’s implicate order and the mind-only buddhist ground consciousness (alayavijnana) dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 258-297 smetham, g. p., quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 258 article quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology graham p. smetham * abstract all animals, of whatever species whatsoever, share a fundamental genetic structure which underpins a hierarchical development of differentiation. it is shown here that when this revolution in our understanding of the functioning of genes and the dna components of genes is placed in the context of the other great twentieth century revolution in science – the quantum revolution – the new metaphysical worldview which emerges goes far beyond the new vistas currently being explored by the evo devo community. in particular, it will become clear that the primary process of evolution is not that which takes place over time on the material plane but, rather, it is that process of development which cascades from a deep quantum level of intentionality through a sequence of immaterial and subtle „implicate orders‟ of „unfoldment‟, to use the terminology coined by physicist david bohm, until there is apparent manifestation on the „material‟ plane‟. this article is adopted from one of the chapters in graham‟s latest book „the grand designer‟ which can be found at www.shunyatapress.com. keywords: quantum evolution, evolutionary development, sheldrake‟s morphogenetic fields, bohm‟s implicate orders, goswami‟s creative universe. the dramatic and far reaching nature of the discoveries which led to the development of the perspective of evolutionary-development biology have, in large degree, still to be appreciated. indeed, as we shall see in the course of this paper, it might be said that to a great extent the hugely significant challenge to the materialistic grounding of the mainstream view within evolutionary thinking has been ameliorated by attempts to claim that, although the implications of the evolutionary-development paradigm are indeed remarkable, they are easily incorporated into the darwinian fold. as sean b. carroll sums up the darwinian perspective in his book on „the new science of evo devo‟ endless forms most beautiful: darwin asked his reader to consider how slight changes, introduced at different points in the process (of evolution) and in different parts of the body, over the course of many thousands or a million generations, spanning perhaps tens of thousands to a few million years, can produce different forms that are adapted to different circumstances and that possess unique capabilities. that is evolution in a nutshell. 1 what carroll does not point out is the overwhelming predominance of a materialist metaphysical paradigm which underpins the darwinian worldview. thus when richard dawkins laid the metaphysical foundations for his exposition of his vision of the blind watchmaker, * correspondence: graham smetham, http://www.quantumbuddhism.com e-mail: qb@delysid.bltc.net http://www.quantumbuddhism.com/ mailto:qb@delysid.bltc.net dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 258-297 smetham, g. p., quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 259 he did so by claiming the validity of asserting a foundational metaphysical materialist worldview „for everyday purposes‟: we peel our way down the hierarchy, until we reach units so simple that, for everyday purposes, we no longer feel the need to ask questions about them. 2 in his book darwin’s dangerous idea daniel dennett, dawkins‟ compatriot in the cause of materialism, is intellectually pugilistic in his rallying cry for the worldview of materialism: an impersonal, unreflective, robotic, mindless little scrap of molecular machinery is the ultimate basis of all the agency, and hence meaning, and hence consciousness, in the universe. 3 thus darwinism and materialism have become almost complementary aspects of a common „naturalist‟ worldview. a worldview within which the „gene,‟ in large part thanks to the strident proselytizing activities on the part of dawkins, became considered to be the ontologically privileged material unit which had somehow magically evolved a desperation to survive. in his book the extended phenotype dawkins makes the following impassioned and wildly anthropomorphic declaration of the ontological primacy of the „gene‟: …we should see through individual organisms. we see through them to the replicating fragments of dna within, and we see the wider world as an arena in which these genetic fragments play out their tournaments of manipulative skill. genes manipulate the world and shape it to assist their replication. it happens that they have „chosen‟ to do so largely by molding matter into multicellular chunks which we call organisms, but this might not have been so. fundamentally what is going on is that replicating molecules ensure their survival by means of their phenotypic effect on the world. it is only incidentally true that those phenotypic effects happen to be packaged up into units called individual organisms. 4 this is an astonishingly implausible claim which basically asserts that all biological organisms, all cultural activities, and consciousness itself are nothing other than expendable epiphenomenal products which have been adventitiously generated in order that the ultimately fundamental units of reality genes – may survive, even though in reality these putatively ultimate units do not materially survive as the same „stuff‟ any more than any other apparently „material‟ aspect of an organism. one of the core tenets of this materialist darwinism was the belief that the genes involved in the evolution of different species would themselves be different, different species would not have common gene structure. thus the evolutionary biologist ernst mayr wrote confidently in the 1960‟s that: much that has been learned about gene physiology makes it evident that the search for homologous genes is quite futile except in very close relatives. if there is only one efficient solution for a certain functional demand, very different gene complexes will come up with the same solution, no matter how different the pathway by which it is achieved. the saying “many roads lead to rome” is as true in evolution as in daily affairs. 5 an excellent example of a pronouncement made on the basis of little evidence but a huge emotional investment in the materialist darwinian worldview, an investment which can still be found in much „scientific‟ writing. however, this presuppositional assumption has now dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 258-297 smetham, g. p., quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 260 been shown by the evolutionary-development revolution in biology to be completely false; as carroll writes: the first shots in the evo devo revolution revealed that despite their great differences in appearance and physiology, all complex animals-flies and flycatchers, dinosaurs and trilobites, butterflies and zebras and humans-share a common “tool kit” of “master” genes that govern the formation and patterning of their bodies and body parts. … the important point to appreciate from the outset is that this discovery shattered our previous notions of animal relationships and of what made animals different, and opened up a whole new way of looking at evolution. 6 in other words, all animals, of whatever species whatsoever, share a fundamental genetic structure which underpins a hierarchical development of differentiation. as we shall see, when this revolution in our understanding of the functioning of genes and the dna components of genes is placed in the context of the other great twentieth century revolution in science – the quantum revolution – the new metaphysical worldview which emerges goes far beyond the new vistas currently being explored by the evo devo community. in particular, it will become clear that the primary process of evolution is not that which takes place over time on the material plane but, rather, it is that process of development which cascades from a deep quantum level of intentionality through a sequence of immaterial and subtle „implicate orders‟ of „unfoldment‟, to use the terminology coined by physicist david bohm, until there is apparent manifestation on the „material‟ plane‟. in order to appreciate the full impact of the „whole new way of looking at evolution‟ it will be useful to appreciate the view that had become central to the hardcore materialist „neodarwinian‟ perspective as presented in the early writings of richard dawkins (he has become rather ambiguous and contradictory on the issue in recent times) and the continued materialist interpretation of evolution preached by daniel dennett. as we have see above, the received, and completely false, wisdom of the academic „authorities‟ in the field prior to evo-devo was that the genes responsible for different species would be different, and the more distant the phyla involved the greater the difference would be expected to be. thus dawkins, writing in 1998, tells us that: the genes that survive in camels will, to be sure, include some that are particularly good at surviving in deserts, and they may even be shared with desert rats and desert foxes. but, more importantly, successful genes will be those that are good at surviving in an environment consisting of the other genes that are typically found in the species. … it is not the genes of any given individual that cooperate well together. they have never been together in that combination, for every genome in a sexually reproducing species is unique … it is the genes of the species at large that cooperate, because they have met before, often, and in the intimately shared environment of the cell… 7 it is impossible not to point out in passing that this is actually incoherent mythology, a neodarwinian piece of, unsubstantiated even at the time, internally inconsistent fantasy which has now been shown, by the evidence, to be beyond the misguided. suppose, for instance, someone were to claim that the genes that survive in camels were not good at surviving in deserts! furthermore is it actually a sane possibility that the various genes within a species would not be good at cooperating? according to dawkins the genes within particular individuals within a species do not cooperate because they have not met before, but, on the dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 258-297 smetham, g. p., quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 261 other hand, the genes of the species have often met before and therefore do cooperate. surely this is an extremely unlikely scenario, the genes of a particular species happily cooperating together, until, that is, they happen to congregate together in an individual of the species! it is also a scenario completely at variance with the evidence of evo-devo which indicates that the genes within any individual do nothing else but cooperate, indeed if one thinks about the issue for even a moment it is difficult to comprehend how an embryo could possibly develop without cooperation, so what the particular „cooperation‟ dawkins is referring to, a cooperation not exhibited by genes within the individual, is difficult to fathom. leaving aside this particular piece of dawkinsian incoherence, the picture of („selfishly‟) selfsufficient, and self-enclosed, genetic material units, carrying items of on-board information, units which become increasingly disparate as species and environment diverge, is clear. thus „surviving genes in camels‟, we are told, „may even be shared with desert rats and desert foxes‟, presumably because of the common environment. the implication, however, is that species inhabiting differing environments will not share commonality of genes. this fundamental, and mistaken, neo-darwinian view, then, is that the more widely species diverge from each other, so also does the genetic make-up of those species. as carroll elucidates the entrenched viewpoint: the classification of organisms, the assignment into like and unlike, has largely been driven by a consideration of form. so the long standing assumption has been the greater the disparity in form, the less, if anything, any two species would have in common at the level of their genes. 8 so here we find carroll indicating that the view which dawkins so often stridently proclaimed to be „scientific fact‟ was actually always an „assumption! it was this neo-darwinian metaphysical mythology that was completely discredited when the evidence became available. carroll writes that „this view was entirely incorrect‟ and he quotes stephen jay gould: the central significance of our dawning understanding of the genetics of development lies not in the simple discovery of something utterly unknown … but in the explicitly unexpected character of these findings, and in the revisions and extensions thus required of evolutionary theory. 9 it is intriguing that gould should paper over the fact that the evo-devo revolution actually indicated the complete fallaciousness of core assumptions of the materialistic appropriation of darwinism that had occurred by using terms such as „revisions and extensions‟. for the revolution in a sense was as profound as the quantum revolution in physics and, as we shall see, has a lot to do with the quantum revolution, although most current proponents of the evodevo perspective seem to be hard at work to preserve an outmoded and inappropriate materialist perspective. in is also revealing that gould refers to the „unexpected character of these findings‟ for one of the first things which should surely strike anyone of insight on coming across the evo-devo is that the elucidation provided actually contains a much greater level of coherency than the previous understanding. consider, for example, myers‟ confident and utterly fallacious claim that „very different gene complexes will come up with the same solution, no matter how different the pathway by which it is achieved.‟ the “many roads lead to rome” view is completely counter intuitive; the notion that genes should diversify and differentiate into dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 258-297 smetham, g. p., quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 262 radical different characters, becoming more and more disparate as the species draw apart and yet at the same time should converge on identical solutions to various evolutionary challenges is surely unlikely, however different the species involved may be. neither was there evidence for it, it was simply considered as being „obvious‟, so obvious that some proponents of completely fallacious worldviews made good names and livings for themselves promulgating falsehoods. for now we know that: natural selection has not forged many times completely from scratch; there is a common genetic ingredient to making each eye type, as well as to the many types of appendages, hearts, etc. these common ingredients must date deep back in time, before there were vertebrates or arthropods, to animals that may have first used these genes to build structures with which to see, sense, eat or move. these animals are the distant ancestors of most modern animals, including ourselves. 10 this is a paradigm which accounts for the facts of evolution far more coherently, as well as being in accord with actual evidence, than the „many roads‟ scenario. in order to prepare the way for an initial appreciation of the evo-devo paradigm it is useful to consider the „object-oriented‟ paradigm within computer modeling which constitutes the initial phase of computer systems development. the object of this approach is to be able to design a computer software system in a hierarchical modular fashion in which the system starts at the base as a highly abstract module and then descends through levels of „objectclasses‟ of increasing complexity; each level adds functionality to the level above. thus in figure 1 we see that at the top of the class tree there is the most „abstract‟ class which is just a bank account. within this class only the information which is common to all bank accounts can be placed, information which is specific to various types of bank account are contained in the classes on lower levels of the tree. a further refinement of this hierarchical structure which is a vital part of the objectorientation paradigm is the idea of „virtual members‟. these are members of a class which form part of the overall structure but cannot be fully specified within the class because the exact form of the member depends upon the implementation of members at a lower level of the hierarchy. so the top level „bank account‟ class might look as shown in figure 2. the personal details of the account holder can be „implemented‟ within this level but the „virtual‟ members will be fully specified at a lower level of the object hierarchy. thus the „virtual‟ members specify an „abstract‟ structure which can be implemented in different ways at a later point depending upon the paths taken through the lower levels of the hierarchy. dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 258-297 smetham, g. p., quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 263 fig 1 fig 2 the findings of the evo-devo revolution now indicate that a similar hierarchical modular development is fundamental within the evolutionary development of species. figure 3 gives a flavor of this perspective in a very crude and reduced form, indicating the principle rather than detail. the essential point is that, whereas the previous view of divergent „random‟ mutation of material gene units asserted the lack of common structure between divergent species it now turns out that in fact there is a common structure, which is clearly apparent within the genetic structure underlying all species. the first indication of this commonality was a result of research into the genetic makeup of fruit flies and mice. in order to elucidate this, a quick outline of the terminology is required. the fundamental process which appears to drive the process of the embryonic development is the division and differentiation of cells (the reason for the word „appears‟ will become apparent later) which is itself determined by the functioning of the strings of dna within the cells. each chromosome within a cell is a long molecule of dna (deoxyribonucleic acid); the chromosome in turn is identified as consisting of smaller strands of dna called genes, so genes are smaller components, each occupying its own particular location within the chromosome, some of which are identified as having particular tasks within the development of the embryo (figure 4a). dna itself is composed of two strands of nucleotides wrapped around each other in the famous double helix configuration; each nucleotide is comprised of one of four distinct bases: adenine (a), cytosine (c), thymine (t), guanine (g), and these bases map on to each other to form the dna helix as indicated in fig 5: a can only link with t, and g with c. dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 258-297 smetham, g. p., quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 264 fig 3 dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 258-297 smetham, g. p., quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 265 fig 4 fig 5 within the functioning of cell the dna is responsible for the manufacturing of proteins through the intermediary production of „messenger‟ rna (mrna). a single strand of mrna is produced from one strand of the dna double helix, a process termed „transcription‟. subsequently the mrna strand is „decoded‟ into a protein sequence; this process is termed „translation‟. proteins are comprised of sequences of amino acids, and this sequence determines the configuration and chemical properties of the target proteins; and these properties determine the function of the protein in the functioning of the organism, whether they function as carriers of oxygen or are constituents of muscle fiber and so on. one of the crucial discoveries which opened the way to the evo-devo paradigm was the discovery by françois jacob and jacques monod of the fundamental switching mechanism which takes place in order to regulate the mode of functioning of genes. in their investigation of the functioning of the intestinal bacterium e.coli jacob and monod discovered the existence of gene „repressor‟ sites which determine whether or not a gene is „on‟ or „off‟ and, therefore, whether gene transcription into mrna takes place. this mechanism is mediated by the production, in certain circumstances, of a dna „binding protein‟; this binding protein binds with a specific dna sequence and thereby turns the gene on or off. dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 258-297 smetham, g. p., quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 266 the next piece of the puzzle was provided by the mapping of the genes on the third (of four) chromosome of the fruit fly onto the parts of the fly‟s anatomy that they directed: …the genes sat close together in two clusters. one cluster, the bithorax complex, contained three genes that affected the back half of the fly; the other, the antennapedia complex, contained five genes that affected the front half of the fly. even more provocative, the relative order of the genes in the two clusters corresponded to the relative order off the body parts they affected… 11 this correspondence between genes and the parts of the fruit fly, and the fruit fly egg, is shown in figure 6. fig 6 – hox genes in the fruit fly. these two pieces of the puzzle linked together beautifully when the proteins which made up the genes were analyzed and it was discovered that all eight genes had a short stretch of a 60 amino acid domain that were all similar in sequence. this shared sequence was called a „homeobox‟ and the corresponding protein domain was called the „homeodomain‟; subsequently the genes were dubbed „hox‟ genes. it then became apparent that the homeodomains were dna-binding domains which were triggered by corresponding proteins, an insight which indicated that genes were switched on or off by the presence of the relevant binding proteins; so the presence of proteins acted as activators of switches that determined the manner of functioning of various hox genes. dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 258-297 smetham, g. p., quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 267 fig 7 carroll gives an example of how hox genes and gene switches function to determine the longitudinal stripe markings in a fly embryo. specific protein activators and repressors bind to various switch locations on the dna strand to the side of the actual gene; this is „similar to the way a specific key fits into a particular lock.‟ thus in fig 7 the combination of the activator and repressor proteins determine that the mrna protein is „expressed‟ and activates a particular stripe in the embryo. the question which naturally arises, of course, is what determines the particular combination of activators and repressors that activate the switches at any particular point in development. it turns out that there is a sequential cascade of activation of switches, so one set of activators and repressors determine the proteins which are operative in the next phase; as carroll says it is a „chicken and egg‟ scenario: ultimately, the beginning of spatial information in the embryo often traces back to asymmetrically distributed molecules deposited in the egg during its production in the ovary … (so the egg did come before the chicken)… however, carroll declines to speculate on where the first „egg‟ came from. the next remarkable discovery was of the same genetic structure and functioning in many diverse animals, „various bugs, earthworms, frogs, cows, and humans‟: …the similarities among the species were astounding … such sequence similarity was just stunning. the evolutionary lines that led to flies and mice diverged more than 500 million years ago, before the famous cambrian explosion that gave rise to most animal types. no biologist had even the foggiest notion that such similarities could exist between genes of such different animals. these hox genes were so important that there sequences had been preserved throughout this enormous span of animal evolution. 12 when the arrangement of the hox genes in mice was figured out the mapping of structure, including the isomorphism between gene order and body structure, between the fruit fly and mice turned out to be, as carroll says, „amazing‟. figure 8 shows the correspondences between the common underlying gene structure and fly and mouse embryo. so, as carroll points out: dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 258-297 smetham, g. p., quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 268 fig 8 it was inescapable. clusters of hox genes shaped the development of animals as different as flies and mice, and now we know that includes just about every animal in the kingdom, including humans and elephants. 13 and it soon became apparent that this commonality extended to other fundamental types of gene complexes. the next type of gene to be shown to be common across species was the socalled eyeless gene (so called because, when mutated in flies, it is responsible for the loss of eyes) which is called aniridia in humans and small eye in mice, together these three genes are collectively known as pax-6 and they have been found to be significant for the development of all kinds of different types of eyes across species. the fact that the gene responsible for the development of eyes is common is dramatic (or, as caroll says, „intriguing and provocative‟) because humans and mice have camera-type eyes whereas flies have compound eyes; so the same gene regulates the development and placement of eyes but the type of eye depends on other factors. this feature was demonstrated in an experiment in which mouse small eye genes were transplanted into various strange places in flies such as the wings. the result was the development of fly type eye structures on the fly wings, structures induced by the presence of mouse eye-producing genes. another component of what carroll calls the „gene tool kit‟ is the distal-less (dll) gene, which was so called because when it is mutated the distal, or outer, parts of fly limbs fail to develop. again these genes are found to be operative in the development of „all sorts of things that stuck out of animal bodies:‟ 14 these included chicken legs, fish fins, the appendages of marine worms (called „parapodia‟), the ampulae and siphons on sea squirts, and even the tube feet on sea dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 258-297 smetham, g. p., quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 269 urchins. this was another example, like pax-6, of a tool kit gene involved in building vastly different structures that only share, at most, the common feature of projecting away from the main body. these animals are also representatives of different major branches of the animal tree. 15 the final component of the gene toolkit mentioned by carroll is the tinman gene, which is so named after the character in the wizard of oz who lacked a heart; flies have an open circulatory system, which means they do not have a heart as such. these genes were found to have mammalian versions (nk2 family) which are significant in heart formation in vertebrates, including ourselves. the multi-functionality of the distal-less gene is remarkable. as carroll points out, fourteen or more different types of appendages project out from the body of a crayfish (fig 9) and the distal less gene is significant in the development of them all. but the distal less gene is not only responsible for land (underwater or dry land) limb development; it is also significant in the placing of spots on butterfly wings: distal-less still kept its old job: it was also deployed in the distal parts of all developing butterfly limbs, just as in all other insects and arthropods. the spots of the distal-less expression in butterfly wings were a new trick, “learned” long after its ancient role in limb-building. remember everything about a toolkit protein‟s action depends on context. 16 it is in passages such as this that carroll subtly reveals his adherence to the old neo-darwinian notion that that the development of species, a process driven by changes in the way in which various gene components are expressed through the operation of the surrounding regulatory switching protein mechanisms, is a result of random mutations which occur over time, which in this particular case allows distal-less gene mechanism to „learn‟ a new role. in the old dawkins style model it was, fallaciously, asserted that the actual material makeup of the genes themselves mutated and thereby produced new phenotypes (fully developed organisms) ready to be filtered and winnowed by the tooth-and-claw fight with the environment. but in the new evo-devo vision, as portrayed by carroll, it is changes in the regulatory switches, rather than the genes, that are responsible for evolutionary changes. the actual mechanism or mechanism responsible for such changes, however, is left somewhat hazy. in the case of the distal-less regulatory mechanism becoming involved in the determination of the patterning of the outer butterfly wing adornment, for instance, we are simply told that it somehow „learned‟ to add this functionality to its repertoire over the course of time. but towards the end of his book carroll nails his materialist and mechanistic colors to the evolutionary flagpole when he considers the remarkable fact that the same features, which are determined by the functioning of the same gene complexes (genes plus regulatory protein mechanisms), are found across diverse species, a discovery which is redolent with resonance of the dreaded notion of „design‟: this vestigial remnant of the neo-darwinian worldview, however, is no more than an implausible echo of what was, in the days of the ascendency of the neo-darwinian mythological worldview, nothing more than a speculative and incoherent fantasy which was adopted in order to preserve a newtonian materialism which was itself heading for extinction. dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 258-297 smetham, g. p., quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 270 fig 9 these instances of evolution repeating itself directly address difficulties some have had in grasping the role of random mutation in the evolutionary process. some people have found it hard to imagine how novelty and complexity arise from a “random process.” the key distinction is that while the generation of genetic variation by mutation is a completely random process, the sorting out of these variations as to which will persist and which will be discarded is determined by a powerful, selective nonrandom process. of the hundreds of millions or billions of individual base pairs in an animal genome, all are equally susceptible to random copying errors or physical damage that cause mutations. but only a tiny fraction of all possible mutations can alter a mammal‟s coat in a viable manner, or reduce a stickleback‟s spines without causing catastrophic collateral damage. in large populations of animals, over eons of time, such mutations will arise simply as a matter of probability. when they do occur, positive selection upon the trait they affect will cause them to spread in populations over time. 17 the extent of the desperation in this presentation is clearly apparent in the fact that it is an account which posits the most unlikely scenario, the notion that accumulation of evolutionary errors is responsible for the astonishingly organized and coordinated growth of increasingly complex and evolved biological organisms, in the face of contrary evidence that there is an inbuilt directionality and at least an minimal intentionality or what paul davies calls a „subtle teleology‟ within the process of evolution. the very example of the functioning of e. coli which carroll uses to illustrate the role of proteins as triggers for the activation of genes mitigates against the mythology of randomness. as professor patricia l. foster, of the biology department of indiana university, points out: when populations of microorganisms are subject to certain nonlethal selections, useful mutants arise … whereas useless mutants do not. this phenomenon, known as adaptive, directed, or selection-induced mutation, challenges the long-held belief that mutations only arise at random and without regard to utility. 18 dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 258-297 smetham, g. p., quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 271 and, of course, the neo-darwinian worldview has nothing to say on the presence of consciousness, and, within humans, full-blown self-consciousness, as a significant feature of the organisms produced by the universal evolutionary process. in his excellent book life’s solution: inevitable humans in a lonely universe professor simon conway morris has also demonstrated the prevalence of the convergence of evolutionary „solutions‟ to survival challenges across widely differing species, a phenomenon which suggests that templates for the structure of various components of plant and animal physiology are seeded into the potentialities underlying the evolutionary process. and the conclusion he draws is that, contrary to the „drunken walk‟ within a maze of mechanistic randomness viewpoint of various materialist evolutionary biologists, there is teleology towards the production of increasing levels of complexity, and associated sentience, within the ground potentiality of the process of evolution such that the end point of an organism having the kind of self-aware intelligence of human beings is an inevitability: so, if convergence is going to be a guiding principle in the understanding of evolution, then of all the areas worth investigating one of the most interesting must surely be to look at what constraints if any, accompany the development of sensory organs. it is here, if anywhere, that we can approach the wider problem of the evolution of the nervous systems, brains, and perhaps ultimately sentience. and this is turn might give some clues as to whether indeed intelligence is some quirky end point of the evolutionary process or whether in reality it is more-or-less inevitable, an emergent property that is wired into the biosphere. 19 in other words conway morris adopts a „anthropic‟ perspective which hold that it is sentience and consciousness which are the driving force and target of the evolutionary process, a viewpoint not entertained willingly amongst the denizens of materialist enclaves, but, as we shall see, a perspective which is now increasingly suggested by quantum evidence. the american cognitive scientist and philosopher jerry fodor, professor of philosophy at rutgers university, in a recent essay why pigs don’t fly, has questioned the neo-darwinian assumption of random „adaptationism‟ and has indicated that there are perhaps more viable alternatives: everybody thinks evo-devo must be at least part of the truth, since nobody thinks that phenotypes are shaped directly by environmental variables. even the hardest core darwinists agree that environmental effects on a creature‟s phenotype are mediated by their effects on the creature‟s genes: its „genome‟. indeed, in the typical case, the environment selects a phenotype by selecting a genome that the phenotype expresses. once in place, this sort of reasoning spreads to other endogenous factors. phenotypic structure carries information about genetic structure. and genotypic structure carries information about the biochemistry of genes. and the biochemical structure of genes carries information about their physical structure. and so on down to quantum mechanics for all i know. 20 and here fodor takes the descent through the levels of the physical world down to the physical description of the functioning of reality which most physicists consider to be ultimate explanatory level: quantum physics. furthermore it is significant that fodor qualifies his statement of the possibility that quantum physics might be significant in the process of evolution by the phrase „for all i know‟, indicating a lack of knowledge to adjudicate the dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 258-297 smetham, g. p., quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 272 possibility. for it seems to be the case that very few writers and commentators on the issue, at least within the fold of evolutionary biologists, do have the necessary acquaintance with the radical findings of quantum theory in order to approach the issue of the possibility that evolution is primarily driven from the quantum level. thus dawkins tells us that, when it comes to quantum theory: …this is where i must make my excuses and leave. sometimes i imagine i have some appreciation of the poetry of quantum theory, but i have yet to achieve an understanding deep enough to explain it to others. 21 what dawkins does not tell us, however, is how, given his incompetence at the quantum level, he can possibly be certain, as he certainly seems to be, that genes are the „selfish‟ ontologically primary drivers of the evolutionary process. for, as fodor indicates, genes can themselves be reduced to their molecular constituents and the functioning of such molecular units depends upon the details of quantum physics. as johnjoe mcfadden, professor of molecular genetics at the university of surrey, points out: watson and crick‟s structure (of dna) was therefore the culmination of centuries of biological progress. the great mysteries were laid bare: how biological information was encoded, how it was inherited and how it was changed. but it also pointed in a quite surprising direction, towards the involvement of that other great triumph of the 20 th century science – quantum mechanics – in the fundamental basis of life and the driving force of evolution.” 22 it is truly remarkable how most so many interested parties working in the field of evolutionary biology remain quite happy to ignore the dramatic discoveries of quantum physics, discoveries which have completely revolutionised our understanding of what appears to be a „material‟ world. for if one thing has been established beyond doubt by the quantum revolution it is that cartesian-newtonian type „matter‟ „does not exist‟, to quote quantum physicist professor henry stapp. furthermore it is now necessary to accept that the ultimate nature of what appears to be the material world is actually, again quoting stapp, „idea-like‟, or of the nature of mind. this viewpoint is becoming increasingly established within quantum philosophy, although there are stubborn pockets of materialist desperation resisting the cascade of quantum evidence. and, furthermore, it is a conclusion which was clearly reached by many of the founding fathers of quantum theory, which is why max planck asserted that: all matter originates and exists only by virtue of a force... we must assume behind this force the existence of a conscious and intelligent mind. this mind is the matrix of all matter. 23 and schrödinger wrote that: mind has erected the objective outside world … out of its own stuff. 24 furthermore, in his 1944 book what is life schrödinger explicitly wondered whether there might be a quantum basis for the genetic mechanism of inheritance. more recently physicist amit goswami has indicated the necessity of placing the operations of a universal field of awareness-consciousness as being fundamental in the orchestration of the evolutionary process: dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 258-297 smetham, g. p., quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 273 …if we do science on the basis of consciousness, on the primacy of consciousness, then we can see in this phenomenon creativity, real creativity of consciousness. in other words we can truly see that consciousness is operating creatively even in biology, even in the evolution of the species. 25 this proposal will be vigorously resisted by the materialist minded cohorts of the greater number of evolutionary biologists within which the notion of the materialist „chance and necessity‟ paradigm predominates; however, it is the kind of perspective which is required by the quantum evidence. in my previous essay the grand designer: can hawking’s godless theory of everything run without god (vol 1, no. 7 – 2010) i demonstrated that if one took the core proposals for the basis of the theory of everything contained within hawking and mlodinow‟s book the grand design seriously then the conclusions they reach, in particular the conclusion that a „whole universe‟ can „just appear out of nothing‟ is clearly at variance with the earlier assertion that at the moment of the big bang the universe „appeared spontaneously, starting off in every possible way,‟ and then subsequently sentient beings somehow „choose‟ or „create‟ for themselves which universe they will occupy through the exercise of perceptual weeding out of possibilities. this perspective clearly requires that at the moment of „creation‟ there must be a quantum field of infinite potentiality which contains its own mechanism of unfoldment, rather than a pure „nothingness‟ which hawking and mlodinow seem to favor. furthermore this universal field must be of the nature of consciousness-awareness. the conclusion that the ultimate nature of the universal process must be of the nature of consciousness follows exactly from hawking and mlodinow‟s adherence to feynman‟s „sum over histories‟ approach to quantum theory, which requires that: the histories that contribute to the feynman sum don‟t have an independent existence, but depend on what is being measured. we create history by our observations, rather than history creating us. 26 in other words it is the exercise of sentient „observation‟, or perception, which creates „our history‟, which also means that sentient perception determines the nature of the universal process backwards in time, and also forwards in time, through the weeding out of potentialities. thus in their chapter „choosing our universe‟ hawking and mlodinow tell us that in one possible universal history the moon is made of „roquefort cheese‟ but somehow the perceptual activities of the sentient beings of the current universe has vetoed this possibility and opted for a moonrock moon; although there may be other universes which do have a roquefort cheese moon, the sentient beings in our universe have, over vast time over scales, „chosen‟ moonrock. 27 this view agrees with the understanding of the visionary physicist john wheeler, who also concludes that the evolution of the universe eventually requires the participation of sentient beings in the determination of its nature: directly opposite to the concept of universe as machine built on law is the vision of a world self-synthesized. on this view, the notes struck out on a piano by the observer participants of all times and all places, bits though they are in and by themselves, constitute the great wide world of space and time and things. 28 and: dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 258-297 smetham, g. p., quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 274 law without law. it is difficult to see what else than that can be the plan of physics. it is preposterous to think of the laws of physics as installed by swiss watchmaker to endure from everlasting to everlasting when we know that the universe began with a big bang. the laws must have come into being. therefore they could not have been always a hundred percent accurate. that means that they are derivative, not primary … events beyond law. events so numerous and so uncoordinated that, flaunting their freedom from formula, they yet formulate firm form … the universe is a self excited circuit. as it expands, cools and develops, it gives rise to observerparticipancy. observer-participancy in turn gives what we call tangible reality to the universe … of all the strange features of the universe, none are stranger than these: time is transcended, laws are mutable, and observer participancy matters. 29 a significant observation in this quote is that the universe „as it expands, cools and develops, it gives rise to observer-participancy. observer-participancy in turn gives what we call tangible reality to the universe…‟ which indicates an interdependent evolutionary process which physicist amit goswami calls a „tangled hierarchy‟ within which the observing aspect and the observed aspect of the evolutionary process develop inter-dependently through a sequence of increasingly „explicate‟, or materialized, levels of manifestation. this viewpoint corresponds closely to the suggestion by the significant trailblazing physicist david bohm who suggested that the appearance of the material world emerges through initially subtle levels of „implicate orders‟ which manifest through quantum layers, which he dubbed „implicate orders‟, towards a final „material‟ manifestation. as we shall see, this view of a vertical downward (or upward depending upon one‟s point of view) evolution through quantum levels of manifestation provides a much more coherent and fertile elucidation of the manner in which the common structures underlying the morphology of biological life came into being. in his book life without genes adrian woolfson presents us with a poetic vision of the sort of field of potentiality that he imagines must have „existed‟ before the dawn of life within the universe: in the beginning there was mathematical possibility. at the very inception of the universe fifteen billion years ago, a deep infinite-dimensional sea emerged from nothingness. its colourless waters, green and turquoise blue, glistened in the nonexistent light of the non-existent sun … a strange sea though, this information sea. strange because it was devoid of location … 30 this field, of course, can only be the quantum wavefunction of the universe, a universal wavefunction which contains: …all possible histories … through which the universe could have evolved to its present state… 31 this perspective, of course, is completely harmonious with the hawking-mlodinow version; the quantum wavefunction of the universe contains all the future evolutionary possibilities for the development of sentient beings and the environments inhabited by then. and from out of the vast entangled web of infinite possibilities for manifestation only certain privileged, because viable within the context of the details of the evolution of this particular universe, members will actually make it into reality: dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 258-297 smetham, g. p., quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 275 an information space of this sort would furnish a complete description of all potentially living and unrealizable creatures… 32 the fact that not all possibilities for the manifestation of sentient beings and the environments inhabited by them are actualized, thereby leaving some potentialities as „unrealized‟ is, again, in line with the hawking-mlodinow perspective, wherein many potentialities, the unlikely possibility of a cheese-moon being an example given by them, are weeded out by the choices that the universal consciousness, which at some point becomes embodied within evolved sentient beings, makes along the way. the dramatic implication, then, is that the potential forms of all sentient beings must be „contained‟ as pure potentiality within the ground of the universal quantum consciousness which awaits unfoldment at the edge of time. the attitude to the notion that the quantum level of reality, the level which just about all physicists now consider to the ultimate and grounding level, is at least inextricably entangled with the phenomenon of consciousness (rosenblum and kuttner – quantum enigma) or, even more radically, consists of a field of pre-individualized awareness-consciousness (stapp, goswami, hameroff and others), on the part of those who lean towards a materialist view of reality is ambiguous to say the least. the quantum evidence is now so now ineluctable that denying it is really not a viable option. however, an option often resorted to is to falsely claim that the quantum evidence is so confusing that the matter has not been decided yet. in a recent book called life ascending, which won the 2010 royal society prize for science books, the author nick lane refers to the views of the scottish physicist graham cairnssmith who suggests that what we call „matter‟ must itself have subjective features and must also in some fashion partake of the nature of consciousness, which was the position advanced by bohm; lane writes that: matter is conscious in some way, with „inner‟ properties, as well as the familiar external qualities that physicists measure. pan-psychism is taken seriously again. it sounds preposterous. but what arrogance to think that we know all there is to know about the nature of matter! we don‟t. we don‟t even understand the way quantum mechanics works. … we don‟t know enough about the deep nature of matter to know how neurons transform brute matter into subjective feelings. 33 this passage illustrates the kind of intellectual schizophrenia which seems to be at the root of current thinking in biology and neurophysiology and other associated disciplines; and it is also necessary to point out in passing that the assertion that „we don‟t even understand the way quantum mechanics works‟ is completely untrue – we have a very precise understanding, it‟s just that most people don‟t like the quantum implication that consciousness is the primary constituent of reality. the fact that the concept of „matter‟ has been thrown into dramatic ambiguity by quantum physics, so much so that the respected physicist henry stapp has repeated many times that cartesian-newtonian type matter „does not exist,‟ and physicist and respected science writer john gribben has written a book entitled the end of the matter myth, not to mention pronouncements such as that made in 1931 by max planck that he regarded „consciousness as fundamental. i regard matter as derivative from consciousness‟ 34 , does not stop misguided biologists and others lamenting that they do not know how „brute matter‟ is „transformed‟ into „subjective feelings.‟ how can a nonexistent, mythological assumed aspect of reality transform into anything? this is not to say that the material world is completely non-existent, this would be a ridiculous assertion. the point concerns the ultimate nature of what appears to be an dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 258-297 smetham, g. p., quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 276 „external‟ material world which is conceived of as being independent of mind. the evidence of quantum theory quite clearly is that what appears to be a sphere of materiality which has its own inner self-enclosed independent essence cannot actually be like this. quantum theory unambiguously tells us that what we thought was independent „matter‟ is actually dependent upon mind. as quantum physicist wojciech h. zurek, the primary instigator of the theory of „quantum darwinism,‟ a quantum viewpoint which is fundamental for understanding the evo-devo evidence, tells us: given almost any initial condition, the universe described by [the quantum wavefunction] evolves into a state containing many alternatives that are never seen to coexist in our world. moreover, while the ultimate evidence for the choice of one alternative resides in our elusive “consciousness,” there is every indication that the choice occurs much before consciousness ever gets involved and that, once made, the choice is irrevocable. 35 although at first sight the implication of the quantum evidence might seem to be that individual consciousnesses „collapse‟ the wavefunction, in fact it is actually more correct to consider the appearance of the material world to be an inter-subjective process which operated at a much deeper quantum level that individuated consciousness, and, furthermore, prior to the manifestation of sentient beings within the process of evolution there must be an inner cognitive function within the field of potentiality which operates to unfold potentialities and thereby also unfold and evolve the future sentient beings destined to inhabit the unfolding universe. nick lane suggest that such a „pan-psychic‟ viewpoint is „preposterous‟ and, although he pays a brief lip-service to the fact that we do not know „all there is to know about the nature of matter‟ he quickly falls back into the familiar, and for many cosy, materialist worldview of the pre-quantum, pre-twentieth century perspective, the perspective of gentlemen fossil collectors and intrepid explorers and species collectors of tropical rain forests. this tendency to constantly fall back into a default position of primary materialism, even whilst in the midst of making observations which should alert the writer in question to the fallacious nature of the perspective is astonishing. lane, for example, in referring to the work of the neuroscientist gerald edelman, tells us that: edelman refers to the process of brain development as neural darwinism, which emphasises the idea that experience selects successful neural combinations. all the basic tenets of natural selection are present; we start out with a massive population of neurons, which can be wired up in millions of different ways to achieve the same ends. the neurons vary amongst themselves and can either grow more robust or wither away; there is competition between neurons to form synaptic connections and differential survival on the basis of success. 36 here lane at first reiterates the recent discovery of neuroplasticity, the fact that, contrary to what the vociferous „experts‟, again on the basis of prejudice and minimal evidence, in the field of neuroscience prior to the appalling silver spring monkey experiments, the mind‟s intentionality is able to determine the wiring of the brain. in the silver spring experiments the nerve ganglia that supplied sensation to the brain from the monkeys‟ arms and legs were cut and various forms of encouragement, such as electric shocks, were used to force the monkeys to use the limbs they could not feel. subsequently it was discovered that significant cortical remapping had occurred, showing that being forced to use limbs with no sensory input had triggered changes in their brains' organization. this evidence of the brain's dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 258-297 smetham, g. p., quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 277 plasticity helped overturn the widely held view that the adult brain cannot reorganize itself in response intentional actions. professor of psychiatry jeffrey schwartz, in his excellent book the mind and the brain says of this discovery: mind, we now see, has the power to alter biological matter significantly; that three pound lump of gelatinous ooze within our skull is truly the mind‟s brain. 37 lane, however, turns this perspective on its head and, in the same way that dawkins gives an inappropriate ontologically privileged status to „selfish‟ genes, gives the brain‟s neurons an equally inappropriate status, for as stapp points out: …no such brain exists; no brain, body, or anything else in the real world is composed of those tiny bits of matter that newton imagined the universe to be made of. 38 by this dramatic assertion stapp is emphasizing the fact that the quantum realm is primary; there is no „newtonian‟ type matter, and therefore no ultimately existing self-sufficient neurons, in existence. the inappropriate positing of the „material‟ brain as being the ultimate source of the phenomenon of consciousness derives from the simplistic observation that there is an obvious connection between damage to various areas of the brain and consequent behavior: …specific brain injuries (lesions) cause specific reproducible deficits. it‟s hardly surprising, but a lesion in the same area causes the same deficit in different people, or for that matter in animals. 39 however, as we shall see, this crude materialist assumption is incorrect. the fact that the brain is ultimately an apparent „material‟ organization which emerges from a deeper level of quantum functioning in no way undermines the apparent coherent „material‟ functioning of the quantum structure of the brain. it simply means that, at the level at which our „material‟ bodies and our sense faculties function, the coherent functioning of the ultimate quantum mindnature, to employ a term of the buddhist dzogchen tradition, manifests as the apparently „material‟ world. but this does not mean that the evidence as to the ultimate quantum mindnature of reality is false. the situation is that a deep implicate field of quantum awareness-consciousness organizes itself through a cascade of quantum „implicate orders‟ that finally produce the explicate structures of the brains of sentient beings in order to manifest as individuated consciousness within the manifested dualistic universe. david bohm encapsulated this vision in his notion of the holomovement: …the notion of the holomovement was enriched by going from a three dimensional space to a multidimensional implicate order and then to a vast „sea‟ of energy in „empty‟ space, so we may now enrich this notion further by saying that in its totality the holomovement includes the principle of life as well. inanimate matter is then to be regarded as a relatively autonomous sub-totality in which, at least as far as we know, life does not significantly manifest. … indeed, the holomovement which is „life implicit‟ is the ground of both „life explicit‟ and of „inanimate‟ matter, and this ground is what is primary, self-existent and universal. 40 this characterization of the universal ground of „life implicit‟, within which the potentialities for sentient beings and their environments have an origin bears an significant resemblance to the buddhist dzogchen account of the universal ground: dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 258-297 smetham, g. p., quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 278 the root of our material-mental universe is this self-existent pristine cognitiveness, a point instant virtual singularity; since its facticity is open-dimensioned and not discernable as any concrete thing, it is a meaning-saturated field as pristine cognitiveness. the radiation field of this open dimension is the intrinsic photic character of pristine cognitiveness. since this is there as its own lucency (in its prismatic character) as yet undifferentiated into color values, it is the quasimirroring pristine cognitiveness. since these modes of pristine cognitiveness have one and the same operational source, differing only in name, this facet is termed the selective mapping pristine cognitiveness. since these modes of pristine cognitiveness are self-existent, identical with respect to their lucency and indivisible, this facet is termed the auto-reflexive identity pristine cognitiveness. since by understanding correctly the meaning-value of this cognitive character of being all intentional ideation is actualized spontaneously and this facet is termed the precisely actualizing pristine cognitions as the operational source of the intelligible universe that the eighty-four thousand portals to life‟s meaning opens up. 41 here the unfolding principle which drives the evolution of the sentient beings both downwardly through implicate orders of manifestation, and also across time, is „pristine cognitiveness‟. this is the fundamental universal cognitive function which is able to trigger the quantum sea of potentiality into action, and through this action, which takes place over vast time scales, sentient beings of all possible varieties consistent with the nature of the manifesting universe come into being, each embodying a tiny quantum of the universal „pristine cognitiveness‟ which provides the driving force for the evolution of the universe. thus, as bohm indicates, „life implicit‟ becomes both „life explicit‟ and „inanimate‟ matter. in the following elucidation the interconnections between the dzogchen account, based on herbert v. guenther‟s excellent exposition matrix of mystery: scientific and humanistic aspects of rdzogs-chen thought, of how a fundamental field of 'pristine cognitiveness‟ materializes into individualized centers of dynamic meaning-experiencing, or sentient beings, and the account based on the quantum insights on the part of bohm is uncanny. according to bohm: we can say that human meanings make a contribution to the cosmos, but we can also say that the cosmos may be ordered according to a kind of „objective‟ meaning. new meanings may emerge in this over all order. that is we may say that meaning penetrates the cosmos, or even what is beyond the cosmos. for example there are current theories in physics that imply that the universe emerged from the „big bang‟. in the earliest phase there were no electrons, protons, neutrons, or other basic structures. none of the laws that we know would have had any meaning. even space and time in their present well-defined form would have had no meaning. all of this emerged from a very different state of affairs. the proposal is that, as happens with human beings, this emergence included the creative unfoldment of generalized meaning. 42 guenther describes the beginning phases of the evolution of the manifested and materialized world of dualistic experience from the „evolutionary zero point‟ according to the dzogchen worldview as follows: it is excitatory intelligence that provides the necessary programming information for initiating a dramatic unfolding process (the big bang) tending towards ever greater dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 258-297 smetham, g. p., quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 279 degrees of complexity (the evolving universe) while simultaneously, throughout all its phases, retaining the intelligence that initiated the process. when this big bang occurs, the surging of intelligence-qua-isotropic radiation develops a special envelop-like structuring of radiation field…the unitary process as an envelop-like structure which results from this surging of intelligence is termed the meaningsaturated field as pristine cognitiveness. 43 at this point there is still no „matter‟, the appearance of the material world comes into manifestation at a later point of quantum evolution from the evolutionary zero point. what we are discussing at this level of development is the cascade of quantum templates of meaning-manifestation, levels of quantum downward evolution from the nondual zero point, levels that bohm termed „implicate orders‟, each implicate order enfolds a new level of meaning evolution in a quantum descent into apparent materiality, and this descent requires the materialization of sentient beings as carriers of individualized awareness of a particular locus of meaning-awareness: later, with the evolution of new forms of life, fundamentally new steps may have evolved in the creative unfoldment of further meanings. that is, we may say that some evolutionary processes occur which could be traced physically, but we cannot really understand them without looking at some deeper meaning which was responsible for the changes. the present view of the changes is that they are random, with selection of those traits that were suited for survival, but that does not explain the complex, subtle structures that actually occurred. 44 here bohm indicates the serious shortcomings of the materialistic and mechanistic view of the evolutionary process enshrined in the materialistic vision of the darwinian evolutionary process. the view pugilistically promoted by dawkins and dennett for instance is that the universe has always been fully materialized and that evolution is nothing more that the nonintentional and mechanical activity of essentially lifeless matter, an extraordinarily counterintuitive, but for some incomprehensible reason, widely accepted belief. in contrast to this, now completely unacceptable, vision of the lifeless magically becoming life through blind mechanical churning of mindless bits and pieces of inert matter, bohm is suggesting that evolution must be driven by an intentionality which acts towards the manifestation of life through increasingly more materialized levels of quantum potentiality. evolution, according to bohm, must essentially be an intentional quantum process by which subtle quantum structures cascade down to less subtle levels to eventually become fully „materialized‟. this process, according to bohm, requires: 1. a set of implicate orders 2. a special distinguished case of the above set, which constitutes an explicate order of manifestation. 3. a general relationship (or law) expressing a force of necessity which binds together a certain set of the elements of the implicate order in such a way that they contribute to a common explicate end… 45 and elsewhere he indicates a set of nested orders: explicate, implicate, super-implicate, super-super-implicate…. in the imagery of dzogchen, as the „excitatory intelligence‟ manifests through the subtle or „implicate‟ quantum levels towards manifestation on a materialized level it creates dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 258-297 smetham, g. p., quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 280 „envelopes‟, which we can identify as quantum demarcation structures which designate boundaries which the cognitive process of materialization, which thereby marks out areas of differentiation between the activity of subjective cognition and the projected stabilized cognized objects, in this way the „pristine cognitiveness‟ hides its unitary nature in an imaginational field of activity, a field of activity within which the possibilities for the evolution of sentient beings and the collective environments shared by the various varieties of sentient beings takes shape: this field envelope exhibits an intentional structure, constituted both as an intending act phase and an intended object phase… 46 this account, which asserts that the cascade into manifestation begins at a deep subtle level of potentiality with the mere glimmer of quantum-intentional movement, prompted by the internal „pristine cognitiveness‟, a subtle quantum intentionality that produces the first implicate order of subtle intentional-subject and intended object, without any further content than this mere subtle intentional duality, easily melds with the most recent „quantum darwinism‟ proposal that the nature of the quantum stuff of reality is epiontic: …quantum states, by their very nature share an epistemological and ontological role – are simultaneously a description of the state, and the „dream stuff is made of.‟ one might say that they are epiontic. these two aspects may seem contradictory, but at least in the quantum setting, there is a union of these two functions. 47 in this new quantum paradigm we find that the insight brought to modern western philosophy by bishop berkeley that „to be is to be perceived‟ is now validated at the fundamental level of quantum theory: the epistemological act of perception actually creates a moment of ontology. and this does not mean that something already existing is known to be existing, it means, rather, that the very perceptual act creates the existence at the quantum level, one might say that the „collapse of the wavefunction‟ actually is one moment of quantum perception which itself is a moment of quantum ontology. furthermore the epiontic paradigm indicates that repeated perception creates a resonant latency for the same perception to occur again, so the more often a perception is repeated the more probable it becomes. this process of „quantum darwinism‟, which i have explored in detail in relation to various formulations in my article bohm’s implicate order, wheeler’s participatory universe, stapp’s mindful universe, zurek’s quantum darwinism and the buddhist mindonly ground consciousness (jcer, vol. 1 issue 8), underlies edelman‟s „neural darwinism‟ as well as biological evolution over time, in the latter context it finds its most explicitly developed formulation in rupert sheldrake‟s proposal of the functioning of quantum morphogenetic fields. the russian physicist and quantum philosopher michael mensky has also formulated a similar perspective. according to mensky consciousness is an interior aspect or quality of the wavefunction which reflexively operates upon quantum potentialities for experiential existence. for individuated consciousness itself to become manifest from fundamental awareness as an explicit experiential aspect of reality it must bring an experienced world into being; and such a world is manifested through the actualisation of the potentialities within the wavefunction and the subsequent selection of primary experiential pathways. according to mensky a crucial question which requires explication is why the alternatives dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 258-297 smetham, g. p., quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 281 which naturally arise are classical, or at least close to classical, in demeanour. mensky gives the following account: if the picture of the world as it appears in consciousness were far from classical, then, due to quantum non-locality, this would be a picture of a world with „locally unpredictable‟ behaviour. the future of a restricted region in such a world could depend on events even in very distant regions. no strategy of surviving could be elaborated in such a world for a localised living being. life (of the form we know) would be impossible. on the contrary, a (close to) classical state of the world is „locally predictable‟. the evolution of a restricted region of such a world essentially depends only on the events in this region or not too far from it. influence of distant regions is negligible. strategy of surviving can be elaborated in such a world for a localised living being. 48 entangled quantum phenomena can instantaneously affect each other over vast cosmic distances. in fact distance does not seem to be an issue for this kind of entangled mutual determination. it follows, therefore, that in a non-classical, quantum-entangled scenario there would be no environments wherein environmental behaviour was determined purely by local events. such environments would not be locally coherent and predictable and consequently they could not support coherent life. if mensky‟s argument is correct then the classical lineaments of a life-supporting manifested reality is fashioned by consciousness itself for its own manifestation! in quantum field theory there in a non-substantial entangled quantum field of potentiality and within the process that mensky envisages it is through the operation of a primitive level of quantum consciousness that this entangled and interdependent field is localised through the quantum evolution of the „classical‟ world of individualised sentience and materiality. furthermore, mensky indicates that the level of consciousness at which the process begins is: …the most primitive, or the most deep, level of consciousness, differing perceiving from not perceiving. 49 such deep levels of consciousness contain shared structures of possible experience. these aspects of the structures of consciousness are coterminous with those that the analytic psychologist c.g. jung called archetypes. although jung‟s archetypes are primarily concerned with deep emotional determinations of aspects of reality, his work led him to suggest, like bohm, that there is a deep level of connection between the physical world and the realm of the subjective. 50 this view of the deep inner and hidden connection between the manifest realms of the objective world and the subjective experiential world was also shared by physicist wolfgang pauli who corresponded for a time with jung on the subject. the experiential templates for the material world, which can be thought of as archetypal templates which interact with the established features of the objective wavefunction that provides the potential for a material world, must be shared, at least in part, by all sentient beings. mensky‟s account of how such deep structures of consciousness, which select the experiences conforming to a stable material world from the wealth of quantum possibility, arise in the first place provides a fertile starting point for the development of the view of evolution as an essentially quantum process which begins with the operation of the interior quantum „pristine cognitiveness‟ operating within the field of quantum potentialities. and the starting point, at the very base of the hierarchical cascade of implicate orders into dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 258-297 smetham, g. p., quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 282 material manifestation is the glimmer of the division into perceiver and perceived. within this division into the possibility of observer and an observed, a fundamental division which takes place at a deep hidden quantum implicate level, the universe becomes self-referring and self-observing, a process which now gives rise to what goswami calls a „tangled hierarchy‟, which can be compared to bohm‟s cascade of „implicate orders‟, of selfobservation through which the fluid quantum nature of the fundamental ground becomes increasingly divided into quantum template „prototype‟ sentient beings and inhabited environments. these prototype quantum potentialities only „exist‟ as quantum potentialities until consciousness intervenes to fully materialise them, a process which goswami and others suggest may occur backwards in time, a quantum viewpoint which means that evolution would be a far more bizarre and complex process than envisaged by the single dimensioned darwinian perspective. for within this quantum perspective it would be the case that until sentient beings began to solidify the process of quantum evolution, backwards in time, the process would be only occurring at the quantum level. this scenario involves the possibility that vast ages prior to the cambrian, for instance, would at that time only be quantum processes, a viewpoint which is consistent with the hawking-mlodinow metaphysical vision of the evolution of the universe and its inhabitants. as goswami indicates: life and by implication we ourselves are here because of the way the universe is designed in possibility so we can collapse the possibility into manifestation. 51 as we shall see, this perspective can bring coherent elucidation to some perplexing evolutionary conundrums such as the meaning of the cambrian „explosion.‟ however, such a perspective seems seriously counter-intuitive and nick lane would almost certainly employ the term „preposterous‟ to describe it. but surely we have to decide whether we take the quantum evidence and implications seriously or not? this understanding of the nature of quantum evolution is consistent with the fact that in quantum field theory the ultimate quantum field contains no substantiality; there is only a field of potentiality which is „operated‟ upon by „creation‟ (and „destruction) operators. this description can easily be viewed as an „objective‟ presentation of the action of a fundamental „pristine cognitiveness‟, also termed within dzogchen as an „excitatory intelligence‟, operating to unfold sentient potentialities. the very first glimmer of epiontic quantum perception, deep within the quantum ground, would simply be a movement of consciousness which gathers into a centre an intentional disposition for perception towards an aspect of the ground of reality which is interdependently posited as being that which is perceived. the first quantum implicate templates, therefore, would simply be that of perceiver-perceived, or „grasper‟ and „grasped‟ as buddhist mind-only philosophy terms the division. at this point there is only the intention to produce a realm of dualistic experience embodied within a multitude of sentient beings, but as yet there is no actual full-blown perceiving going on, we are still in the early phases of quantum implicate manifestation and there is the mere potentiality for a division into perceiving beings and perceived entities. the next movement towards manifestation would be to divide the perceiving aspect into actual varieties of perception: some form of sight or echo-location etc., hearing, smelling, touching, tasting. this step will be accompanied by the kind of objects which can be perceived according to which sense faculty and so on. also there must be a determination as to mode of movement according to the potential environment. these determinations will begin at a very subtle „virtual‟ quantum level, and in this way the actual basic templates of dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 258-297 smetham, g. p., quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 283 possible sentient beings might be determined within quantum implicate orders prior to actual manifestation on the apparently „material‟ world. this process will cascade down, through many quantum implicate levels, or „orders‟, to ever more explicate „gross‟ levels of manifestation, until, of course, an actual teaming experiential dualistic interconnected manifold of perceiving creatures and concomitant perceived worlds is „created‟ from out of the epiontic field of quantum potentiality. such a view accounts for aspects of evolution far more coherently than the currently accepted materialistic darwinian paradigm and also for such anomalies as the cambrian explosion. a good example to consider is the case of the distal-less gene which has been discussed above. as with the example of the crayfish the distal-less gene complex has a remarkable range of applications. conway morris describes the situation as follows: as with pax-6 the original function of this gene is not certain, but some evidence suggests that its primary role was linked with the development in the embryo of the nervous system, and especially the sensory organs. now it so happens that in arthropods many of the sensory organs are located on the appendages, and accordingly when there was need for improved sensory perception so parts of the body protruded to extend the sensory range of the sensory cells. only later were such outgrowths on occasion employed for such purposes as locomotion. the widespread expression of the gene distal-less is, therefore, effectively a reflection of the recurrent and independent of such limbs: in a sense distal-less hitchhikes as a sensory protrusions and is subsequently transformed to allow an additional function such as a leg or an antenna. 52 so it appears that the same gene complex responsible for organizing protrusions for extending the range of sensory apparatus were „only later‟ „employed for such purposes as locomotion. the impression which is easily gleaned from such presentations is that there must be a sequence of animals across which a sense protrusion is, dues to chance random mutation, gradually transformed into walking apparatus. but the notion that there could have been an intermediate animal which used the same protrusion to see and walk, or smell and walk or hear and walk etc. is clearly difficult to contemplate seriously. this sense of dissonance is even more pronounced with the transformation which is supposed to have taken place, via „natural selection‟, from gills to wings: the gill-to-wing theory always had evidence in its favor (just not enough weight to settle the matter). but, if indeed insect wings came from crustacean gill branches, does this mean that some kind of crayfish or shrimp just crawled onto land and started flying? no, not at all. there were many evolutionary steps between animals that carried a set of respiratory appendages and the origin of powered insect flight on two pairs of wings as we know it today. 53 but such a dogmatic and dubious belief in the power of gradualist „natural selection‟ cannot mask the fact that, if this account were to be correct, there must be a point in the evolution from gill to wing when the final creature in the evolutionary sequence abandoned the gill function completely and threw in its lot with a life on the wing, just as a few mutations back there must have been an animal using its wings for extracting the odd fix of oxygen from water. does this sound plausible? the biologist lisa nagy has asked: dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 258-297 smetham, g. p., quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 284 should vertebrate and insect limbs be considered homologous [meaning descended from a common ancestor] because they are patterned by similar gene networks? or is the similarity an example of molecular convergence… 54 in light of the discussion so far, however, the most plausible and coherent explanation of the phenomenon is that what carroll calls „toolkit genes‟ reflects the fact that there are „toolkit‟ morphogenetic templates or prototypes for various modules of animal construction which reside as quantum „virtual‟ morphogenetic field modules within quantum implicate orders. rupert sheldrake describes the process of embryonic development as follows: the development of multicellular organisms takes place through a series of stages controlled by a succession of morphogenetic fields. at first the embryonic tissues develop under the control of primary embryonic fields. then … different regions come under the influence of secondary fields, in animals those of limbs, eyes, ears etc. … generally speaking, the morphogenesis brought about by the primary fields is not spectacular, because it establishes the characteristic differences between cells in different regions that enable them to act as the morphogenetic germs of the organ fields. then in the tissues developing under their influence, germs of subsidiary fields, fields which control the morphogenesis of structures within the organ as a whole… 55 thus the development of the embryo is controlled by a nested hierarchical of morphogenetic fields, which are, according to sheldrake, „quantum probability fields‟ 56 akin to bohm‟s implicate orders. this, of course, is exactly what we should expect in a quantum evo-devo universe; the development of the embryo cascades through hierarchical levels of quantum morphogenetic fields in the same way that evolution also took place through a sequence of quantum implicate orders. figure 10 shows the very basic and partial beginnings of a hierarchical tree diagram indicating the kind of structure which one can conceive as underlying the upper implicate levels of the manifestation of various animals. the first division of the unified quantum ground is, as indicated above, the mere glimmer of perception; a movement of intentionality on the part of the universal „pristine cognitiveness‟ in the direction of producing a manifested world by unfolding as many of the potentialities, which are latent within the possibilities for sentient life contained within the ultimate field of potentiality, as is coherently possible. if the quantum evo-devo perspective is correct, then, in contrast to the neo-darwinian materialist random-chance story in which the natural environment exists fully and materially formed prior to life making a bid for survival, the true evolutionary process is one in which sentient beings and their environments evolve interdependently through quantum implicate levels. thus the various requirements for body structure, sensory organs, means of movement dependent upon the environment and so no are fulfilled by the evolutionary process, both synchronically through quantum implicate orders and diachronically (over time), by a modular „pick and mix‟ process. the modular „design‟ of the duckbilled platypus is intriguing in this context. when the naturalist george shaw, keeper of the department of natural history at the british museum, received a specimen from captain john hunter in australia he remarked that it was “impossible not to entertain some doubts as to the genuine nature of the animal, and to surmise that there might have been practiced some arts of deception in its structure.” 57 dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 258-297 smetham, g. p., quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 285 whilst it is true, of course, that at the fully manifested level all sentient beings inhabit the „same‟ material world in the sense that the quantum ground of potentiality within which all sentient beings exist have the same potentialities awaiting unfoldment, each type of sentient being will unfold a different continuum experience of the „material‟ world. but all the possible worlds inhabited by the varieties of sentient beings are clearly consistent and coherent in their overlapping features. the entire interconnected system is a coherently inter fig 10 dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 258-297 smetham, g. p., quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 286 dependent creation etched out of the potentialities within the ultimate quantum field of universal awareness. darwin himself was not unfamiliar with the notion of an inter-dependent aspect within the process of evolution for at the beginning of his chapter the struggle for existence in his the origin of species we can read: how have all those exquisite adaptations on the part of one organization to another part, and to the conditions of life, of one distinct organic being to another being been perfected? we see these beautiful co-adaptations most pleasantly in the woodpecker and mistletoe… 58 it would have been impossible, of course, for darwin to have been aware of the quantum origin. this view of the process of the unfolding of the multifarious possibilities within the quantum ground of reality through a universal unfolding of potential perceiving organisms can be immediately applied to some iconic darwinian scenarios. we shall consider darwin‟s finches and the african cichlids. the crucial darwinian point concerning the galapagos finches is that the beaks were supposed to have evolved by natural selection to fit the environmental surroundings, in this case the kind of nuts available being the evolutionary environmental factor (fig 11). this process is generally considered to have taken place gradually over a long time span due to random mutation. but the evidence gathered by researchers trying to support the neodarwinian gradualist account actually undermines it: he describes the evidence they gathered demonstrating the correlation of beak size with food supply … and follows that with a good summary of the observations that the grants made of beak size on the island of daphne major after a drought. as the available supply of edible seed dwindled, only tough hard-to-open seeds were left, and only birds with larger, deeper beaks could eat them. subsequent generations showed a dramatic increase in overall beak size in the population. 59 this, however, does not indicate a mechanism which hangs around for a random mutation to ride to the rescue of the starving finches; it indicates an exquisitely tuned responsive interaction between the population about to inhabit an environment and the conditions of the environment immediately prior to the habitation by the subsequent generations. it is as if the experiences of the finches inhabiting the environment during the drought had left a trace within a deep level of the quantum field which then determined the form of the subsequent generations of finches. this corresponds exactly to rupert sheldrake‟s notion of a „morphogenetic field‟, a kind of memory within nature, and the buddhist alayavijnana, the ground consciousness, and bohm‟s „implicate order‟. all of these, of course, map onto the notion of the universal quantum field of reality. the way that such a mechanism could function is easily comprehended when one recalls that according to quantum theory it must be the case that all possibilities for manifestation are contained within the universal quantum wavefunction. this is the basis for the everettdewitt many-worlds theory of the functioning of reality, which says that all the possibilities within the universal wavefunction do actually happen in different experiential worlds. dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 258-297 smetham, g. p., quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 287 the quantum mindnature vision of the functioning of reality, which gives rise to a quantum evo-devo perspective asserts that whilst all the possibilities for the type of finch beak are contained within the universal wavefunction, which one is expressed depends upon the environmental conditions that the finches are about to be expressed into, so to speak. there is a „morphic resonance‟ between the implicate finch template about to manifest and the possibilities for manifestation such that the most appropriate manifestation for the environmental conditions occurs. this perspective is not only consistent with the current evidence, it also adds completion and depth were at the moment there is only detail. work on the actual mechanism underlying the phenomenon of the morphing finch beak has been carried out by dr. cliff tabin and a team of developmental biologists at harvard medical school. the key to the process was found to lie within the operation of the bmp4 (bone morphogenetic protein number 4) gene which signals for the production of the bmp4 protein. this gene turns out to be remarkably multitalented as it also coordinates the development of the embryo. fig 10 in order to verify the significance of the bmp4 gene in the morphology of beaks the researchers artificially increased the production of bmp4 in chicken embryos and the beaks of the chicks became wider and more robust. researchers also found that a different gene was responsible for the expression of another protein, calmodulin, which resulted in long probing beaks. so the operations of just two genes, which coordinate the expression to the amounts of two different proteins, appear to control the morphology of beaks. this leads to significant insights. new morphic forms can arise through the subtle operation of existing genes. it appears as if there is an overall template for a finch, for instance, which could be conceived of as being of the form of a sheldrakian „morphogenetic field‟, which is then tweaked in its expression by the detailed operation of the genes underlying the template. viewed from the perspective of zurek‟s quantum darwinism, it becomes clear that both the morphogenetic template field of the finch and the information which determines the actual expression of the details of the template, the exact form of the beak for instance, must reside in a quantum information field. this is clearly homologous to bohm‟s notion of the dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 258-297 smetham, g. p., quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 288 implicate order. this is a dramatic insight bringing together crucial insights from cutting edge quantum theory and evolutionary biology, and we can only expect exciting developments are close at hand within this field. what is quite clear from the evidence so far, however, is that the materialistic notion of gradual step by step random mutation which is promulgated with pugilistic fervor by richard dawkins and others turn out to be completely false. the only reasonable picture that can be drawn in the light of all the evidence available clearly points to the „emergence‟ of the subjective perceiving aspect of the overall quantum process, together with the objective environmental container (the terms „container‟ and „contained‟ are used within buddhist philosophy), in co-dependence on the overall interconnected field conditions. such a coordinated co-arising through levels of quantum resonance is completely consonant with quantum non-locality. i hope that john wheeler would have approved of my appropriation of his famous graphic image in figure 11 which illustrates this viewpoint. it has been suggested by some evo-devo enthusiasts that the emerging perspective clearly shows that some form of subtle teleology is clearly indicated within the process of reality. the form of this teleology, however, has yet to be explicated. the quantum mindnature perspective, with its assertion of the minimalist teleology of a self-perceiving function within the quantum ground of reality, as is clearly indicated by the phenomenon of the collapse of the wavefunction, provides exactly the form of teleology that is required to explain the developmental evolution at all levels, even that of the cosmos itself. also, quite clearly this perspective completely elucidates the nature of the „goldilocks enigma‟ of the anthropic finetuning of the universe. fig 11 dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 258-297 smetham, g. p., quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 289 another „iconic‟ darwinian phenomenon is that of the african fish called cichlids which have evolved into such a huge diversity of species that they have become one of the best known evolutionary radiations. the cichlids have evolved into a dramatic diversity of different shapes and sizes, with a variety of jaw types which are adapted for different kinds of foods. research has shown that exactly the same process operates in this case as in the case of darwin‟s finches. all of the different types of cichlid have the same gene profile but the astonishing diversity is produced by the expression of the basic gene profile into different forms according to the environmental opportunities. it seems that the same template will be expressed in any form which will fit into an environmental niche. this is exactly what one would expect of a creative self-perceiving universe which operates in order to maximize the number of perceiving organisms, of all possible types, according to the possibilities offered by the surrounding environments. this process, however, is not one in which the environment is fixed and given but, as we have seen previously, it is a process of interdependent co-origination between perceiving organisms and their environment. a simple analogy that dawkins offers in order to illustrate the „sieving‟ process of the environment which he considers to be fundamental to „natural selection‟ is that of a hole which is able to sort balls into those bigger than it and those smaller: the result of one sieving process are fed into a subsequent sieving, which is fed into …, and so on. 60 the random jiggling of the sea of endless possibility, thrown up by the chance workings of completely non-conscious, non-intentional molecular interactions is ordered, in small gradual steps, by the taming influence of the natural sieve (fig 12). dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 258-297 smetham, g. p., quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 290 fig 12 dawkins‟ balls this picture, however, has one small, but vastly significant mistake. where does the sieve come from? in the example of the balls and the hole, for instance, the hole is external to the random system of balls waiting to be ordered. the theory of evolution, if it is to claim an ultimate significance, should be self-contained, that is to say it should apply to the universe as a whole, without recourse to external agencies. this is, after all, exactly the kind of metaphysical requirement that dawkins appeals to in his refutation of the notion of a creator god. and the fact that dawkins does consider his vision to have ultimate metaphysical relevance is clearly apparent; he tells us, for instance, that: darwinism is true, not just on this planet but all over the universe wherever life may be found. 61 the sieve, therefore, must be internal to and generated by the evolutionary process itself. the only other alternative is that the sieve is already in place, expectantly waiting for emergent life to make a bid for survival so to speak. the only metaphysically viable possibility is that the sieve is generated by the very process which dawkins is trying to explain by means of the sieve; which means that the sieve must be itself generated by its own process of sieving! this might seem like a tall order, but in fact it is easily elucidated in the quantum mindnature evo-devo perspective. the environment, which arises interdependently through the quantum evo-devo evolutionary process, is relatively stable in relation to the flexibility of perceiving organisms; this is indicated by figure 13. in this image we can see that the kind of evolutionary sieve that dawkins requires can be generated by the evolutionary process itself. the process of a self-resonating, self-manifesting process of evolution which is depicted in fig 13 is a beautiful example of a process of dependent origination; both aspects, subjective and objective, of the manifestation arise in dependence upon the other. indeed, as we have seen, darwin himself was not unfamiliar with the notion of a co-dependent aspect within the process of evolution. dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 258-297 smetham, g. p., quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 291 fig 13 at the end of his recent reworking of his controversial 1981 book a new science of life rupert sheldrake writes that: the hypothesis of formative causation is a testable hypothesis about objectively observable regularities of nature. it cannot explain the origination of new forms and new patterns of behaviour, nor can it explain subjective experience. such explanations can be given only by theories of reality more far-reaching than those of natural science, in other words by metaphysical theories. 62 if the formative causation hypothesis was to be shown to be correct by experimentation and observation, sheldrake goes on to say, this would not mean that the materialist-mechanistic worldview would necessarily be shown to be invalid, it would, however, have to compete with other metaphysical theories. in this section we shall briefly examine how the quantum mindnature metaphysical perspective constitutes a precise and coherent account of how formative causation would naturally emerge from the internal perceiving operations at the quantum level. dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 258-297 smetham, g. p., quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 292 the following brief outline of sheldrake‟s proposal is based on his own summary in a new science of life. he suggests the existence of morphogenetic fields which are responsible for molding the physical stuff of reality into the forms that is adopts. morphogenetic fields provide: …further type of causation … responsible for the forms of all material morphogenetic units (sub-atomic particles, atoms, molecules, crystals, quasicrystalline aggregates, organelles, cells, tissues, organs, organisms). form, in the sense used here, includes not only the shape of the outer surface of the morphogenetic unit but also its internal structure. 63 the morphogenetic field which moulds any particular morphogenetic unit provides a „virtual form‟ which directs, through some natural mechanism (the inverse quantum zeno effect) the way in which the physical „stuff‟ is organized. inorganic morphogenesis is rapid but organic morphogenesis takes place through a hierarchy of levels (akin to bohm‟s nested implicate orders) of developmental pathways, each pathway is called a „chreode‟. thus the development of an organism takes place through the operation of a succession of nested morphogenetic fields. morphogenetic fields are established over time through a process of „morphogenetic resonance‟ which depends on „patterns and structures of vibration‟ 64 once the morphogenetic structure is established there is a continued action of morphogenetic resonance which stabilizes the unit and, furthermore, the stability of the morphogenetic field itself depends on the repeated manifestation of the morphogenetic unit it gives rise to, so there is an interdependent relationship between the morphogenetic field and its morphogenetic unit. this means that „phenomena become more probable the more often they occur.‟ 65 the isomorphism between sheldrake‟s notion of morphogenetic fields and the probabilistic quantum wavefunction is quite clear: …morphogenetic fields are not precisely defined but are probability structures that depend on the statistical distribution of previous similar forms. the probability distributions of electronic orbitals described by solutions of the schrödinger equation are examples of such probability structures, and are similar in kind to the probability structures of the morphogenetic fields of morphogenetic units at higher levels. 66 morphogenetic fields, then, are exactly the kind of quantum probability fields which would be created or built up by the kind of processes involved in the quantum mindnature perspective. the close connection between the formative causation hypothesis and the quantum mindnature perspective resides in the fact that it is the quantum process of repeated perception or activation at the quantum level that builds up the probability structures within wavefunctions; it is this internal quantum process, therefore, that creates morphogenetic fields. in other words morphogenetic fields can be considered to be classical level expressions of thee deep operations of the quantum level of consciousness. as we have seen the manifestation of the dualistic realm of experience takes place through a hierarchy of quantum levels, beginning with the merest spontaneous movement of the ground consciousness towards the activity of perception. this movement of universal intentionality, which is a naturally innate function of universal „empty‟ consciousness, has the effect of activating, and thereby strengthening the latencies of, potentialities within the dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 258-297 smetham, g. p., quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 293 ground of reality. once the process has began the quantum process of manifestation cascades through increasingly more complex levels of manifestation. sheldrake himself says that the hypothesis of formative causation itself does not explain the genesis of the cascade of the manifestation of the evolutionary process; it only describes the mechanisms involved once the process gets going: the action of the morphogenetic field of a morphogenetic unit on the morphogenetic fields of its parts, which are morphogenetic units at lower levels, can be thought of in terms of the influence of this higher level probability structure on lower level probability structures; the higher-level field modifies the probability structures of the lower-level fields. 67 this process of higher-level fields controlling and modifying lower-level fields is, sheldrake tells us, illustrated by the way in which molecules modify the fields of the atoms which make it up. the hierarchical morphogenetic field control mechanism underlies important biological phenomena such as protein folding. furthermore the inverse zeno effect which is involved in the operation of enzymes is exactly such a quantum phenomenon that seems to control a „classical‟ level manifestation. the evidence which has been claimed for the formative causation hypothesis is controversial and is generally discounted by mainstream workers in the field. and, because the power of the dominance of the materialist worldview is still overwhelming (which itself is surely an example of „the presence of the past!‟) the kind of evidence required in order to convince skeptics would have to be irresistible. this is because there seems to be a deeply ingrained antagonistic prejudice towards theories which threaten materialistic approaches to understanding the process of reality. the approach adopted within the quantum mindnature perspective in challenging the mechanistic-materialist worldview begins from a significantly different point because it takes the quantum evidence as it is now as the ground for developing a metaphysical overview, an overview which precisely coheres with all significant current quantum perspectives. as this work shows the breadth, scope and depth of the overarching and detailed metaphysical perspective is so dramatic that it is difficult to conceive of an alternative metaphysical perspective bringing together diverse areas of discourse together in such a detailed and precise manner. it was not anticipated at the outset, for instance, that the natural evolutionary development of the quantum mindnature perspective itself would account for the process of evolution as well as otherwise unexplained phenomena within the field of evolutionary development. and one of the significant implications of this perspective is that something akin to formative causation must be operating at, and through, the quantum level. sheldrake identifies four possible metaphysical theories which count account for the formative causation hypothesis: modified materialism: is definitely not a feature of the quantum mindnature perspective. it is actually difficult to see how any kind of materialism can account for morphogenetic fields which are non-local. quantum phenomena are, of course, non-local, but quantum phenomena are not „material‟ in the manner in which „classical‟ materialism conceives of „matter.‟ as stapp says there is „no room‟ for „classical matter in a quantum universe. dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 258-297 smetham, g. p., quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 294 the conscious self: according to sheldrake: the conscious self can be thought as not interacting with a machine, but with morphogenetic fields. these morphogenetic fields are associated with the body and depend on its physical and chemical states. but the self is neither the same as the morphogenetic field, nor does its experience simply parallel the changes brought about within the brain by energetic and formative causation. it „enters into‟ the morphogenetic fields, but it remains over and above them. 68 the suggestion which sheldrake makes for how the „self‟ can influence the physical body closely parallels michael mensky‟s viewpoint proposed in the extended everett concept paper and it also incorporates elements of stapp: …how does [the self] act upon the external world through morphogenetic fields? there are two ways in which it could do so: first, by selecting between different possible morphogenetic fields, causing one course of action rather than another; and second, by serving as the creative agency through which new morphogenetic fields come into being … in both cases it would act like a formative cause, but one that is, within limits, free and undetermined from the point of view of physical causation. it could indeed be thought of as the formative cause of causes. 69 the creative universe: sheldrake‟s version of the creative universe is based upon henri bergson‟s proposal of the élan vital, a vital spark at the core of reality driving the process of manifestation and evolution. the translation that sheldrake makes of bergson‟s term is „vital impetus‟, and quite clearly this perspective is completely in accord with the view developed within this work that the ground of reality has as an innate function of its own nature the mere requirement of perception of its own potentialities. the drive towards perception is exactly the élan vital driving the process of reality. as sheldrake indicates this metaphysical viewpoint implies a hierarchy of levels of individuated consciousnesses: such creative agencies could give rise to new morphogenetic fields by a kind of causation very similar to … conscious causation … in fact, if such creative agencies are admitted at all, then it is difficult to avoid the conclusion that they must in some sense be conscious selves. 70 according to sheldrake such a viewpoint cannot account for how or why the universal process got underway in the first place and does not provide a „goal‟ for the process. however, the metaphysical perspective proposed by the quantum mindnature universe, which is based on the evidence of quantum theory, supplies the explanation of both genesis and „goal‟, although the goal is not achieved once and for all time but is, rather, a continuous process, by the same simple and natural observation: there is at the heart of the universal consciousness an inner pressure towards perception of the latent potentialities of the „empty‟ ground of reality. this pressure towards perception is evidenced in the ‟collapse of the wavefunction‟. as sheldrake points out this perspective does not imply any independent „transcendent‟ creator. the creative force is simply an innate aspect of the universal process of reality. dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 258-297 smetham, g. p., quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 295 transcendent reality: the notion of a transcendent creative agency is fraught with difficulty because of the different ways in which the term „transcendent‟ may be understood. some presentations of this position leave the detailed delineation of the metaphysical structure of the „transcendence‟ being claimed conveniently ambiguous so that various dubious claims can be implied. the significant issue is whether the creative agency conceived of is asserted to be substantially and effectively independent of the realm of manifestation that it is supposed to be creator of. this is the position of most fundamentalist christian beliefs which picture an independent god fashioning a separate domain for his created creatures, giving them a set of laws to follow and then stepping back to survey the disastrous results. for buddhist philosophy such a simplistic picture is simply logically incoherent. if the supposedly „creative‟ agency were to be completely independent and separate of the creation, which is to say an absolutely and irrevocably different and separate nature, then it could not have any creative relationship with something that it is totally separate and independent of. the kind of „transcendence‟ which is incorporated into the quantum mindnature perspective is the subtle advaita (non-dual) metaphysical structure which asserts that there is an ultimately non-dual creative process of reality that creates a vast illusion of dualistic experience. from this perspective there is not so much a „creation‟ as a continuous process of creating on the part of the non-dual creative ground. the details of this perspective, as shown in this work, are remarkably subtle; one of the subtleties being the fact that the sentient being caught up in the dualistic play of illusion are themselves agents of the creative force. if we construe the phrase „transcendent conscious being‟ in following passage as referring to the non-dual creative aspect of an interdependent and interconnected process of reality, sheldrake‟s characterization of the notion of transcendent reality comfortably applies to the quantum mindnature universe: if this transcendent conscious being were the source of the universe and everything within it, all created things would in some sense participate in its nature. the more or less limited „wholeness‟ of organisations at all levels of complexity could then be seen as a reflection of the transcendent unity on which they depended, and from which they are ultimately derived. 71 such a view precisely applies to the metaphysical position developed in detail within this work. the illusory and limited sense of selfhood that is part of the dualistic experience of non-enlightened sentient beings is precisely a reflection and embodiment of the unity of nondual creative source and, furthermore, the change of state from the unenlightened perspective to an enlightened perspective is itself an illusion though which the illusion of separation dissolves. this subtle advaita metaphysics of a transcendent and immanent reality embraces and includes the previous two positions of „conscious selves‟ (although they are ultimately illusory) and the „creative universe‟: …this fourth metaphysical position affirms the causal efficacy of the conscious self, and the existence of a hierarchy of creative agencies immanent within nature, and the reality of a transcendent source of the universe. 72 dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 258-297 smetham, g. p., quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 296 the quantum mindnature metaphysical perspective developed in this work on the basis of all the currently available quantum evidence and interpretations provides exactly such a metaphysical perspective which elucidates and explains how the mechanisms of formative causation would be produced through the epiontic operations of the quantum levels of the universal ground consciousness which is the quantum mindnature matrix of the universe. 1 endless forms p5 2 blind watchmaker 3 dennett – darwin‟s dangerous idea p27 4 extended phenotype p5 5 endless forms p72 6 endless forms p9 7 reweaving the rainbow p213 8 endless forms p54 9 p72 10 p72 11 p61 12 p64 13 p65 14 p69 15 p70 16 p208 17 p290 18 foster p. l. (1993) „adaptive mutation: the uses of adversity‟ in annual review of microbiology vol 47 p467-504 19 conway morris p148 20 new york review of books 21 dawkins, richard (2006). unweaving the rainbow p50 22 quantum evolution mcfadden 23 das wesen der materie” (the nature of matter), speech at florence, italy, 1944 (from archiv zur geschichte der maxplanck-gesellschaft, abt. va, rep. 11 planck, nr. 1797) 24 schrödinger, e. (1944) p121. 25 interview with – in what is enlightenment. 26 see the grand design p140 27 see the grand design p140 28 barrow, john d., davies, paul c. w., harper, charles l. (eds) (2004) p577 – wheeler, j a (1999) „information, physics, quantum: the search for links.‟ in feynman and computation: exploring the limits of computers, ed a. j. g. hey, p309 (314). cambridge, ma: perseus books. 29 wheeler quoted in barrow, john d., davies, paul c. w., harper, charles l. (eds) (2004) p73 – freeman j. dyson: „thought-experiments in honor of john archibald wheeler.‟ 30 woolfson, adrian (2000) p74 31 barrow, d. john & tipler, frank j. (1986) p105 32 woolfson, adrian (2000) p76 33 life ascending p252 34 the observer (january 25th, 1931) 35 decoherence and the transition from quantum to classical – revisited p4 36 life ascending p247 37 schwartz, jeffrey m. & sharon begley (2003) p369 38 stapp, henry (2007) p139 39 life ascending p240 40 essential bohm p102 41 matrix of mystery p52 42 essential bohm p180 43 matrix of mystery p51 44 essential bohm p180 45 eb p103 46 matrix of mystery p51 47 barrow, john d., davies, paul c. w., harper, charles l. (eds) (2004) p136 – wojciech h. zurek: „quantum darwinism and envariance.‟ 48 rosenblum, bruce and kuttner, fred (2006) p179 dna decipher journal | march 2011 | vol. 1 | issue 2 | pp. 258-297 smetham, g. p., quantum evo-devo universe: quantum evolution and the evidence of evolutionary-developmental biology issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 297 49 mensky, michael: „reality in quantum mechanics, extended everett concept, and consciousness‟ p6 50 jung, c.g.(1977) p538 51 creative evolution p113 52 life‟s solution p242 53 endless forms p176 54 nagy in american zoologist 55 a new science of life p136 56 a new science of life p104 57 http://www.museumofhoaxes.com/hoax/hoaxipedia/duckbilled_platypus/ 58 darwin, charles (1859) 59 jonathan wells and darwin‟s finches. 60 dawkins, richard (2006) the blind watchmaker p45 61 dawkins, richard (2006). the blind watchmaker 62 nsol p237 63 nsol p143 64 nsol p144 65 nsol – back cover blurb 66 nsol p145 67 nsol p105 68 nsol p240 69 nsol p241 70 nsol p243 71 nsol p244 72 nsol p244 dna decipher journal | october 2021 | volume 11 | issue 1 | pp. 21-35 21 pitkänen, m., & rastmanesh, r., homeostasis as self-organized quantum criticality article homeostasis as self-organized quantum criticality m. pitkänen1 and r. rastmanesh2,3 1independent researcher. 1 2member of the nutrition society, london, uk. 3member of the american physical society, usa. abstract cold shock proteins (csps) and heat shock proteins (hsps) have a great deal of similarity and have much more general functions, so it is easier to talk about stress proteins (sps) having two different modes of operation. the attempt to understand various functions of sps led to much more general problem: how self-organized quantum criticality (soqc) is possible? criticality means by definition instability but soqc is stable, which seems to be in conflict with the standard thermodynamics. in fact, living systems as a whole are quantum critical and manage to stay near quantum criticality, which means soqc. this is nothing but homeostasis usually understood as a complex control system needed to keep living systems in flow equilibrium. zero energy ontology (zeo) forming the basics of tgd (topological geometrodynamics) inspired quantum measurement theory extends to a quantum theory of consciousness and living systems and predicts that the arrow of time changes in ordinary (”big”) state function reductions. zeo leads to a theory of quantum self-organization and time reversal means that dissipation in reversed direction looks like extraction of energy from the environment for the observer with standard time direction. the change of the arrow of time transforms critical states from repellers to attractors and makes soqc possible. soqc and homeostasis would result automatically rather than being forced. magnetic body (mb) is another key notion. mb has a maximal temperature known as hagedorn temperature th crucial for understanding soqc and functioning of sps. th would relate closely to physiological temperature in biomatter. 1 introduction this article started as an attempt to understand the properties of cold shock proteins (csps) and heat shock proteins (hsps) in tgd framework. as a matter of fact , these proteins have great deal of similarity and have much more general functions, so it is easier to talk about stress proteins (sps) having two different modes of operation. time as we proceed, it will be revealed that this issue is only one particular facet of a much bigger problem: how self-organized quantum criticality (soqc) is possible? criticality means by definition instability but soqc is stable, which seems to be in conflict with the standard thermodynamics. in fact, living systems as a whole seem to be quantum critical [kauffman 2015] and manage to stay near criticality, which means soqc. note that the self-organized criticality (soc) is generalized to soqc. topological geometrodynamics (tgd) [pitkänen 2020a] [pitkänen 2014c, pitkänen 2016] is a 43 year old proposal for a unification of fundamental interactions. zero energy ontology (zeo) [pitkänen 2020c] is basic aspect of quantum tgd and allows to extend quantum measurement theory to a theory of consciousness and of living systems. zeo also leads to a quantum theory of self-organization [pitkänen 2019a] predicting both arrows of time. could zeo make soqc possible as well? 1correspondence: matti pitkänen http://tgdtheory.com/. address: rinnekatu 2-4 a8, 03620, karkkila, finland. email: matpitka6@gmail.com. email: matpitka6@gmail.com. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.com/ mailto:matpitka6@gmail.com dna decipher journal | october 2021 | volume 11 | issue 1 | pp. 21-35 22 pitkänen, m., & rastmanesh, r., homeostasis as self-organized quantum criticality 1.1 summary of the basic properties of csps and hsps let’s consider a summary of csps and hsps or briefly sps. 1. there is a large variety of cold shock proteins (csp) and heat shock proteins (hsps). csps and hsps are essentially the same proteins and labelled by hspx, where x denotes the molecular weight of the protein in kdaltons. the value range of x includes the values {22, 60, 70, 90, 104, 110} and hsps are classified into 6 families: small hsps, hspx, x ∈ {40, 60, 70, 90, 110}. at least hsp70 [wikipediae] and hsp90 [wikipediaf ] have atpase at their end whereas hsp60 has atp binding site [wikipediad]. csps and hsps consist of about 103 − 104 amino acids so that x varies by one order of magnitude. their lengths in the un-folded active configuration are below 1 micrometer. csps/hsps [wikipediac, wikipediab, nuray and ferhan 2001, szaz et al 2003] are expressed when the temperature of the organism is reduced /increased from the physiological temperature. csps possess cold-shock domains [wikipediaa] consisting of about 70-80 amino-acids thought to be crucial for their function. part of the domain is similar to the so called rnp-1 rna-binding motif. in fact, it has turned that csp and hsp are essentially the same object and stress protein (sp) is a more appropriate term. wikipedia article about cold shock domain [wikipediaa] mentions escherichia coli as an example. when the temperature is reduced from 37 ◦c to 10 ◦c, there is 4-5 hours lag phase after which growth is resumed at a reduced rate. during lag phase expression of around 13 proteins containing cold shock domains is increased 2-10 fold. csps are thought to help the cell to survive in temperatures lower than optimum growth temperature, by contrast with hsps, which help the cell to survive in temperatures greater than the optimum, possibly by condensation of the chromosome and organization of the prokaryotic nucleoid. what is the mechanism behinds sp property is the main question. 2. sps have a multitude of functions involved with the regulation, maintenance and healing of the system [petrauskas et al 2011, kellner et al 2019, feidantsis et al 2019, biter et al 2013, szaz et al 2003]. they appear in stress situations like starvation, exposure to cold or heat or to uv light, during wound healing or tissue remodeling, and during the development of the embryo. sps can act as chaperones [kellner et al 2019] and as atpases [fouvet et al 2018, christopher et al]. sps facilitate translation, and protein folding in these situations, which suggests that they are able to induce local heating/cooling of the molecules involved in these processes. csps could be considered like ovens and hsps like coolants; systems with very large heat capacity acting as a heat bath and therefore able to perform temperature control. sps serve as kind of molecular blacksmiths or technical staff stabilizing new proteins to facilitate correct folding and helping to refold damaged proteins. the blacksmith analogy suggests that this involves a local ”melting” of proteins making it possible to modify them. what ”melting” could mean in this context? one can distinguish between denaturation in which the folding ability is not lost and melting in which it is lost. either local denaturation or even melting would be involved depending on how large the temperature increase is. in a aqueous environment the melting of water surrounding the protein as splitting of hydrogen bonds is also involved. one could also speak also about local unfolding of protein. 3. there is evidence for large change ∆cp of heat capacity cp (cp = de/dt for pressure changing feed of heat energy) for formation ion nucleotide-csp fusion [christopher et al]. this could be due to the high cp of csp. the value of heat capacity of sps could be large only in vivo, not in vitro. 4. hsps can appear even in hyper-thermophiles living in very hot places. this suggests that csps and hsps are basically identical more or less but operate in different modes. csps must be able to extract metabolic energy and they indeed act as atpases. hsps must be able to extract issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2021 | volume 11 | issue 1 | pp. 21-35 23 pitkänen, m., & rastmanesh, r., homeostasis as self-organized quantum criticality thermal energy. if they are able to change their arrow of time as zeo suggests, they can do this by dissipating with a reversed arrow of time. to elucidate the topic from other angles, the following key questions should be answered: 1. are csps and hsps essentially identical? 2. can one assign to sps a high heat capacity (hhc) possibly explaining their ability to regulate temperature by acting as a heat bath? one can also ask whether hhc is present only in vivo that is in a aqueous environment and whether it is present only in the unfolded configuration of hp? 1.2 the notion of quantum criticality the basic postulate of quantum tgd is that the tgd universe is quantum critical [pitkänen 2014c, pitkänen 2016] [pitkänen 2015a, pitkänen 2015c]. there is only a single parameter, kähler coupling strength αk mathematically analogous to a temperature and theory is unique by requiring that it is analogous to critical temperature. kähler coupling strength has discrete spectrum labelled by the parameters of the extensions of rationals. discrete p-adic coupling constant evolution replacing continuous coupling constant evolution is one aspect of quantum criticality. what does quantum criticality mean? 1. quite generally, critical states define higher-dimensional surfaces in the space of states labelled for instance by thermo-dynamical parameters like temperature, pressure, volume, and chemical potentials. critical lines in the (p,t) plane is one example. bringing in more variables one gets critical 2-surfaces, 3-surfaces, etc. for instance, in thom’s catastrophe theory [zeeman 1977] cusp catastrophe corresponds to a v -shaped line, whose vertex is a critical point whereas butterflly catasrophe to 2-d critical surface. in thermodynamics the presence of additional thermodynamical variables like magnetization besides p and t leads to higher-dimensional critical surfaces. 2. there is a hierarchy of criticalities: there are criticalities inside criticalities. critical point is the highest form of criticality for finite-d systems. triple point, for instance, for water in which one cannot tell whether the phase is solid, liquid or gas. this applies completely generally irrespective of whether the system is a thermo-dynamical or quantal system. also the catastrophe theory of thom gives the same picture [zeeman 1977]. the catastrophe graphs available in the wikipedia article illustrate the situation for lower-dimensional catastrophes. 3. in tgd framework finite measurement resolution implies that the number of degrees of freedom (dfs) is effectively finite. quantum criticality with finite measurement resolution is realized as an infinite number of hierarchies of inclusions of extensions of rationals. they correspond to inclusion hierarchies of hyperfinite factors of type ii1 (hffs). the included hff defines the dfs remaining below measurement resolution and it is possible to assign to the detected dfs dynamical symmetry groups, which are finite-dimensional. the symmetry group in never reachable ideal measurement resolution is infinite-d super-symplectic group of isometries of ”world of classical worlds” (wcw) consisting of preferred extremals of kähler action as analogs of bohr orbits. super-symplectic group extends the symmetries of superstring models [pitkänen 2014c] [pitkänen 2010b, pitkänen 2010a, pitkänen 2015b, pitkänen 2019b]. 4. criticality in living systems is a special case of criticality and as the work of kauffman [kauffman 2015] suggests of quantum crticality as well. living matter as we know, it most probably corresponds to extremely high level of criticality so that very many variables are nearly critical, not only temperature but also pressure. this relates directly to the high value of heff serving as iq. the higher the value of heff , the higher the complexity of the system, and the larger the fluctuations and the issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2021 | volume 11 | issue 1 | pp. 21-35 24 pitkänen, m., & rastmanesh, r., homeostasis as self-organized quantum criticality scale of quantum coherence. there is a fractal hierarchy of increasingly quantum critical systems labelled by a hierarchy of increasing scales (also time scales). in zeo classical physics is an exact part of quantum physics and quantum physics prevails in all scales. zeo makes discontinuous macroscopic bsfrs to look like smooth deterministic time evolutions for the external observer with opposite arrow of time so that the illusion that physics is classical in long length scales is created. number theoretical physics or adelic physics [pitkänen 2017a] is the cornerstone of tgd inspired theory of cognition and living matter and makes powerful predictions. p-adic length scale hypothesis deserves to be mentioned as an example of prediction since it has direct relevance for sps. 1. p-adic length scale hypothesis predicts that preferred p-adic length scales correspond to primes p ' 2k: l(k) = 2(k−151)/2l(151), l(151) ' 10 nm, thickness of neuronal membrane and a scale often appearing molecular biology. 2. tgd predicts 4 especially interesting p-adic length scales in the range 10 nm25 µ. one could speak of a number theoretical miracle. they correspond to gaussian mersenne primes mg,k = (1 + i)k−1 with prime k ∈ {151, 157, 163, 167} and could define fundamental scales related with dna coiling for instance. 3. the p-adic length scale l(k = 167) = 2(167−151)/2l(151) = 2.5 µ m so that sps could correspond to k ∈ {165, 167, 169} . l(167) corresponds to the largest gaussian mersenne in the above series of 4 gaussian mersennes and to the size of cell nucleus. the size scale of a cold shock domain in turn corresponds to l(157), also associated with gaussian mersenne. note that the wavelength defined by l(167) corresponds rather precisely to the metabolic currency .5 ev. 4. hspx, x ∈ {60, 70, 90} corresponds to a mass of x kdaltons (dalton corresponds to proton mass). from the average mass 110 dalton of amino acid and length of 1 nm one deduces that the straight hsp60, hsp70, and hsp90 have lengths about .55 µm, .64 µ, and .8 µm. the proportionality of the protein mass to length suggests that the energy scale assignable to hspx is proportional to x. (hsp60, hsp70, hsp90) would have energy scales (2.27, 1.95,1.5 ev) for heff = h naturally assignable to biomolecules. the lower boundary of visible photon energies is a 1.7 ev. remark: one has h = heff = nh0 for n = 6. what if one assumes n = 2 giving heff = h/3 for which the observations of randel mills [mills et al 2003] give support [pitkänen 2017b]? this scales down the energy scales by factor 1/3 to (.77,.65,0.5) ev not far from the nominal value of metabolic energy currency of about .5 ev. there are strong motivations to assign to hsps the thermal energy e = t = .031 ev at physiological temperature: this is not the energy emax = .084 ev at the maximum of the energy distribution, which is by a factor 2.82 higher than e. the energies above are however larger by more than one order of magnitude. this scale should be assigned with the mbs of sps. 5. the wavelengths assignable to hsps correspond to the ”notes” represented by dark photon frequencies. there is an amusing co-incidence suggesting a connection with the model of bio-harmony [pitkänen 2014a, pitkänen 2014b]: the ratios of energy scales of hsp60 and hsp70 to the hsp90 energy are 3/2 and 1.3, respectively. if hsp90 corresponds to note c, hsp60 corresponds to g and hsp70 to note e with ratio 1.33. this gives c major chord in a reasonable approximation! probably this is an accident. note also that the weights x of hspxs are only nominal values. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2021 | volume 11 | issue 1 | pp. 21-35 25 pitkänen, m., & rastmanesh, r., homeostasis as self-organized quantum criticality 1.3 hagedorn temperature, hhc, and self-organized quantum criticality (soc) self-organized criticality (soc) is an empirically verified notion. for instance, sand piles are soqc systems. the paradoxical property of soqc is that although criticality suggests instability, these systems stay around criticality. in standard physics soqc is not well-understood. tgd based model for soqc involves two basic elements: zeo and hagedorn temperature. 1. zeo predicts that quantum coherence is possible in all scales due to the hierarchy of effective planck constants predicted by adelic physics. ”big” (ordinary) state function reductions (bsfrs) change the arrow of time [pitkänen 2020c]. dissipation in reversed arrow of time looks like generation of order and structures instead of their decay that is self-organization. hence soqc could be made possible by the instability of quantum critical systems in non-standard time direction. the system paradoxically attracted by the critical manifold in standard time direction would be repelled from it in an opposite time direction as criticality indeed requires. 2. surfaces are systems with infinite number of dfs. strings satisfy this condition as also magnetic flux tubes idealizable as strings in reasonable approximation. the number of dfs is infinite and this implies that when one heats this kind of system, the temperature grows slowly since heat energy excites new dfs. the system’s maximum temperature is known as hagedorn temperature and it depends on string tension for strings. in the tgd framework, magnetic flux tubes can be approximated as strings characterized by a string tension decreasing in long p-adic length scales. this implies a very high value of heat capacity since very small change of temperature implies very large flow of energy between the system and environment. th could be a general property of mb in all scales (this does not yet imply soqc property). an entire hierarchy of hagedorn temperatures determined by the string tension of the flux tube, and naturally identifiable as critical temperatures is predicted. the temperature is equal to the thermal energy of massless excitations such as photons emitted by the flux tube modellable as a black body. remark: if the condition heff = hgr [pitkänen 2018], where hgr is gravitational planck constant introduced originally by nottale [nottale an da rocha 2003], holds true, the cyclotron energies of the dark photons do not depend on heff , which makes them an ideal tool of quantum control. hagedorn temperature would make them soqc systems by temperature regulation if csp type systems are present they can serve as ovens by liberating heat energy and force the local temperature of environment to their own temperature near th . their own temperature is reduced very little in the process. these systems can also act as hsp/csp type systems by extracting heat energy from/providing it to the environment and in this manner reduce/increase the local temperature. system would be able to regulate its temperature. a natural hypothesis is that th corresponds to quantum critical temperature and in living matter to the physiological temperature. the ability to regulate the local temperature so that it stays near th has interpretation as self-organized (quantum) criticality (soc). in the tgd framework these notions are more or less equivalent since classical physics is an exact part of quantum physics and bsfrs create the illusion that the universe is classical in long (actually all!) scales. homeostasis is a basic aspect of living systems. system tends to preserve its flow equilibrium and opposes the attempts to modify it. homeostasis involves complex many-levels field back circuits involving excitatory and inhibitory elements. if living systems are indeed quantum critical systems, homeostasis could more or less reduce to soqc as a basic property of the tgd universe. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2021 | volume 11 | issue 1 | pp. 21-35 26 pitkänen, m., & rastmanesh, r., homeostasis as self-organized quantum criticality 2 the basic ideas about sps the tgd based model for sps relies on the notion of mb carrying dark matter as heff > h phases and the notions of heat transfer and heat capacity. the basic idea is that at least in aqueous environment the mbs of biomolecules in general have a large number of dfs and act as heat reservoirs with a stable temperature near a hagedorn temperature. mbs of sps have also high heat transfer rates between the thermal environment of the ordinary matter. zeo in particular time reversal makes it possible to realize thermal regulation in terms of soqc. on the other hand, information carrying biomolecules cannot have high heat transfer rate with environment. 2.1 conditions on the heat transfer rates between the systems involved to avoid lengthy explanations, it is appropriate to introduce some shorthand notations. denote by jh(x − y ) heat transfer rate between systems x and y . denote by e. denote bb(x) the biological body of system x. x can denote the ordinary biomolecule (dna,rna,protein) denoted by bm or stress protein sp. there are several conditions on the model explaining the hhc 1. jh(mb(sp )−e) should be high so that the mb of sp can rapidly adapt to temperature changes and extract thermal energy from the environment and act as an oven or a coolant. jh(mb(sp )−bm should be high so that csps could rapidly warm up bms for processes like translation, transcription and folding. jh(mb(sp )−bm can be also high if heat transfer occurs indirectly via mb(bm). this requires that both jh(mb(bm)−bm and jh(mb(sp )−mb(bm) are high. however, the large value of jh(mb(bm)−bm implies that bms can take care of temperature regulation without the help of sps. hence this option does not seem to be consistent with empirical facts. hence jh(mb(bm)− bm must be low. there is also a deeper rational for this. the mbs of ordinary bio-molecules must carry information and cannot be thermalized so that the energy transfer rate between them and their bb and between them and the environment must be low. 2. in csp mode the mbs of sps should actively extract energy from fats. the bms should extract thermal energy from mbs of sps. in hsp mode mbs of sps at temperature than that of the local thermal environment (including bms) should cool it by absorbing thermal energy from it. the following table summarizes the constraints on the symmetric matrix of heat transfer rates jh(a,b) for various combinations of subsystems x and y . the shorthand notations are (sp,bm,e) for (stress protein, basic biomolecule, environment) and mb(x) for the mb of molecule x. environment e is taken as the thermal environment at the level of ordinary matter. the diagonal heat transfer rates are not considered. h/l for the matrix element jh(x,y ) of the table means that its value can be large/small. the symbol ”*” means that this particular transfer is not relevant. x/y sp mb(sp ) bm mb(bm) e sp ∗ h ∗ ∗ ∗ mb(sp ) h ∗ h ∗ h bm ∗ h ∗ l ∗ mb(bm) ∗ ∗ l ∗ ∗ e ∗ h ∗ ∗ ∗ (2.1) in the minimal scenario the only constraints are on jj(sp,mb(sp ) (h), jj(bm,mb(sp ) (h), and jj(bm,mb(bm) (l). the natural question is what makes it possible for the mbs of sps to gain energy. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2021 | volume 11 | issue 1 | pp. 21-35 27 pitkänen, m., & rastmanesh, r., homeostasis as self-organized quantum criticality 1. the first manner to get energy is heat transfer from the environment. passive heat transfer would involve either ordinary photons transformed to dark photons and absorbed by mb(sp) or active heat extraction in time reversed mode involving emission of dark photons transformed to ordinary photons and absorbed by ordinary matter. the energies should be in the range of thermal energies at physiological temperatures. 2. the negative energy photons from the mb of biomolecule can be also received by other mbs acting as analogs of population reversed laser. thermalisation is expected to occur if there is large number of this kind of states. mb should allow almost continuum of cyclotron energy state in the energy resolution defined by the size scale of the molecules. 3. at least some sps such as hsp70 and hsp90 could act as atpases providing the heat energy at their mbs to drive adp→ atp process. they would act as general purpose quantum heat engines with mb acting as a heat bath running the atpase machinery. heat engine function requires a heating of the mb sp to a temperature above the local physiological temperature but below the hagedorn temperature: in zeo time reversal for the mb of sp allows this: it would look like extraction of thermal energy from the environment. part of the energy heating mb of sp could come from the binding of atp to atpase part of ps. this energy is in the range of 3-7 ev for nucleotides and could heat the mb of sp. one could also consider remote metabolism for the molecules receiving the metabolic energy quantum with a negative energy photon inducing atp → adp . note that the metabolic energy quantum .5 ev is in infra-rede (ir) range and corresponds to 2.4 µm wavelength very near to the largest p-adic length scale l(167) in the quadruplet of primes k ∈ {151, 157, 163, 167} defining four gaussian mersennes and defining the size scale of nucleus. now, consider the extraction of heat energy from the environment: 1. the energies assignable to the photon wavelengths defined by the lengths of hspx proteins are proportional to 1/x and above 1.5 ev, which is considerably above the energy of thermal photon at the maximum of planck distribution for energy is emax = .084 ev). 2. the energy transfer would be based on energy resonance and is possible only if the cyclotron frequency spectrum of dark particles contains energies possessed by molecules in their spectrum in infrared range. this poses a condition on the cyclotron energies e = ~effeb/m assumed to be in bio-photon energy range: this requires that heff = nh0 = ~gr = bmm/v0 is large: one has e = gmb/v0 does not depend on the mass of charged particle. cyclotron energies involve also the contribution from a longitudinal motion along the flux tube. the energy scale for dark photon is now ~eff/l and also universal since l scales as ~gr. if l is small the energy scale is so large that longitudinal dfs are not excited and thermalization does not occur. same is true if b is large enough. magnetic field strength is expected to scale like 1/l2(k), where l(k) is the p-adic length scale characterizing the molecule. the endogenous magnetic field bend = 2be/5 identified as the monopole flux part of the earth’s magnetic field is expected to define an important value in the spectrum of magnetic fields. the corresponding p-adic length scale corresponds to the length scales assignable to sps. also octaves of this value are expected and the model of bio-harmony [pitkänen 2014a, pitkänen 2014b] suggests that the preferred values are given by 12-note scale. for short linear molecules the energy scales would be too high to allow thermalization so that these molecules can serve as information molecules. for long dna one has length scale hierarchy and thermalization can occur only in long enough length scales. human dna has total length of order 1 meter but if the size of dna defines the p-adic length scale, then dna does not thermalize since the size of nucleus is not larger than l(167) = 2.5 µm. note that dna defines a length scale hierarchy issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2021 | volume 11 | issue 1 | pp. 21-35 28 pitkänen, m., & rastmanesh, r., homeostasis as self-organized quantum criticality in codons, genes, and also coiling scales define hierarchy levels. when the length of the molecules is longer than the wavelength of thermal photon at room temperature, one expects thermalisation to occur. sps have lengths below 1 µm. 3. the thermalization should take place for the mbs of sps. there are two energy scales associated with the cyclotron energies and the free motion along the flux tube respectively. thermal energy scale could correspond to either of these length scales. (a) cyclotron energy scale is given by ec = gmb/v0 for heff = hgr and the scales are proportional to b. longitudinal energy scale dose not depend on heff since the flux tube length scales like heff . since b scales like 1/l2(k), cyclotron length scale increases for small protein sizes. this suggests that thermalization is associated with the cyclotron df and appears for large enough p-adic length scales characterizig protein size. (b) longitudinal energy scale naturally corresponds to the lengh of protein for heff = n. the energy scale of longitudinal excitations is consirably above the thermal energy scale so that thermalization would not be possible. it might be however possible to transfer energy from these dfs to the mb of sp where it is transformed to thermal energy. 2.2 a new physics model for hhc now, consider a more concrete new physics model for hhc: 1. hhc suggests the existence of new dfs to which energy is stored so that temperature is not raised as new dfs become available. 2. in the theory of extended objects like strings, the very large number (infinite) of degress of freedom (dfs) implies a maximal temperature th known as hagedorn temperature. flux tubes are extended objects. this suggests that the mbs of sps are near to the hagedorn temperature defining the maximal temperature for their mbs. also the assumption that the physiological temperature is near but usually below th : this condition allows sp to act as heat engine. this cannot be true for the information carrying biomolecules such as dna, rna and proteins since thermalization destroys information. therefore they must have a temperature much below th . 3. in a hot environment the existence of hagedorn temperature th for the mb of hsp means that the thermal energy is transferred from the environment to the mb of hsp. this tends to reduce the local temperature of the environment towards th . hsp would act as an ideal coolant. their presence would faciliate the basic functions of cells. 4. csp and its mb would be at temperature near th and could act as an oven. their presence around dna, rna, and proteins would raise their temperature locally and facilitate transcription, translation and protein folding and unfolding otherwise prevented by a low temperature. 5. sps could act as heat engines providing heat energy to molecular motors [wikipediag]. this entails sp to have a temperature higher than the temperature of environment. in zeo this is possoble by using a time reversed mode for sp to extract energy from the environment. many sps have atpase at their end and this would make them universal heat engines providing the work as metabolic energy currency for any molecular user. 6. quite generally, by their atpase property, many sps could act as metabolic energy sources in stressful situations this comprises many other situations in addition to low and high temperatures. metabolic energy feed increases heff and would increase the scale quantum coherence reduced in the damage of dna, proteins and tissue, for instance. after this, the system could self-organize to the healed state. for instance, csps could induce local melting of misfolded proteins leading to a issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2021 | volume 11 | issue 1 | pp. 21-35 29 pitkänen, m., & rastmanesh, r., homeostasis as self-organized quantum criticality repair. csps act as chaperones and their basic tool would be local ”melting” (remind our operational definition of ”melting”) by feeding heat energy allowing to establish a correct conformation. 7. the mbs of sps could extract their thermal energy from the thermal energy of the environment in time reversed mode allowed by zep allowing the temperature of sp to even exceed that of environment in the final state of bsfr. consider a quantitative estimate. 1. for a typical flux tube length is larger than the radius of the flux tube. the critical temperature identified as hagedorn temperature corresponds to a typical thermal energy of the flux tube and is determined by flux tube length and its string tension. the critical temperature is inversely proportional to the length of the flux tube. 2. critical temperature th roughly corresponds to the energy of a photon with wavelength equal to the flux tube length l : e = th ∼ heff/l. for heff = h the flux tube length corresponds to the length scale of csp but for large values of heff = hgr it corresponds to a scale of even earth. the energies and temperature th are however the same irrespective of the value of heff and thus length of flux tube. 3. the rough estimate is that for physiological temperatures tph around th , the length for heff = h the wave length for a thermal photon at temperate 310 k the maximum of energy distribution is around 14.7 µm: note that the sizes of most animal and plant cells are oin the rage of 10-100 µm. for the wavelength distribution the wavelength for the maximum is roughly 7 µm. csps and hsps consist of about 100-1000 amino acids or so. length would be in the range .1-1 µm. the energies of photons with a wave length of straight sp are definitely above thermal energy range. some questions are in order. 1. if the new dfs are associated with mb, what can one say about the value of heff serving as iq could be? sps are possessed already by bacteria which suggests that the value of heff cannot be very large. acting as a chaperon is a control function, which suggests a higher than normal value of heff . higher than normal value ignites intriguing question whether they have higher iq (as a value of heff characterizing number theoretic complexity) than other proteins helping to survive in difficult situations. on the other hand, the thermalization means that sp flux tubes cannot carry information unlike the flux tubes of basic bio-molecules with their mbs at very low temperature. 2. cell membrane must stay flexible as temperature is lowered. this is known to be achieved by a generation of unsaturated bonds to lipids. this involves desaturase enzyme creating c-c double bond. desaturase enzymes are not sps. sps can however faciliate the transcription and translation of desaturase enzymes. 2.3 physiological temperature as hagedorn temperature, local temperature regulation, and self organized quantum criticality the notions of quantum criticality, self-organized quantum criticality (soc) and hagedorn temperature leads to a new physics based model for the explanation of sp functions. 1. hagedorn temperature th as a maximal temperature of mb of stress protein would be crucial for its functioning. why the physiological temperature is around 310 k is one of the puzzles of biology. the work of kauffman [kauffman 2015] suggests that the interpretation as a quantum critical temperature is appropriate. tgd predicts a hierarchy of quantum critical temperatures. the natural guess would be that this quantum critical temperature is hagedorn temperature realized issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2021 | volume 11 | issue 1 | pp. 21-35 30 pitkänen, m., & rastmanesh, r., homeostasis as self-organized quantum criticality at the level of mb asymptotically: in practice, the temperature of mb would be somewhat below th . this would facilitate temperature regulation or perhaps even make it possible. at quantum criticality also long length scale quantum fluctuations are possible and this makes modifications of the system possible say damaged proteins. if the temperature t of the environment at bb is above th , the thermal energy flows to mb of sp and its temperature t is reduced. mb can also make bsfr reversing the arrow of time and extract thermal energy from the environment. 2. self-organized criticality (soc) generalizes to self-organized quantum criticality (soqc) in the tgd framework. soc is well-known but it is not understood. for instance, sand piles are soc systems. they tend to approach a critical state, which looks paradoxical since just the opposite should hold for critical systems by their defining property which makes them unstable! critical system is optimal for measuring and representing since it has a large number of different states with roughly the same energy. therefore biosystems should be critical systems. the basic objection against soc and soqc is that scs are unstable by definition. in zeo this objection can be circumvented. quantum coherence is possible in all scales and in bsfrs the arrow of time is changed. this transforms the critical manifold from a repeller to an attractor and time reversals make soqc possible. the occurrence of soqc would be direct empirical proof for the zeo and its most dramatic predictions. what is the distinction between csp and hsp modes of sps? soqc according to zeo suggests that time reversal could explain this difference. how do the time reversals for csp and hsp modes differ? the following picture is suggestive. 1. the time reversal occurs for the mb of sp in hsp mode so that they extract thermal energy from environment. 2. the time reversal occurs for the mbs molecules interacting with sps in csp mode so that they can extract heat energy from the mb of csp. it has been already told that homeostasis in presence of quantum criticality is essentially quantum critical soc. 2.4 ∆cp > 0 for hsp90-nucleotide binding as support for the model chistopher et al have studied enthalpy driven reactions involving nucleotide or ansamycin bimnding to hsp90: the title of the article [christopher et al] is ”structuralthermodynamic relationships ofinteractions in the n-terminal atp-binding domain”. these reactions occurring in constant pressure are enthalpy driven meaning that heat is liberated in these reactions the second option would be entropy driven reaction in which the large entropy gain makes reaction possible. the formation of a bound state means a reduction of dfs suggesting a decrease of the heat capacity cp of the combined system. researchers however find ∆cp > 0 when another reactant is nucleotide but not for the ansamycin case. intuitively, the number of dfs should increase to explain this. the authors of the article discussed a number of explanations for their unexpected finding. the presence of mb means new hidden dfs and the neglect of its presence could lead to thermodynamical anomalies. could ∆cp > 0 in an enthalpy driven reaction leading to a formation of bound state be such an anomaly? 1. suppose hsp90 has mb can have large cp and that it is at the temperature of the environment. the temperature varies in the range 2-25 ◦c being considerably below the physiological temperature 37 c proposed to correspond to a maximal temperature hagedorn temperature for the magnetic issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2021 | volume 11 | issue 1 | pp. 21-35 31 pitkänen, m., & rastmanesh, r., homeostasis as self-organized quantum criticality flux tubes of sps. cp for the mb of sp is expected to increase as the temperature rises since new dfs are thermally excited. cp could be rather high already for the initial state if it corresponds to the sum of heat capacities for nucleotide/ansamycin and hsp90. the size of the mb of nucleotide for heff = h should be small if it correlates with the size of nucleotide/ansamycin. nucleotide is an information molecule and therefore its mb should be at a low temperature and have low cp (thermal energies cannot excite the states at low temperature). 2. since binding reaction is in question, cp for the combined system should be reduced unless something happens at the level of mbs. could the heat capacity of mb of hsp90 increase for nucleotide binding? could even the value of ∆h for the nucleotide case be larger than thought due to the fact that part of ∆h is transferred to mb of hsp90? (a) a lot of heat is liberated in the exothermic binding reaction in both cases. the measure part of the liberated heat goes to the standard dfs discussed in the article. part of ∆h is transferred to the mb of hsp90 and can heat it to a higher local temperature. new dfs open and heat capacity of mb of cps90 increases so much that the net heat capacity can increase despite the reduction of ordinary contribution to cp. this would happen for the nucleotide but not for ansamycin. why would the fraction of liberated heat going to the mb of hsp be so small for ansamycin that ∆cp remains negative? (b) could the heat ∆h liberated in the nucleotide case be considerably larger than assumed and larger than for ansamycin plus csp. this is quite possible since only the fraction going to the environment is measured, not that transferred to mb. theoretical estimates do not of course take the possible presence mb into account. if ∆h for the nucleotide case is larger than believed, then mb of hsp90 can be heated more and ∆cp > 0 is possible. (c) the inspection of tables of [christopher et al] shows that the values of ∆h for the nucleotide case are in the range 3-8 ev per reaction and correspond to uv energies. for reactions ∆cp < 0 the values of ∆h are of order .3 ev and correspond to ir photons but with energies larger than thermal energies. the difference is more than order of magnitude and suggests a similar difference for ∆h transferred to mb, which supports the proposed explanation. 2.5 some functions of sps in tgd perspective 2.5.1 sps as heat baths for molecular heat engines and providers of heat energy to atps heat is produced as a side effect of metabolism and hsps could extract this heat using remote metabolism and transform it to heat energy resourses liberated when needed. sps could be used for heating as in the basic biological processes like transcription and transcription. sps could also act as heat engines transforming heat energy to work in the case of molecular motors [wikipediag]. there are reports about the role of hsps in doing molecular work [kellner et al 2019, bonventre et al 1999, biter et al 2013]: the new element would be heat energy coming from the mb of sp. at least sps such as hsp60, hsp70, hsp90, hsp104 binding to atp could serve as general purpose heat engines transforming heat energy at their mb to metabolic energy currency used in various biological processes. 1. all processes produce heat and the very idea of hsps would the that hsps gather this heat energy and act as heaters as in the case of transcription, translation, and replication or as heat engines liberating the heat energy as ordered energy. action as atpase would make hsp a general purpose molecular heat engine. currently, we know that hspx for x ∈ {60, 60, 90, 104} at least act as atpases. ***very important question: is atpase property a general property of hsps?**** issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2021 | volume 11 | issue 1 | pp. 21-35 32 pitkänen, m., & rastmanesh, r., homeostasis as self-organized quantum criticality by the second law of thermodynamics these heat engines have some maximal efficiency proportional to the difference of the temperatures for heat bath now mb and the system receiving the energy. hence hsp mbs must be at a temperature higher than the systems receiving the energy. the formation of hsp90-atp bound state would liberate binding energy about 3-7 ev per reaction (metabolic energy quantum is .5) ev and this heats mb of hsp and would lead to the reported increase of heat capacity. 2. there is, however, a reason to worry. by carnot’s law maximal effectiveness is proportional to ∆t/t , where ∆t is the temperature difference between the system receiving the work and heat bath, now the mb of sp, and t the temperature of the heat bath. is the temperature difference high enough to give a reasonable effectiveness? zeo provides a quantum manner to get rid of worries. time reversal could make possible for the mb of hsp to develop a temperature higher than that of environment by what looks for an observer extraction of thermal energy from the environment but is actually bsfr leading to final state which dissipates in reverse time direction to a state in which the temperatures are equal. th should be however somewhat higher than the physiological temperature. 2.5.2 heat shock protein 70 and atp in homeostasis atp depletes in stress situations due to the lack of ordinary metabolic energy feed as in ischemia. the role of hsp70 and its co-function with atp in this kind of situation is discussed in [bonventre et al 1999] . also hsp70 involves atpase and the lack of the ordinary metabolic energy could be replaced by thermal metabolic energy feed from the mbs of say hsp70. 2.5.3 sps and infection one can distinguish between immune response, which is specific to the invader organism (say bacterium or virus) or molecule and non-specific immune response involving inflammation and fever. infection includes both the effects of the invader and those caused by the non-specific immune response. 1. the invader specific immune response would be basically an action of the mb: this is the basic vision of tgd. already the mb of water recognizes the invader molecules by the cyclotron energy spectrum of their mbs: this is just water memory [smith 2001, ho 2011, montagnier et al 2009] discussed from tgd point view in [pitkänen 2011]. ”homeopathy” is he ugly synonym for ”water memory” and involves mechanical agitation feeds energy to the mbs of water clusters forming a population mimicking invader molecules. mbs of water clusters are varying its flux tube thicknesses and in this manner changing corresponding cyclotron frequencies to get in tune with possible invaders: this is similar to what we do when we search for a radio station. when a hit occurs, mb of the water cluster fixes the flux tube thickness. after getting to resonance, the mbs of water molecules clusters can reconnect with u-shaped flux tubes to corresponding bacterial flux tubes: a pair of flux tubes connecting the water cluster mb to the invader molecule is formed. invader is caught. the chemical side of the immune system emerged later and would involve sequences of dark proton triplets associated with proteins as addresses 3n-fold resonance. 2. when bacteria infect cells, they induce inflammation and fever by raising the body temperature as a non-specific immune response. inflammation can be seen as the body’s protective response against infection. the fever helps immune cells to migrate to infection by a process known as chemotaxis. what fever and inflammation could mean in the proposed picture about sps? a possible explanation is as follows. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2021 | volume 11 | issue 1 | pp. 21-35 33 pitkänen, m., & rastmanesh, r., homeostasis as self-organized quantum criticality 1. quite generally, the loss of quantum coherence as a reduction of heff induced by the attack by bacteria should transform ordered energy to heat and produce entropy and also raise the temperature inducing fever. one possible mechanism producing heat in the loss of quantum coherence could be the decay of dark cyclotron condensates and dark photon states to biophotons with heff = h and with energies around hagedorn energy of order the energy associated with the physiological temperature. also the decay of dark proton sequences in the reduction heff → h to ordinary protons would liberate energy as photons: pollack’s experiments show that ir irradiation produces exclusion zones (ezs) most effectively so that the energy would be in ir range. 2. inflammation involves hsps, in particular hsp70 [krause et al 2015]. if the heat produced by the infection causing the fever can be seen as an entropic waste energy, sps such as hsp90 would do its best to transform it to ordered energy realized as metabolic energy quanta with the nominal value around .5 ev. as discussed, this would mean a formation of bound states liberating energy for instance, hmp90-atp bound state would liberate energy with part going to the mb of hsp70/90 and part to a local environment. hmp70/90 acting as atpases in the bound state and generate metabolic energy quanta by the adp → atp process. the liberated binding energy could cause the observed raise of cp of the mb of hmp90 and allow it to absorb more effectively heat energy from the environment by temporary time reversal and transform it to metabolic energy quanta. hsps would be thus generated to absorb the surplus heat to be used as a metabolic energy resource and fever would be reduced as a consequence. 3 speculative mechanisms explaining some biological observations in the sequel some speculative applications will be considered. 3.1 obesity, failing diets, and sps the effects of diets on hsp expression and activation have recently been studied, see for instance [feidantsis et al 2013, renes et al 2016, habich et al 2017, saad, sabbah and rezk 2019]. during the initial phase of diet the weight is lost. after that the weight often starts to regain. does a new energy source emerge or is the level of metabolic energy consumption reduced so that the weight regain starts although the nutrient feed stays at the same albeit reduced level? 1. the fractality of tgd universe suggests an analogy to our society. living organism is a molecular society, and the fractality of the tgd universe encourages looking at the situation from the point of view of our own society. our energy resources have been depleting and we have learned to save energy, and also to recycle thermal energy to increase thermal efficiency. could the organism learn to use remote metabolism to extract thermal energy from the environment besides sps. note that the thermal energy of a thermal photon at room temperature is rather near to the coulomb energy of a unit charge assignable to the cell membrane voltage perhaps defining another metabolic energy currency. 2. the tgd explanation relies on the proposed ability of at least some sps to act as atpases transforming heat energy of their mb to ordered energy realized as metabolic energy quanta. the binding of sps to atp [christopher et al] would also liberate binding energy transformed to heat, which is partially transferred to mb as heat energy serving as an additional metabolic energy source. also the reduction of heat losses would mean more effective use of metabolic energy. people having obesity predisposition might generate hsp60 or hsp70 and hsp90 even in situations without stress. also psychological stress such as depression might generate hsps [bahrami et al 2019]. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2021 | volume 11 | issue 1 | pp. 21-35 34 pitkänen, m., & rastmanesh, r., homeostasis as self-organized quantum criticality hsp60 is known to be associated with obesity [habich et al 2017]. hsp60 is associated with mitochondria and has atp binding site but does not have atpase. could atp binding site give hsp60 a role analogous to that of atpase using heat energy of mb of hsp70 to generate atp from adp? a more plausible option is that the binding of atp provides energy for hsp60 and only hsp70 and hsp90 act as atpases. hsp70 [mayer et al 2019] expression is considerably higher in obesity without metabolic syndrome but lower in obesity with metabolic syndrome [saad, sabbah and rezk 2019]. this would suggest that the diet induces expression of hsp70 and therefore brings an additional metabolic energy source available. in metabolic syndrome the level of hsp70 utilizing thermal energy and reducing entropy of the system would be abnormally low. besides the expression of hsp70, also its activation is needed [wang et al 2017]. if the activation takes a considerable time, one could understand why it takes time for the additional metabolic energy source to emerge. 3. the ability to act as heat engines and atpases relies on zeo: the mbs of sps could extract thermal energy from the environment in a mode with reversed arrow of time: instead of a disappearance of the necessary temperature gradient it would be generated. one can also say that system learns during diet to use remote metabolism. the phenomenon of remote metabolism or quantum credit card has been previously proposed by pitkänen [pitkänen 2013]: system would actively extract energy rather than receive it passively. the receiver of effective negative energy signal would be analogous to a population reversed laser assignable to mb. quantum credit card would facilitate rapid access to energy via bypassing ”bureaucratic formalities”. this mechanism applies also to information transfer and makes communications possible with effective signal velocity exceeding the maximal signal velocity. quite recently, it has been learned that quite simple physical systems can ”breathe” by extracting the energy of brownian motion [kuzkin,krivtsov 2020]: the finding is discussed from the point of view of zeo in [pitkänen 2020d]. 4. the utilization of metabolic energy becomes more effective during diet and there is less waste of energy. less nutrients would be required and if the dietary consumption stays at the same albeit reduced levels, fat begins to be regenerated. dietary stress would induce the generation of sps. sps acting as aptases would extract thermal energy from the environment and also from the liberated binding energy in the formation of sp-atp complex and liberate it as ordered energy by adp→ atp process. the slow rate for the generation of enzymes needed to generate and activate sps might be the reason for the slow response 5. one could see the situation also in the following manner. zeo and time reversal are involved with the extraction of thermal energy from the environment by the mbs of sps. one can also say that the system learns during the diet to use remote metabolism. the time reversal would be the analog of sleep period. also we get metabolic energy resources during sleep and the same mechanism could be involved. this could be also seen as hibernation/sleeping at the molecular level and the hibernation/sleep even at the level of organisms could rely on the same mechanism. 3.2 sleigh dogs which run for days without eating, and starving bacterial colonies suppose that the general view about sps is correct. assume also there is a fractal hierarchy of mbs. not only those of biomolecules and of smaller systems, but also of cells, organelles, organs, bodies, larger units like populations... assume also that heff = hgr holds true so that the cyclotron energy spectrum does not depend on the mass of the dark charged particle. this implies that mbs at all levels of the hierarchy can communicate issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | october 2021 | volume 11 | issue 1 | pp. 21-35 35 pitkänen, m., & rastmanesh, r., homeostasis as self-organized quantum criticality with the lowest level and also exchange energy and serve as metabolic energy sources. sps would thus allow the transfer of energy to all these levels. this admittedly speculative picture could explain the reported ability of sled dogs to run several days without eating [robson 2008]: they could store the energy to their mbs and use it during substrate lack. a possible storage to their collective mb would increase further the energy storage ability. this would mean a connection to collective levels of consciousness predicted by tgd and receival of metabolic energy feed as dark photons from these levels [pitkänen 2013]. heff hierarchy indeed makes possible energy transfer and communications between widely different scales characterizing a hierarchy of conscious entities. this picture could partially explain also why bacteria in media lacking substrate form tightly bound colonies looking like multicellulars. they could store energy to their mb and use it during its substrate lack. perhaps also the dissipation is reduced because heff increases. the cells could also learn to extract thermal energy of the cellular environment besides the thermal energy of sps, which is more or less another manner to say the same. starvation could have been the evolutionary pressure leading to the formation of multicellulars. indeed, the embryos of multicellulars are found to form tightly bound bacterial colonies [yin et al 2019]: the tgd based model is discussed in [pitkänen 2020b]. there is also anecdotal evidence about analogous abilities of tibetan monks and people regarded as saints. to summarize, the proposed general model involves several new physics elements. the new view about space-time and fields, the new view about quantum theory based on zeo predicting time reversal in bsfrs and a new view about self organization and a realization of soqc, the heff hierarchy labelling dark matter as phases of ordinary matter predicted by number theoretic vision about tgd, and the hierarchy of collective levels if consciousness having as a correlate the hierarchy of mbs carrying dark matter in tgd sense. this vision can be defended only by its internal consistency and ability to solve a long list of deep problems of recent day physics. received january 19, 2021; accepted october 1, 2021 references [bahrami et al 2019] bahrami a et al. depression in adolescent girls: relationship to serum vitamins a and e, immune response to heat shock protein 27 and systemic inflammation. j affect disord, 2152:68–73, 2019. doi: 10.1016/j.jad.2019.04.048. 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[wikipediag] molecular motor. available at: https://en.wikipedia.org/wiki/molecular_motor. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://www.researchgate.net/publication/343601103_ballistic_resonance_and_zero_energy_ontology https://www.researchgate.net/publication/343601103_ballistic_resonance_and_zero_energy_ontology http://tinyurl.com/o4o8srm https://pubmed.ncbi.nlm.nih.gov/31517511/ http://tinyurl.com/qkzwk5t https://en.wikipedia.org/wiki/cold_shock_domain https://en.wikipedia.org/wiki/cold_shock_response https://en.wikipedia.org/wiki/cold_shock_response https://en.wikipedia.org/wiki/heat_shock_protein https://en.wikipedia.org/wiki/heat_shock_protein https://en.wikipedia.org/wiki/hsp60 https://en.wikipedia.org/wiki/hsp70 https://en.wikipedia.org/wiki/hsp90 https://en.wikipedia.org/wiki/molecular_motor introduction summary of the basic properties of csps and hsps the notion of quantum criticality hagedorn temperature, hhc, and self-organized quantum criticality (soc) the basic ideas about sps conditions on the heat transfer rates between the systems involved a new physics model for hhc physiological temperature as hagedorn temperature, local temperature regulation, and self organized quantum criticality cp>0 for hsp90-nucleotide binding as support for the model some functions of sps in tgd perspective sps as heat baths for molecular heat engines and providers of heat energy to atps heat shock protein 70 and atp in homeostasis sps and infection speculative mechanisms explaining some biological observations obesity, failing diets, and sps sleigh dogs which run for days without eating, and starving bacterial colonies unraveling the tree of life dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 073-109 king, c., the tree of life: tangled roots and sexy shoots issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 73 article the tree of life: tangled roots and sexy shoots tracing the genetic pathway from the first eukaryotes to homo sapiens chris king* abstract the picture conveyed by the significance of endosymbiosis, genome fusion and horizontal transfer as key evolutionary processes complementing the vertical transmission of the tree of life, makes clear that evolution is not just a matter of competitive survival of the fittest gene, individual, or species, but of dynamic survival of genes in a surviving ecosystem. although dawkins' (1978) notion of the "selfish gene" was pivotal in drawing attention to the fact that it was the survival of genes and not organisms, or even species, that was the key evolutionary process, attributing the human sentiment of selfishness to a gene is somewhat of a self-serving advertising distraction on the part of the author, which diminishes the subtlety and complexity of the sometimes apparently paradoxical ways genes actually interact to bring about beneficial outcomes in the evolutionary dynamics of the ecosystem. although the idea of selection of genes has been pivotal in defining the need to consider evolutionarily stable strategies under genetic variation in ways which have been subsequently confirmed time and time again in situations such as the sexual genetics of social insects such as bees and ants, social selection is by no means ineffectual, or much of sociobiology, including the biological basis of morality as an extension of reciprocal altruism, would cease to exist. moreover, from what we have seen, particularly about horizontal gene transfer, and the capacity of mobile elements to induce modulated changes in nuclear genomes, it is not the 'selfishness' of a genetic element alone that results in survival of both a gene and its hosts, but dynamic feedbacks,, and relationships which ultimately contribute to a massive sharing of information in the manner of parallel genetic algorithms fundamental to the replicative genetic process, which enable global forms of genetic and genome optimization central to the overall viability of life as complex systems. key words: tree of life, genetic pathway, eukaryotes, homo sapien, dna, rna, evolution. introduction this article is a fully referenced research review to overview progress in unraveling the details of the evolutionary tree of life, from life's first occurrence in the hypothetical rna-era, to humanity's own emergence and diversification, through migration and intermarriage, using research diagrams and brief discussion of the current state of the art, as of 2009, in response to summaries of some of these developments (lawton 2009, lane 2009). the tree of life, in biological terms, has come to be identified with the evolutionary tree of biological diversity. it is this tree which represents the climax fruitfulness of the biosphere and the genetic foundation of our existence, embracing not just higher eukaryotes, plants, animals and fungi, but protista, eubacteria, and archaea, the realm, including the extreme heat and salt-loving organisms, which appears to lie almost at the root of life itself. * correspondence: chris king http://www.dhushara.com e-mail: chris@sexualparadox.org http://en.wikipedia.org/wiki/evolutionary_tree http://en.wikipedia.org/wiki/tree_of_life http://en.wikipedia.org/wiki/eukaryote http://en.wikipedia.org/wiki/protista http://en.wikipedia.org/wiki/eubacteria http://en.wikipedia.org/wiki/archaea http://www.dhushara.com/ mailto:chris@sexualparadox.org dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 073-109 king, c., the tree of life: tangled roots and sexy shoots issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 74 fig 1: the tree of life (king http://www.dhushara.com/book/unraveltree/life4ck.jpg) http://www.dhushara.com/ dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 073-109 king, c., the tree of life: tangled roots and sexy shoots issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 75 the universal common ancestor following a phase of biogenesis possibly based on cosmic symmetry-breaking (king 1978, 2004), based on new breakthroughs concerning rna synthesis (sutherland et. al. 2009) recent research suggests that the last universal common ancestor (luca) of all life on the planet may have arisen from a phase interface between alkaline hydrogen-emitting undersea vents and the archaic acidified iron-rich ocean (martin and russel 2003), giving rise to an active iron-sulphur reaction phase still present in living cells and associated with electron transport and some of the most ancient proteins, such as ferredoxin, in which differential dynamics in membranous micropores in the vents managed to concentrate polypeptides and polynucleotides to biologically sustainable levels (baaske et. al. 2007, budin et. al. 2009), giving rise to the rna era, while at the same time providing a free energy source based on proton transport across membranous microcellular interfaces resulting from fatty acids also being concentrated above their critical aggregate concentration . fig 1a: proposed scheme for the universal common ancestor (martin and russel 2003) the universal common ancestor of the three domains of life may have thus been a proton-pumping membranous interface from which archaea and bacteria emerged as free-living adaptions. this is suggested by fundamental differences in their cell walls and other details of evolutionary relationships among some of the oldest genes. it has also been proposed, on the basis of the highly-conserved commonality of transcription and translation proteins to all life, but the apparently independent emergence of distinct dna replication enzymes in archaea/eucaryotes and eubacteria, that the last universal common ancestor had a mixed rna-dna metabolism based on reverse transcriptase, pinpointing it to the latter phases of the rna era (leipe et. al. 1999). dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 073-109 king, c., the tree of life: tangled roots and sexy shoots issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 76 fig 1b: hypothetical branching and evolution of rna and dna replication machinery (leipe et. al. 1999). three domains of life life today is informationally based on the sequences of the four bases a, g, t and c in dna, with messenger copies of the genetic sequence in mrna forming intermediates in the assembly of proteins, as the cell's primary active chemical and structural agents. this is achieved through a process of translation at the ribosome a supra-molecular complex composed of some 50 chaperoning proteins surrounding a core composed of three rrna units, fed by amino-acid coupled trnas. the rnas carry out the essential function, supporting the idea that translation was at first a purely rna-based process of protein construction. in line with this and other rna fossils found particularly in eukaryotes, it is widely believed that life began based on rna, which shares both the capacity for complementary replication of dna and the formation of 3-dimensional chemically reactive conformations, similar to proteins, after which the ribosome evolved, transferring the reactive burden on to proteins sequenced through the genetic code. some time later, the informational genome was consolidated into more stable dna. fig 2: the initial tree of rrnas shows three distinct founding domains (woese 1987) dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 073-109 king, c., the tree of life: tangled roots and sexy shoots issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 77 originally the bacteria and archaea were thought to be one large diverse family of prokaryotes until carl woese (1977, 1978, 1987, 1990) and others investigated the evolutionary tree of ribosomal rnas and found that there were three distinct founding evolutionary domains, then named eubacteria, archaebacteria along with the eukaryotes. this gave the eukaryotes a closer founding status as well, by contrast with the idea that the procaryotic bacteria came first and then, somehow the higher eukaryote organisms with their complex cellular structures, including among others the endoplasmic reticulum, along with the nuclear envelope and golgi apparatus all parts of a common complex of internal membranous partitions and the architecture of microtubules, including centrioles, and the eukaryote flagellum, as well as the eukaryotes endosymbiont mitochondria and chloroplasts fig 3: key structural differences separating the larger rrna units of the three domains (woese 1987). in addition to their evolutionary sequence divergence, the smaller 30s ribosomal rnas of each domain, show distinct structural features characteristic of their own domain, but also emphasizing structural links between bacteria and archaea on the one hand and archaea and eukaryotes on the other, qualitatively confirming the central place of the archaea in the divergence. fig 4: small and large rrna subunits of the eubacteia thermus thermophilus and the archaeon haloarcula marismortui. rna orange and yellow, protein blue and active site green. (wikipedia ribosome) the validity of the rna-era concept and the capacity for rnas to be both replicating informational and active ribo-enzymes is emphasized by the continuing dependence of the ribosome on rrna http://www.dhushara.com/book/unraveltree/10_small_subunit.gif http://www.dhushara.com/book/unraveltree/10_small_subunit.gif http://en.wikipedia.org/wiki/ribosome dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 073-109 king, c., the tree of life: tangled roots and sexy shoots issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 78 rather than the protein components is emphasized by the 3-dimensional realizations of the two subunits in fig 4, which show that the rrna molecules are still carrying out the central task of protein assembly with only minor modification due to the 'chaperoning' proteins, despite 3.8 billion years of evolution. norman pace subsequently enlarged the scope and accuracy of the rrna tree, including a greater diversity of organisms. this tree has become the basis of several other studies (see e.g. fig 10). the copernican principle asserts that the earth is a typical rocky planet in a typical planetary system, located in an unexceptional region of a common barred-spiral galaxy, hence it is probable that the universe teems with complex life. this is supported to a reasonable extent by the discovery of an increasing number of planets including some putative "goldilocks" zone planets where water would be liquid and life as we know it could potentially exist. set against this, the rare earth hypothesis argues that the emergence of complex life requires a host of fortuitous circumstances including a galactic habitable zone, a central star and planetary system having the requisite character, the circumstellar habitable zone, the size of the planet, the advantage of a large satellite, conditions needed to assure the planet has a magnetosphere and plate tectonics, the chemistry of the lithosphere, atmosphere, and oceans, the role of "evolutionary pumps" such as massive glaciation and rare bolide impacts, and whatever led to the still mysterious cambrian explosion of animal phyla. this might mean that planets able to support a bacterial level of life are not so uncommon, but those supporting complex multicellular life might be. fig 5: further elaboration of the rrna tree (pace 1997) http://en.wikipedia.org/wiki/rare_earth_hypothesis dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 073-109 king, c., the tree of life: tangled roots and sexy shoots issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 79 fig 6: lower right: a third rrna tree which suggests archaea lie very close to the root is contrasted with that for the enzyme hmgcoa reductase, which also shows evidence of horizontal transfer to an archaean (ex doolittle 2000). bringing this question to a pivotal crux in our context, the emergence of mitochondria as endosymbionts has been proposed to be a critical bottleneck which allowed complex life to evolve only once, because, only in this effectively fractal cellular architecture, can the membrane surface areas necessary to support the chemical reactions enabling the vastly larger number of genes in a complex organism's genome to maintain metabolic stability (lane and martin 2010). whether such endo-symbiosis is rare. or a common extreme of parasitic relationships would then determine how likely or unlikely complex life might be. offset against both the uniqueness of the mitochondrial endo-symbiosis and the closely linked, but independent question of the origin of the nucleus and nuclear envelope, has been the discovery of mimiviruses and mamaviruses infecting amoeba (raoult et, al. 2004) and related very large aquatic viruses such as crov infecting single celled plankton species, which despite their recent discovery, appear from ocean gene analyses to be potentially ubiquitous and widespread in the oceans and possibly playing a crucial role in regulating the atmospheric-oceanic pathways, such as carbon sequestration (fisher, allen, wilson and suttle 2010). these form an intermediate genetic position between viruses and cells, having the largest genomes, with extensive cellular machinery and larger than the smallest completely autonomous bacterial and archaeal genomes. as an illustration of genes in mimivirus normally appearing only in cellular genomes, the mimivirus has genes for central protein-translation components, including four amino-acyl transfer rna synthetases, peptide release factor 1, translation elongation factor ef-tu, and translation initiation factor 1. the genome also exhibits six trnas. other notable features include the presence of both type i and type ii topoisomerases, components of all dna repair pathways, many polysaccharide synthesis enzymes, and one intein-containing gene. inteins are protein-splicing domains encoded by mobile intervening sequences (ivss). they self-catalyze their excision from the host protein, ligating their former flanks by a peptide bond. they have been found in all domains of life (eukaria, archaea, and eubacteria), but their distribution is highly sporadic. only a few instances of viral inteins have been described. self-splicing type i introns are a different type of mobile ivs, selfhttp://www.newscientist.com/article/dn18734-why-complex-life-probably-evolved-only-once.html http://www.newscientist.com/article/dn18734-why-complex-life-probably-evolved-only-once.html http://www.k8science.org/news/news.cfm?art=1288 http://en.wikipedia.org/wiki/mimivirus http://en.wikipedia.org/wiki/mamavirus http://www.newscientist.com/article/dn19625-giant-virus-with-tiny-victims-carries-a-monster-genome.html dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 073-109 king, c., the tree of life: tangled roots and sexy shoots issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 80 excising at the mrna level. they are rare in viruses. mimivirus exhibits four instances of selfexcising intron, all in rna polymerase genes. evolutionary diversification of mimiviruses from nucleocytoplasmic large dna viruses (fisher et. al.) and in relation to the three domains of cellular life based on the concatenated sequences of seven universally conserved protein sequences (raoult et. al.) mimiviruses also host parasitic virophages, affectionately named sputnik as viral satellites, which piggy back on the metabolism of the large viral factories set up by these giant viral genomes causing the mimiviruses to sicken, and these virophages also contains genes that are linked to viruses infecting each of the three domains of life eukarya, archaea and bacteria (la scola et. al. 2008). it has thus been suggested that they have a primary role in the establishment of cellular life and that they may have been instrumental in the emergence of the nuclear envelope. fig 7: evolution of iron-sulphur cluster proteins of mitochondria is linked to αproteobacteria (emelyanov 2003) http://www.nature.com/news/2008/080806/full/454677a.html dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 073-109 king, c., the tree of life: tangled roots and sexy shoots issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 81 tangled roots of horizontal transfer despite the division into three domains, further investigations of proteins in the three domains began to reveal a much more confused and complicated picture. firstly the ribosomal proteins, like the rrnas show distinct, easily differentiated morphologies with some correspondences linking one pair of domains and other another pair (forterre 2006b, woese 2000). secondly, the proteins in eukaryotes appear to have a mixed origin with the informational ones having an evolutionary relationship with archaea but the metabolic enzymes appearing to have a bacterial origin. this suggests that the eukaryote genome has either resulted from one, or more symbiotic fusions e.g. an archaeal and a bacterial genome and/or that there has been a high degree of horizontal gene transfer between bacteria and eukaryotes. the evidence for symbiotic inclusions is clear from the fact that all eukaryotes, except for a few primitive anaerobic varieties, such as the metamonad human gut parasite giardia lamblia, all have endosymbiotic respiring mitochondria, which are evolutionarily related to α-proteobacteria such as rickettsiae (emelyanov 2003). plants also have photosynthetic chloroplasts derived from cyanobacteria. α-proteobacteria, including rickettsiae (and related wollbachia and agrocbacterium), obligately live in the cytoplasm of other cells and so are naturally adapted to becoming an endosymbiont of a glycolytic organism by providing respiring energy to the host's metabolism resulting in the mitochondrion. giardia still retains traces of mitochondrial proteins so appears to have lost its respiring organelles, rather than occupying a place in the tree before mitochondria were incorporated into eucarya (adam 2000). fig 8: tangled roots (doolittle 2000) http://en.wikipedia.org/wiki/giardia http://en.wikipedia.org/wiki/proteobacteria http://en.wikipedia.org/wiki/rickettsiae http://en.wikipedia.org/wiki/cyanobacteria dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 073-109 king, c., the tree of life: tangled roots and sexy shoots issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 82 the picture of horizontal transfer is even more tangled in bacterial and archaeal genomes, which contain a great number of shared and exchanged genes, probably through viral transfer. this has led generally to doolittle (1998), woese (2002), and others, proposing a tangled root to the tree of life involving a transition from a regime in which thre was a much higher rate of horizontal exchange and effective global optimization of genomes, to tree-like vertical evolution of genomes, once the more complex genomes of the eukaryote domains became established. subsequently, to try to clarify the taxonomic relationships founding the tree of life, peer bork and his team produced a refined evolutionary tree by selecting only universal proteins that had not been subjected to horizontal transfer, providing the most detailed tree root diagram to date, although admittedly on only a skeleton gene set comprising some 1% of the respective genomes. the phylogenetic tree has its basis in a cleaned and concatenated alignment of 31 universal protein families and covers 191 species whose genomes have been fully sequenced. fig 9: high resolution tree of the three domains of life (ciccarelli, bork et. al. 2006).purple eubacteria, green archaea, red eukaryotes. dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 073-109 king, c., the tree of life: tangled roots and sexy shoots issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 83 fig 9b: tree diagram of the birth, transfer, duplication and loss of key genes in the redox and electron transport pathways, in a founding burst of gene evolution between 3.3 and 2.7 billion years ago (david and alm 2010). then lawrence david and eric alm (2010) produced the above tree investigating the central genes common to a wide spectrum of life forms, involving the founding steps of redox reactions and electron transport, demonstrating a rapid evolutionary innovation during an archaean genetic expansion between 3.3 and 2.7 billion years ago. they mapped the evolutionary history of 3983 gene families that occur in a wide range of modern species. they were able to show that 27 per cent of these gene families appeared in a short evolutionary burst. many of the genes from this time were involved in electron transport a key step in respiration and photosynthesis, which ultimately led to oxygen-producing photosynthesis and the "great oxygenation event" 2.4 billion years ago, when the atmosphere became oxygen rich. this lends support to the idea that the collective primordial genome functioned as a supercomputer (king 2010) based on parallel genetic algorithms combined with horizontal genetic transfer, whose bit computation rate through mutation and recombination is sufficient to generate the functional conformations, through protein folding, to solve the key metabolic pathways over a period no longer than 300 million years. bacteria engage in much more radical forms of pan-sexuality than higher organisms, involving viruses and plasmids, themselves separate mobile genetic elements, acting as agents of genetic transfer, accelerating the pace of bacterial evolution (maxmen 2010). this enables the genetic sequences of bacteria, archaea and protists to move around in the genome and to be exchanged between cells, and even between different species. sexual exchange of material can happen both through viral exchange and through a conjugation plasmid, which can spool dna from one bacterium into another, resulting in a net donation of genes from one strain or species to another, which ensures a broad exchange of genetic material throughout bacterial ecosystems, resulting in rapid accumulation of advantageous genes exemplified by plasmid borne infectious drug resistance. dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 073-109 king, c., the tree of life: tangled roots and sexy shoots issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 84 to give a very rough idea of the computing power of the combined bacterial genome alone, taking into account bacterial soil densities (~10 9 /g), effective surface area (~10 18 cm 2 ), genome sizes (~10 6 ), combined reproduction and mutation rates (~10 -3 /s) gives a combined presentation rate of new combinations of up to 10 30 bits per second, roughly 10 13 times greater than the current fastest computer at 2 petaflops or about 10 17 bit ops per second. corresponding rates for complex life forms would be much lower, at around 10 17 per second because they are fewer in total number and have lower reproduction rates and longer generation times, but they are still vying with the computation rates of the fastest supercomputer on earth. fig 10: horizontal transfers across the bacterial tree under two thresholds 10, 5 genes (dagan et. al.). this picture of bit rates coincides closely with the archaean expansion scenario noted above and suggests that evolution has been a two-phase process in which the much higher bit rates of the collective single-celled genome under promiscuous sexuality and horizontal transfer has arrived at a global genetic solution to the protein folding problems of the central metabolic, electro-chemical and even root developmental pathways, which are then later capitalized on by multi-celled organisms, through gene duplication and loss as well as the creation of new specialized genes at a much lower rate. the massive extent of horizontal transfer in eubacteria, as well as archaea has also become clear suggesting large components of procaryote genomes are effectively globally optimized for their niches by frequent genetic transfer. dagan et. al. have characterized the extent of horizontal transfer dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 073-109 king, c., the tree of life: tangled roots and sexy shoots issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 85 for a series of thresholds as well as establishing specific modularity of horizontal transfer of functions between groups. fig 11: evolutionary root of the tree of life and its diversification into archaea, bacteria and eukaryotes appears to have gone through an early period of cool temperature consistent with an rna era, followed by a hot period (anathaswamy, boussau et. al.) surviving archaea are known to inhabit extreme environments, including hot volcanic pools, hydrothermal vents and extreme salty environments and several arrangements of the root of the tree, including bork's team's work suggest a hot origin for life. however other research (brochier and philippe, boussau et. al.), concludes the base root may have been at about 25 o c, a more viable temperature for a simple rna metabolism, with a succeeding period of high temperature adaptions shortly after the differentiation of the three domains in evolutionary time. fig 12: genetic diffusion at the root of the tree (dagan and martin) critics of the validity of the tree root concept, such as dagan and martin emphasize the small proportion (1%) of the genome used in bork's study and stress both the lateral (or horizontal) gene transfer events uniting the prokaryote realms and the apparent chimaeric nature of the eukaryote http://en.wikipedia.org/wiki/archaea dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 073-109 king, c., the tree of life: tangled roots and sexy shoots issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 86 genome, which appears to contain both archaea-related informational genes and eubacterial metabolic ones, in addition to obvious endosymbiont events of the mitochondrion and chloroplast. fig 13: pattern of invasions of the spin element (lisch) the case for horizontal transfer of genes between unrelated eukaryote species through infectious elements invading new and hence non-resistant species is also well established. the spin element is present in a diverse unrelated set of species, spanning amphibians, reptiles, marsupials and mammals while absent from closely related species (lisch). the eukaryote nuclear genome as a genetic fusion fig 14: the proposed ring of life (rivera and lake) in a further study, rivera and lake used a new algorithm to take account of possible genetic fusion events by forming a genetic ring through matching partial trees into a most parsimonious whole, inferring that the eukaryote genome has arisen from a fusion of an archaeal (possibly eocyte) genome with that of either a cyanobacterium or possibly a γ-proteobacterium. http://en.wikipedia.org/wiki/eocyte dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 073-109 king, c., the tree of life: tangled roots and sexy shoots issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 87 the method used cannot definitively determine whether or not the eubacterial genome could have come from the mitochondrial event, which, to an even greater extent than the more recent chloroplast, has resulted in a high net transfer of genes from the mitochondrial chromosome to the nucleus, leaving open the possibility that in addition to the mitochondrial symbiosis, and the later chloroplast one, there may have been an additional genetic fusion. lane and archibald have cited further major endosymbiosis events involving complex three genome interaction in protista, where both green and red algae have been incorporated by endosymbiosis into other protists, which demonstrate both that endosymbiois has occurred many times and the genomic complexity of nuclear symbiont gene exchange. fig 15: proposed fusion between two genomes informational, from archaea (red), and metabolic, from eubacteria (blue) as well as mitochondrial genes migrating to the nucleus (green) (horiike et. al.). up to 75% of nuclear genes whose ancestry has been elucidated may come from bacteria (lane). the idea of a genetic fusion between an archaea and a γ-proteobacterium is also supported by several other lines of research including evolution of glycolytic enzymes (emelyanov), ‘homology-hit analysis’ of non-mitochondrial genes determined the number of yeast orthologous orfs in each functional category to the orfs in six archaea and nine bacteria at several thresholds, suggesting an archaeal parasite engulfed by a eubacterium (horiike et. al.) the proposal that close association between a central methanogenic archaebacterium (archaea) and a close-knit surrounding clump of ancestral sulfate-respiring δ-proteobacteria could have also led to the nucleus and endoplasmic reticulum (moreira and lopez-garcia). http://www.newscientist.com/article/mg20227121.600-has-the-mystery-of-sex-been-explained-at-last.html?full=true dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 073-109 king, c., the tree of life: tangled roots and sexy shoots issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 88 fig 16: gene replacement tree root (makarova) hartman and federov's list of putative chronocyte genes correspond to the 359 above. other theories stick to the three domain paradigm and propose that a primitive eukaryote precursor possibly still retaining an rna-based genome, as suggested by woese (1998) might be the case for the progenote (first root life form) to be the last universal common ancestor of all three domains, possibly including genes for endoplasmic reticulum and microtubules, engulfed both and archaea and a eubacterium. hartman and federov cite a collection of such genes, including those for ribosomal proteins as well, naming the organism as a chronocyte. this is also consistent with the much greater complexity of use of rna in eukaryotes, including alternative splicing, the use of introns, interfering-rnas in gene regulation, micro-rnas and the use of the nucleus to contain a diversely functioning rna informational metabolism not unlike that of a putative progenote. viral influences on the nuclear genome fig 17: proposed viral contribution of dna polymerases fva etc. founder viruses (forterre). other cellular and viral genealogies are possible and the scheme is merely representative. dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 073-109 king, c., the tree of life: tangled roots and sexy shoots issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 89 forterre looks likewise to a three component origin, but his emphasis is on the idea that viruses have contributed major components to the genome of all three groups, possibly providing each of three rna-based cell lineages with independent transitions to dna-based genomes by contributing dnapolymerases, thus radically improving the stability and competitiveness of these cell lines who became the eventual survivors. in addition to the ribosomal proteins and rrnas having distinct qualitative features in each domain, many dna informational proteins exist in different nonhomologous families (usually with several versions for one family). there are already six known non-homologous families of cellular dna polymerases. in the case of dna polymerases of the b family, there is one version in bacteria (only found in some proteobacteria), one in archaea, and several in eukarya. the distribution of the different versions and families of cellular dna informational proteins among domains is erratic most of the time and does not fit with any of the models proposed for the universal tree, suggesting abrupt insertion into the cellular genomes by viral transfer. fig 18: evolutionary tree of dna polymerase amino termini (villareal and defilippis). villareal and defilippis have likewise investigated the idea that dna viruses are the origin of dna replication proteins, by investigating the amino terminus and constructing an evolutionary tree which shows dna polymerases of dna viruses, eukaryotes (α,δ), archaea, e coli and two phages rooted in a tree consistent with a viral origin. this idea has a great deal of plausibility because viruses are now know to have a potentially primal origin, rather than being recent escapees from cellular genomes which have undergone reductive parasitic changes to their genome. viruses clearly also have retained both rna-rna, dna-dna and retrotranscription dna-rna-dna using both rna and dna stages in their capsid viral forms, so they retain all the transitional states between rna and dna-based replication. dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 073-109 king, c., the tree of life: tangled roots and sexy shoots issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 90 fig 19: bacterial dna polymerases also show viral members (underlined) close to the root of the tree (file et. al.). furthermore the retroviruses and related mobile genetic elements have a common ancient evolutionary origin, which is related to telomerase, which itself uses an rna primer to initiate chromosome duplication. there is thus a plausible case that telomerase is in fact a biological fossil of a retroviral conversion of the founding eukaryote cell line to a dna genome. the symbiotic face of eukaryote mobile elements in 1978, following the work of darryl reanny (1974-6), i proposed (1978, 1992) that viruses and transposable elements, far from just being selfish genes (dawkins 1976), formed part of a dynamical system of genetic symbiosis between the hosts and the mobile genetic elements, because the mobile elements permitted forms of coordinated gene expression and the formation of new genes in a modular manner, which would otherwise be impossible, achieving in return perpetuation of their own genomes over evolutionary time scales. most of the details of this proposal have proved to be realized. by some reckonings, 40 to 50 per cent of the human genome consists of dna imported horizontally by viruses, some of which has taken on vital biological functions. coding sequences comprise less than 5% of the human genome, whereas repeat sequences account for at least 50% and probably dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 073-109 king, c., the tree of life: tangled roots and sexy shoots issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 91 much more. transposable line or long-intermediate repeat retroelements common to vertebrates, with a history running back to the eukaryote origin are specifically activated in both sperms and eggs during meiosis (branciforte and martin, tchénio et. al., trelogan and martin). these replicate from transcribed rna copies of themselves thus using rna to instruct dna copies, indicating an origin in rna-based life, as does the active rna processing of our own eukaryote cells. their rna-based reverse transcriptase shows homologies with the telomerase essential for maintaining immortality in our germ line, indicating a common and symbiotic origin. 100,000 partially defective lines and their 300,000 dependent smaller fellow traveler alu sines make up a significant portion of the human and mammalian genomes, along with pseudogenes, apparently defective copies of existing genes translocated by elements such as lines. fig 20: human transposable element evolutionary history of l1-lines (cream), alu elements (lt. blue), retrovirus-like ltr (long-terminal repeat) elements (green) and dna transposons (dk. brown). older lines and sines are in yellow and dk. blue. this history extends back over 200 million years indicating the very ancient basis of this potentially symbiotic relationship (human genome consortium). these elements travel passively down the germ line with chromosomal dna, so their specific activation during meiosis suggests they may perform a role of coordinated regulatory mutation. this suggests that the type of symbiotic sexuality embraced by bacteria and plasmids also continues to function in higher organisms in a form of sexual symbiosis between our chromosomes and transposable genetic elements. this is consistent with the 1.4% point mutation divergence between humans and chimps, being overshadowed by an additional 3.9% divergence to 5.4% overall (britten), when insertions and deletions are accounted. sines, such as human alu, a free-rider on the line reverse transcriptase derived from the small cellular rna used to insert nascent proteins through the membrane, are in turn implicated in active functional genes (reynolds, schmid) particularly some involved in cellular stress reactions, again suggesting genetic symbiosis. humans have about 13 times as many rna edits as non-primate species, including inosine insertions associated with alu elements, as well as intron deletions (holmes ) and newly inserted exons (ast), which may differentiate humans from other apes through alternative splicing of genes expressed in the brain. rna editing is abundant in brain tissue, where editing defects have been linked to depression, epilepsy and motor neuron disease. there is a new dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 073-109 king, c., the tree of life: tangled roots and sexy shoots issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 92 alu insert about every 100 births. as many as three quarters of all human genes are subject to alternative splice editing. fig 21: pseudogene-mediated production of endogenous small interfering rnas (endosirnas). pseudogenes can arise through the copying of a parent gene (by duplication or by retrotransposition). (a) an antisense transcript of the pseudogene and an mrna transcript of its parent gene can then form a double-stranded rna. (b) pseudogenic endo-sirnas can also arise through copying of the parent gene as in a and then nearby duplication and inversion of this copy. the subsequent transcription of both copies results in a long rna, which folds into a hairpin, as one half of it is complementary to its other half. in both a and b, the double-stranded rna is cut by dicer into 21-nucleotide endo-sirnas, which are guided by the risc complex to interact with, and degrade, the parent gene's remaining mrna transcripts. the mrna from genes is in red and that from pseudogenes is in blue. green arrows indicate dna rearrangements (sasidharan and gerstein). recent explosion of the area of interfering mirnas as regulatory elements in gametogenesis and development (großhans) has provided an explanation of how pseudogenes, including those retrotransposed via line elements, can gain functional regulatory significance even though they do not produce translatable mrnas. although the data from the human genome project indicated that human lines are becoming less active as a group by comparison with the corresponding elements in the more rapidly evolving mouse genome, there remain about 60 active human line elements which are known to be responsible for mutations in humans. more recent investigation (boissinot et. al.) shows that the most recent families are highly active. around four million years ago shortly after the chimp-human split, a new family ta-l1 line-1 emerged and is still active, with about half the ta insertions being polymorphic, varying across human populations. moreover 90% of ta-1d, the most recent subfamily are polymorphic, showing highly active lines remain present. lines are more heavily distributed on the sex chromosomes with x chromosomes containing 3 times as many full length potentially active elements and the y chromosome 9 times as many! this is consistent with a continuing mutational dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 073-109 king, c., the tree of life: tangled roots and sexy shoots issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 93 load on humans which is removed more slowly from the sex chromosomes by crossing over in proportion to the degree to which crossing over is inhibited in each (i.e. totally on the y and largely in males in the x but not in females). sexual recombination is a protection from mutational error in a process called muller's ratchet. fig 22: evolution of reverse transcriptases from a common ancestor bearing a line archetype (xiong and eickbush, nakamura et. al.). the root of their evolution goes back to the transfer from rna to dna at the beginning of life. they form a complementary evolutionary tree to that of cellular life as genetic symbionts of metazoa travelling down the germ line. their group includes telomerases essential to the reproductive cycle. lines are preferentially expressed in both steriodogenic and germ-line tissues in mice (branciforte and martin, trelogan and martin), suggesting stress could interact with meiosis. l1 expression occurs in embryogenesis, at several stages of spermatogenesis including leptotene, and in the primary oocytes of females poised at prophase 1. conversely the sry-group male determining gene sox has been found to regulate line retrotransposition (tchénio et. al.). similarly line elements have been proposed to be 'boosters' in the inactivation of one x chromosome that happens in female embryogenesis (lyon). this could enable somatic stress to have a potential effect on translocation in the germ-line which might enable form of genetic adaption in long-lived species such as humans. both l1 and alu elements may be able to self-regulate rates of replication, through the existence of stealth drivers, viable elements which maintain a low transcription rate of active elements, with little genomic impact and hence little negative selection. these occasionally seed daughter master elements, which may replicate actively to form new families when conditions permit. this picture is consistent with long periods of quiescence, punctuated by bursts of 'saltatory' replication leading to large copy numbers (han et. al.). dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 073-109 king, c., the tree of life: tangled roots and sexy shoots issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 94 endogenous retroviruses and the placenta endogenous retroviruses, or ervs, which also travel down the germ line as free-riders, although some may retain infectious capacity, may be essential for placental function, as every mammal tested has placental blooms of endogenous retroviruses which appear to both aid the formation of the syncytium, the super-cellular fused membrane that enables diffusion from the mother to the baby and the immunity suppression, which prevents rejection of the embryo, both characteristics of retroviruses such as hiv. mi and colleagues (2000) found a placental gene whose sequence was homologous to several retroviral envelope proteins. the sequence, now called syncytin, is identical to the envelope protein of the herv-w retrovirus (blond et. al.) which exists in around 40 apparently defective viral copies, including those in which the two syncytin viral env genes are fully functional (mi et. al.). syncytin is expressed at high levels in the syncytiotrophoblast (and at low levels in the testes) and nowhere else. most of the other genes of the provirus have been mutated, suggesting that the envelope glycoprotein function was specifically selected. if cultured cells are made to express syncytin, they will fuse together, and this fusion can be blocked with antibodies against syncytin. herv-w is only found in primates, but mice have similar retroviral blooms and erv-related syncytin genes have also been found in them (dupressoir et. al.). the ability of mammals and thus ourselves to form a viable placenta and give birth to live young may thus depend on the mammals having harnessed a viral gene somewhere in our evolutionary lineage. the defective copies of endogenous retroviruses may also serve to protect the host against further infection by becoming transcribed and causing incorporation of defective elements into the replicating virus (best et. al.). fig 23: the evolutionary tree of endogenous retrovirus classes along with other infectious retroviruses such as hiv span virtually all metazoa. when retrotranspons are included (fig 22) they extend to all eukaryote realms. http://en.wikipedia.org/wiki/endogenous_retrovirus dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 073-109 king, c., the tree of life: tangled roots and sexy shoots issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 95 emergence and diversification of modern humans fig 24: one hypothetical evolutionary tree for humans and related apes. there is much debate about the actual form of such a tree. homo sapiens appears to have evolved into a single dominant species on the planet, after preceding period in which fossil evidence suggests there were several different anthropoid species coexistent. the final stage of this process was the disappearance of homo erectus and neanderthal, the latter after a well-defined period of coexistence in europe at the end of the last ice age. our own evolutionary and cultural roots appear to lie in africa, with evidence of culture and cosmetics running back over 100,000 years, in addition to evidence for tools and weapons. an alternative regional development theory has proposed that humans evolved through a considerable amount of interbreeding over the whole african and asian continental region, however genetic evidence is coming to point towards an african origin with only at most very occasional cross fertilization with related species. fig 25: human-neanderthal-chimp divergences (green et. al.) according to genetic analysis, neanderthals diverged from homo sapiens ~500,000 years ago. there has been no major interbreeding, but possibly some transfer of genes e.g. from human males to neanaderthal females, although candidate human genes conferring natural advantage do have a profile consistent with transfer from neanderthals (green et. al.). dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 073-109 king, c., the tree of life: tangled roots and sexy shoots issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 96 fig 26: the "out of africa" hypothesis may be consistent with a degree of regional development involving some sexual interbreeding with neanderthals and homo erectus (new scientist). specific genes such a s pdha1 consist of two families with the last common ancestor 1.8 million years ago, and microcephalin variants appearing 40,000 years ago also have differences suggesting an original divergence 1 million years ago suggesting 'introgression' from neanderthals (jones). an even more ancient divergence in the pseudogene rrm2p4 in east asian people suggests interbreeding with homo erectus. some evidence from skeletons is also consistent with this picture. however more recent sequencing of the neanderthal nuclear genome (callaway) suggests little or no interbreeding with homo sapiens and has cast doubt on the existence of the microcephalin variant in neanderthals, as well as a gene associated with increased fertility in icelanders also attributed to transfer from neanderthals. comprehensive investigation of the neanderthal genome (green, r. e. et al. (2010) science 328, 710-722., nature | doi:10.1038/news.2010.225) suggests that there was a period of interbreeding between neanderthals and humans in the near east around the time of the first migration out of dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 073-109 king, c., the tree of life: tangled roots and sexy shoots issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 97 africa, rather than more recently in europe, as the putative sequences are shared by non-african french, han and papuan, but not by the african yoruba or san. it is estimated that among the former, 1-4% of the genome derives from neanderthal sequences, although there is little evidence for these corresponding to the specific genes suggested by lahn's team. other transfers could have occurred but are not apparent in the research. the situation has been complicated by two finds. firstly we have the 'hobbit' human remains found on flores, named homo floresiensis. these are variously claimed to be a separate human species possibly related to homo erectus, or disclaimed as microcephalic human pygmy peoples. more recently we have the discovery of remains of denisovians, a further species branching off from the neanderthals. genetic analysis of the remains indicates a significant interbreeding specifically with melanesian people of some 6% (reich d, et. al. 2010 genetic history of an archaic hominin group from denisova cave in siberia nature doi:10.1038/nature09710). chromosomes contain a variety of markers that can be used to compare diverse populations and infer an evolutionary relationship between them. these include the slowly varying protein polymorphisms of coding regions which are useful for long-term trends, single nucleotide polymorphisms, and noncoding region changes (mutation rates about 2.5 x 10 -8 per base pair per generation and useful for reconstructing evolutionary history only over millions of years) insertion and deletion events (about 8% of polymorphisms, extending from one to millions of nucleotides), particularly those driven by transposable elements such as the lines and even more frequent sines, non-coding micro-satellites (mutation rate 10 -5 10 -2 due to repeat slippage) and mini-satellite regions of repeating dna (mutation rates as high as 2 x 10 -1 due to meiotic recombination in sperm) that both evolve rapidly and are not subject to the strong selection of coding regions which can differentiate changes over the much shorter time scales of modern human migration. the insertions and deletions of the million or so alu elements in the human genome are particularly useful, as the most active sub-population of about 1000 alu is actively transcribing and undergoing rapid change. a subpopulation of alu are capable of generating new coding regions (exons), when inserted into non-coding introns between spliced sections of a translated mrna, because one basepair change within alu leads to formation of a new exon reading into the surrounding dna. this is not necessarily deleterious because alternative splicing still allows the original protein to be made as well. we have the highest number of introns per gene of any organism, and thus have to have gained an advantage from this costly error-prone process. alus may have given rise, through alternative splicing, to new proteins that drove primates' divergence from other mammals. recent studies have shown that the nearly identical genes of humans and chimps produce essentially the same proteins in most tissues, except in parts of the brain, where certain human genes are more active and others generate significantly different proteins through alternative splicing of gene transcripts. our divergence from other primates may thus be due in part to alternative splicing. if we consider the likely effects of the out of africa hypothesis, we would expect that founding african populations not subject to active expansion and migration would have greater genetic diversity and that the genetic makeup of other world populations would come from a subset of the african diversity, consisting of those subgroups who migrated. in the case of mitochondrial mtdna (mutation rate about 2.5 x 10 -7 ) and its hyper-variable d-loop (mutations rates as high as 4 x 10 -3 ), which is transmitted only down the maternal line (see tishkoff and verrelli for caveat) and the non-recombining majority of the y-chromosome which is transmitted only down the paternal line, each with no recombination, we would expect greater diversity going deeper into the historical tree of divergence, with certain existing groups who have http://en.wikipedia.org/wiki/homo_floresiensis http://www.nature.com/news/2010/101222/full/4681012a.html dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 073-109 king, c., the tree of life: tangled roots and sexy shoots issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 98 retained the founding patterns of survival and have not undergone rapid population expansions to retain an increasingly diverse source variation. all these features are broadly observed in the genetic data to date. fig 27: (a) mtdna tree for african groups showing haplotypes of !kung, mbuti and biaka as well as the line coming out of africa (chen et. al.). (b) diagram of world migration and regional differentiation of successive mtdna haplotypes (gilbert). (c) mtdna distances between founding african groups including hadza (clicks) khwe is from (knight et. al.). recent mtdna evidence suggests a first wave of migration down the coast of asia all the way to australia (forster et. al.). most studies of non-coding regions of autosomal, x-chromosome, and mitochondrial mtdna genetic variation (which are desirable markers because they are not so subject to selection and thus have relatively neutral drift) show higher levels of genetic variation in african populations compared to non-african populations, using many types of markers. although some studies of y-chromosome variation have observed higher heterozygosity levels in non-african populations, the african populations have higher levels of pairwise sequence differences, consistent with these populations being ancestral. high levels of diversity in african populations alone do not prove that african populations are ancestral. a recent bottleneck event and/or colonization and extinction events among non-african populations, or a more recent onset of population growth in non-africans, could also cause a decrease in genetic diversity (tishkoff and verrelli). in fact the complete inter-fertility of all human populations and the relative lack of genetic divergence by comparison with the few remaining chimp colonies in the wild (hrdy 183) does indicate a significant bottleneck. the genetic data is consistent with a human emergence from a population of only 10,000 around 100,000 years ago. this is also consistent with the delayed maturation, long birth spacings as a result of prolonged lactation and high infant mortality seen in gather-hunter populations such as the !kung. at such low growth rates a population of 100 would take 50,000 years to reach 10,000 (hrdy 183). dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 073-109 king, c., the tree of life: tangled roots and sexy shoots issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 99 fig 28: patterns of male migration. the genographic project a partnership between national geographic and ibm will collect dna samples from over 100,000 people worldwide to provide a high-resolution genetic map of human migration. however studies of protein polymorphisms as well as mtdna haplotypes, x-chromosome and ychromosome haplotypes, autosomal microsatellites and minisatellites, alu elements, and autosomal haplotypes indicate that the roots of the population trees constructed from these data are composed of african populations and/or that africans have the most divergent lineages, as expected under a recent african origin rather than a multi-regional emergence model. additionally, studies of autosomal, x-chromosomal haplotype and mtdna variation indicate that africans have the largest number of population-specific alleles and that non-african populations harbor a subset of the genetic diversity that is present in africa, as expected if there was a genetic bottleneck when modern humans migrated out of africa. analysis of genetic variation among ethnically diverse human populations indicates that populations cluster by geographic region (i.e., africa, europe/middle east, asia, oceania, new world) and that african populations are highly divergent. the mtdna studies hypothesize a primal female ancestor the african eve around 150,000 years ago (chen et. al.) while the y-chromosome adam is more recent, at around 90,000 years ago (underhill et. al.) consistent with the greater reproductive variance of males than females. differences between the y and mtdna distributions indicate how migration, intermarriage and female exogamy have affected the gene pool. fig 29: (right) genographic project study of mitochondrial origins shows a deep split separating khoisan mitochondrial inheritance from other groups, including those migrating out of africa, suggesting a separation of some 100,000 years possibly caused by long term drought in africa (behar et al.) the genetic patterns of both these and autosomal microsatellites (zhivotovsky et. al.) are consistent with founding african diversity with migratory radiations to form other world populations, with deep founding radiations to the forest people such as the biaka and mbuti, khoisan click-language speaking !kung-san bushmen of botswana and the sandawe of tanzania, and possibly the hadzabe, dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 073-109 king, c., the tree of life: tangled roots and sexy shoots issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 100 as well as the forest people such as the mbuti and biaka 'pygmies' who have adopted the bantu languages of the farming neighbours with which they now share semi-symbiotic relationships. along with some ethiopian and sudanese sub-populations, these groups may represent some of the oldest and deeply diversified branches of modern humans.such recent genetic evidence has laid bare the relationships between some of the founding human groups spread across africa from the 'cushite' horn of ethiopia to the southern kalahari. mitochondrial dna studies have highlighted the ancient origin of the !kung san and of pygmy peoples of the congo basin such as the mbuti and the biaka. y-chromosome studies have shown the !kung share a most ancient haplotype with sub-populations from ethiopia and the sudan. according to an overall survey of genetic research by sarah tishkoff of the university of maryland, the most deeply ancestral known human dna lineages may be those of east africans, such as the sandawe, who share many phenotypic features and a click language with the !kung. this suggests southern khoisan-speaking peoples originated in east africa. the most ancient populations are now believed to also include the sandawe, burunge, gorowaa and datog people of tanzania. the burunge and gorowaa migrated to tanzania from ethiopia within the last 5,000 years consistent with an ancient founding population in this area. echoes of the earliest language spoken by ancient humans tens of thousands of years ago may have been preserved in the distinctive clicking sounds still spoken by some existing african tribes. fig 30: (a) non-recombining y-chromosome evolutionary tree (underhill et. al.) (b) geographical distribution showing the ancient haplotype shared by the san and ethiopian and sudanese sub-populations. (c) genetic distances between khoisan and forest peoples sharing m112 a y-chromosome allele common only in these groups showing great genetic distance between hadzabe and san peoples (knight et. al.) . (d) autosome satellite analysis confirming ancient divergence of san and forest peoples leading to migration from africa (zhivotovsky et. al.). dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 073-109 king, c., the tree of life: tangled roots and sexy shoots issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 101 highlighting unique features of human genetic evolution, are two key genes whose mutations cause microcephaly, consistent with increased brain size, whose rapid spread through the human population may coincide with spurts in human culture. microcephalin (evans et. al.) appeared ~37,000 years ago coinciding with the birth of culture and aspm spread from the near east around 5000 years ago (mekel-bobrov et. al.). however studies linking these variants have failed to find differences in intelligence and results remain highly controversial (doi:10.1126/science.314.5807.1872). nevertheless, these results are consistent with an overall examination of linkage disequilibrium in single nucleotide polymorphisms (moyzis et. al.) which indicate that about 7% of our genes have been subject to selection in the last 50,000 years, a figure similar to domestication of maize, including genes for protein metabolism, disease resistance and brain function. in a counterpoint to these studies, (hein, rohde et. al.) estimate that the repeated spreading of family trees by sexually recombining mobile populations and differences in reproductive rates leads to an estimate of the most recent common ancestor of our global populations existing just 3,500 years ago, excepting these most isolated groups. fig 31: human divergence trees calculated by single nucleotide polymorphisms (snps) top left (li et. al.) lower right (jakobsson et. al.) and for haplotypes and copy number variation between populations (li et. al.). further studies of the nuclear genome, using snps (single nucleotide polymorphisms), cnvs (copy number variation) and haplotype have thrown up reasonably consistent maps of regional divergence of principal human groups, demonstrating correspondence to the "out of africa" hypothesis and consistent with major patterns of migration. dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 073-109 king, c., the tree of life: tangled roots and sexy shoots issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 102 the evolutionary tree of human ethnic and migratory peoples bears an interesting relationship with the corresponding tree of languages, which has been resolved at least as far as the founding indoeuropean languages (gray and atkinson). fig 31a: in 2009, tishkoff et. al. reported on a major study of african and african american evolution containing the most detailed information on african diversity to date. dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 073-109 king, c., the tree of life: tangled roots and sexy shoots issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 103 fig 32: evolutionary tree of indo-european languages suggests a possible radiation corresponding to the kurgans occurred around 4,900 bc (6,900 bp) and that they were preceded by hittite migrations into anatolia. time scales in red are bp (gray and atkinson). significantly tocharian appears in buddhist writings from china's xinjiang province, indicating early far-eastern spread. inset: hypothetical relationship between indoeuropean and wider language groups such as afro-asiatic. dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 073-109 king, c., the tree of life: tangled roots and sexy shoots issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 104 fig 33: hypothetical core of all human languages from "the shape and fabric of language evolution" further work associated with gray and atkinson's research. dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 073-109 king, c., the tree of life: tangled roots and sexy shoots issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 105 conclusion: the tree of life, the selfish gene, and climax genetic diversity the picture conveyed by the significance of endosymbiosis, genome fusion and horizontal transfer as key evolutionary processes complementing the vertical transmission of the tree of life, makes clear that evolution is not just a matter of competitive survival of the fittest gene, individual, or species, but of dynamic survival of genes in a surviving ecosystem. although dawkins' (1978) notion of the "selfish gene" was pivotal in drawing attention to the fact that it was the survival of genes and not organisms, or even species, that was the key evolutionary process, attributing the human sentiment of selfishness to a gene is somewhat of a self-serving advertising distraction on the part of the author, which diminishes the subtlety and complexity of the sometimes apparently paradoxical ways genes actually interact to bring about beneficial outcomes in the evolutionary dynamics of the ecosystem. the mandala of evolution (dion wright) (detail). although the idea of selection of genes has been pivotal in defining the need to consider evolutionarily stable strategies under genetic variation in ways which have been subsequently confirmed time and time again in situations such as the sexual genetics of social insects such as bees and ants, social selection is by no means ineffectual, or much of sociobiology, including the biological basis of morality as an extension of reciprocal altruism, would cease to exist. moreover, from what we have seen, particularly about horizontal gene transfer, and the capacity of mobile elements to induce modulated changes in nuclear genomes, it is not the 'selfishness' of a genetic element alone that results in survival of both a gene and its hosts, but dynamic feedbacks,, and relationships which ultimately contribute to a massive sharing of information in the manner of parallel genetic algorithms fundamental to the replicative genetic process, which enable global forms of genetic and genome optimization central to the overall viability of life as complex systems. just as a predator, such as a lion survives, not because it is a selfish beast thinking only of eating the next gazelle, but because the predator, although it is surviving by killing individual antelopes, is maintaining a degree of stability in population dynamics, without which, the herbivores might multiply causing a massive famine, leading to cycles of boom and bust and the potential extinction or attrition of antelopes, lions and the grasslands. dna decipher journal | january 2011 | vol. 1 | issue 1 | pp. 073-109 king, c., the tree of life: tangled roots and sexy shoots issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 106 likewise, although we may think of individual genes, transposable elements, or 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(2009) the genetic structure and history of africans and african americans www.sciencexpress.org 30 april doi:10.1126/science.1172257 . dna decipher journal | december 2023 | volume 13 | issue 1 | pp. 81-92 81 pitkänen, m., expanding earth hypothesis and pre-cambrian earth exploration expanding earth hypothesis and pre-cambrian earth matti pitkänen 1 abstract in this article i continue to develop the tgd version of the expanding earth hypothesis. the key topics are more detailed views of the pre-cambrian biology, geology, and thermal evolution and of what happened in the cambrian explosion induced by the increase of the radius of earth by factor 2. one ends up with a detailed model for the phase transition leading to the increase of the earth radius. this phase transition requires a considerable energy feed provided by the phase transition thickening monopole flux tubes of the magnetic body of earth and liberating energy. the analogy with the recent mars pre-cambrian earth had a solid core analogous to the inner core. in the phase transition to a liquid outer core with much larger volume. part of the newly formed outer core could in turn have transformed to form a part of the mantle increasing its thickness. 1 introduction in this article i continue to develop the tgd version of the expanding earth hypothesis [4]. more detailed views of the pre-cambrian biology, geology, and thermal evolution of earth and of what happened in the cambrian explosion induced by the increase of the radius of earth by factor 2 will be discussed. the expanding earth hypothesis (eeh) is discussed in various articles [10, 7, 14]. 1. cosmic expansion according to general relativity (grt) predicts that astrophysical objects should expand smoothly. this does not happen. in the tgd universe, the expansion would be basically a quantum phenomenon and take place in rapid jerks and such a jerk would have induced cambrian explosion (ce). 2. expandng earth hypothesis (eeh) statrd that the radius of earth increased rather rapidly by a factor of about two in cambrian explosion (https://cutt.ly/x2zawae) (ce) that started about 541 million yours ago and lasted about 13-25 million years. 1.1 vision of the evolution of life on pre-cambrian earth the recent view of pre-cambrian era has problems. how to solve faint sun paradox (https://rb.gy/ mfhavz): was some additional source of energy present and heat the surface of earth to make liquid water possible? what happened in great oxygenation even (goe) (https://cutt.ly/k2jaxv9)? did deep oceans really exist? did snowball earth (https://rb.gy/qkoiah) precede cambrian expolosion (ce) ()https://cutt.ly/x2zawae)? what happened in ce? tgd view of eeh leads to a vision of how underground oceans could have served as seats for highly evolved photosynthesizing life, which bursted to the surface and formed the recent oceans. 1. life would have evolved in underground oceans shielded from meteoritic bombardment and cosmic rays. the radius of earth increased rapidly by a factor of about 2 during the cambrian explosion (ce). the multicellular life utilizing photosynthesis bursted to the surface of earth and formed recent oceans. 1correspondence: matti pitkänen http://tgdtheory.com/. address: rinnekatu 2-4 a8, 03620, karkkila, finland. email: matpitka6@gamail.com. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://cutt.ly/x2zawae https://rb.gy/mfhavz https://rb.gy/mfhavz https://cutt.ly/k2jaxv9 https://rb.gy/qkoiah https://cutt.ly/x2zawae http://tgdtheory.com/ mailto:matpitka6@gmail.com dna decipher journal | december 2023 | volume 13 | issue 1 | pp. 81-92 82 pitkänen, m., expanding earth hypothesis and pre-cambrian earth there would have been no large oceans before the ce. hydrothermal vents could have existed. the possible lifeforms were very simple bacteria, which photosynthesized using h2s since there was now water and oxygen. earth was like mars now: mars has no oceans and no oxygen. there are indications of underground reservoirs of water and signs of simple life forms. 2. highly developed multicellular animals and photosynthesizing algae bursted to the surface. note that algae are responsible for the production of most oxygen also in the recent oceans. if hydrothermal vents contained sulphur based life it disappeared because the generation of the basic building blocks of biomolecules was too slow. interestingly, the radius of mars is roughly 1/2 of that for earth. could mars have underground oceans teeming with life? when does the radius increase by factor two? 3. there is however a problem. how is photosynthesis possible underground? it is dark there! the basic proposal is that solar photons with energies in the visible and possibly infrared range arrive as dark photons along monopole flux tubes, which extend above the earth and carry dark matter. the strength of the magnetic field would be about .2 gauss and fraction 2/5 of the nominal value of the earth’s total magnetic field involving also a non-monopole part. 4. also dark photons from the interior of earth propagating along the flux tubes or associated with them could have served as an energy source. the temperature in the earth’s inner core (with radius about 20 percent of the earth’s radius) corresponds to about 5,500 k, which corresponds to a thermal energy scale of about .55 ev, which corresponds to the nominal value of the metabolic energy quantum. the energy at the maximum of the energy distribution is roughly 3 times larger than this energy and would be around 1.65 ev. the energy at the maximum wavelength of thermal energy distribution is 5 times higher and about 2.75 ev, which is the upper bound for the energy range 2-2.75 ev of visible photons. if the temperature of the inner core before ce has not differed appreciably from that now, which could hold true if the inner core was already before ce in the expanded state as also water containing regions, the idea about dark photons from the inner core as a metabolic energy source, which would make possible the evolution of photosynthesis in underground oceans, makes sense. 1.2 a model for the phase transition increasing the radius of earth by factor 2 the idea about relatively fast growth of the earth radius by factor 2 (during 13-25 million years) raises the eyebrows of standard physicists. how can such a large change of density make sense? it seems safe to exclude the possibility that the mass of earth has increased roughly by a factor of 8 (mass should have arrived from dark magnetic flux tube structure to which the core of earth is associated as a tangle). it must be admitted that the question of how this scaling could have occurred has remained poorly understood. in this article, a model for how this scaling could have occurred is proposed. the key question that i was not previously aware of, relates to the energetics. where did the required energy compensating for the decrease of the gravitational binding energy and providing the energy required by the expansion come from? some new physics seems to be necessary. in the tgd framework, the quantum phase transitions of the magnetic body (mb) increases the thickness of the flux tubes and reduce their string tension determined by kähler magnetic energy and volume energy (to which a hierarchy of values of cosmological constant can be assigned). this leads to a liberation of energy and this energy feed could have made possible to induce ordinary phase transitions requiring energy. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2023 | volume 13 | issue 1 | pp. 81-92 83 pitkänen, m., expanding earth hypothesis and pre-cambrian earth the analogy between recent mars and pre-cambrian earth suggests that the earth had only a single core analogous to the recent inner core which is solid and consists mostly of fe and ni. the most natural phase transition would have transformed part of this core to the outer core which is liquid and has a smaller density and has also lower temperature. this could have forced at least the horizontal expansion of the mantle. the thickness of the mantle could have increased in a further transformation of the newly formed outer core to mantle or transfer of material from the outer core to the mantle. 2 a possible view of the expansion of earth? the most natural tgd inspired guess is that a phase transition at the level of mb, increasing flux tube thickness, induces a phase transition at the level of ordinary matter by providing energy in the case that it requires energy. there are several questions to be answered. 2.1 did the inner core participate the expansion? did the inner core (https://cutt.ly/p2jsljb) participate in the expansion? 1. could it be that the outer core emerged and this led to a generation of convective currents giving rise to the maxwellian part of the magnetic field. the temperature at the boundary of the inner core is the same as the solar surface temperature. note that in the ”standard model” the weak interactions within the mantle are assumed to produce energy. the recent radius of the inner core is r/5 and so small that there is no need for it to participate in the expansion: one would 4r/5 → 8r/5 for the outer and he radius would increase by factor 9/5: not far from 2. 2. could it be that the outer core with the recent thickness 2400 km emerged in a phase transition transforming the fe-li solid of the inner core to fe-liquid of the outer core so that the inner core could have reduced in size? was the mantle+crust with recent thickness 2390 km (the recent earth radius is 2890+2400+1220= 6370 km) scaled in the transition by factor 2 also in the radial direction or only horizontally? the scaling of the earth radius by factor 2 gives the condition d(mantle, i) + d(inner, i) = (1/2)[d(mantle, f) + d(outer, f) + d(inner, f)] . one has d(mantle, f) = 2890 km, d(outer, f) = 2200 km, d(inner, f) = 1220 km. (a) if the mantle thickness was scaled by factor 2 (d(mantle, i) = d(mantle, f)/2), one has d(inner, i) = 1810 km, which is larger than 1220 km as required. for this option the initial value of the mantle thickness could have been small and the thickness of the inner core correspondingly larger. (b) the second option is that the newly formed outer core partially transformed to mantle and increased its thickness so that no radial scaling of the mantle was needed. this option is perhaps the most plausible one. (c) for the no-scaling option (d(mantle, i) = d(mantle, f)) one would have d(inner, i) = 365 km, which is suspiciously small and smaller than 1220 km. therefore the scaling of the mantle thickness is the more realistic option. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://cutt.ly/p2jsljb dna decipher journal | december 2023 | volume 13 | issue 1 | pp. 81-92 84 pitkänen, m., expanding earth hypothesis and pre-cambrian earth 2.2 how the outer core was formed? what happened in the formation of the outer core? 1. the proposal is that regions of dark water with an increased value of heff = hgr were generated in the mantle. inside these regions photosynthesis occurred using the dark photons carrying metabolic energy from the inner core and outer core. the range of energies is the same as in the radiation from sun [14]. 2. did the expansion of the volume force a formation of underground oceans in mantle containing dark water, which then bursted to the surface? was the formation of oceans necessary? were dark matter blobs enough? did they condense to form larger dark water volumes, which eventually bursted to the surface? 3. the material in the core of earth derives basically from chondrites, which contain water and also organic molecules. this suggests that the water of the underground oceans in the mantle derives from the chondrites and that the presence of the basic biomolecules in chondrites was essential for the evolution of life inside earth. 4. in the case of water, superionic ice [2] (https://cutt.ly/uxuikuq and https://cutt.ly/3xuiwhx) existing at extreme pressures is a possible candidate for the exotic phase of water. superionic ice is proposed to appear in the mantles of giant planets such as uranus and neptune and in [10, 7] the possibility that it could occuring the earth’s mantle was considered. the density of superionic ice is slightly less than 4 times the density of ordinary ice. could superionic ice in the mantle have transformed to dark water with a volume larger a factor 42/3. this would have contributed to the increase of the volume of the mantle. note that the transition could have led to expansion only in horizontal directions increasing the 2-dimensional volume by a factor 4. 5. one can compare the situation with that in recent mars. for mars, the inner and outer core are one and the same thing so that the situation corresponds to that in pre-cambrian earth. also the radii were nearly the same. on mars, the temperature at the surface of the core is about 2000 k (e = .21 ev). if the temperature for the pre-ce earth was the same, the temperature of the core came 1.5 times higher and inner core 2.5 times higher in the phase transition. this could be understood if energy was liberated in the thickening of the flux tubes. 2.3 the energetics of the transition what can one say of the energetics of the phase transition? 1. expansion requires energy. where did the energy come from? the fraction of gravitational energy earth from its mass is of the order of gm/r ∼ 10−9 and its reduction in the expansion was of the same order of magnitude 10−9. energy was needed to induce the expansion. also the reduction of the average density and the increase of temperature required energy. where did the energy come from? did it come from the increase of the flux tube thickness reducing string tension? 2. magnetic and volume energy should have been liberated in the model based on the thickening of cosmic strings or flux tubes. generation of ordinary matter or a phase transition for an ordinary matter can be imagined. the liberated energy could have driven the expansion as an explosion. also the heating of the matter would be an outcome. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://cutt.ly/uxuikuq https://cutt.ly/3xuiwhx dna decipher journal | december 2023 | volume 13 | issue 1 | pp. 81-92 85 pitkänen, m., expanding earth hypothesis and pre-cambrian earth 3. the increase of hgr by a factor 2 is one option that one can imagine. the reduction of the quantized velocity parameter β0 by factor 1/2 could have happened β0 → β0/2? this process should have had as a counterpart ordinary phase transition liberating energy. one can consider two options for the phase transition at the level of the mb. the first option would correspond to a thickening of cosmic string to monopole flux tube and second option to that of an already thickened cosmic string. a more realistic mechanism involves the expansion of an already thickened flux tube with much smaller liberated energy. factor of order 10−9 is enough. 1. the phase transition for the ordinary matter would have been induced by a phase transition at the level of the mb of the system involving thickening of the flux tubes. the ordinary matter would have been in the form fe and ni inside in the inner core. 2. the ordinary phase transition could have been melting of the inner core at its outer surface so that it would have gradually generated the outer core as a liquid layer between outer and inner cores. the process would still continue. temperature would have increased in the melting from 2000 k to about 5000 k in the inner core and from 2000 k to 3000 in the outer core. the energy liberated in the thickening of the flux tubes would have provided this energy. the expansion of the core and the liberated energy would have driven the expansion of the volume above the contracting inner core. this process could have also forced the expansion of the outermost layer with recent thickness about .444 re . it is also possible that the newly formed outer core transformed partially to mantle so that no radial expansion of the mantle was not needed. 3 tgd view of the pre-cambrian era in the sequel a tgd view general view of pre-cambrian era is proposed followed by a discussion as a series of questions. the basic idea is to take the recent mars as a guideline in attempts to understand pre-cambrian earth. 3.1 a rough overall view of pre-cambrian era the recent view of pre-cambrian era has problems. how to solve faint sun paradox (https://rb.gy/ mfhavz): was some additional source of energy present and heat the surface of earth to make liquid water possible? what happened in great oxygenation even (goe) (https://cutt.ly/k2jaxv9)? did deep oceans really exist? did snowball earth (https://rb.gy/qkoiah) precede ce? 3.1.1 energetics during the pre-cambrian era the basic assumption is thermal flow equilibrium in which the energy from the sun is temporarily stored and leaves the system in time determined by the planet. in the tgd framework, the flow of energy from the interior of earth forces us to challenge this picture. 1. the total energy flux from the sun would have been by a factor 1/4 smaller than now although local flux would have been the same. one can wonder whether this had some implications. if the biosphere is controlled by mb having quantum coherence in the scale of earth, this might be the case. as a matter of fact, during ce the phase transition generating inner core would have feeded energy liberated in the thickening of flux tubes of the mb of earth to also to the surface of earth. inner core and core could have also served as source of metabolic energy for the photosynthesizing life forms in underground oceans [14]. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://rb.gy/mfhavz https://rb.gy/mfhavz https://cutt.ly/k2jaxv9 https://rb.gy/qkoiah dna decipher journal | december 2023 | volume 13 | issue 1 | pp. 81-92 86 pitkänen, m., expanding earth hypothesis and pre-cambrian earth 2. solar energy input and reradiation of energy by greenhouse gases storing the energy temporarily. oceans bind 90 percent of the solar energy in the recent earth. in the tgd framework, oceans would have been absent during the pre-cambrian era and could not have stored energy in large scales so that the situation would have been similar to that in recent mars. this would explain why multicellular life was virtually absent during pre-cambrian period. lakes and small oceans could have been present and the energy from the earth interior could have warmed them. also volcanic activity could have transferred energy to the earth’s surface as it does also nowadays. reradiation would have been missing unless greenhouse gases were present locally. 3. sunlight absorption depends on various factors. the spin of earth and the tilt of the orbit with respect to the rotation plane affect the absorption in the time scale of 104−105 years. milankovitch cycle for the ice ages relates to this dependence. the duration of the carbon cycle corresponds to millions of years. also weathering and volcanic activity affect the absorption. greenhouse gases are an important factor on recent earth. also the distribution of continents affects the absorption (https://cutt.ly/62jsqsu). 3.1.2 the atmosphere of earth before ce what about the surface pressure before ce? 1. pressure is determined by the concentrations of molecules and atoms in the atmosphere. the abundances of o and n were small before ce: the situation could have been as in mars today. 2. the composition of the earth’s earliest atmosphere is not known with certainty. present nitrogen, n2, and carbon dioxide, co2, which are also the predominant nitrogenand carbon-bearing gases produced by volcanism today. these are relatively inert gases. the leakage of molecules in ce earth was not as intense as in mars today since the gravitational field was 10 times stronger than in mars. leakage partially explains low surface pressure if the production of gases has roughly the same rate. 3. it is interesting to compare the percentages of various gases in the recent earth and recent mars . in the recent earth: the fractions of n and o are 78 % and 21 % respectively. the variation of oxygen fraction is between 10 and 35 per cent during the last 541 million years (https://cutt. ly/22jsuzr). in recent mars the fractions of co2, n and o are 96 %, 1.9 %, and .15 % respectively. the partial pressure of oxygen present in the martian atmosphere is po = .95× 10−2 atm which corresponds to the value of po in the beginning of the second stage of goe at earth. recent mars could give some hints of the situation in ce earth. co2 or other greenhouse gases should have been present. also methane ch4 was prosent. these gases could have been produced in the interior of earth as in mars and responsible for the warm earth. 4. ideal gas approximation gives the estimate p = nt . hydrodynamic equilibrium requires that the pressure gradient is equal to gravitational force density, which determined by the density of the atmosphere and by the strength of the gravitational field, which was 4 times stronger for precambrian earth according to tgd. note that the gravitational energy of protons in the earth’s gravitational field is of order 1 ev and twice the nominal value .5 ev of the metabolic energy quantum [13]. the transfer of oxygenated fluid from underground oceans would have made oxygenation possible in pre-ce earth. this would have caused local oxidation of iron without deep oceans. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://cutt.ly/62jsqsu https://cutt.ly/22jsuzr https://cutt.ly/22jsuzr dna decipher journal | december 2023 | volume 13 | issue 1 | pp. 81-92 87 pitkänen, m., expanding earth hypothesis and pre-cambrian earth 5. the climax of the goe caused be accelaring expansion of earth corresponds ce. before goes there is a slow oxygenation, which in the standard model is assumed to be caused by the photosynthesis of cyanobacteria. what really happened during ce is a mystery as is also ce. in the tgd framework, the underground oceans would played a key role. also cyanobacteria could have emerged from the underground oceans. 3.1.3 maybe deep oceans are not necessary? according to the wikipedia article (https://cutt.ly/k2jaxv9), the end of the deposition of banded iron formation at 1.85 billion years ago is interpreted as marking the oxygenation of the deep ocean. banded iron formation largely disappears from the geological record at 1.85 billion years ago, after peaking at about 2.5 billion years ago. banded iron formations can form only when abundant dissolved ferrous iron is transported into depositional basins, and an oxygenated ocean blocks such transport by oxidizing the iron to form insoluble ferric iron compounds. but are deep oceans really needed? one can compare the situation with the situation in recent mars. mars is red and contains oxidized iron. 1. rivers and water flow at its surface and there are no deep oceans in the recent mars. the simplest assumption is that the situation could have been the same always. this applies also to the existence of the maxwellian part of the magnetic field requiring an inner core. although the martian atmosphere has a low oxygen content, the iron rich material is oxidized in presence of water and develops rust giving the color red. also in mars, band iron formations consisting of non-oxidized iron and dating to times before the beginning of martian goe, should exist. the flow of a non-oxygenated water could have transported ferrous iron to the depositional basis. 2. the amount of oxygen in the martian atmosphere is very low but he oxygenated water percolating from the underground oceans could induce the oxidation of iron. the same mechanism could be at work on the early earth. the beginning of the oxygenation would correspond to the emergence of oxygen based life forms to the underground oceans. 3.2 comparison with the recent mars the resemblances between mars https://cutt.ly/s2jaofj and pre-cambrian earth according to tgd inspire the question whether the recent mars could be like the pre-cambrian earth after the initiation of goe. could one use these resemblance to understand pre-cambrian earth in the tgd universe. 1. for mars the radius and distance from the sun are r = .53×re and d = 1.523au . similar tilt of a rotation axis. the mass of mars is m = .107me so that the surface gravitation is .38 g. for pre-ce earth surface gravitation is roughly 10 times stronger. 2. surface temperatures in mars vary from 20 c to -153 c at poles. the average temperature is -62 c. the temperature drops rapidly with height and with the time of day since the atmosphere is very thin and cannot store heat energy. the ratio of energy fluxes to mars and earth is equal d/d(mars) = .43 so that there is no big difference between mars and earth. 3. surface pressure at mars is p(mars) = 0.0628 atm which is 6.3 % of the pressure p(eart) = 1 atm. the martian atmosphere contains 0.174 % oxygen and 2.8 % nitrogen. at the earth, the corresponding abundances are 29 % o and 78 % n. oxygen partial pressures for oxygen is po(mars) = 0.01 atm. there are active sources of gases, such as methane, in the interior of mars. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://cutt.ly/k2jaxv9 https://cutt.ly/s2jaofj dna decipher journal | december 2023 | volume 13 | issue 1 | pp. 81-92 88 pitkänen, m., expanding earth hypothesis and pre-cambrian earth 4. on mars there are no oceans and continents are absent. if earth is like mars, the oceans could have been absent also on earth. instead of them small lakes and rivers could have been present as in the recent mars. they would have contained oxygenated water from oceans inside the earth interior, where photosynthesis was producing oxygen. continents would have been absent so that the existing vision about the history of the continental drift before ce, should be obsolete albeit natural if one assumes that the radius of earth has always been the recent one. 5. could mars be experiencing the analog of goe? during the second stage of the great oxidation event (goe) (see the picture https://cutt.ly/d2jaed3 in wikipedia article https://cutt.ly/ k2jaxv9), the oxygen content of the atmosphere gradually increased during period 2.45-.84 ga to values of .02 and .04 atm but it is assumed that oxygen was absorbed by the oceans and seabed rock. during the third stage of goe, the oxygen content did not change. it is assumed that the oxygen started to gas out from oceans but was absorbed by land surfaces. at the fourth state of goe, ce occurred and the oxygen content increased rapidly to the recent 21 per cent. the recent value po(mars) = 0.01 atm is below .02 atm at the end of the second phase of goe but would correspond to the value of po ≃ .01 on earth in the beginning of the secon state of goe. could it be that goe on mars has begun? the naive guess is that there is still 2.45 gy to the recent situation on earth. 6. the interior of mars consists of a crust, a mantle consisting of silicates and a solid metal core consisting of fe and ni as the solid inner core of earth. crust has a typical thickness of 50 km, which is not far from that on earth. there is no liquid outer core, which in the case of earth is responsible for the convective ionic currents creating the maxwellian part of the magnetic field (note that the monopole part needs no source). in mars the magnetic field is indeed absent in large scales. martian auroras have been observed however. in the tgd framework, this suggests that only the dark part of the martian magnetic field has a considerable strength whereas the maxwellian part is very small. this suggests that in the case of earth the emergence of the maxwellian part of the magnetic field made possible the shielding of life against cosmic rays and that life did not have any other option than to evolve in the womb of gaia. 7. for the recent earth, the volume fraction of the outer core of earth 16.5 %. the outer core carries the convective currents giving rise to the maxwellian part of the magnetic field of earth. the inner core however feeds heat energy to the outer core and has a considerable effect on its dynamics. this conforms with the idea that the inner core serves as a source of heat energy. 8. the temperature t = 1900 − 2000 k at the boundary of martian core corresponds to a thermal energy ≃ .2 ev, which is below the metabolic energy quantum .5 ev. on the recent earth, one has t = 3000 k (.3 ev) at the upper boundary of the outer core and t = 5000 k (.5 ev) at the upper boundary of the inner core: the latter is the temperature at the surface of the sun. these observations lead to the proposal [14] that the energy feed from the inner and outer cores, realized as dark photons, could have served as a metabolic energy source for the evolving life in the underground oceans. also the solar photons might have transformed into dark photons propagating along the flux tubes of the monopole part of the earth’s magnetic field to the interior of earth. one can even ask whether this mechanism might be still at work at polar regions of earth covered by ice or at the bottom of oceans. 3.3 some questions related to the pre-cambrian period pre-cambrian period cambrian explosion (ce) are not well-understood and there are several paradoxical aspects involved. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://cutt.ly/d2jaed3 https://cutt.ly/k2jaxv9 https://cutt.ly/k2jaxv9 dna decipher journal | december 2023 | volume 13 | issue 1 | pp. 81-92 89 pitkänen, m., expanding earth hypothesis and pre-cambrian earth 3.3.1 why so few multicellular fossils from pre-cambrian period? there is very little evidence for multicellulars from pre-cambrian period whereas fossils of mono-cellulars (cyanobacteria) exist. the oldest multicellular fossils are 1.2 billion years old. multicellular fossils with an age of 600 million years and thus preceding ce, which began 541 million years ago have been also found (https://cutt.ly/d2jagzb). the multicellular organisms preceding ce are much simpler than plants and animals that emerged in ce. the standard explanation for the nearly complete absence of multicellular fossils is that they have disappeared almost completely because they had no hard parts. what is however very strange is that suddenly the fossils of rather complex multicellulars emerge suddenly in ce [3]. 3.3.2 questions related to energetics the first questions relate to energetics. 1. faint sun paradox means that solar radiation was only 70 per cent from the recent temperature. the earth surface was however warm since liquid water existed. could earth’s interior have served as a source of heat energy? this seems to require new physics. 2. in the tgd framework one can ask whether a quantum phase transition proceeding at the level of mb (mb) of earth could have induced ordinary phase transition at the level of ordinary matter, say solid-liquid phase transition of the fe-ni at its boundary giving rise to the outer core. this would have made convective charged currents generating the maxwellian part of the magnetic field of earth providing a shield against cosmic rays. this kind of induction of ordinary phase transitions by quantum phase transitions could be crucial for the evolution of life [13, 12]. 3. could the energy liberated in the phase transition of the mb increasing the thickness of the flux tubes have driven this solid-liquid phase transition and have also feeded heat energy to the surface of earth increasing the temperature. also the increase of the gravitational potential energy in the increase of the radius by factor 2 requires a lot of energy. note that nuclear physics cannot be involved with the energy production. basic stable isotopes of fe and ni have atomic numbers 56 and 58. ni has also a= 60, 61, 62, 64 as stable isotopes. fe has stable isotopes with a=54,57,58 besides a=56. ordinary nuclear processes cannot transform ni nuclei fe nuclei and new physics is needed. 3.3.3 did large oceans really exist? the existence of oceans covering most of the surface of earth is assumed in the standard view of precambrian period. but did earth have oceans at its surface before ce? 1. could it be that the situation before ce was like in the recent mars. this plus the assumption that the radius of earth was only 1/2 of the recent radius would totally change the views about pre-ce earth both biologically, geologically, and thermodynamically. 2. the simplest working hypothesis is that plate tectonics was not present before ce. standard view (https://cutt.ly/i2zf8v8) however is that roughly 750 million years ago, the earliest-known supercontinent rodinia, began to break apart. did the breaking apart of rodinia initiate the expansion of earth, which gradually accelerated? if so, the area covered by the analogues of oceans between continents was much smaller than on the recent earth. the narrow fissures would have contained water which had bursted from the underground oceans and brough multicellular life forms. the analogues of continents would have later recombined to form pannotia 600–540 ma. did the expansion involve a pulsation leading to the formation of pannotia, which then split again to issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://cutt.ly/d2jagzb https://cutt.ly/i2zf8v8 dna decipher journal | december 2023 | volume 13 | issue 1 | pp. 81-92 90 pitkänen, m., expanding earth hypothesis and pre-cambrian earth continents separated by narrow analogs of oceans. the multicellular lifeforms giving rise to 600 ma old fossils could have emerged from underground oceans in the breaking apart of pannotia. 3.3.4 snowball earth hypothesis from tgd point of view the assumption is that snowball earth dating back to 650 ma, involving several large scale glaciations, preceded ce. the earth would have suffered a global glaciation but evidence exists only for local glaciations. what could be the tgd counterpart of the snowball earth? milankovitch cycles (https://cutt. ly/12zkeof) with a period of order 100,000 years were present and could have caused local glaciations explaining the observed glaciations. the two large scale glaciations associated with snowball earth could relate to the expansion of earth. did the glaciation take place for the oceans defined by the narrow fissures between the analogues of continents formed in the splitting of rodinia? 3.3.5 the great oxygenation event the great oxygenation event oxidized the atmosphere and made oxygen based life possible at the surface of earth. 1. the oxygen content of the atmosphere and assumed oceans was very low before ce and could not support oxygen based life. during the great oxygenation event (goe) (see the wikipedia article (https://cutt.ly/k2jaxv9), which started for about 2.45 gy ago, the oxygenation of atmosphere proceeded very slowly (see the wikipedia picture https://cutt.ly/d2jaed3). in ce (ce) the oxygen content of the atmosphere increased very rapidly to the recent level of about 21 per cent. the oxidation is made manifest by the observed layers of oxidized iron. the absence of oxygen for more than 2.45 gy ago is demonstrated by layers of iron based compounds, which are not oxidized. 2. usually it is assumed that the oceans were present during the pre-cambrian period and that the sea water was oxidized gradually. on mars the situation is however different. there are local sources of oxygenated water such as lakes and rivers but no oceans. there is also evidence for underground life on mars. could the situation on earth have been like in mars during the pre-cambrian earth? could the underground oceans, serving as a kind of womb shielding the evolving life from meteoric bombardment and cosmic rays, have made possible the evolution of the photosynthesizing life and multicellulars producing oxygen, which bursted to the surface of earth in ce? 3. suppose that the water from the underground oceans, containing highly developed multicellulars, bursted to the surface during the goe. what could be the time scale of the process? was goe implied by this process and did it accelerate during ce? did this increasing rate of bursts lead to oceans of increasing size so that the scale of glaciations was dramatically increased during the last two glaciations before ce. 3.3.6 was ce a quantum phase transition in earth scale? the tgd view of ce explains the sudden appearance of multicellulars and also implies that the gravitation would have been 4 times stronger before ce so that the possible lifeforms surviving at the surface of earth are expected to have a flat shape. the reduction of surface gravitation after ce in turn could in turn explain the emergence of giant plants and animals. in the tgd framework the evolution of life would have involved quantum criticality and quantum phase transitions closely related to ordinary criticality and phase transitions [12]. ce would be naturally a quantum phase transition in the scale of earth involving in an essential manner gravitational planck issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://cutt.ly/12zkeof https://cutt.ly/12zkeof https://cutt.ly/k2jaxv9 https://cutt.ly/d2jaed3 dna decipher journal | december 2023 | volume 13 | issue 1 | pp. 81-92 91 pitkänen, m., expanding earth hypothesis and pre-cambrian earth constant hgr making possible dramatic reduction of gravitational binding energy in the scaling up of earth radius by factor 2. in the tgd framework the standard ontology of quantum theory is replaced with zero energy ontology (zeo) solving the basic paradox of the quantum measurement theory [6, 9, 8, 11]. interesting questions relate to the proposal that a pair of ”big” state function reductions (bsfrs) in astrophysical scales (counterpart for quantum tunnelling) changing the arrow of time was in question. could one interpret the time reversed classical time evolution after the first bsfr, that is goe, as a classical correlate for the pair of bsfr making the process effectively to look like deterministic and smooth classical process [1, 5]? acknowledgements: i want to thank my friend heikki haila for enlightening discussions concerning glaciations. received january 15, 2023; accepted december 8, 2023 references [1] minev zk et al. to catch and reverse a quantum jump mid-flight, 2019. available at: https: //arxiv.org/abs/1803.00545. [2] prakapenka vb et al. structure and properties of two superionic ice phases. nature physics, 17(11):1– 6, 2021. available at: https://www.researchgate.net/publication/355212207_structure_and_ properties_of_two_superionic_ice_phases. [3] gould sj. wonderful life. penguin books, 1991. [4] pitkänen m. expanding earth model and pre-cambrian evolution of continents, climate, and life. in genes and memes: part ii. available at: https:/tgdtheory.fi/pdfpool/expearth.pdf, 2006. [5] pitkänen m. copenhagen interpretation dead: long live zeo based quantum measurement theory! available at: https:/tgdtheory.fi/public_html/articles/bohrdead.pdf., 2019. [6] pitkänen m. some comments related to zero energy ontology (zeo). available at: https: /tgdtheory.fi/public_html/articles/zeoquestions.pdf., 2019. [7] pitkänen m. empirical support for the expanding earth model and tgd view about classical gauge fields. https://tgdtheory.fi/public_html/articles/expearthnewest.pdf., 2021. [8] pitkänen m. negentropy maximization principle and second law. available at: https:// tgdtheory.fi/public_html/articles/nmpsecondlaw.pdf., 2021. [9] pitkänen m. some questions concerning zero energy ontology. https://tgdtheory.fi/public_ html/articles/zeonew.pdf., 2021. [10] pitkänen m. updated version of expanding earth model. https://tgdtheory.fi/public_html/ articles/expearth2021.pdf., 2021. [11] pitkänen m. about the number theoretic aspects of zero energy ontology. https://tgdtheory.fi/ public_html/articles/zeonumber.pdf., 2022. [12] pitkänen m. comparison of orch-or hypothesis with the tgd point of view. https://tgdtheory. fi/public_html/articles/penrose.pdf., 2022. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://arxiv.org/abs/1803.00545 https://arxiv.org/abs/1803.00545 https://www.researchgate.net/publication/355212207_structure_and_properties_of_two_superionic_ice_phases https://www.researchgate.net/publication/355212207_structure_and_properties_of_two_superionic_ice_phases https:/tgdtheory.fi/pdfpool/expearth.pdf https:/tgdtheory.fi/public_html/articles/bohrdead.pdf https:/tgdtheory.fi/public_html/articles/zeoquestions.pdf https:/tgdtheory.fi/public_html/articles/zeoquestions.pdf https://tgdtheory.fi/public_html/articles/expearthnewest.pdf https://tgdtheory.fi/public_html/articles/nmpsecondlaw.pdf https://tgdtheory.fi/public_html/articles/nmpsecondlaw.pdf https://tgdtheory.fi/public_html/articles/zeonew.pdf https://tgdtheory.fi/public_html/articles/zeonew.pdf https://tgdtheory.fi/public_html/articles/expearth2021.pdf https://tgdtheory.fi/public_html/articles/expearth2021.pdf https://tgdtheory.fi/public_html/articles/zeonumber.pdf https://tgdtheory.fi/public_html/articles/zeonumber.pdf https://tgdtheory.fi/public_html/articles/penrose.pdf https://tgdtheory.fi/public_html/articles/penrose.pdf dna decipher journal | december 2023 | volume 13 | issue 1 | pp. 81-92 92 pitkänen, m., expanding earth hypothesis and pre-cambrian earth [13] pitkänen m. how animals without brain can behave as if they had brain. https://tgdtheory.fi/ public_html/articles/precns.pdf., 2022. [14] pitkänen m. krebs cycle from tgd point of view. https://tgdtheory.fi/public_html/ articles/krebs.pdf., 2022. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://tgdtheory.fi/public_html/articles/precns.pdf https://tgdtheory.fi/public_html/articles/precns.pdf https://tgdtheory.fi/public_html/articles/krebs.pdf https://tgdtheory.fi/public_html/articles/krebs.pdf introduction vision of the evolution of life on pre-cambrian earth a model for the phase transition increasing the radius of earth by factor 2 a possible view of the expansion of earth? did the inner core participate the expansion? how the outer core was formed? the energetics of the transition tgd view of the pre-cambrian era a rough overall view of pre-cambrian era energetics during the pre-cambrian era the atmosphere of earth before ce maybe deep oceans are not necessary? comparison with the recent mars some questions related to the pre-cambrian period why so few multicellular fossils from pre-cambrian period? questions related to energetics did large oceans really exist? snowball earth hypothesis from tgd point of view the great oxygenation event was ce a quantum phase transition in earth scale? dna decipher journal| november 2011| vol 1.| issue 3| pp. 298-307 298 pitkänen m., gariaev p. quantum model for remote replication article quantum model for remote replication matti pitkänen 1 and peter gariaev. 2 abstract a model for remote replication of dna is proposed. the motivating experimental discoveries are phantom dna, the evidence for remote gene activation by scattered laser light from similar genome, and the recent findings of montagnier’s and gariaev’s groups suggesting remote dna replication. phantom dna is identified as dark nucleon sequences predicted by quantum tgd with dark nucleons defining naturally the analogs of dna, rna, trna, and amino-acids and realization of vertebrate genetic code. the notion of magnetic body defining a hierarchy of flux quanta realize as flux tubes connecting dna nucleotides contained inside flux tubes connecting dna codons and a condensed at flux sheets connecting dna strands is an essential element of the model. dark photons with large value of planck constant coming as integer multiple of ordinary planck constant propagate along flux quanta connecting biomolecules: this realizes the idea about wave dna. biomolecules act as quantum antennas and those with common antenna frequencies interact resonantly. biomolecules interacting strongly in particular dna nucleotideswould be characterized by same frequency. an additional coding is needed to distinguish between nucleotides: in the model for dna as topological quantum computer quarks (u,d) and their antiquarks would code for the nucleotides a,t,c, and g would take care of this. the proposed role of quarks in biophysics of course makes sense only if one accepts the new physics predicted by quantum tgd. dna codons (nucleotide triplets) would be coded by different frequencies which correspond to different values of planck constant for photons with same photon energy propagating along corresponding flux tubes. this allows to interpret the previously proposed tgd based realization of so called divisor code proposed by khrennikov and nilsson in terms of quantum antenna mechanism. in this framework the remote replication of dna can be understood. dna nucleotides interact resonantly with dna strand and attach to the ends of the flux tubes emerging from dna strand and organized on 2-d flux sheets. in montagnier’s experiment the interaction between test tubes a and b would be mediated by dark photons between dna and dark nucleon sequences and amplify the dark photon beam, which in turn would induce remote replication. in the experiment of gariaev scattered laser light would help to achieve the same purpose. dark nucleon sequences would be generated in montagnier’s experiment by the homeopathic treatment of the test tube b. dark nucleon sequences could characterize the magnetic body of any polar molecule in water and give it a ”name” written in terms of genetic codons so that genetic code would be much more general than usually thought. the dark nucleon sequence would be most naturally assigned with the hydrogen bonds between the molecule and the surrounding ordered water being perhaps generated when this layer of ordered water melts as the molecule becomes biologically active. water memory and the basic mechanism of homeopathy would be due to the ”dropping” of the magnetic bodies of polar molecules as the water is treated homeopathically and the dark nucleon sequences could define an independent life form evolving during the sequence of repeated dilutions and mechanical agitations taking the role environmental catastrophes as driving force of evolution. the association of dna, rna and amino-acid sequences associated with the corresponding dark nucleon sequences would be automatic since also also they are polar molecules surrounded by ordered water layers. the transcription of the dark nucleon sequences associated the with the polar invader molecule to ordinary dna sequences in turn coding of proteins attaching to the invader molecules by the quantum antenna mechanism could define the basic mechanism for functioning and evolution of the immune system. 1matti pitkänen http://tgd.wippiespace-com/public_html. address: köydenpunojankatu 2 d 11 10940, hanko, finland. email: matpitka@luukku.com. 2 peter gariaev. address: peter gariaev. address: russia, moscow 123056, maliy tishinskiy per. 11/12 25, to peter gariaev. email: gariaev@mail.ru. issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. http://tgd.wippiespace-com/public_html mailto:matpitka@luukku.com mailto:gariaev@mail.ru dna decipher journal| november 2011| vol 1.| issue 3| pp. 298-307 299 pitkänen m., gariaev p. quantum model for remote replication 1 introduction the idea about remote replication, transcription and translation of genes in terms of electromagnetic field patterns is very attractive and would be in accordance with the wave dna vision. this requires a coding of dna nucleotides. i have proposed several codings of this kind. 1. in dna as topological quantum computer model [1] quark and anti-quark at the ends of a flux tube connecting dna nucleotide to a lipid of the nuclear or cell membrane takes care of the coding. also sequences of dark nucleons giving rise to dark nuclei realize the analogs of dna, rna, trna, and amino-acids as well as vertebrate genetic code [8, 3]. dark nucleons sequences could correspond to the phantom dna discovered by gariaev’s group [13]. 2. quantum antenna hypothesis represents one of the oldest ideas of tgd inspired quantum biology [6]: molecules would act like quantum antennas. frequency coding would be very natural for groups of molecules participating in the same reaction: the flux tubes connecting the molecules would carry the radiation inducing resonant antenna interaction and phase transitions reducing planck constant would bring the reacting molecules near to each other. magnetic flux tubes connecting the molecules would be essential element of the mechanism. remote replication would represent an example about a situation in which ~ changing phase transition does not take place. if one wants coding of individual molecules -such as dna nucleotidesby frequency in turned coded by the value of ~ for given photon energy (e = hf), one is forced to make ad hoc assumptions and it is difficult to find any plausible scenario. quantum antenna mechanism could make possible remote replication for which the findings of montagnier’s group as well as remote transcription for which the work of gariaev’s group gives some evidence. 3. one can consider also a coding by field patterns. in fact, the quark and antiquark at the ends of the flux tube generate a color magnetic field coding for the quark pair since the classical color field depends on the color of the quark and its antiquark. gariaev’s group has proposed that the change of polarization direction could provide a possible mechanism of coding of dna sequences to radiation patterns [11]. the proposal is discussed from tgd point of view in [7]. the mechanism changing the polarization direction should reduce to different propagation velocities for the two circular polarizations. the other polarization should act more strongly with the dna related structures and this should cause the slowing down of propagation since it would correspond to sequence of absorptions and emissions. the constraint that this occurs coherently for dnas and codes the dna sequence is very powerful condition. it is however difficult to imagine how this mechanism alone could give rise to remote replication of dna or similar processes: the coding from radiation pattern to dna sequences is the bottle neck. therefore this mechanism will not be discussed in the following. in the sequel a model for the coding of dna in terms of radiation patterns is discussed. there are three experimental guidelines: the phantom dna [13] identified as dark nucleon sequences in tgd framework and the evidence for remote activation of dna transcription [11] both discovered by gariaev’s group are assumed as the first two key elements of the model. the remote replication of dna suggested by the experimental findings of montagnier’s group serves as a further guideline in the development of the model. also the results of the latest experiment of gariaev’s group in many respects similar to that of montagnier’s experiment but differing in certain crucial aspects from it are used as input. polymerase chain reaction (pcr) is the technique used in the experiments of montagnier’s group [10] and later in somewhat modified experiment by gariaev’s group involving irradiation of the second test tube by laser light. dna polymerase catalyzes the formation of dna from existing dna sequences serving as a template. since the catalytic interaction of dna polymerase takes place with already existing dna sequence, the only possibility is that first some conjugate dna sequences are generated by remote replication after which dna polymerase uses these sequences as templates to amplify them to original dna sequences. whether the product consists of original dna or its conjugate can be tested. the model inspires the proposal that the magnetic body of a polar molecule codes for it using dark nucleon sequences assignable to the hydrogen bonds between the molecule and surrounding ordered water layer. quantum antenna mechanism would allow the immune system to modify itself by developing issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. http://en.wikipedia.org/wiki/pcr dna decipher journal| november 2011| vol 1.| issue 3| pp. 298-307 300 pitkänen m., gariaev p. quantum model for remote replication ordinary dna coding for amino-acids attaching to and thus ”catching” the polar molecule. the mechanism could be behind water memory and homeopathic healing. every polar molecule in living matter would have dark nucleon sequence or several of them (as in the case of amino-acids) serving as its name. this would also associate unique dark nucleon sequence also with the magnetic body of dna so that dna-dark dna association would be automatic. same applies to mrna and trna and amino-acids. 2 the findings that one should understand it is good to start by summarizing the experimental findings that the model should explain. 1. one should be able to identify phantom dna [13]. this identification explains the findings about phantom dna if ordinary and dark dna have common resonance frequencies and therefore behave like resonantly interacting quantum antennae. 2. the earlier findings of gariaev’s group suggesting remote gene expression [11], which becomes also possible if the dnas of the sender can activate the dna of the receiver by radiation. direct activation could be based on electromagnetic signal between dna of the sender and ordinary conjugate dna of the receiver. scattering from ordinary and possibly also phantom dna and would generate this kind of signal. the challenge is to explain why the activation obeys genetic code in the sense that a given dna sequence activates only similar dna sequence. 3. the claim of montagnier’s team [12, 9] is that the radiation generated by dna affects water in such a manner that it behaves as if it contained the actual dna. a brief summary of experiment of montagnier and collaborators is in order. (a) two test tubes containing 100 bases long dna fragments were studied. both tubes were subjected to 7 hz electromagnetic radiation. earth’s magnetic field was eliminated to prevent its possible inteference (the cyclotron frequencies of earth’s magnetic field are in eeg range and one of the family secrets of biology and neuroscience since seventies is that cyclotron frequencies in magnetic fields have biological effects on vertebrate brain). the frequencies around 7 hz correspond to cyclotron frequencies of some biologically important ions in the endogenous magnetic field of .2 tesla explaining the findings. this field is 2/5 of the nominal value of the earth’s magnetic field. (b) what makes the situation so irritating for skeptics who have been laughing for decades for homepathy and water memory is that the repeated dilution process used for the homeopathic remedies was applied to dna in the recent case. the solution containing no detectable amounts dna (dilution factor was 10−12) was placed in second test tube whereas the first test tube contained 100 bases long dna in the original concentration. (c) after 16 to 18 hours both tubes were subjected to polymerase chain reaction (pcr), which builds dna from its basic building bricks using dna polymerase enzyme. what is so irritating from the point of view of skeptic was that dna was generated also in the test tube containing the highly diluted water. water in presence of second test tube seems to be able to cheat the polymerase by mimicking the presence of the actual dna serving in the usual situation as a template for builing copies of dna. one could also speak about the analog quantum teleportation. note that the presence of both test tubes and therefore some kind of communication between the samples is absolutely esential for the process to take place: repeated dilution is not enough. 4. peter gariaev’s team has carried out an analogous experiment recently in which one has two test tubes containing water. tube a contained dna fragments and tube b contained only water and dna nucleotides plus dna polymerase just as as in montagnier’s experiment. the analog of the homeopathic procedure was not however applied to tube b. the experiments use a drop of dna in water in gamma concentration in tube a. this dna (with length of 600 base pairs) was scanned by laser radiation from helium-neon laser. the scattered radiation having a wide spectrum issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal| november 2011| vol 1.| issue 3| pp. 298-307 301 pitkänen m., gariaev p. quantum model for remote replication of frequencies down to khz frequencies was applied on tube b at distance of 3 m in refrigerator (+4 celsius) containing distilled water solution of dna nucleotides and dna polymerase inducing polymer chain reaction pcr amplifying dna template if present. the generation of dna sequences in tube b with the same mass distribution as in tube a by polymer chain reaction (pcr) is observed suggesting that the necessary dna template is generated as a direct copy or conjugate of the original in test tube a by some unknown mechanism. nucleotide sequences have not been analyzed to see whether they are identical or conjugates of those in tube a. 3 the model of remote replication consistent with dna as topological quantum computer model the basic assumptions are that the scattered radiation, the flux tubes of the magnetic body of dna along which the radiation propagates, and quarks and antiquarks at the ends of the flux tubes from system able to serve as a template for the formation of conjugate of ordinary dna. to understand how remote remote replication could take place, some further assumptions are necessary. 1. the flux tubes emanating from dna are parallel and condensed at 2-d flux sheet having dna at is first boundary so that dna nucleotides can attach to the flux tubes at the second boundary. the attached nucleotides would be along the same line and would form dna sequence in remote replication process. 2. quantum antenna interaction takes place between group of molecules participating a given reaction so that they have common antenna frequency as resonance frequency. the frequencies characterize the radiation propagating along magnetic flux tubes connecting the molecules, and could come as sub-harmonics of the frequency of (in the case considered) visible light from the formula e = hnf, hn = nh , n = 1, 2, 3, ... . here e is the fixed energy of photon. hn denotes value of planck constant which in tgd universe can have infinite number of values coming as multiplies of the ordinary planck constant h. for a given photon energy e one obtains harmonics of the basic wavelength λ = c f(n) = nλ0 . wave length would correspond to the length of the flux tube proportional to n. dnas with flux tubes characterized by different values of n would correspond to different levels in the evolutionary hierarchy. in tgd inspired theory of consciousness the value of hn serves as the measure for the time scale of planned action and memory span and neurons of frontal lobe would represent the highest level in the hierarchy, 3. if resonance frequency is same for all nucleotides, frequency cannot distinguish between dna nucleotides. in the model of dna as topological quantum computer the quark (u or d) and antiquark (u or d ) at the ends of the flux tube code for a, t,c,g. this model is the simplest one and does not require any additional assumptions about frequency coding. it also allows resonant interaction at several frequencies: the scattering of visible light from dna indeed produces a wide spectrum of frequencies interpreted in terms of dark variants of visible photons. one can criticize the assumption that particular quark or antiquark is associated with the flux tube ending at particular nucleotide. at this moment this assumption does not have a convincing dynamical explanation. presumably this explanation would rely on the minimization of the interaction energy. 4. what is needed is a model explaining why the resonant antenna frequency does not depend on nucleotide: obviously the frequency should relate to something shared by all nucleotides. an energy issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal| november 2011| vol 1.| issue 3| pp. 298-307 302 pitkänen m., gariaev p. quantum model for remote replication level associated with sugar-phosphate backbone of dna is what comes first in mind. a more exotic option is transition involved with quark-antiquark pair. since electromagnetic field for nonvacuum extremals is accompanied by classical color field, the exchange of gluons between quark and antiquark suggests itself as the quantum antenna interaction distinguishing between nucleotides. quantum antenna mechanism is extremely general and flexible and might be a fundamental mechanism of bio-catalysis allowing also communication between visible and dark matter sectors. antenna mechanism is of course central also in ordinary communications. if the biologically most relevant interactions of biomolecules via quantum antenna mechanism then also water memory and the claimed effects of homeopathically treated water might be understood [3]. the testing of the dark photon aspect of the hypothesis would require the detection of the dark photons somehow: the decay to a bunch of n ordinary photons with same wavelength is the obvious manner to achieve this. 3.1 identification of phantom dna the observed residual coherent scattering from a chamber from which ordinary dna is removed inspired the notion of phantom dna [13]. the questions are what phantom dna is and is it relevant to remote replication of the ordinary dna. phantom dna observed in the scattering experiments could correspond to dark nucleon sequences realizing vertebrate genetic code with dark nucleons consisting of three quarks representing both dna,rna, trna, and aminoacids as particular nucleon states [5, 3]. the resonant interaction between ordinary and dark dna would explain why light at same frequencies scatters also from dark dna in phantom dna experiments. in montagnier’s experiments it could give rise to a positive feedback amplifying the radiation from second sample containing dna. water would be living in the sense that it contains ”dark dna” and dark dna might allow remote transcription to ordinary dna sequences in presence of ordinary dna codons (triplets) and vice versa. skeptic can of course ask whether one could explain the experimental findings without assuming phantom dna. 1. in gariaev’s experiments [13], which inspired the notion of phantom dna part of dna could ”drop” to parallel space-time sheets and have the same effect on the scattered radiation as the ordinary dna. this explanation would however require the many-sheeted space-time of tgd probably equally abominable to skeptic as phantom dna. 2. in montagnier’s experiment and also in the recent experiment of gariaev the ordinary dna contained by water droplet could diffuse to dark space-time sheets and enter from flux tube a to flux tube b along the same magnetic flux tubes as radiation propagates. dna polymerase would allow to amplify this leaking dna and produce conjugate dna. the irradiation of the original dna would generate the flux sheets serving as a route for the transfer. the killer test is to check whether it is indeed conjugate of the original dna which is produced. again many-sheeted space-time is required. 3. for the option based on dna as topological quantum computer hypothesis discussed above the remote replication would take place via the direct formation of conjugate dna template and dna polymerase produces from this copies of the original dna whereas for ”trivial” option conjugate dna is produced. phantom dna would not be absolutely necessary. it is however questionable whether the intensity of the radiation is high enough and the resonant interaction with phantom dna which could give rise to a positive feedback might be needed to amplify the radiation. 3.2 dark dna and frequency coding by quantum antenna mechanism the remote transcription of dark dna (phantom dna) to ordinary dna and vice versa would have quite far reaching implications for evolution since dark dna/rna/trna/amino-acids could define a virtual world serving as r&d lab where new dnas could be developed and if needed translated to ordinary dna. the dark dna could be also transferred through cell membranes without difficulty, in particular to germ cells. also the genetic transfer between different organisms would become possible. second issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal| november 2011| vol 1.| issue 3| pp. 298-307 303 pitkänen m., gariaev p. quantum model for remote replication possibility is that the magnetic flux tubes mediating the dark photons traverse the cell membranes so that even the transfer of dark nucleons through the cell membrane is un-necessary. the implications for genetic engineering would be obvious. could one generalize the quantum antenna mechanism to the interaction between dark nucleons representing dna triplets as entangled states of three quarks and ordinary dna codons consisting of three unentangled nucleotides? could similar mechanism realize genetic code assigning to dark dna dark variants of rna, trna and amino-acids via the analogs of transcription and translation processes? it seems that frequency coding, which somewhat disappointingly did not look natural for remote replication of ordinary dna, is ideal for these processes so that the original idea of wave dna would be realized at the level of dark-visible and dark-dark interactions. the flux tubes would be associated with entire codons -dna triplets rather than individual nucleotides. different dna triplets do not form interacting groups in the sense that they should be connected by flux tubes. therefore the simplest possibility would be frequency coding with specific resonance frequency for each dna triplet. no quarks at the ends of the flux tubes connecting codons are needed. remark:: a hierarchy of flux quanta is essential and must distinguish between its levels. flux tubes associated with nucleotides at flux tubes associated with dna codons at flux sheets traversing dna strands. if one assumes that octaves correspond to the same frequency this would require odd multiples λ(n) = (2n+ 1)λ0 , n = 0, ..., 63 of λ0 so that the longest wavelength would be 127λ0. in the number theoretic model of the genetic code based on the notion of combinatorial hierarchy [2] codons are indeed labeled by 64 integers in the range 0, ..., 127 = 27 − 1. these integers are however not assumed to be odd. one can also consider the possibility that the frequencies are coded by the value of planck constant and this option leads to an interpretation of the earlier proposed realization of divisor code [8] to be discussed later on. support for this option comes from the phenomenon of phantom dna demonstrating that resonant scattering of light from dna and dark dna occurs for the same frequencies. can one imagine remote transcription of dark dna to ordinary dna using only nucleotides as building bricks? this process would require coupling of dna nucleotides to dark nucleons representing dna triplets and it is not easy to imagine any simple mechanism making this possible. already existing dna triplets seem to be necessary. 3.3 common explanation for the findings of montagnier and gariaev in the experiments of montagnier’s group [9] the outcome is remote replication whereas the earlier experiments gariaev’s group [13, 11] give evidence for phantom dna and remote activation of dna transcription by scattered laser light able to represented genetic code. there must be interaction between the test tubes in montagnier’s experiments and in the recent experiments of gariaev’s group observing remote replication there is explicit interaction between the test tubes due to the scattered laser radiation. hence one expects a common underlying mechanism based on radiation between the tubes and phantom dna. 1. the tgd based explanation [3] of montagnier’s findings relies on the assumption that the homeopathic procedure generated a population of dark dna nucleotides in the diluted system. the sequence of dilutions and shakings was like a series of environmental catastrophes driving the evolution of dark dna and also feeding metabolic energy to the system. the outcome was dark dna population mimicking the original dna in the test tube b. in the presence of dna polymerase in tube b and second test tube a containing ordinary dna the dark dna was somehow able to generate ordinary dna in tube b. the detailed mechanism for this remained open. 2. could the scattered laser light have the same effect as the homeopathic procedure? this would require a direct transcription of dark dna to ordinary dna in the presence of dna polymerase and nucleotides (only them!). it is very difficult to understand how this could happen. dna polymerase very probably does not have the same catalyzing effect on dark dna sequences as on ordinary dna sequences. it is also difficult to imagine the build-up of ordinary dna from issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal| november 2011| vol 1.| issue 3| pp. 298-307 304 pitkänen m., gariaev p. quantum model for remote replication nucleotides using dark nucleon sequences as templates: if frequency coded codons would serve as building bricks, situation would be simpler as already found. 3. one must not forget that the presence of the test tube a was essential in the experiment of montagnier: communications between the test tubes crucial for the outcome must have taken place. the consistency between the two experiments could be achieved if the dna in test tube a generated the counterpart of the scattered laser signal in gariaev’s experiments but certainly as a much weaker signal. 4. this signal should have been amplified somehow by the presence the dark dna sequences in tube b so that it would have been able to generate critical amounts of conjugate of the original dna amplified by dna polymerase to the copy of the original. what suggests itself is a positive feedback loop ordinary dna sequences → dark dna sequences → ordinary dna sequences..... causing the amplification of the weak signal so that it is able to induce remote replication by the proposed mechanism. this kind of feedback of signals propagating between magnetic bodies was assumed also in the model for the strange images produced by the irradiation of dna sample by ordinary light interpreted as photographs of magnetic flux tubes containing dark matter [4]. this model explains also the findings of the recent experiment (unpublished) of gariaev. in this case the amplification by feedback mechanism could be present but might not be needed since the scattered laser radiation could give strong enough signal to produce the needed amount of conjugate dna serving as a template. what is nice from tgd point of view that the consistency between the two experiments gives support also for the notion of dark dna and its identification as phantom dna. 3.4 summing up the basic assumptions of the mechanism the basic assumptions of the model of remote replication deserve a short summary. 1. bio-molecules would serve as receiving and sending quantum antennas forming populations with communications between members just like higher organisms. the molecules participating the same reaction would naturally have same antenna frequencies. quarks and antiquarks at the ends of the flux tubes would code for different nucleotides and the frequencies associated with the nucleotides would be identical. the character of classical electromagnetic field would code for a particular nucleotide. 2. remote replication and other remote polymerization processes would differ from the ordinary one only in that the phase transition reducing the value of planck constant for the flux tube would not take place and bring the molecules near each other. note that the fractal hierarchy of flux quanta: nucleotide flux tubes, codon flux tubes and flux sheets associated with dna strands is essential. 3. the immediate product of remote replication would be the conjugate of the original dna sequence and dna polymerase would amplify it to the copy of the original dna sequence. this prediction could be tested by using very simple dnas sequencessay sequences consisting two nucleotides which are not conjugates. for instance, one could check what happens if conjugate nucleotides are absent from the target (neither conjugate nor original dna sequence should be produced). if the target contains conjugate nucleotides but no originals, only conjugate dna sequences would be produced one might hope in sufficiently large amounts to be detectable. 4. frequency coding would be natural for quantum antenna interactions between ordinary dna and its dark variant and also between dark variants of dna, rna, trna, and amino-acids. the reason is that dark nucleons represent the genetic code by entanglement and it is not possible to reduce the codon to a sequence of letters. 4 possible implications the proposed realization of remote replication seems to have rather far reaching implications for the understanding of the mechanism of homeopathy and basic mechanisms of immune system as well as to issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal| november 2011| vol 1.| issue 3| pp. 298-307 305 pitkänen m., gariaev p. quantum model for remote replication the understanding of how dna -dark nucleon sequence association. one can also interpret the proposed tgd based realization of the divisor code [8] suggested by khrennikov [14] as frequency coding of dna triplets by the value of planck constant assignable to flux tubes emerging from dna triplets. 4.1 possible relevance for homeopathy and immune system tgd inspired vision about water memory assumes that the magnetic bodies of molecules dis-solved into water represent the molecules in terms of cyclotron frequencies characterizing its magnetic body. molecules can lose their magnetic bodies as the hydrogen bonds connecting the molecule to the magnetic body are split. the population of these lost magnetic bodies would define a representation for the dissolved substance able to mimic it. the hitherto unanswered questions concern the detailed structure of the magnetic body of the molecule and how it codes for the molecule. the hydrogen bonds connecting the molecule to the ordered water forming a kind of ice covering the molecule in the inactive state should be crucial aspect of the coding. if dark nucleon sequences are associated with the hydrogen bonds of this ”ice layer” or generated in their splitting as i have proposed, one can ask whether dark nucleon sequences could characterize the molecular magnetic body. if so, cyclotron resonance frequencies or more general frequencies associated with the dark dna sequences could code for the molecule. dna sequences would define a universal language allowing for the system to name for polar molecules. quantum antenna mechanism would in turn associate ordinary dna sequences with the dark nucleon sequences coding for the molecule. hence one can imagine a development of a mechanism allowing the organism to modify its dna by adding to it genes coding for proteins characterized by the same resonance frequencies as the magnetic bodies of the invader molecules. these proteins would couple strongly to the invader molecules via quantum antenna mechanism and the phase transition reducing planck constant would allow them to catch the invader molecules by attaching to them. the fact that the dna of immune system evolves very rapidly conforms with this vision. 4.2 frequency coding for dna sequences by the value of planck constant as a realization of divisor code the realization of dark magnetic bodies of polar molecules in terms of dark nucleon sequences allows to understand the association of dark dna with ordinary dna, rna, and trna making among other things possible the transcription of dark dna to dna and vice versa. dark nucleon sequences would be associated with the magnetic bodies of dna, mrna, and trna. this would apply also to aminoacid sequences. dark dna would separate from ordinary dna as it loses its magnetic body in the splitting of hydrogen bonds and suffers denaturation. similar mechanism would cause denaturation of other biomolecules and would mean that they ”lose their names” and thus information content and become mere organic molecules instead of living bio-molecules. this kind of association would make the emergence of the genetic code and its generalization to the naming of molecules by dna sequences trivial. genetic code can be understood from the proposed natural correspondence between dark nucleon sequences and dna, rna, trna, and acmino-acids). i have however developed also another realizaton based on tgd based realization of so called divisor code first suggested by khrennikov and nilsson [14] and the following argument allows to interpret in terms of frequency for fixed value of photon energy with frequencies coded by the value of planck constant. 1. the observation of khrennikov and nilsson is following. consider the integers n in the range 1,...,21 and obviously labeling amino-acids and let k(n) the number of divisors of n. define b(k) as the number of integers n for which the number of divisors is k. it turns out that the numbers b(k) are rather near to the numbers a(k) of amino-acids coded by k codons. this suggests that given amino-acid a is coded by a product of prime p(a), which alone characterizes it, and integer n(a) in the range 1, ..., 21. the product of integers characterizing the codon coding for a would be characterized by the product of p(a) and some factor r(a) of n(a). with these assumptions given codon would code for only single amino-acid and the number of dnas coding for amino-acid a is the number of the factors r(a) of n(a). the codons coding for a would be coded by integers p(a)r(a) such that r(a) divides n(a). the safest assumption would be that the primes p(a) satisfy issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal| november 2011| vol 1.| issue 3| pp. 298-307 306 pitkänen m., gariaev p. quantum model for remote replication p(a) > 19 so that p(a) does not divide n(a) for any a. if p(a) is as small as possible the value spectrum of p(a) is {23, 29, 31, 37, 41, 43, 47, 53, 59, 61, 67, 71, 73, 79, 83, 89, 97, 101, 103, 107, 109} . if one assumes that the two additional aminoacids coded in some cases by non-vertebrate genetic code correspond to primes also the primes 113, 127 are included. what is interesting is that mersenne prime m7 = 27 − 1 = 127 appears in the model of genetic code based on the notion of combinatorial hierarchy [2]. this model assumes that dna codons correspond to 64 integers in the range 1, ..., 127. this realization of the genetic code cannot however be consistent with the divisor code realized in the proposed manner since it would require that the integers n(a)p(a) belong to the range 1, .., 127. the prime factors of these integers can however belong to this range. 2. the tgd inspired proposal [8] was that the flux tube assignable to amino-acid a corresponds to ~ = p(a) × n(a)~0 whereas the dna triplet (for quark-antiquark coding nucleotide rather than triplet) coding for it is characterized by ~ = p(a)× r(a)~0 such that r(a) divides n(a). 3. this proposal could be interpreted in terms of frequency coding by quantum antenna mechanism. for a given photon energy e wave length would be coded by the value of ~ and one would have λn = nλ0, n = p(a)n(a) for amino-acids and n = p(a)r(a) for codons. the condition that flux tube lengths are same for different dna triplets would be satisfied if the common length of the flux tubes is an integer multiple of λ0 proportional to the product of all integers appearing as factors in the integers coding for amino-acids. the common length of the flux tubes would be therefore proportional to the product ∏ a p(a) ∏ a ra. references books related to tgd [1] m. pitkänen. dna as topological quantum computer. in genes and memes. onlinebook. http: //tgd.wippiespace.com/public_html/genememe/genememe.html#dnatqc, 2006. [2] m. pitkänen. genes and memes. in genes and memes. onlinebook. http://tgd.wippiespace. com/public_html/genememe/genememe.html#genememec, 2006. [3] m. pitkänen. homeopathy in many-sheeted space-time. in bio-systems as conscious holograms. onlinebook. http://tgd.wippiespace.com/public_html/hologram/hologram.html# homeoc, 2006. [4] m. pitkänen. model for the findings about hologram generating properties of dna. in genes and memes. onlinebook. http://tgd.wippiespace.com/public_html/genememe/genememe.html# dnahologram, 2006. [5] m. pitkänen. nuclear string hypothesis. in p-adic length scale hypothesis and dark matter hierarchy. onlinebook. http://tgd.wippiespace.com/public_html/paddark/paddark.html# nuclstring, 2006. [6] m. pitkänen. quantum antenna hypothesis. in quantum hardware of living matter. onlinebook. http://tgd.wippiespace.com/public_html/bioware/bioware.html#tubuc, 2006. [7] m. pitkänen. the notion of wave-genome and dna as topological quantum computer. in genes and memes. onlinebook. http://tgd.wippiespace.com/public_html/genememe/genememe.html# gari, 2006. issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. http://tgd.wippiespace.com/public_html/genememe/genememe.html#dnatqc http://tgd.wippiespace.com/public_html/genememe/genememe.html#dnatqc http://tgd.wippiespace.com/public_html/genememe/genememe.html#genememec http://tgd.wippiespace.com/public_html/genememe/genememe.html#genememec http://tgd.wippiespace.com/public_html/hologram/hologram.html#homeoc http://tgd.wippiespace.com/public_html/hologram/hologram.html#homeoc http://tgd.wippiespace.com/public_html/genememe/genememe.html#dnahologram http://tgd.wippiespace.com/public_html/genememe/genememe.html#dnahologram http://tgd.wippiespace.com/public_html/paddark/paddark.html#nuclstring http://tgd.wippiespace.com/public_html/paddark/paddark.html#nuclstring http://tgd.wippiespace.com/public_html/bioware/bioware.html#tubuc http://tgd.wippiespace.com/public_html/genememe/genememe.html#gari http://tgd.wippiespace.com/public_html/genememe/genememe.html#gari dna decipher journal| november 2011| vol 1.| issue 3| pp. 298-307 307 pitkänen m., gariaev p. quantum model for remote replication [8] m. pitkänen. three new physics realizations of the genetic code and the role of dark matter in bio-systems. in genes and memes. onlinebook. http://tgd.wippiespace.com/public_html/ genememe/genememe.html#dnatqccodes, 2006. biology [9] dna waves and water. http://arxiv.org/abs/1012.5166. [10] polymerase chain reaction. http://en.wikipedia.org/wiki/pcr. [11] p. gariaev et al. the dna-wave biocomputer, volume 10. chaos, 2001. [12] s. ferris j.-l. montagnier l. montagnier, j. aissa and c. lavall’e. electromagnetic signals are produced by aqueous nanostructures derived from bacterial dna sequences. interdiscip. sci. comput. life sci., 2009. [13] g. g. komissarov a. a. berezin a. a. vasiliev p. p. gariaev, v. i. chudin. holographic associative memory of biological systems. proceedings spie the international society for optical engineering. optical memory and neural networks, pages 280–291, 1991. [14] a. khrennikov m. nilsson. a number theoretical observation about the degeneracy of the genetic code. http://arxiv.org/abs/q-bio/0612022. issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. http://tgd.wippiespace.com/public_html/genememe/genememe.html#dnatqccodes http://tgd.wippiespace.com/public_html/genememe/genememe.html#dnatqccodes http://arxiv.org/abs/1012.5166 http://en.wikipedia.org/wiki/pcr http://arxiv.org/abs/q-bio/0612022 introduction the findings that one should understand the model of remote replication consistent with dna as topological quantum computer model identification of phantom dna dark dna and frequency coding by quantum antenna mechanism common explanation for the findings of montagnier and gariaev summing up the basic assumptions of the mechanism possible implications possible relevance for homeopathy and immune system frequency coding for dna sequences by the value of planck constant as a realization of divisor code dna decipher journal | december 2019 | volume 9 | issue 3 | pp. 123-145 123 pitkänen, m., cosmic string model for formation of galaxies, & dna structure article cosmic string model for formation of galaxies, & dna structure matti pitkänen 1 abstract the view about the role of new nuclear physics predicted by tgd in the model of solar interior gives excellent guidelines for attempts to develop a more detailed understanding about tgd counterparts of blackholes as volume filling flux tube tangles. one ends up to rather detailed picture making correct predictions about minimum radii of blackholes and neutron stars. the idea about ordinary stars as blackhole like objects emerges. the standard blackhole thermodynamics is replaced by two thermodynamics. the first thermodynamics is assignable to the flux tubes as string like entities having hagedorn temperature th as maximal temperature. the second thermodynamics is assignable to gravitational flux tubes characterized by the gravitational planck constant hgr. cosmic strings are assumed to form a fractal hierarchy and that in tgd inspired biology cosmic strings thickened to monopole flux tubes are behind various linear biomolecules organized around them as ordinary matter. this leads to ask whether dna double strand and the organization of dna double strands to chromosomes might be more general phenomenon. chromosomes consist of 4 strands, which allows to ask whether something similar happens even at the level of superclusters and that the topology of quadrupole field is involved. keywords: cosmic string model, galaxy, formation, dna strand, tgd framework. 1 introduction the view about the role of new nuclear physics predicted by tgd in the model of solar interior [25] gives excellent guidelines for attempts to develop a more detailed understanding about tgd counterparts of blackholes as volume filling flux tube tangles. 1.1 brief description of the model for for the formation of galaxies and stars tgd based cosmology predicts that the primordial cosmology was dominated by cosmic strings identified as 4-surfaces having 2-d m4 projection in h = m4xcp2. cp2 projection is a complex surface of cp2. the dimension of m4 projection is unstable against perturbations and during cosmological evolution the m4 projection thickens. this leads to a model for the formation of galaxies as tangles along cosmic strings in turn containing stars and even planets as sub-tangles. 1. twistor lift of tgd [15] predicts that cosmological constant at the level of space-time surface (to be distinguished from that associated with grt limit of tgd) is length scale dependent. this solves the basic problem caused by the huge value of cosmological constant in the very early universe. in zero energy ontology length scale dependent λ having spectrum coming in some negative powers of 2 characterizes the space-time sheets assignable to individual system and the corresponding causal diamond (cd) and is determined by its p-adic length scale. for instance, sun has its own cosmological constant predicted by the model solving the puzzle due to larger abundances obtained in solar-seismological determinations than in spectroscopic and meteoritic determinations. dark nuclear states of nuclei inside solar core contribute also to the nuclear abundances [25]. 1correspondence: matti pitkänen http://tgdtheory.fi/. address: rinnekatu 2-4 8a, 03620, karkkila, finland. email: matpitka6@gmail.com. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.fi/ mailto:matpitka6@gmail.com dna decipher journal | december 2019 | volume 9 | issue 3 | pp. 123-145 124 pitkänen, m., cosmic string model for formation of galaxies, & dna structure 2. the energy of flux tubes consists of kähler magnetic energy and volume energy. quantum classical correspondence strongly suggests that this energy is identifiable as dark matter even for minimal value of heff . 3. phase transitions reducing the value of cosmological constant are possible. cosmic strings (or rather their m4 projections) start to thicken and lose magnetic energy by transforming to ordinary matter. this is analogous to the decay of the inflaton field to matter. this generates einsteinin space-time with space-time surfaces having large and increasing 4-d m4 projection. flux tubes and cosmic strings are however still present. the expansion of flux tubes in phase transitions reducing λ gives rise to a jerk-wise accelerated expansion at the level of astrophysical objects. for given phase transition the accelerated expansion eventually stops since the expansion increases volume energy. the expansion periods however repeat being induced by phase transitions reducing length scale dependent quantized cosmological constant λ associated with the volume action coming as powers of 2 and making flux tubes unstable against thickening and transformation of magnetic energy to ordinary matter. the recent accelerated expansion corresponds to this kind of period being thus analogous to inflation and is predicted to stop since volume energy increases. the expansion rate is predicted to oscillate so that the expansion takes place as jerks and there is evidence for this [2] (see (http://tinyurl.com/oqcn2hp) discussed from tgd point of view in [13]. 4. in particular, the tgd counterpart of inflation would have led from cosmic string dominated primordial cosmology in which einsteinian space-time does not make sense to a radiation dominated phase in which einsteinian space-time makes sense. expanding earth model [21] allowing to understand cambrian explosion is one application of tgd based quantum cosmology. 1.2 the notion of length scale dependent cosmological constant in this section the notion of length scale dependent cosmological constant is considered in more detail. tgd predicts that cosmological constant λ characterizing space-time sheets is length scale dependent and depends on p-adic length scale. furthermore, expansion would be fractal and occur in jerks. this is the picture that twistor lift of tgd leads to [15]. quite generally, cosmological constant defines itself a length scale r = 1/λ1/2. r = (8π)1/4 √ rlp essentially the geometric mean of cosmological and planck length defines second much shorter length scale r. the density of dark energy assignable to flux tubes in tgd framework is given as ρ = 1/r4. in tgd framework these scales corresponds two p-adic length scales coming as half octaves. this predicts a discrete spectrum for the length scale dependent cosmological constant λ [15] . for instance, one can assign to ..., galaxies, stars, planets, etc... a value of cosmological constant. this makes sense in many-sheeted space-time but not in standard cosmology. cosmic expansion is replaced with a sequence of fast jerks reducing the value of cosmological constant by some power of 2 so that the size of the system increases correspondingly. the jerk involves a phase transition reducing λ by some negative power of 2 inducing an accelerating period during which flux tube thickness increases and magnetic energy transforms to ordinary matter. thickening however increases volume energy so that the expansion eventually halts. also the opposite process could occur and could correspond to a ”big” state function reduction (bsfr) in which the arrow of time changes. an interesting question is whether the formation of neutron stars and super-novas could involve bsfr so that these collapse phenomena would be kind of local big bangs but in opposite time direction. one can also ask whether blackhole evaporation could have as tgd analog bsfr meaning return to original time direction by a local big bang. tgd analogs of blackholes are discussed in [22]. evidence for the anisotropy of the acceleration of cosmic expansion has been reported (see http: //tinyurl.com/rx4224f). thanks to wes johnson for the link. anisotropy of cosmic acceleration would fit with the hierarchy of scaled dependent cosmological constants predicting a fractal hierarchy issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/oqcn2hp http://tinyurl.com/rx4224f http://tinyurl.com/rx4224f dna decipher journal | december 2019 | volume 9 | issue 3 | pp. 123-145 125 pitkänen, m., cosmic string model for formation of galaxies, & dna structure of cosmologies within cosmologies down to particle physics length scales and even below. the phase transitions reducing the value of λ for given causal diamond would induce accelerated inflation like period as the magnetic energy of flux tubes decays to ordinary particles. this would give a fractal hierachy of accelerations in various scales. consider now some representative examples to see whether this picture can be connected to empirical reality. 1. cosmological constant in the length scale of recent cosmology corresponds to r ∼ 1026 m (see http://tinyurl.com/k4bwlzu). the corresponding shorter scale r = (8π)1/4 √ rlp is identified essentially as the geometric mean of r and planck length lp and equals to r ∼ 4 × 10−4 m: the size scale of large neuron. this is very probably not an accident: this scale would correspond to the thickness of monopole flux tubes. 2. if the large scale r is solar radius about 7 × 108 m, the short scale r ' 1012 m is about electron compton length, which corresponds to p-adic length scale l(127) assignable to mersenne prime m127 = 2127− 1. this is also the size of dark proton explaining dark fusion deduced from holmlid’s findings [16, 17]: this requires heff ∼ 212! remark: dark proton sequences could be neutralized by a sequence of ordinary electrons locally. this could give rise to analogs of atoms with electrons being very densely packed along the flux tube. the prediction of the tgd based model explaining the 10 year old puzzle related to the fact that nuclear abundances in solar interior are larger than outside [25] (see http://tinyurl.com/ y38m54ud) assumes that nuclear reactions in sun occur through intermediate states which are dark nuclei. hot fusion in the sun would thus involve the same mechanism as ”cold fusion”. the view about cosmological constant and tgd view about nuclear fusion lead to the same prediction. 3. if the short scale is p-adic length l(113) assignable to gaussian mersenne mg,113 = (1 + i)113 − 1 defining nuclear size scale of r ∼ 10−14 m, one has r ∼ 10 km, the radius of a typical neutron star (see http://tinyurl.com/y5ukv2wt) having a typical mass of 1.4 solar masses. a possible interpretation is as a minimum length of a flux tube containing sequence of nucleons or nuclei and giving rise to a tangle. neutron would take volume of about nuclear size size of the magnetic body of neutron? could supernova explosions be regarded as phase transitions scaling the stellar λ by a power of 2 by making it larger and reducing dramatically the radius of the star? 4. short scale r ∼ 10−15 m corresponding to proton compton length gives r about 100 m. could this scale correspond to quark star (see http://tinyurl.com/y3n78tjs)? the known candidates for quark stars are smaller than neutron stars but have considerably larger radius measured in few kilometers. weak length scale would give large radius of about 1 cm. the thickness of flux tube would be electroweak length scale. starting from this picture, one ends up to rather detailed picture making correct predictions about minimum radii of blackholes and neutron stars. the idea about ordinary stars as blackhole like objects emerges naturally since flux tubes are universal objects in tgd universe and could be also inspired by the fashion of dualizing everything to blackholes. the standard blackhole thermodynamics is replaced by two thermodynamics. the first thermodynamics is assignable to the flux tubes as string like entities having hagedorn temperature th as maximal temperature. the second thermodynamics is assignable to the gravitational flux tubes characterized by the gravitational planck constant hgr: hawking temperature tb is scaled up by the ratio ~gr/~ to tb,d and is gigantic as compared to the ordinary hawking temperature but the intensity of dark hawking radiation is extremely low. the condition th = tb,d for thermodynamical equilibrium fixes the velocity parameter β0 = v0/c appearing in the nottale formula for ~gr and suggests β0 = 1/heff for the dark nuclei at flux tubes issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/k4bwlzu http://tinyurl.com/y38m54ud http://tinyurl.com/y38m54ud http://tinyurl.com/y5ukv2wt http://tinyurl.com/y3n78tjs dna decipher journal | december 2019 | volume 9 | issue 3 | pp. 123-145 126 pitkänen, m., cosmic string model for formation of galaxies, & dna structure defining star as blackhole like entity in tgd sense. this also predicts the hagedorn temperature of the counterpart of blackhole in grt sense to to be hadronic hagedorn temperature assignable to the flux tube containing dark nuclei as dark nucleon sequences so that there is a remarkable internal consistency. in zero energy ontology (zeo) quasars and galactic blackholes can be seen as time reversals of each other. the cosmological time anomalies such as stars older than the universe can be understood. in zeo the time evolution for the zero energy states associated with causal diamonds (cds) by sequences of small state function reductions (weak measurements) gives rise to conscious entity, self. self dies and reincarnates with an opposite arrow of time in big (ordinary) state function reduction reversing the arrow of time. these reincarnations define kind of universal karma’s cycle. if the karma’s cycle leaves the sizes of cds bounded and their position in m4 unaffected, quantum dynamics reduces to a local dynamics inside cds defining sub-cosmologies. in particular, the age distributions and properties of stars depend only weakly on the value of cosmic time stars older than the universe become possible in standard view about time. the flux tube picture about galaxies and larger structures is discussed with application to some anomalies strongly suggesting the presence of coherence in scales of even billion light years. also ”too” fast spinning galaxies are discussed. the local galaxy supercluster laniakea is discussed in the flux tube picture as a flux tube tangle in scale of .5 gly. 2 blackholes, quasars, and galactic blackholes i have discussed a model of quasars in [22] (see http://tinyurl.com/y2jbru4k) . the model is inspired by the notion of meco and proposes that quasar has a core region analogous to black hole in the sense that the radius is apart from numerical factor near unit rs = 2gm . this comes from mere dimensional analysis. 2.1 blackholes in tgd framework in tgd the metric of blackhole exterior makes sense and also part of interior is embeddable but there is not much point to consider tgd counterpart of blackhole interior, which represents failure of grt as a theory of gravitation: the applicability of grt ends at rs . the following picture is an attempt to combine ideas about hierarchy of planck constant and from the model of solar interior [25] deriving from the 10 year old nuclear physics anomaly [4, 6]. 1. the tgd counterpart of blackhole would be maximally dense spaghetti formed from monopole flux tube. stars would not be so dense spaghettis. a still open challenge is to formulate precise conditions giving the condition rs = 2gm . the fact that condition is ”stringy” with t = 1/2g taking formally the role of string tension encourages the spaghetti idea with length of cosmic string/flux tube proportional to rs . 2. the maximal string tension allowed by tgd is determined by cp2 radius and estimate for kähler coupling strength as 1/αk ' 1/137 and is roughly tmax ∼ 10−7.5/g suggesting that in blackhole about 107.5 parallel flux tubes with maximal string tension and with length of about rs give rise to blackhole like entity. kind of dipole core consisting of monopole flux tubes formed by these flux tubes comes in mind. the flux tubes could close to short flux tubes or flux tubes could continue like flux lines of dipole magnetic field and thicken so that the energy density would be reduced. 3. this picture conforms with the proposal that the integer n appearing in effective planck constant heff = n × h0 can be decomposed to a product n = m × r associated to space-time surface which is m-fold covering of cp2 and r-fold covering of m4. for r = 1 m-fold covering property could be interpreted as a coherent structure consisting of m almost similar regions projecting to m4: one issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/y2jbru4k dna decipher journal | december 2019 | volume 9 | issue 3 | pp. 123-145 127 pitkänen, m., cosmic string model for formation of galaxies, & dna structure could say that one has field theory in cp2 with m-valued fields represented by m4 coordinates. for r = 1 each region would correspond to r-valued field in cp2. this suggests that newton’s constant corresponds apart from numerical factors 1/g = m~/r2, where r is cp2 radius (the radius of geodesic circle). this gives m ∼ 107.5 for gravitational flux tubes. the deviations of m from this value would have interpretation in term of observed deviations of gravitational constant from its nominal value. in the fountain effect of super-fluidity the deviation could be quite large [11]. smaller values of heff are assigned in the applications of tgd with the flux tubes mediating other than gravitational interactions, which are screened and should have shorter scale of quantum coherence. could one identify corresponding planck constant in terms of the factor r of m: heff = r~0? tgd leads also to the notion of gravitational planck constant ~gr = gmm/v0 assigned to the flux tubes mediating gravitational interactions presumably these flux tubes do not carry monopole flux. 4. length scale dependent cosmological constant should characterize also blackholes and the natural first guess is that the radius of the blackhole corresponds to the scaled defined by the value of cosmological constant. this allows to estimate the thickness of the flux tube by a scaling argument. the cosmological constant of universe corresponds to length scale l = 1/ √ λ ∼ 1026 m and the density ρ of dark energy corresponds to length scale r = ρ−1/4 ∼ 10−4 m. one has r = (8πr)1/4 √ llp giving the scaling law (r/r1) = (l/l1)1/2. by taking l1 = rs(sun) = 3 km one obtains r1 = .7×10−15 m rather near to proton compton length 1.3×10−15 m and even nearer to proton charge radius .87××10−15 m. this suggests that the nuclei arrange into flux tubes with thickness of order proton size, kind of giant nucleus. neutron star would be already analogous structure but the flux tubes tangled would not be so dense. denoting the number of protons by n , the length of flux tube would be l1 ' nlp ≡ xrs (lp denotes proton compton length) and the mass would be nmp. this would give x as x = (lp/lpl) 2 ∼ 1038. note that the ratio of the volume filled by the flux tube to the m4 volume vs defined by rs is vtube vs = 3 8 ( lp lpl )2 × ( lp rs )2 ∼ 10( rs(sun) rs )2 . (2.1) the condition vtube/vs < 1 gives a lower bound to the schwartschild radius of the object and therefore also to its mass: rs > √ 10rs(sun) and m > √ 10m(sun). the lower bound means that the flux tube fills the entire m4 volume of blackhole. blackhole would be a volume filling flux tube with maximal mass density of protons (or rather, neutrons -) per length unit and therefore a natural endpoint of stellar evolution. the known lower limit for the mass of stellar blackhole is few stellar masses (see http://tinyurl.com/ycd4w4m4) so that the estimate makes sense. 5. an objection against this picture are very low mass stars with masses below .5m(sun) (see http: //tinyurl.com/ceoo6sj) not allowed for k ≥ 107. they are formed in the burning of hydrogen and the time to reach white dwarf state is longer than the age of the universe. could one give up the condition that flux tube volume is not larger than the volume of the star. could one have dark matter in the sense of n2-sheeted covering over m4 increasing the flux tube volume by factor n2. 6. this picture does not exclude star like structure realized in terms of analogs of protons for scaled up variants of hadron physics m89 hadron physics would have mass scale scaled up by a factor 512 with respect to standard hadron physcs characterized by mersenne prime m107. the mass scale would correspond to lhc energy scale and there is evidence for a handful of bumps having interpretation as m89 mesons. it is of course quite possible that m89 baryons are unstable against transforming to m107 baryons. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/ycd4w4m4 http://tinyurl.com/ceoo6sj http://tinyurl.com/ceoo6sj dna decipher journal | december 2019 | volume 9 | issue 3 | pp. 123-145 128 pitkänen, m., cosmic string model for formation of galaxies, & dna structure 7. the model for star [25] inspired by the 10 year old nuclear physics anomaly led to the picture that protons form at least in the core dark proton sequences associated with the flux tube and that the scaled up compton length of proton is rather near to the compton length of electron: there would be zooming up of proton by a factor about 211 ∼ mp/me. the formation of blackhole would mean reduction of heff by factor about 2−11 making dark protons and neutrons ordinary. 2.2 can one see also stars as blackhole like entities? the assignment of blackholes to almost any physical objects is very fashionable, and the universality of the flux tube structures encourages to ask whether the stellar evolution to blackhole as flux tube tangle could involve discrete steps involving blackhole like entities but with larger planck constant and with larger radius of flux tube. 1. could one regard stellar objects as blackholes labelled by various values of planck constant heff? note that heff is determined essentially as the dimension n of the extension of rationals [12, 18]. the possible p-adic length scales would correspond to the ramified primes of the extension. p-adic length scale hypothesis selects preferred length scales as p ' 2k, with prime values of k preferred. mersennes and gaussian mersennes would be in favoured nearest to powers of 2. the most general hypothesis is that all values of k in the range [127, 107] are allowed: this would give half-octaves spectrum for p-adc length scales. if only odd values of k are allowed, one obtains octave spectrum. 2. the counterpart of schwartchild radius would be rs(k) = (l(k)/l(107))2rs corresponding to the scaling of maximal string tension proportional to 1/g by l(107)/l(k)2, where k is consistent with p-adic length scale hypothesis. the flux tube area would be scaled up to l(k)2 = 2k−107l(107)2, and the constant x ≡ x(107) would scale to x(k) = 2k−107x. scaling guarantees that condition v (tube)/vs does not change at all so that the same lower bound to mass is obtained. note that the argument do not give upper bound on the mass of star and this conforms with the surprisingly large masses participating in the fusion of blackholes producing gravitational radiation detected at ligo. 3. the favoured p-adic length scales between p-adic length scale l107 assignable to black hole and l(127) corresponding to electron compton length assignable to solar interior are the p-adic length scale l(113) = 8l(127) assignable to nuclei, and the length scale l(109), which corresponds to p near prime power of two. (a) for k = 109 (assignable to deuteron) the value of the mass would be scaled by factor 4 to a lower about 12 km to be compared with the typical radius of neutron star about 10 km. the masses of neutron stars around about 1.4 solar masses, which is rather near to the lower bound derived for blackholes. neutron star could be seen the last phase transition in the sequence of p-adic phase transition leading to the formation of blackhole. (b) could k = 113 phase precede neutron stars and perhaps appear as an intermediate step in supernova? assuming that the flux tubes consist of nucleons (rather than nuclei), one would have rs(113) = 64rs giving in the case of sun rs(113) = 192 km. (c) for k = 127 the p-adic scaling from k = 107 would give schwartschild radius rs(127) ∼ 220rs . for sun this would give rs(127) = 3 × 109 m is roughly by factor 4 larger than the radius of the solar photosphere radius 7× 108 meters. k = 125 gives a correct result. this suggests that k = 127 corresponds to the minimal value of temperature for ordinary fusion and corresponds to the value of dark nuclear binding energy at magnetic flux tubes. the evolution of stars increases the fraction of heavier elements created by hot fusion and also temperatures are higher for stars of later generations. this would suggest that the value of issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2019 | volume 9 | issue 3 | pp. 123-145 129 pitkänen, m., cosmic string model for formation of galaxies, & dna structure k is gradually reduced in stellar evolution and temperature increases as t ∝ 2(127−k)/2. sun would be in the second or third step as far the evolution of temperature is considered. note that the lower bound on radius of star allows also larger radii so that the allowance of smaller values of k does not lead to problems. 2.3 what about blackhole thermodynamics? blackhole thermodynamics is part of the standard blackhole paradigm? what is the fate of this part of theoretical physics in light of the proposed model? consider first the natural picture implied the vision about blackhole as space-filling flux tube tangle. 1. the flux tubes are deformations of cosmic strings characterized by cosmological constant which increases in the sequence of increasing the temperature of stellar core. the vibrational degrees of freedom are excited and characterized by a temperature. the large number of these degrees of freedom suggests the existence of maximal temperature known as hagedorn temperature at which heat capacity approaches to infinity value so that the pumping of energy does not increase temperature anymore. the straightforward dimensionally motivated guess for the hagedorn temperature is suggested by p-adic length scale hypothesis as t = x~/l(k), where x is a numerical factor. for blackholes as k = 107 objects this would give temperature of order 224 mev for x = 1. hadron physics giving experimentally evidence for hagedorn temperature about t = 140 mev near to pion mass and near to the scale determined by λqcd, which would be naturally relate to the hadronic value of the cosmological constant λ. the actual temperature could of course be lower than hagedorn temperature and it is natural to imagine that blackhole cools down. the hagedorn temperature and also actual temperature would increase in the phase transition k → k − 1 increasing the value of λ(k) by a factor of 2. 2. the overall view about the situation would be that the thermal excitations of cosmic string die out by emissions assignable perhaps to black hole jets and also going to the cosmic string until a state function reduction decreasing the value of k occurs and the process repeats itself. the naive idea is that this process eventually leads to ideal cosmic string having hagedorn temperature t = ~/r and possible existing at very low temperature: this would conform with the idea that the process is the time reversal of the evolution leading from cosmic strings to astrophysical objects as tangles of flux tube. this would at least require a phase transition replacing m107 hadron physics with m89 hadron physics and this with subsequent hadron physics. one must of course consider also all values of k as possible options as in the case of the evolution of star. the hadron physics assignable to mersenne primes and their gaussian counterparts could only be especially stable against a phase transition increasing λ(k). 2.3.1 what happens to blackhole thermodynamics in tgd? blackhole thermodynamics (see http://tinyurl.com/y7pvj23x) has produced admirable amounts of literature during years. what is the fate of the blackhole thermodynamics in this framework? it turns out that the the dark counterpart of of hawking radiation makes sense if one accepts the notion of gravitational planck constant assigned to gravitational flux tube and depending on masses assignable to the flux tube. the condition that dark hawking radiation and flux tubes at hagedorn temperature are in thermal radiation implying tb,dark = th . the emerging prediction th is consistent with the value of the hadronic hagedorn temperature. 1. in standard blackhole thermodynamics the blackhole temperature tb identifiable identifiable as the temperature of hawking radiation (see http://tinyurl.com/md6mmvg) is essentially the surface issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/y7pvj23x http://tinyurl.com/md6mmvg dna decipher journal | december 2019 | volume 9 | issue 3 | pp. 123-145 130 pitkänen, m., cosmic string model for formation of galaxies, & dna structure gravity at horizon and equal to tb = κ/2π = ~/4πrs is analogous to hagedorn temperature as far as dimensional analysis is considered. one could think of assigning tb to the radial pulsations of blackhole like object but it is very difficult to understand how the thermal isolation between stringy degrees of freedom and radial oscillation degrees of freedom could be possible. 2. the ratio tb/th ∼ lp/4πrs would be extremely small for ordinary value of planck constant. situation however changes if one has tb = ~eff 4πrs , (2.2) with ~eff = n~0 = ~gr, where ~gr is gravitational planck constant. the gravitational planck constant ~gr was originally introduced by nottale [1] [10, 9] assignable to gravitational flux tube (presumably non-monopole flux tube) connecting dark mass md and mass m (m and m touch the flux tubes but do not define its ends as assumed originally) is given by ~gr = gmdm v0 , (2.3) where v0 < c is velocity parameter. for the bohr orbit model of inner planets nottale assumes md = m(sun) and β0 = v0/c ' 2−11. for blackholes one expects that one has β0 < 1 is not too far from β0 = 1. the identification of md is not quite clear. i have considered the problem how v0 and md are determined in [20, 19] [14]. for the inner planets of sun one would have β0 ∼ 2−11 ∼ me/mp. note that the size of dark proton would be that of electron, and one could perhaps interpret 1/β0 as the heff/~ assignable to dark protons in sun. this would solve the long standing problem about identification of β0. 3. one would obtain for the hawking temperature tb,d of dark hawking radiation with heff = hgr tb,d = ~gr ~ tb = 1 8πβ0 × md m ×m . (2.4) for k = 107 blackhole one obtains tb,d th = ~gr ~ × tb × l(107) x~ = 1 8πβ0(107) × md m × l(107)m x~ . (2.5) for m = mp this gives tb,d th = ~gr ~ tb × l(107) x~ = 1 8πxβ0(107) × md m × mp 224 mev . (2.6) the order of magnitude of thermal energy is determined by mp. the thermal energy of dark hawking photon would depend on m only and would be gigantic as compared to that of ordinary hawking photon. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2019 | volume 9 | issue 3 | pp. 123-145 131 pitkänen, m., cosmic string model for formation of galaxies, & dna structure 4. thermal equilibrium between flux tubes and dark hawking radiation looks very natural physically. this would give tb,d th = 1 (2.7) giving the constraint ~gr ~ tb × l(107) x~ = 1 8πxβ0 × md m mp 224 mev = 1 . (2.8) on the parameters. for m/md = 1 this would give xβ0 ' 1/6.0 conforming with the expectation that β0 is not far from its upper limit. 5. if ordinary stars are regarded as blackholes in the proposed sense, one can assign dark hawking radiation also with them. the temperature is scaled down by l(107)/l(k) and for sun this would give factor of l(107)/l(125) = 2−9 if one requires that rs(k) corresponds to solar radius. this would give tb(dark, k)→ ~gr ~ × l(107) l(k) tb = 2(k−107)/2 8πβ0 × md m ×m . (2.9) for k = 125 and md = m this would give tb(dark, 125) = m/2π. the condition tb,d = th for k = 125 would require scaling of β0(107) to β(125) = 2−9β0(107) ' 2−11. this would give β0(107) ' 1/4 in turn giving x ' .66 implying th ' 149 mev. the replacement of mp = 1 gev with correct value mp = .94 gev improves the value. this value is consistent with the value of hadronic hagedorn temperature so that there is remarkable internal consistency involved although a detailed understanding is lacking. 6. the flux of ordinary hawking thermal radiation is t 4 b/~3. the flux of dark hawking photons would be t 4 b,dark/~3gr = (~gr/~)t 4 b and therefore extremely low also now also. in principle however the huge energies of the dark hawking quanta might make them detectable. i have already earlier proposed that tb(hgr) could be assigned with gravitational flux tubes so that thermal radiation from blackhole would make sense as dark thermal radiation having much higher energies. one can however imagine a radical re-interpretation. bhe is not the thermal object emitting thermal radiation but bhe plus gravitational flux tubes are the object carrying thermal radiation at temperature th = tb . for this option dark hawking radiation could play fundamental role in quantum biology as will be found. 7. what about the analog of blackhole entropy given by sb = a 4g = π l2pl t 2 b , (2.10) where a = 4πr2s is blackhole surface area. this corresponds intuitively to the holography inspired idea that horizon decomposes to bits with area of order l2p ? issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2019 | volume 9 | issue 3 | pp. 123-145 132 pitkänen, m., cosmic string model for formation of galaxies, & dna structure the flux tube picture does not support this view. one however ask whether the volume filling property of flux tube could effectively freeze the vibrational degrees of flux tubes. or whether these degrees of freedom are thermally frozen for ideal blackhole. if so, only the ends of he flux tubes at the surface or their turning points (in case that they are turn back) can oscillate radially. this would give an entropy proportional to the area of the surface but using flux tube transversal area as a unit. this would give apart from numerical constant sb = a 4l(k)2 . (2.11) 2.3.2 constraint from ~gr/~ > 1 what values of mass m can interact quantum gravitationally and are thus allowed in hgr for given md? 1. the notion of hgr makes sense only for hgr > h. if one has hgr < h assume hgr = h. an alternative would be hgr =→ h0 = h/6 for hgr < h0. this would given gmdm/v0 > ~min (~min = ~ or ~/6) leading m > β0~ 2rs(md) × ~min ~ . (2.12) this condition is satisfied in the case of stellar blackholes for all elementary particles. 2. one can strengthen this condition so that it would satisfied also for gravitational interactions of two particles with the same mass (md = m). this would give m mpl > √ β0 . (2.13) for β0 = 1 this would give m = mpl, which corresponds to a mass scale of a large neuron and to size scale 10−4 m. β0(125) = 2−11 gives mass scale of cell and size scale about 10−5 meters. β0(127) ' 2−12 corresponding to minimum temperature making hot fusion possible gives length scale about 10−6 m of cell nucleus. a possible interpretation is that the structure in cellular length scale have quantum gravitational interaction via gravitational flux tubes. biological length scales would be raised in special position from the point of view of quantum gravitation. 3. also interactions of structures smaller than the size of cell nucleus with structures with size larger the size of cell nucleus are possible. by writing the above condition as (m/mpl)(md/mpl) > β0, one sees that from a given solution to the condition one obtains solutions by scaling m→ xm and md →md/x. for β0(127) ' 2−11 corresponding to the scale of cell nucleus the atomic length scale 10−10 m and length scale 10−4 m of large neuron would correspond to each other as ”mirror” length scales. there would be no quantum gravitational interactions between structures smaller than cell nucleus. there would be master-slave relationship: the smaller the scale of slave, the larger the scale of the master. 2.3.3 quantum biology and dark hawking radiation the scaling formula β0(k) ∝ 1/l(k) with flux tube thickness scale given by l(k) allows to estimate β0(k). in this manner one obtains also biologically interesting length scales. an interesting question is whether the scales for the velocities of ca waves (see http://tinyurl.com/qs3j5cp) and nerve pulse conduction velocity could relate to v0. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/qs3j5cp dna decipher journal | december 2019 | volume 9 | issue 3 | pp. 123-145 133 pitkänen, m., cosmic string model for formation of galaxies, & dna structure 1. the tube thickness about 10−4 m, which corresponds to ordinary cosmological constant being in this sense maximal corresponds to the p-adic length scale k = 171. the scaling of β0 ∝ 1/l(k) gives v0(171) ∼ 4.7 µm/s in eggs the velocity of ca waves varies in the range 5-14 µm/s, which roughly corresponds to range k ∈ {171, 170, 169, 168}. in other cells ca wave velocity varies in the range 15-40 µm/s. k = 165 corresponds to 37.7 µm/s near the upper bound 40 µm/s. the lower bound corresponds to k = 168. k = 167, which corresponds to the larges gaussian mersenne in the series assignable to k ∈ {151, 157, 163, 167} the velocity is 75 µm/s. 2. for k = 127 gives v0 ∼ 75 m/s. k = 131 corresponds to v0 = 18 m/s. these velocities could correspond to conduction velocities for nerve pulses in accordance with the view that the smaller the slave, the larger the master. i have already earlier considered that dark hawking radiation could have important role in living matter. the hawking/hagedorn temperature assuming x = 1/6.0 k = l(171) has peak energy 38 mev to be compared with the membrane potential varying in the range 40-80 mev. room temperature corresponds to 34 mev. for k = 163 defining gaussian mersenne one would have peak energy about .6 ev: the nominal value of metabolic energy quantum is .5 ev. k = 167 corresponds to .15 ev and 8.6 µm cell size. even dark photons proposed to give bio-photons when transforming to ordinary photons could be seen as dark hawking radiation: gaussian mersenne k = 157 corresponds to 4.8 ev in uv. could cmb having peak energy of .66 mev and peak wavelength of 1 mm correspond to hawking radiation associated with k = 183? interestingly, cortex contains 1 mm size structures. to sum up, these considerations suggest that biological length scales defined by flux tube thickness and cosmological length scales defined by cosmological constant are related. 2.4 zero energy ontology, cosmology, and astrophysics zero energy ontology replaces ordinary ontology in tgd based view about quantum states and quantum jump [26]. 1. in zeo zero energy states are superpositions of space-time surfaces inside causal diamond (cd) identified as preferred extremals of the basic action principle of tgd. cd is cartesian product of causal diamond cd of m4 and of cp2. the preferred extremals analogous to bohr orbits have boundaries ends of space-time at the light-like boundaries of cd. there is a fractal hierarchy of cds and given cd is an imbedding space correlate for a conscious entity self consciousness is universal. 2. zero energy states can be seen as superpositions of state pairs with members assigned to the opposite boundaries of cd. zeo predicts that in ordinary or ”big” state function reductions (bsfrs) the arrow of time of system changes and remains unaffected in ”small” state functions (ssfrs), which are tgd counterpart for ”weak” measurements and associated with a sequence of unitary evolution for the state assignable to the active boundary cd, which also shifts farther from the passive boundary. passive boundary is unaffected as also members of state pairs at it. 3. subjective time is identified as a sequence of ssfrs and correlates strongly with clock time identifiable as the distance between the tips of cd and increasing in statistical sense during the sequences of ssfrs. 4. bsfr corresponds to state function reduction at active boundary of cd which becomes passive. this forces the state at passive boundary to change. passive boundary becomes active. bsfr means the death of self and reincarnation with an opposite arrow of time. thus the notion of life cycle is universal and life can be lieved in both directions. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2019 | volume 9 | issue 3 | pp. 123-145 134 pitkänen, m., cosmic string model for formation of galaxies, & dna structure 5. what happens to cd in long run? there are two options. (a) the original assumption was that the location of formerly passive boundary is not changed. this would mean that the size of cd would increase steadily and the outcome would be eventually cosmology: this sounds counter-intuitive. classically energy and other poincare charges are conserved for single preferred extremal could fail in bsfrs due to the fact that zero energy states cannot be energy eigenstates. (b) the alternative view suggested strongly m8 −h duality [12] is that the size of cd is reduced in bsfr so that the new active boundary can be rather near to the new passive boundary. one could say that the reincarnated self experiences childhood. in this case the size of cd can remain finite and its location in m8 more or less fixed. one can say that the self associated with the cd is in a kind of karma’s cycle living its life again and again. since the extension of rationals can change in bsfr and since the number of extensions larger than given extension is infinitely larger than those smaller than it, the dimension of extension identifiable in terms of effective planck constant increases. since n = heff/h0 serves as a kind of iq, one can say that the system becomes more intelligent. 2.4.1 cosmic redshift but no expansion of receding objects: one further piece of evidence for tgd cosmology universe is not expanding after all, controversial study suggests was the title of very interesting science news article (see http://tinyurl.com/o6vyb9g) telling about study, which forces to challenge big bang cosmology. the title of course involved the typical exaggeration. the idea behind the study was simple. if universe expands and also astrophysical objects such as stars and galaxies participate the expansion, they should increase in size. the observation was that this does not happen! one however observes the cosmic redshift so that it is too early to start to bury big bang cosmology. this finding is however a strong objection against the strongest version of expanding universe. that objects like stars do not participate the expansion was actually known already when i developed tgd inspired cosmology for quarter century ago, and the question is whether grt based cosmology can model this fact naturally or not. the finding supports tgd cosmology based on many-sheeted space-time. individual space-time sheets do not expand continuously. they can however expand in jerk-wise manner via quantum phase transitions increasing the p-adic prime characterizing space-time sheet of object by say factor two of increasing the value of heff = n×h for it. this phase transition could change the properties of the object dramatically. if the object and suddenly expanded variant of it are not regarded as states of the same object, one would conclude that that astrophysical objects do not expand but only comove. the sudden expansions should be observable and happen also for earth. i have proposed a tgd variant of expanding earth hypothesis along these lines [21]. 2.4.2 stars as reincarnating conscious entities? one can apply zeo to the evolution of stars. the basic story (see http://tinyurl.com/ceoo6sj) is that the star is formed from he interstellar gas cloud, evolves and eventually collapses to a white dwarf, degenerate carbon-oxygen core, supernova or even blackhole if the mass of the remnant resulting in explosion throwing outer layers of the star away is in the range of 3-4 solar masses. only very massive stars end up to supernovas. the type of the star depends on the abundances of various elements in the interstellar gas from which they formed and believed to contain heavier elements produced by earlier supernovas. there are however several anomalies challenging the standard story. there are stars older than universe (see http://tinyurl.com/s698l86). there is also evidence that the abundances of heavier issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/o6vyb9g http://tinyurl.com/ceoo6sj http://tinyurl.com/s698l86 dna decipher journal | december 2019 | volume 9 | issue 3 | pp. 123-145 135 pitkänen, m., cosmic string model for formation of galaxies, & dna structure elements in the early cosmology are essentially the same as for modern stars [3] (see http://tinyurl. com/qkk26dv). tgd based explanation is discussed in [25]. karma’s cycle option for the stellar evolution could explain these anomalies. 1. stars would be selves in karma’s cycle with their magnetic bodies reincarnating with a reversed arrow of time in a collapse to blackhole/white hole like entity (bhe/whe) depending on the arrow of time. this would follow by a stellar evolution leading to an asymptotic state bhe/whe corresponding to maximum size of cd followed by a collapse to bhe or whe. also ordinary stars would correspond to bhes/whes characterized by p-adic length scale l(k) longer than l(107) assignable to grt blackholes. in standard time direction whe would look like blackhole evaporation. 2. this would allow stars older than the universe and suggests also universal abundances. note however that the abundances would strongly depend on the abundances of the interstellar gas and matter produced by the magnetic energy of flux tube. ”cold fusion” as dark fusion could produce elements heavier than fe and light elements li, be, b, whose abundances for fusion in stellar core is predicted to be much much smaller than the observed abundances in the case of old stars. the lifetimes of stars depend on their type. also a universal age distribution of stars in stellar clusters not depending appreciably on cosmic time is highly suggestive. i remember of even writing about this. unfortunately i could not find the article. to put it more generally, the hierarchy of cds implies that the universe decomposes effectively to sub-universes behaving to some degree independently. the view about karma’s cycles provides a more precise formulation of the pre-zeo idea that systems are artists building themselves as 4-d sculptures. in particular, this applies to mental images in tgd based view about brain. 1. one could perhaps say that also quantum non-determinism has classical correlates. cds would be the units for which time-reversing bsfrs are possible. also ssfrs affecting cds could have classical space-time correlates. m8 −h duality [12] predicts that the time evolution for space-time surface inside cds decomposes to a sequence of deterministic evolutions glued together along m4 time t = rn hyperplanes of m4 defining special moments in the life of self at which the new larger cd receives a new root t = rn. the non-deterministic discontinuity could be localized to the 2-d vertices represented by partonic 2-surfaces at which the ends of light-like partonic orbits meet. 2. the m4 hyperplanes t = rn correspond to the roots of a real polynomial with rational coefficients defining the space-time surfaces at the level of m8 as roots for the real or imaginary part in quaternionic sense for the octonionic continuation of the polynomial. these moments of time could correspond to ssfrs. 3. the finite classical non-determinism is in accordance with the classical non-determinism is predicted at the limit of infinitely large cd and vanishing cosmological constant at which classical action reduces to kähler action having a huge vacuum degeneracy due to the fact than any space-time surface having lagrangian manifold (vanishing induced kähler form) as cp2 projection is a vacuum extremal. the interpretation of this degeneracy interpreted in terms of 4-d spin glass degeneracy would be that at the limit of infinitely large cd the extension of rationals approaches to algebraic numbers and the roots t = rn becomes dense and the dynamics becomes non-deterministic for vacuum extremals and implies non-determinism for non-vacuum extremals. 2.4.3 no time dilation for the periods of processes of quasars there are strange findings about the time dilation of quasar dynamics challenging the standard cosmology [7]. one expects that the farther the object is the slower its dynamics looks as seen from earth. lorentz invariance implies red shift for frequencies and in time domain this means the stretching of time intervals so that the evolution of distant objects should look the slower the longer their distance from the observer issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/qkk26dv http://tinyurl.com/qkk26dv dna decipher journal | december 2019 | volume 9 | issue 3 | pp. 123-145 136 pitkänen, m., cosmic string model for formation of galaxies, & dna structure is. in the case of supernovae this seems to be the case. what was studied now were quasars at distances of 6 and 10 billion years and the time span of the study was 28 years [8]. their light was red shifted by different amounts as one might expect but their evolution went on exactly the same rhythm. this looks really strange. in grt the redshift violates conservation of four-momentum. in tgd cosmic redshift reduces to the fact that the tangent spaces of the space-time surface for target and receiver differ by a lorentz boost. redshift does not mean non-conservation of four-momentum but only that the reference frames are different for target and observer. the size for the space-time sheets assignable to the systems considere must be large, of the order of the size scale l defined by the size of the recent cosmology to which one assigns the hubble constant. in the flux tube picture this means that the flux tubes have length of order l but thickness would be about r = 10−4 meters the size scale of large neuron. photons arrive along flux tubes connecting distant systems. note that cmb corresponds to 10 times longer peak wavelength. i have already earlier discussed this time anomaly [13] but what i have written is just the statement of the problem and and some speculations about its solution in terms of zeo. a valuable hint is that the time anomaly appears for quasarsvery heavy objects but not for supernovae much lighter objects. this suggests that the redshift depends on the masses of the objects considered. 1. one considers an approximately periodic process. it is quite possible that this process is not classical deterministic process at space-time level but that one has sequence of ssfrs (weak measurements) or even bsfrs for a subsystem of the target. these processes replace quantum superposition of space-time surfaces inside cd with a new one and ssfr also increases its size in statistical sense. a natural lorentz invariant ”clock time” for the target is the distance between the tips of cd light-cone proper time. both m4 linear coordinates and light-cone robertson-walker coordinates are natural coordinates for space-time sheets with 4-d m4 projection. ”clock time” must be mapped to m4 linear time for some space-time sheet. the minkowski coordinates for the cd are determined only modulo lorentz boost leaving the light-like boundary of cd invariant. in general the m4 coordinates of the target and observer are related by a lorentz boost and this gives rise to cosmological redshift and also gravitational reshift. 2. the information about ssfr or bsfr at the target must be communicated to the observer so that the space-time sheets in question must be connected by flux tubes carrying the photons. cd must contain both systems and naturally has cosmological size given by l so that flux tubes have thickness about r. the m4 time coordinate must be common to both systems. the natural system to consider is center of mass system (cm) in which the sum of the momenta of two systems vanishes. 2.4.4 did cosmology have any ”dark ages”? a further potential time anomaly of the recent cosmology relates to thedark agesof the universe. between the decoupling of cmb radiation from matter and the formation of stars there should have been adark agesduring which there was only neutral hydrogen. star formation generated radiation at energies high enough to ionize hydrogen and the ionized interstellar gas started to produce radiation. the 21 cm line of neutral hydrogen serves as a signature of neutral hydrogen. this line is redshifted and from the lower bound for the redshift one can deduce the time when ”dark ages” ended. the popular article tells (see http://tinyurl.com/wzegzxk) that the recent study using murchison widefield array (mwa) radio telescope by jonathan pober and collaborators gave an unexpected result. only a new lower upper bound for this redshift emerged: the upper bound corresponds to about 2 meters [5] (see http://tinyurl.com/qttq3gl). the conclusion of the experimenters is optimistic: soon the upper bound for the redshift should be brought to light. in tgd based view about cosmology and astrophysics (http://tinyurl.com/tkkyyd2) one can formulate two questions. 1. one can ask whether there were any ”dark ages” at all! issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/wzegzxk http://tinyurl.com/qttq3gl http://tinyurl.com/tkkyyd2 dna decipher journal | december 2019 | volume 9 | issue 3 | pp. 123-145 137 pitkänen, m., cosmic string model for formation of galaxies, & dna structure 2. an alternative question is whether the ”dark ages” in distant geometric past are prevailing anymore! this would be like asking whether the hitler of thirties is the hitler we know anymore. the point is that in tgd framework one must distinguish between subjective time and geometric time and this leads to some rather dramatic modifications of the prevailing view about time. the following arguments encourage a positive answer to the first question and negative answer to the second question. the following arguments encourage positive answer to the first question and negative answer to the second question. the answer to the first question relies of tgd based view about nuclear physics solving anomalies of standard nuclear physics and leading to a new view about stellar evolution. 1. in tgd framework the formation of stars could have preceded by a pre-stellar period during which dark fusion giving rise to dark proton sequences dark nuclei at monopole flux tubes happened: this is pollack effect in biology. this would have been ”cold fusion” period in the stellar evolution and would have occurred spontaneously at low temperatures. it would have already produced abundances, which are not far from modern ones and one of the recent surprises is that the abundances at very early period are already near to modern ones. 2. the model predicts also the possibility of neutral states for which electrons are at flux tubes parallel to dark proton flux tubes and have the same scaled up size (due to non-standard value of heff = nh0, which is smaller by factor about 1/2000) as dark protons. in solar interior dark protons would have compton size of electron so that heff for them would be about 2000 times higher h = m4 × cp2 than h. also smaller and larger value of heff are possible. for blackholes the protons at flux tubes would be ordinary: heff = h. 3. the transformation of dark nuclei having much smaller binding energy would have liberated nuclear binding energy and the resulting photons having energy up to gamma ray energies would have ionized the neutral hydrogen. zero energy ontology (zeo) leads to a negative answer to the question whetherdark ages still prevail in distant past. 1. in zeo universe consists at the level of imbedding space h = m4 × cp2 of a fractal hierarchy of cd = cd × cp2, where cd is causal diamond of m4. cds have interpretation as a hierarchy of sub-cosmologies. each cd defines a correlate for a conscious entity and increases in size in each ”small” state function reduction (ssfr) defining a counterpart of weak measurement. the flow of experienced time corresponds to the increase of distance between tips of cd. second boundary of cd is however fixed passive as also members of state pairs at it defining zero energy states. the active boundary recedes farther away from the passive one. this gives rise to the arrow of time for given life of cd. 2. in a ”big” (ordinary) state function reduction (bsfr) the roles of boundaries of cd change. active becomes passive and vice versa. the arrow of time changes. self dies and reincarnates with opposite arrow of time. the simplest possibility is that the size of cd can decrease in bsfr meaning that the formerly passive boundary becomes much nearer to active. in this case cd begins to grow from a small size: self has ”childhood”. in this case it can happen that self never reaches a size larger than some upper bound and lives again and its life. each life is more evolved since the extension of rationals involved with space-time surface increases in statistical sense in bsfr. this is nothing but karma’s cycle but in all scales. 3. at the level of stars this would mean that star could undergo evolution as karma’s cycle also in cosmological remote past as an object located at fixed point of h. the abundances would be more or issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2019 | volume 9 | issue 3 | pp. 123-145 138 pitkänen, m., cosmic string model for formation of galaxies, & dna structure less the same as for modern stars. this would explain the mystery of stars older than the universe and solve also other time anomalies of the standard cosmology. this explanation is consistent with the first one and actually the first one is needed to explain abundances of nuclei heavier than fe and the light nuclei li, b, be much higher than predicted by standard model. thus both questions would have positive answer. 2.4.5 observation of a time reversal of a blackhole like object? a very strange object behaving like time reversal of blackhole has been observed (http://tinyurl.com/ umzxaoe). usually blackhole eat the surrounding matter and also prevent the formation of stars since they are powerful emitters of gamma rays this is not in accordance with the naive view about blackholes. the weird blackhole does not emit gamma rays and the environment around it cools and this makes possible star formation. instead of eating the surrounding matter it should feed matter to surroundings making possible the star formation. the most obvious tgd identification of the mystery object relies on zero energy ontology allowing both arrow of time. the arrow of time chances in ordinary state function reduction the ”big” one as opposed to ”small” one corresponding to weak measurement. this predicts time reversed blackhole like objects (bhes) analogous to white holes: white hole like objects (whes). whes could appear in the very early states of the galactic evolution. they could feed the magnetic energy of monopole flux tubes to environment transformed to ordinary matter in turn forming galaxies. as a matter of fact, monopole flux tubes portions emanating it much lines of magnetic field would be formed and their local thickening and formation of tangles would give rise to stars. if the time reversal idea is taken very seriously whes should suck gamma rays from environment inducing cooling making the star formation easier. this would be dissipation in non-standard direction of time identifiable as the basic metabolic mechanism associated with all kinds of self-organization process: quantum coherence at the level of magnetic body would be essential and induce long range coherence of ordinary matter as forced coherence. whe could be also created in bsfr for a bhe. 2.4.6 do quasars and galactic blackholes relate by time reversal in zeo? this picture combined with zero energy ontology (zeo) based view about ordinary state functions changing the arrow of time and occurring even in astrophysical scales leads to a tentative view about quasars and galactic blackholes as time reversals of each other. 1. quasars could be seen as analogs of white holes feeding the mass of cosmic string out to build the galactic tangle and part of the mass of thickening tangle would transform to ordinary matter. they would initiate the formation of galaxy meaning emergence of increasing values of heff in the hierarchy of planck constant. cosmic string would basically feed the mass and energy liberated in the decay of magnetic energy at cosmic strings thickening to flux tubes to ordinary matter and serving in the role of metabolic energy driving self-organization. 2. galactic blackholes could be perhaps indeed analogs of blackholes as time reversals of quasars ”big” (ordinary) state function reduction would transform quasar as white hole to a galactic blackhole. now the system would be drawing back the mass from the surroundings to the flux tube and maybe cosmic string. the process could be like breathing. in zero energy ontology breathing could indeed involve a sequence of states and their time reversals. this raises also the question whether the evolution of stars could be seen as a time reverse for the formation of blackholes: kind of growth followed by a decay perhaps since the values of planck constant heff would be reduced. the climax of his evolution would correspond to maximal values of heff . the evolution of life would be certainly this kind of climax. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/umzxaoe http://tinyurl.com/umzxaoe dna decipher journal | december 2019 | volume 9 | issue 3 | pp. 123-145 139 pitkänen, m., cosmic string model for formation of galaxies, & dna structure 2.5 objections against grt blackholes the basic theoretical objection against blackholes was due to einstein himself. the collapse of matter to single point is simply impossible. this objection has been however forgotten since doing calculations is much more pleasant activity than hard thinking, and an enormous literature have been produced based on this idealization. there is no doubt that blackhole like entities (bhes) with about schwartschild radius exist, but general relativity does not allow to say anything about the situation inside possibly existing horizon. 2.6 badly behaving blackholes there is an excellent video (thanks to howard lipman for a link) challenging the standard view about blackholes. in the sequel list some arguments that i remember. tgd was born as a solution to the fundamental difficulty of grt due to the loss of classical conservation laws. in tgd framework bhes correspond to volume filling flux tube tangles. also galactic bhes would correspond to a volume filling flux tube tangles. in tgd framework also stars could be seen as bhes having the flux tube thickness characterized by p-adic length scale as an additional parameter. grt blackholes correspond to flux tube thickness about proton compton length. for instance, sun can be seen as a bhe and the size is predicted correctly. the model for bhes makes large number of correct predictions. 1. the minimal radii/masses of grt blackholes and neutron stars are predicted correctly. 2. ordinary blackhole thermodynamics is replaced with the thermodynamics associated with monopole flux tubes carrying galactic dark mass characterized by hagedorn temperature and the thermodynamics gravitational flux tubes characterized by hawking temperature but for gravitational planck constant hgr so that it is gigantic as compared to the ordinary hawking temperature. in thermal equilibrium these temperatures are same and this predicts hadronic string tension correctly. consider now the empirical objections against bh paradigm in light of tgd picture. 1. the observations by alma telescope show that stars can be formed surprisingly near to galactic bhes (see http://tinyurl.com/ry746pg). for instance, 11 young stars just forming have been found at distance of 3 ly from galactic bhe of milky way. this is impossible since the intense tidal forces and uv and x ray radiation should make impossible the condensation of stars from gas clouds. tgd explanation: galaxies are formed as tangles on long thickened cosmic string responsible for galactic dark matter as dark energy. same mechanism give rise to stars as sub-tangles generating at least part of the ordinary matter as decay of the magnetic energy of the flux tube as it thickens. ordinary matter already present could concentrate around the tangle. one learns from the discussion in the above link that star formation involves bipolar flow consisting two jets in opposite directions believed to take care of angular momentum conservation: the star formed is thought to be formed from a rotating gas cloud (rotation would be around flux tube) having much larger angular momentum and part of must be carried out by jets naturally parallel to the flux tube. also this gives support for the view that stars are tangles along flux tube. there are also hundreds of massive and much older stars in the vicinity of galactic bhe. note that in tgd also these stars could be seen as bhes but with different p-adic length scale characterizing the thickened flux tube. the reason why galactic bhe does not swallow these objects could be that they are bound states around flux tube (or even cosmic string outside the star), which is rather rigid by its string tension. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/qpvbocl http://tinyurl.com/ry746pg dna decipher journal | december 2019 | volume 9 | issue 3 | pp. 123-145 140 pitkänen, m., cosmic string model for formation of galaxies, & dna structure 2. ”non-hungry” bhes are found. tgd explanation: in zero energy ontology to which quantum tgd relies, one must distinguish between bhes and their time reversals, white hole like objects (whes), analogous to white holes. whes would not be ”hungry” but feed matter into environment. the counterparts or jets would flow into whe and matter would flow out from whe. 3. the standard theoretical belief is that in a dense star cluster only single blackhole can exist. if there are several blackholes, they start to rotate around each other and fuse to a larger blackhole. a case with two blackholes have been however observed. tgd explanation: a possible explanation is that the objets are whes and their behavior is time reversal of bhes. 4. the velocities of particles in the jets associated with a galactic bhes are near light velocity and require extremely high energies and thus strong magnetic fields. no strong magnetic field has been however observed. tgd explanation: in tgd maxwellian magnetic fields are replaced with flux tubes carrying quantized monopole flux not possible in maxwellian world. their existence allows to understand the presence of magnetic fields in even cosmological scales, the maintenance problem of earth’s magnetic field, and the recent findings about the magnetic field of mars [24]. ordinary magnetic fields correspond to vanishing total flux and are indeed weak: it is these magnetic fields outside the jet which would have been measured. galaxies are tangles in monopole flux tube and this is the carrier of very strong magnetic field associated with jets parallel to the flux tube. 5. very distant galactic blackholes with distances in scale of million light years have radio jets in the same direction. this is very difficult to understand in the standard view about cosmology. tgd explanation: the galactic bhes would be associated with the same long cosmic string forming galaxies as tangles. 2.6.1 too heavy blackhole in milky way the standard model for blackhole formation predicts an upper bound on the mass of blackhole depending also on environment since the available amount of matter in environment is bounded. in the case of milky way the bound is about 20 solar masses. now however a blackhole like entity (bhe) with mass about 70 solar masses has been discovered (see http://tinyurl.com/w7xlb78). i am grateful for wes johnson for the link. also the masses of bhes producing the gravitational radiation in their fusion have been also unexpectedly high, which suggets that standard view about bhes is not quite correct. the proposed model for bhes as a volume filling flux tube gives correct lower bounds for masses of neutron star and tgd counterpart of blackhole but does not give upper bound for the mass. for time reversed bhes analogs of white holes (whes) possibly identifiable as quasars the mass of whe comes from a tangling long cosmic string and there is no obvious upper bound. even galactic bhes could correspond to whes, which have made quantum jump to bhes at the level of magnetic body: in this state the flux tube forming the counterpart of maxwellian magnetic field is fed back from environment. a breathing spaghetti would be in question. in standard model the mechanism for the formation of blackhole is different since there is no flux tube giving the dominant dark energy/dark matter contribution to the mass. therefore the upper bound for mass if there exists such is expected to increase. in tgd framework the dominant contribution would come from the monopole flux tubes giving rise tgd counterpart of magnetic field which extends at least over the region containing stars assumed to correspond sub-tangles of the galactic flux tangle. intuitively it seems clear that the upper bound is higher than in grt. if the spaghetti straightens the tangled flux tube would untangle one could have upper bound. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/w7xlb78 dna decipher journal | december 2019 | volume 9 | issue 3 | pp. 123-145 141 pitkänen, m., cosmic string model for formation of galaxies, & dna structure the simplest model predicts that only the flux tube mass contributes to the mass of bhe. the mass of the ordinary matter going to bhe would transform back to dark energy/mass of the flux tube. the process would be time reversal of the process making sense in zero energy ontology [26] in which the magnetic energy of flux tube transforms to ordinary matter: time reversal for the tgd counterpart of inflation. 3 anomalies related to galactic dynamics wes johnson sent also two links related to the long range correlation between the dynamics of quasars and galaxies. the first result was about correlations of quasar spins in billion light-year scale. second result was about coherence between the galactic spin and motions of surrounding galaxies at least up to 6 mly. the explanation of both findings is in terms of cosmic strings thickened to flux tubes, which are the basic element in the tgd based model for the formation of quasars and galaxies. third anomaly relates to ”too” fast spinning galaxies. 3.1 correlated galactic spins in billion light-year scale the first link is to a popular article ”alignment of quasar polarizations with large-scale structures (see http://tinyurl.com/rcoam7g) telling about alignment of quasar polarization with large scale structure in scale of gly, which is a really huge scale. this suggests that the quasar spin axes are aligned with a linear structure connecting the quasars. the correlations between spin directions of quasars over distances of billion light-years have been observed. these correlations have been observed earlier over much shorter distances for quasars/galaxies along the well-known linear structures. this suggests that the linear structures are much longer than previously thought. this is what i have been preaching for decades. there would exist a fractal tensor network of cosmic string/monopole flux tubes over entire cosmos having local flux tube tangles as nodes. networks inside networks inside.... the flux tubes would carry dark matter in tgd sense making possible quantum coherence in arbitrarily long length scales. 1. tgd predicts a fractal hierarchy of flux tubes formed from cosmic strings: 4-d surfaces in m4×cp2 having 2-d strings world sheet as m4 projection. 2. galaxies reside along linear structures which would correspond to what i call cosmic strings: galaxies would be tangles along these strings thickened locally to monopole flux tubes: part of their magnetic energy would have transformed partially to matter and formed the visible part of galaxy. volume energy would correspond to length scale dependent cosmological constant. they would explain also flat velocity spectra associated with spiral galaxies. there would be no dark matter halo. cosmic strings and their monopole flux tube portions would be remnant from cosmic string dominated period, which transformed to grt type cosmology via an inflation type period as cosmic strings thickened to flux tubes. these strings containing the galaxies as tangles would form a network correlating the dynamics of individual galaxies and making possible correlations and synchrony even over distances of about 1 billion ly. 3. the correlations between spin directions of galaxies is what has been been could be inherited from past when the galaxies along strings were much closer to each other. angular momentum conservation would take care that correlation are preserved. 4. macroscopic quantum coherence even in cosmological scales is however possible by hierarchy of planck constants explaining dark matter as heff = n× h0 phases of ordinary matter. we could be seeing quantum coherence of dark matter inducing ordinary coherence of matter in cosmic scales. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/rcoam7g dna decipher journal | december 2019 | volume 9 | issue 3 | pp. 123-145 142 pitkänen, m., cosmic string model for formation of galaxies, & dna structure remark: i have asked whether all self-organization phenomena involving energy feed (needed to increase heff responsible for quantal long range correlations at dark level) could be induced by dark matter at magnetic flux tubes [23]. a further interesting question is whether self-organization is dissipation in reversed time direction so that also it would be due to second law but in generalized sense required by zeo. 3.2 mysterious coherence in several-megaparsec scales between galaxy rotation and neighbor motion second link was to article ”mysterious coherence in several-megaparsec scales between galaxy rotation and neighbor motion” by lee et al (see http://tinyurl.com/sbmcn6g). the article states that there is a ”mysterious” coherence between the rotational direction of galaxy and the average motion of its nearest neighbours within 6 mpc, possibly even up to 11 mpc. this coherence cannot result from collisions with nearby galaxies like coherence below 1 mpc and is proposed to originate from the collective motion of a structure containing the galaxies affecting the directions of angular momenta of galaxies: the coherence would be induced from that of the collective motion. in tgd framework the natural identification for the collective structure would be as a long monopole flux tube containing the galaxies or at least a subset of them as tangles. there could be of course several monopole flux tubes in the sample studied. it was indeed found that the coherence was especially strong when neighbors of the galaxy at center were restricted to red galaxies. red galaxies could correspond to the same flux tube. alternatively, the collective motion affects them less than other galaxies as the article suggests. 3.3 galaxies spinning ”too” fast the anomalous findings relating to cosmology and astronomy are proliferating i am grateful for wes johnson for a flow of links. this particular link (see http://tinyurl.com/qv2vpw3) gives pictures provided by nasa about spiral galaxies spinning ”too” fast. the problem is that centrifugal acceleration destabilizes the system spinning too fast. this suggests that the structure of galaxy is not what our models involving ordinary matter and dark matter halo are somehow wrong. tgd suggests an improved view allowing to understand also ”too” fast spinning rates. suppose that galaxies are tangles along monopole cosmic string such that string has thickened to flux tube. monopole cosmic string would be rotating. these monopole tangles would serve as tgd counterparts for the magnetic field of galaxy which has no maxwellian counterpart. no currents are needed for their maintenance. 1. monopole flux tube has closed cross section, which is non-contractible 2-surface, pinch is impossible. in other words, the conservation of monopole flux prevents its splitting so that centrifugal acceleration cannot break the flux tube even at the highest spinning velocities. only radial deformation increasing the size is possible. 2. ordinary matter generated as the magnetic energy of the flux tubes has transformed to ordinary matter in process analogous to inflation in turn is gravitationally bound with the flux tube so that the galaxy manages to keep also the ordinary matter. 3.4 galaxy which existed 1 billion years after big bang galaxy gn-z11 (see http://tinyurl.com/tg7sscu) existed 1 billion years after the big bang and gave rise to stars with a rate much faster than milky way. there should have been any stars giving rise to the galaxies by the usual mechanism of gravitational condensation. tgd explanation is simple. galaxies formed as tangles to long cosmic string, which thickened and liberated part of its magnetic energy to ordinary matter, which formed the stars of the galaxy as local issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/sbmcn6g http://tinyurl.com/qv2vpw3 http://tinyurl.com/tg7sscu dna decipher journal | december 2019 | volume 9 | issue 3 | pp. 123-145 143 pitkänen, m., cosmic string model for formation of galaxies, & dna structure tangles inside tangle. the formation of stars was faster because local cosmological constant was larger and the rate for the transformation of magnetic energy to ordinary matter was higher. the periods of star formation should correspond to the phase transitions decreasing the local cosmological constant. also in younger galaxies the star formation is highest near the galactic blackhole, even at distances smaller than 3 ly, where it should not happen at all. the mechanism would be the same. for the flux tubes extending farther from galactic center the local cosmogical constant is smaller and the rate for the formation of stars is slower. 4 local super-cluster laniakea as flux tube structure in the following i try to concretize the ideas about monopole flux tube network as a basic structure behind formation of astrophysical structures by discussing the supercluster laniakea in this framework (the idea came from the question of wes johnson about how i understand laniakea in tgd framework). there are two excellent videos about laniakea (see https://www.youtube.com/watch?v=renyyrwxpho and http://tinyurl.com/ufvw6v5). consider first the structure of laniakea. 1. wikipedia contains a nice article about laniakea (see http://tinyurl.com/zfphldm). laniakea is a local supercluster containing also milky way so that it is own home supercluster. local supercluster is defined as a basin of a local flow of galaxies directed to the center of the super-cluster. there is a video giving view about the structure and dynamics of laniakea is warmly recommended (see https://vimeo.com/104910552). laniakea contains about 105 galaxies, decomposes to four smaller super-cluster like entities and contains about 500 galaxy clusters. 2. the general picture supports the idea about fractal spaghetti formed by monopole flux tube or several of them. the presence of four smaller super-cluster type entities suggests quadrupole field as a rough starting point as one tries to gues the analog as field line topology. the first very naive guess is that the tangle defining the supercluster represents roughly the topology of quadrupole magnetic field in the first approximation: there would be pair of dipoles. one cannot of course fix the number of cosmic strings. the simplest starting point hypothesis is that there is just single closed cosmic string forming a structure analogous to that of quadrupole magnetic field. reconnection can split smaller closed cosmic string from a closed cosmic string and this could correspond to a decay of galaxy to smaller galaxies. therefore single cosmic string is certainly an approximation. remark: recall that cosmic strings are closed and one can have for instance helical structures: say two closed cosmic strings analogous to dna double strands or single closed single having strands as pieces of it. remark: also non-monopole flux tubes are involved and the proposal is that gravitational interactions are mediated along these flux tubes emanating radially from the source. the flux for them is vanishing and there is no current needed to create the field. these flux tubes are not topologically stable against splitting. 3. cosmic strings are assumed to form a fractal hierarchy and that in tgd inspired biology cosmic strings thickened to monopole flux tubes are behind various linear biomolecules organized around them as ordinary matter. this leads to ask whether dna double strand and the organization of dna double strands to chromosomes might be more general phenomenon. chromosomes consist of 4 strands, which allows to ask whether something similar happens even at the level of superclusters and that the topology of quadrupole field is involved. interestingly, also milky way consists of four arms assignable spiral density waves for ordinary matter so that it is not clear whether the arms can be assigned with four poles of quadrupole. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://www.youtube.com/watch?v=renyyrwxpho http://tinyurl.com/ufvw6v5 http://tinyurl.com/zfphldm https://vimeo.com/104910552 dna decipher journal | december 2019 | volume 9 | issue 3 | pp. 123-145 144 pitkänen, m., cosmic string model for formation of galaxies, & dna structure fermi spheres are a peculiarity milky way possibly possibly related to a quadrupole structure of monopole flux tube topology suggesting two cosmic strings meeting at the nucleus of galaxy. there is evidence that milky way could be seen as being formed in a kind of cosmic collision. i have asked whether this is due to a cosmic highway accident at crossroad at which two cosmic string are pass by very near to each other is in question. this could make sense if tangle as a quadrupole corresponds to two dipoles. consider next the dynamics of laniakea. reader can build his/her own views with the help of the beautiful videos (see https://www.youtube.com/watch?v=renyyrwxpho and http://tinyurl.com/ ufvw6v5) demonstrating the velocity flow of visible parts of galaxies, which would be associated with tangles moving along cosmic strings. 1. wikipedia mentions that laniakea is not gravitationally bound. also this suggests that the galaxies associated with it are tangles of one or more cosmic strings. the dynamics would correspond to s motion in gravitational field with constraint forcing the galaxy to move along the cosmic string. 2. the motion of galactic tangles and that of ordinary matter formed from it along cosmic string is free in absence of external forces: this distinguishes tgd from halo model having a spherical symmetry. this would mean rather lose binding but strong correlation produced by the cosmic string. most galaxy motions are directed inward towards great attractor: this would have explanation in terms of gravitational attraction. a good guess is that motion are along flux tube/cosmic string. references [1] nottale l da rocha d. gravitational structure formation in scale relativity. available at: http: //arxiv.org/abs/astro-ph/0310036, 2003. [2] mead lr ringermacher hi. observation of discrete oscillations in a model-independent plot of cosmological scale factor vs. lookback time and a scalar field model. available at: http:// arxiv.org/abs/1502.06140, 2015. [3] banados e et al. a metal-poor damped lyα system at redshift 6.4. the astrophysical journal. available at:http: // tinyurl. com/ qkk26dv , 885(1), 2019. [4] sauval j scott p asplund m, grevesse n. the chemical composition of the sun. annual review of astronomy and astrophysics.available at: https: // doi. org/ 10. 1146/ annurev. astro. 46. 060407. 145222 , 47:481–522, 2009. [5] pober jc et al. first season mwa phase ii eor power spectrum results at redshift 7. arxiv:1911.10216 [astro-ph]. available at:https://arxiv.org/abs/1911.10216, 2019. [6] ferguson jf asplund m serenelli am, basu s. new solar composition: the problem with solar models revisited. arxiv:0909.2668 [astro-ph]. available at:https://arxiv.org/pdf/0909.2668. pdf, 2009. [7] zyga l. discovery that quasars don’t show time dilation mystifies astronomers. available at: http: //www.physorg.com/news190027752.html, 2010. [8] hawkins mr. on time dilation in quasar light curves. month not r astron soc. available at: http://www3.interscience.wiley.com/journal/123345710/abstract, 405(3):1940–1946, 2010. [9] pitkänen m. quantum astrophysics. in physics in many-sheeted space-time. online book. available at: http://www.tgdtheory.fi/tgdhtml/tgdclass.html#qastro, 2006. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://www.youtube.com/watch?v=renyyrwxpho http://tinyurl.com/ufvw6v5 http://tinyurl.com/ufvw6v5 http://arxiv.org/abs/astro-ph/0310036 http://arxiv.org/abs/astro-ph/0310036 http://arxiv.org/abs/1502.06140 http://arxiv.org/abs/1502.06140 http://tinyurl.com/qkk26dv https://doi.org/10.1146/annurev.astro.46.060407.145222 https://doi.org/10.1146/annurev.astro.46.060407.145222 https://arxiv.org/abs/1911.10216 https://arxiv.org/pdf/0909.2668.pdf https://arxiv.org/pdf/0909.2668.pdf http://www.physorg.com/news190027752.html http://www.physorg.com/news190027752.html http://www3.interscience.wiley.com/ journal/123345710/abstract http://www.tgdtheory.fi/tgdhtml/tgdclass.html#qastro dna decipher journal | december 2019 | volume 9 | issue 3 | pp. 123-145 145 pitkänen, m., cosmic string model for formation of galaxies, & dna structure [10] pitkänen m. tgd and astrophysics. in physics in many-sheeted space-time. online book. available at: http://www.tgdtheory.fi/tgdhtml/tgdclass.html#astro, 2006. [11] pitkänen m. criticality and dark matter. in hyper-finite factors and dark matter hierarchy. online book. available at: http://www.tgdtheory.fi/tgdhtml/neuplanck.html#qcritdark, 2014. [12] pitkänen m. does m8−h duality reduce classical tgd to octonionic algebraic geometry? available at: http://tgdtheory.fi/public_html/articles/ratpoints.pdf, 2017. [13] pitkänen m. more about tgd inspired cosmology. in physics in many-sheeted space-time. online book. available at: http://www.tgdtheory.fi/tgdhtml/tgdclass.html#cosmomore, 2016. [14] pitkänen m. about the nottale’s formula for hgr and the possibility that planck length lp and cp2 length r are identical giving g = r2/~eff . in hyper-finite factors and dark matter hierarchy. online book. available at: http://www.tgdtheory.fi/tgdhtml/neuplanck.html#vzerovariableg, 2018. [15] pitkänen m. how the hierarchy of planck constants might relate to the almost vacuum degeneracy for twistor lift of tgd? available at: http://tgdtheory.fi/public_html/articles/hgrtwistor. pdf, 2016. [16] pitkänen m. strong support for tgd based model of cold fusion from the recent article of holmlid and kotzias. available at: http://tgdtheory.fi/public_html/articles/holmilidnew.pdf, 2016. [17] pitkänen m. cold fusion, low energy nuclear reactions, or dark nuclear synthesis? available at: http://tgdtheory.fi/public_html/articles/krivit.pdf, 2017. [18] pitkänen m. philosophy of adelic physics. available at: http://tgdtheory.fi/public_html/ articles/adelephysics.pdf, 2017. [19] pitkänen m. about the physical interpretation of the velocity parameter in the formula for the gravitational planck constant. available at: http://tgdtheory.fi/public_html/articles/vzeronew. pdf, 2018. [20] pitkänen m. about the physical interpretation of the velocity parameter in the formula for the gravitational planck constant . available at: http://tgdtheory.fi/public_html/articles/vzero. pdf, 2018. [21] pitkänen m. expanding earth model and pre-cambrian evolution of continents, climate, and life. available at: http://tgdtheory.fi/public_html/articles/expearth.pdf, 2018. [22] pitkänen m. tgd view about quasars? available at: http://tgdtheory.fi/public_html/ articles/meco.pdf, 2018. [23] pitkänen m. quantum self-organization by heff changing phase transitions. available at: http: //tgdtheory.fi/public_html/articles/heffselforg.pdf, 2019. [24] pitkänen m. could mars have intra-planetary life? available at: http://tgdtheory.fi/public_ html/articles/mars.pdf, 2019. [25] pitkänen m. solar metallicity problem from tgd perspective. available at: http://tgdtheory. fi/public_html/articles/darkcore.pdf, 2019. [26] pitkänen m. some comments related to zero energy ontology (zeo). available at: http:// tgdtheory.fi/public_html/articles/zeoquestions.pdf, 2019. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://www.tgdtheory.fi/tgdhtml/tgdclass.html#astro http://www.tgdtheory.fi/tgdhtml/neuplanck.html#qcritdark http://tgdtheory.fi/public_html/articles/ratpoints.pdf http://www.tgdtheory.fi/tgdhtml/tgdclass.html#cosmomore http://www.tgdtheory.fi/tgdhtml/neuplanck.html#vzerovariableg http://tgdtheory.fi/public_html/articles/hgrtwistor.pdf http://tgdtheory.fi/public_html/articles/hgrtwistor.pdf http://tgdtheory.fi/public_html/articles/holmilidnew.pdf http://tgdtheory.fi/public_html/articles/krivit.pdf http://tgdtheory.fi/public_html/articles/adelephysics.pdf http://tgdtheory.fi/public_html/articles/adelephysics.pdf http://tgdtheory.fi/public_html/articles/vzeronew.pdf http://tgdtheory.fi/public_html/articles/vzeronew.pdf http://tgdtheory.fi/public_html/articles/vzero.pdf http://tgdtheory.fi/public_html/articles/vzero.pdf http://tgdtheory.fi/public_html/articles/expearth.pdf http://tgdtheory.fi/public_html/articles/meco.pdf http://tgdtheory.fi/public_html/articles/meco.pdf http://tgdtheory.fi/public_html/articles/heffselforg.pdf http://tgdtheory.fi/public_html/articles/heffselforg.pdf http://tgdtheory.fi/public_html/articles/mars.pdf http://tgdtheory.fi/public_html/articles/mars.pdf http://tgdtheory.fi/public_html/articles/darkcore.pdf http://tgdtheory.fi/public_html/articles/darkcore.pdf http://tgdtheory.fi/public_html/articles/zeoquestions.pdf http://tgdtheory.fi/public_html/articles/zeoquestions.pdf introduction brief description of the model for for the formation of galaxies and stars the notion of length scale dependent cosmological constant blackholes, quasars, and galactic blackholes blackholes in tgd framework can one see also stars as blackhole like entities? what about blackhole thermodynamics? what happens to blackhole thermodynamics in tgd? constraint from gr/>1 quantum biology and dark hawking radiation zero energy ontology, cosmology, and astrophysics cosmic redshift but no expansion of receding objects: one further piece of evidence for tgd cosmology stars as reincarnating conscious entities? no time dilation for the periods of processes of quasars did cosmology have any "dark ages"? observation of a time reversal of a blackhole like object? do quasars and galactic blackholes relate by time reversal in zeo? objections against grt blackholes badly behaving blackholes too heavy blackhole in milky way anomalies related to galactic dynamics correlated galactic spins in billion light-year scale mysterious coherence in several-megaparsec scales between galaxy rotation and neighbor motion galaxies spinning "too" fast galaxy which existed 1 billion years after big bang local super-cluster laniakea as flux tube structure dna decipher journal | july 2022 | volume 12 | issue 1 | pp. 37-50 37 pitkänen, m., the hen & egg problems of biology from tgd viewpoint article the hen & egg problems of biology from tgd viewpoint matti pitkänen 1 abstract biology has several hen and egg problems. what came first: dna,rna, amino-acids or protocell membrane? did metabolism precede genetic code or vice versa? the stimulus leading to this article could have been the finding that organic molecules are formed in interstellar space at ultralow temperatures of few kelvin in which chemistry should freeze completely. therefore the formation of glycine peptides, which has been demonstrated in the laboratory, should be impossible. the paradox disappears in the tgd framework as do also the hen and egg problems. magnetic body carrying dark matter as heff = nh0 phases allows a universal realization of genetic code and of the analogs of basic bio-molecules in terms of dark nucleon and dark photon triplets. chemical realization emerged later and the question is whether they emerged simultaneously or whether there was some natural order for the chemical steps. the prebiotic form of metabolic machinery based on hydrogen bonds and dark protons emerged at the same time. a metabolism with metabolic energy quantum assignable electrons which corresponds to average energy of a photon of microwave background is predicted and shows itself via miniature potentials of the neuronal membrane. 1 introduction biology has several hen and egg problems. what came first: dna,rna, amino-acids or proto-cell membrane? did metabolism precede genetic code or vice versa? the stimulus leading to this article could have been the finding that organic molecules are formed in interstellar space at ultralow temperatures of few kelvin in which chemistry should freeze completely. therefore the formation of glycine peptides, which has been demonstrated in the laboratory by the group of serge krasnosutski in an environment simulating interstellar space at 10 k temperature [11], should be impossible. in fact, all organic molecules should be absent in so low temperatures but it has been found that interstellar space contains organic molecules at few kelvin temperatures, in particular amino acid glycine (https://cutt.ly/hsyqpmp) although the independent confirmation is lacking in this case. what can one say about the hen egg problem and prebiotic period in the tgd framework? it is good to start by briefly summarizing the relevant ideas of the tgd inspired quantum biology. more detailed summaries can be found in various articles related to dark variant of biochemistry [41, 32, 38], to dark realizations of genetic code [30, 35, 34, 37, 40], and to the models for cell membrane as generalized josephson junction [18, 19, 20, 29], of pollack effect [31], and of water memory and morphogenesis [24] [39]. 1. the basic notion is magnetic body (mb) carrying dark matter as heff = nh0 phases of the ordinary matter and behaving quantum coherently in length scale proportional to heff . mb would control biomatter. communications to mb, sensory input, would be in terms of generalized dark josephson radiation from the cell membrane and the control by mb in terms of dark cyclotron radiation. the sensory input would be from the entire cell membrane and induced by the attachment of the ligands to the receptors. 1correspondence: matti pitkänen http://tgdtheory.com/. address: rinnekatu 2-4 a8, 03620, karkkila, finland. email: matpitka6@gamail.com. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://cutt.ly/hsyqpmp http://tgdtheory.com/ mailto:matpitka6@gmail.com dna decipher journal | july 2022 | volume 12 | issue 1 | pp. 37-50 38 pitkänen, m., the hen & egg problems of biology from tgd viewpoint 2. the notion of a magnetic body having flux tubes as body parts leads to a model of bio-catalysis in which molecules are replaced with nodes of flux tube network. molecules can find each other as part of this dynamical network involving reconnection of u-shaped flux tubes and their shortening in a reduction of heff liberating energy making to overcome the potential wall making the reaction low. dark photon and dark nucleon triplets provide a realization of genetic code [30, 34, 35, 40]. the states of dark nucleon triplets provide also a realization of basic bio-molecules. 1. z6, z4, and z2,rot or z2,refl act as symmetry groups for the 3 icosahedral hamiltonian cycles. each cycle, one of type xz6, one of type z4, and one of type z2, defines 12-note scale and 20 3-chords identified as icosahedral faces and dna codons. the notes along the cycle are obtained as a quint cycle, that is by scaling the frequency of the note by factor 3/2 at each edge of the oriented cycle. the orbits of faces under zn are assigned with amino-acids (aas). this assumption has a concrete interpretation in terms of the resonance mechanism for bio-communications [40]. this gives 60 3-chords and the numbers of triangles at the orbits of triangles and the numbers of triangles at orbits correspond nicely to the numbers of dna codons coding for aas. 4 codons are however missing. the fusion with a unique tetrahedral code gives 64 chords and a dark 3-photon realization of the genetic code. also the identification of dtrna, dtrna, and daa in terms of icosahedral code is possible as found quite recently [40]. also the dark realization of genetic codons in terms of dark proton triplets allows this. 2. z6 allows unique icosahedral harmony defined by 12-note scale realized as an icosahedral hamiltonian cycle. the corresponding aas correspond to 3 dna 6-plets and one dna 2-plet. z4 corresponds to 2 bioharmomies with 5 amino-acids which correspond to dna 4-plets. z2,rot and z2,refl correspond to 10 2-plets both. z2,rot corresponds to 3 icosahedral harmonies and z2,refl to 5 icosahedral harmonies. this makes 1× 2× (3 + 5) = 16 bio-harmonies if the common key of the 12-note scale for the 3 icosahedral harmonies does not matter and the orientation of the hamiltonian cycle does not matter. one can also consider the possibility that the key and the orientation of the cycle for the 3 icosahedral harmonies matter. the change of the orientation replaces the quint cycle with a quart cycle (cg corresponds to quint and cf to quart). 3. the interpretation of bioharmonies is as correlates for moods, emotional states. there is evidence for this interpretation from the strange finding that rna is able to transmit conditioning based on negative or positive emotions generated by stimulus (https://cutt.ly/6sulnqk) discussed in the tgd framework in [33, 36]. the interpretation would be that drna represents the effect of stimulus by its bio-harmony characterizing emotional state, and can induce molecular emotional expression in ddna-dna pairing and also in daa-aa pairing and dx-x pairing in general. dx-x pairing by energy resonance mechanism would correspond to emotional expression. something in x would depend on bio-harmony. in the case of dna and rna this something could be the methylation state and its analogs so that there would be a direct connection with epigenesis. epigenesis would realize the dynamics of emotional expression. the paradox created by the existence of organic molecules in interstellar space at temperatures of few kelbin and the findings of krasnosutski’s group [11] disappears in the tgd framework as do also the hen and egg problems. magnetic body carrying dark matter as heff = nh0 phases allows a universal realization of genetic code and of the analogs of basic bio-molecules in terms of dark nucleon and dark photon triplets. chemical realization emerged later and the question is whether they emerged simultaneously or whether there was some natural order for the chemical steps. the prebiotic form of metabolic machinery based on hydrogen bonds and dark protons emerged at the same time. a new kind of metabolism with metabolic issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://cutt.ly/6sulnqk dna decipher journal | july 2022 | volume 12 | issue 1 | pp. 37-50 39 pitkänen, m., the hen & egg problems of biology from tgd viewpoint energy quantum assignable to electrons instead of protons is predicted. the metabolic energy quantum corresponds to the typical energy of a photon of microwave background. the miniature potentials of the neuronal membrane have this magnitude. 2 hen egg problem, dark biomolecules, and resonance mechanism the notions of magnetic body, dark matter as heff = nh0 phases, dark analogs of information molecules, and resonance mechanism could allow a solution to the hen egg problem of biology: which came first, dna, rna, aas or proto-cell membrane. i have considered the hen egg problem in [23] and proposed a model of proto-cell in [42]. hen egg problem usually means that something is missing from the conceptual picture and tgd based quantum biology suggests what this missing piece could be. the general solution of the problem in tgd would be that dark analogs of information molecules emerged first simultaneously as galois confined states of dark proton-triplets and dark photon-triplets. this made possible resonance communications and the basic recognition mechanism by 3-resonance for dark 3-photons. dx-x pairing was based on energy resonance and these composites were able to find each other by resonance. the reduction of heff for connecting flux tubes in their shortening liberated energy making it possible to overcome the potential wall preventing chemical reactions to occur. this is not as easy as it looks at first since metabolic energy is needed to build the valence bonds and metabolic machinery is absent in early life. the challenge is to develop a more detailed picture around these basic ideas. i have already earlier considered several proposals for the first steps of the evolution of basic bio-molecules [21, 22, 23] but without the recent, rather detailed, view about resonance mechanism combined with the notion of dark 3n-photon and 3n-nucleon as a dark analog of basic biomolecule [40]. 2.1 did the dx-x pairing occur simultaneously for all basic biomolecules? consider first the pairing of basic information molecules x (dna, rna, trna codons and aas). their polymers are not considered in this section. the simplest vision is that the dark variants of basic biomolecules emerged by pollack effect [6, 7, 5, 8, 9] in water irradiated by solar light. 1. pollack effect generated exclusion zones (ezs) as negatively charged regions. part of protons were transferred to magnetic monopole flux tubes of mbs assignable to water clusters and created phases of water with a hexagonal lattice-like structure. 2. an attractive possibility is that the notion of hydrogen bonds generalizes. the monopole flux tubes could be accompanied by hydrogen bonds. this predicts a length scale hierarchy of hydrogen bonds implying long range quantum correlations in arbitrarily long scales and allowing to understand the strange thermodynamic anomalies of water. the length of the dark flux tube is proportional to heff as also the total energy consisting of kähler magnetic and volume contribution. 3. galois confinement as a universal bind mechanism would give rise to sequences of dark protons as bound states. the states of dark proton triplet correspond to ddnas, drnas, dtrnas and daas. the pairing of the dark analogs of biomolecules with ordinary biomolecules to form pairs dx-x gave rise to the observed basic biomolecules. dx-x pairing requires that the ordinary biomolecules have transition energies, which correspond to the cyclotron transition energies of dx for the value of heff considered. ordinary cyclotron transitions and vibrational transitions are good candidates in this respect. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 1 | pp. 37-50 40 pitkänen, m., the hen & egg problems of biology from tgd viewpoint 4. energy resonance condition for the pairs gives powerful conditions and selects the allowed biomolecules. the selection has not been completely unique. in trna the third letter of the chemical codon paired with one of the 32 dtrnas need not be an ordinary nucleotide and in some viruses adenosine (a) is replaced with 2-amino-adenine (”z”) [10] (https://cutt.ly/hsrbs0k). 2.2 did proto-cell and peptides emerge first? it is not at all clear whether the dark variants of the polymers of basic bio-molecules can emerge spontaneously. the problem is that the formation of valence bonds requires energy. this forces us to consider the tgd counterparts of the usual purely chemical proposals in which basic building bricks dna, rna and aas form polymers. now one considers an analog of polymerization at the level of dda, drna, and daa. the findings of montagnier et al [3, 2, 4] discussed from the tgd view point in [39] suggests that remote dna replication occurs in absence of dna template but that the presence of dna polymerase is necessary. dark dna sequences generated by remote replication would appear as a template. this suggests ddna-dna pairing could occur by polymerization and require the presence of enzymes and metabolic energy feed. could proteins (ps) have served in the role of egg in the chemical sense in the tgd framework? could the resonance mechanism together with the tgd view about bio-catalysis make it possible to generate dp-p pairs by a polymerization-like process using dp as a template? 1. the large heff between dp and p would be shortened in a given polymerization step. energy would be liberated as the dark flux tube bond between dp and p is shortened. this energy should make it possible to overcome the potential wall preventing the formation of the peptide bond and also provide the energy of the peptide bond, which is about .08-.16 ev and considerably smaller than metabolic energy quantum about .5 ev. 2. the thermal energy at room temperature using the definition et = kt is .025 ev. second definition of thermal energy is as the energy for which the distribution of black-body radiation as function of energy is maximum: this gives the energy is et ' .12 ev and rather near to the josephson energy of the cell membrane for charge z= 2e is about .1 ev. 3. the energetic requirements for aa polymerization might be satisfied by using irradiation with photon energy around thermal energy at room temperature. an interesting possibility considered in [23, 42] is that a proto-cell membrane formed from lipids was present from the beginning and before the polymerization. lipid membranes can form spontaneously and in tgd universe they act as generalized josephson junctions [18, 20] and induce josephson radiaton, which would make possible communications from cell membrane to mb. could the josephson radiation from the cell membrane with energy of order .1 ev provide the metabolic energy for the polymerization process of aas? 4. in the case of dna and rna the carbon bond energy between two codons is about 3.2 ev and considerably larger so that the polymerization without enzymes looks highly implausible. note also that also the formation of lipids is a problem since c-c bonds have energy 3.47 ev. 2.3 empirical and experimental support for the model of peptide formation there is evidence for amino acid glycine in interstellar space (https://cutt.ly/hsyqpmp) but the independent confirmation is lacking. also the formation of glycine peptides has been observed in laboratory conditions mimicking the interstellar medium (ism). the following summarizes the results described in the article of serge krasnokutski et al [11] published in nature. the following summarizes krasnosutski’s non-technical description of the results (https: //cutt.ly/dsym1sn). issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://cutt.ly/hsrbs0k https://cutt.ly/hsyqpmp https://cutt.ly/dsym1sn https://cutt.ly/dsym1sn dna decipher journal | july 2022 | volume 12 | issue 1 | pp. 37-50 41 pitkänen, m., the hen & egg problems of biology from tgd viewpoint 1. the ultra-low temperatures, common in astrophysical environments, have been believed to freeze out any chemistry in the dense areas of the ism. already the discovery of a high abundance of small organic molecules in molecular clouds was a great surprise. but also the formation of amino acids, nucleobases, lipids, and sugars in space has been confirmed. 2. what about the polymers of aas? it has been conjectured that the condensation of carbon atoms at the surface of dust particles make possible the formation of organic molecules. serge krasnokutski et al indeed demonstrated the formation of glycine polymers from amino ketenes (glycine corresponds nh2-ch2-cooh, aminoketene to nh2-ch-co and polyglycine to nh-ch2-co) under laboratory conditions simulating the ism conditions at temperature t=10 k (https://cutt.ly/3syt169). a spontaneous(!) formation of relatively short peptides (less than 10-11 monomeric units) was found. the polymerization of amino acids under energetic processing (e.g. heat, pressure, or uv irradiation) is known to occur. therefore, a further increase in chain length can be expected in natural environments. moreover, by adding other species instead of a proton to the α-carbon atom of amino ketene (nearest to the functional group) during the polymerization, a variety of different peptide chains can be formed. furthermore, chemical and photochemical modifications of glycine residues in peptides into other amino acid residues were also demonstrated in many works. thus, the glycine peptides observed in our experiments can be converted into different proteins. 3. these findings fit nicely with the proposed mechanism for the formation of proteins (or at least short peptides). the mechanism is not chemical, and no radiation is needed since the generalized josephson radiation would provide the energy of the aa-aa bond, and the formation rate does not vanish at ultralow temperatures. 2.4 how did lipids, small organic molecules, and dna and rna polymers emerge? there is a temptation to say that after the emergence of proto-cell membrane and peptides, the rest was history. this is not so simple. 1. the formation of the proto-cell membrane could occur spontaneously if lipids are available. lipids however have c-c bonds with bond energy 3.47 ev and c==c bonds with energy 6.28 ev. these energies are in the uv range. 2. also the energies of valence bonds associated with dna, rna, and also other basic biomolecules are in this range. the freezing of the chemistry at ultralow temperatures does not allow the generation of these bonds since the metabolic machinery provided by atp molecules is not present. simple organic molecules and even amino-acids are however detected in the interstellar medium. it seems that life-as-nothing-but-chemistry dogma must be wrong. 3. the josephson radiation associated with proto-cell membrane with an energy scale of .1 ev could help in the formation of peptides but cannot help in the more general case. could the splitting of a hydrogen bond provide the metabolic energy quantum of .5 ev in the absence of atp machinery? the formation of water involving o-h bonds and their dynamics at temperatures of few k do not sound plausible unless one leaves the framework of the standard chemistry. metabolic machinery involves a lot of control and the standardization made possible by the metabolic energy quantum. this involves a lot of control. what could have served as a controller and energy source for bond formation at ultralow temperatures of few kelvin and in the absence of the complex metabolic machinery based on atp. in the tgd universe, mb carrying dark matter is the answer to the question. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://cutt.ly/3syt169 dna decipher journal | july 2022 | volume 12 | issue 1 | pp. 37-50 42 pitkänen, m., the hen & egg problems of biology from tgd viewpoint 1. the existence of bend was originally deduced by blackman [14] and other researchers. they found that elf em fields had quantum-like effects on the vertebrate brain. these effects could be understood in terms of cyclotron transitions in the ”endogenous” magnetic field bend ' 2be/5 if the value heff of planck constant was much larger than h, heff/h ∼ 1013 was required in order to scale the energy of 10 hz photon to that of a visible photon with frequency 1014 hz. 2. the large value of heff suggests its identification as gravitational planck constant ~eff = ~gr = gmm/v0 given by nottale’s hypothesis [1]. m denotes here earth’s mass and m the mass of the charged particle. this predicts that cyclotron frequencies in bend correspond to dark photon energies in the visible and uv uv range. most remarkably, the energies do not depend on the mass m of charged particles. this realizes the equivalence principle. 3. visible-uv energy range is associated also with biophotons [13, 12] discussed from tgd view point in [25, 26]. this motivates the identification of biophotons as decay products of dark photons or possibly even dark n-photons resulting in heff → h transition. dark photons or n-photons in this energy. note that the nottale hypothesis and the notion of a monopole magnetic flux tube make sense only in the tgd universe. 4. heff/h0 = n is identifiable as a dimension of extension of rationals in number theoretic vision about tgd. n serves as a kind of iq [27, 28]. mb with heff = hgr corresponds to a rather high level of number theoretic complexity assignable to the mb of earth as a quantum system. mb has a long scale of quantum coherence even of the order of the scale of earth and is by its high ”iq” the natural ”boss” and controls the dynamics of the ordinary biomatter. the molecular transitions induced by the transformations of dark cyclotron (3n-)photons would serve as a natural control tool of mb. the cyclotron condensates at mb can provicde quantized metabolic currencies in the absence of atp machinery. 5. mb could generate already at few kelvin temperatures various biologically important molecules by providing the metabolic energy for the formation of various valence bonds, such as carbon and peptide bonds and make possible the formation of lipids, dna and rna molecules and their polymers and also other basic organic molecule. josephson radiation would in turn make possible the generation of proteins. gravitation would be a key player in living systems and play an especially important role in the very early stage. the chemistry at ultralow temperatures would provide a direct experimental handle to the biophysics associated with mb. 2.5 what can one say about pre-trna? what could be the prebiotic counterpart of trna? 1. dtrna should have a molecular counterpart. the simplest guess is that it corresponds to an rna type codon appearing in trna but somehow differing from it. pre-trna could simply be the (aac-h)3’ end of the acceptor stem with aac replaced with xyz, where zyz denotes the codon part of trna. the addition of a hydrogen atom would relate pre-trna codon to ordinary rna codon. 2. the bond energy for the pre-trna-aa pair as the energy of the ester bond would be about .5 ev, which corresponds to the metabolic energy quantum. energy is therefore required to ”charge” pre-trna. this requires metabolic energy and in the absence of atp machinery, the energy should come from its predecessor. what prebiotic metabolism could be, will be discussed in the next section. 3. if this step works, the polymerization of trnas involving the transformation of the ester bond of pre-trna-aa to aa-aa peptide bond can occur spontaneously since the peptide bond has bond issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 1 | pp. 37-50 43 pitkänen, m., the hen & egg problems of biology from tgd viewpoint energy of order .1 ev. this would give rise to polypeptides. this process would be like a translation process for rna but without an rna template and therefore the outcome would be random. also the rna polymerization in this manner can be considered, now however the rna-rna valence bond has considerably higher bond energy. 4. if drna-rna sequences are formed, they might be transformed to aa sequences by pre-translation process using pre-trna and resonance mechanism pairing drnas and dark counterparts of pretrna-aa pairs. this would define the pre-translation process. 2.6 what could the prebiotic metabolic machinery be? metabolic machinery should have a prebiotic counterpart and have energy about .5 ev as metabolic energy quantum. 1. could the splitting of a hydrogen bond with bond energy about .5 ev provide the energy needed in the formation of pre-trna-aa ester bond? ir photons are most effective in causing pollack effect in water: could also they induce pre-trna-aa pairing? both options would require the presence of water. in principle, the proposed mechanism could lead to a generation of water molecules (the energy of o-h bond is 4.81 ev) already at temperatures of few kelvin. 2. could mb somehow provide the metabolic energy quantum? gravitational flux tubes are in a central role in the tgd inspired quantum biology. in [43] it was observed that the gravitational binding energy of a nucleon in the gravitational field of earth is .67 ev. this is somewhat larger than the metabolic energy quantum. a dark proton at a distance of about .34re , re earth radius, from the surface of earth has gravitational binding energy of .5 ev. the bond energy of the hydrogen bond is .5 ev. could it correspond to the reduction of the gravitational binding energy due to the delocalization of a dark proton to a gravitational flux tube? could the hydrogen bond become dark gravitational u-shaped monopole flux tube with heff = hgr so that the proton of the ordinary hydrogen bond would become gravitationally dark? the size scale of earth would define the length scale of this flux tube. the flux tube could however still connect the same atoms. the transformation hgr → h induces a dramatic shortening of the u-shaped gravitatonal flux tube loop and the gravitationally dark proton at the gravitational flux tube of mb transforms to an ordinary proton. this localization has interpretation as falling of the proton to the surface of earth. could the liberated energy have an interpretation as a ametabolic energy quantum? for a dark variant of hydrogen bond a gravitational flux tube between atoms should form a very long loop at which the gravitationally dark proton would reside. this kind of picture about dark flux tubes associated with gauge interactions has been suggested earlier. for instance, color flux tubes assignable to nuclear protons could extend to distances of the order of atomic size. 3. phosphate is electronegative and forms hydrogen bonds. phosphate ionization could be interpreted as a formation of a dark hydrogen bond. this would explain why phosphate ions have such a central role in metabolism. effective ionization serves as the signature of the delocalization. also other electronegative ions could play the role of phosphate and arsenite has done this in some bacterial systems (https://cutt.ly/zs1fzng). the pre-biotic counterpart of metabolic machinery should have involved phosphate ions or some other electronegative ions forming dark hydrogen bonds. 4. also the valence electrons of valence bonds can become dark by the lengthening of the valence bond to a u-shaped gravitational flux loop. for electrons the gravitational binding energy at height issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://cutt.ly/zs1fzng dna decipher journal | july 2022 | volume 12 | issue 1 | pp. 37-50 44 pitkänen, m., the hen & egg problems of biology from tgd viewpoint .34re is about .25 mev and .5 mev for their cooper pairsm. note that .3 mev corresponds to the energy of photons in the microwave background. could this define a second metabolic energy quantum important in scales by a factor mp/me ∼ 211 longer than nanoscale about 1 nm assignable to dna. this is the length scale of the cell nucleus, microtubules and axons. intriguingly, the minimal fluctuations of membrane potentials correspond to the so-called miniature end plate potentials .4 mv (https://cutt.ly/hsjin76). 5. a gravitational valence bond, connecting a metal atom with an atom with an opposite valence, would lead to effective ionization of the metal atom. for instance, biologically important bosonic ions such as ca++, mg++, fe++ and zn++ associated with their oxides could correspond to effective ions like this. the signature would be a pairing with a neutral oxygen atom by a gravitational valence bond. i have introduced the notion of dark ion to explain the findings of blackman [14] and others and dark ion could correspond to this kind of pair. the original variant of the model assumed that the entire ion is dark, the later version assumed that the valence electron of free atom is dark, and the model consider here assumes that the valence bond is dark. 6. the effective ionization requires energy ∆e to compensate the increment of the gravitational potential energy given by ∆e = (〈vgr(r)〉 − vgr(re)). here egr(r) is gravitational potential energy proton or electron, and re denotes the radius of earth, and r is the distance of the point of flux tube from the center of earth. this estimate neglects the kinetic energy of the dark particle at the flux loop. this assumption is not consistent with the localization near the top of the loop so that the estimate can serve only as a rough order of magnitude estimate. 7. the maximal value for ∆e for electron cooper pair (dark cooper pair is at infinite distance) corresponds to vgr(re) = .36 mev to be compared with the energy scale .3 mev defined by the temperature of 3 k microwave background and to the value .4 mev of the miniature potential. this suggests that, in the case of the electron, the reduction of kinetic energy contributes more than 10 per cent to the ∆e. for a single dark proton one has vgr(re) ' .34 ev, which is below the nominal value of the metabolic energy currency about .5 ev. if a single dark proton is involved, the reduction kinetic energy should contribute at least 32 per cent to ∆e. for a dark proton cooper pair, one has the maximal value of ∆e = .68 ev somewhat above the metabolic energy quantum. these findings support the idea that both proton and electron cooper pairs give rise to metabolic energy quanta. the challenge would be to understand the mechanism for the formation of proton cooper pairs. 8. the transformation of electrons and protons between ordinary and gravitationally dark states would be a key process of metabolism and biocatalysis. this conforms with the fact that proton and electron exchanges play a key role in biology. for instance, phosphorylation means that the receiving molecule gains phosphate, which can form gravitationally a dark hydrogen bond so that the system becomes metabolically active. this would correspond to the activation in bio-catalysis. dna base pairs are connected by 2 (a-t) or 3 (g-c) hydrogen bonds. if these strands can appear as dark gravitational strands, the maximum of 2 (3) metabolic quanta could be liberated in a-t (g-c) pairs via a transformation to ordinary hydrogen bonds. could this serve as a yet-unidentified source of metabolic energy in the replication and transcription? 9. in the same way, in a redox reaction, the electron donor is oxidized and the electron receiver is reduced. reduced molecule gains the ability to have a gravitationally dark electron, and therefore becomes metabolically active in the electronic sense. redox reaction would be the electronic counterpart for phosphorylation. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://cutt.ly/hsjin76 dna decipher journal | july 2022 | volume 12 | issue 1 | pp. 37-50 45 pitkänen, m., the hen & egg problems of biology from tgd viewpoint 2.6.1 could the metabolism of cilia and flagella rely on gravitationally dark electrons? the metabolism of cilia and flagella (https://cutt.ly/wdkyzzx) is poorly understood. according to [17] (https://cutt.ly/edkw2bu) the recent measurements in sea urchin sperm (length ∼ 50 µm long, diamter 0.2 µm ) show that the energy consumed per flagellar beat corresponds to ' 2 × 105 atp molecules. there is no gtp inside cilium as in the case of axonal mts (https://cutt.ly/5dkygb2). it is difficult to understand how atp machinery could provide the metabolic energy feed. this motivates the question about whether local ciliary metabolism could rely on the transformation of valence electrons of some biologically important ions to dark electrons at the gravitational mb and vice versa? the reduction of hgr for electrons would provide the metabolic energy related by a factor me/mp ' 2−11 to the ordinary. according [17], about 4 × 108 gravitationally dark electrons would transform to ordinary ones in a single stroke of cilium. electronic metabolic energy quantum would relate like cent to dollar and make possible a more refined metabolism with fine tuning. electronic metabolism could also be an essential part of ordinary metabolism. consider now the idea more quantitatively. 1. what could be the electronic analog of atp machinery. all biologically important ions can be considered as effective ions with some valence electrons at gravitational mb. in particular, the bosonic ions ca++, mg++ and fe++ could have bose-einstein condensates of gravitationally dark cooper pairs at the gravitational mb. ca++ waves play a key role in cellular biology, fe++ is essential for oxygen based metabolism, and mg++ is important in bio-catalysis: for instance, atp must bind to mg ions in order to become active. 2. suppose that one replaces h with hgr in the schrödinger equation for the valence electrons. the binding energies are scaled down by 1/n2, n = ~gr/~ = gmme/v0~ = 2πrs,e/leβ0, rs,e ' .9 cm, le = h/me ' 2.4× 1012 m. for β0 = 1, this gives n ' 2.4× 1010. the radii a of bohr orbits would be scaled up by n2 ∼ 5.8 × 1020 from a(z) = z2a0, a0 ' .5 × 10−10 m giving a ' 2.9 × z2 × 1010 m for z ≥ 3 (li), a is longer than the astronomical unit au = 15 × 1010 m (distance from earth to sun). the electromagnetic binding energy would be very near to zero. the gravitational interaction would dominate and cannot be neglected. the schrödinger equation would reduce in an excellent approximation to that for the gravitational potential. note however that the description of dark gravitational particles in terms of wave functions concentrated at flux tubes is the more realistic option than ordinary schrödinger equation assuming total delocalization. 3. what could be the mechanism transforming valence electrons to dark electrons? this should happen for positively charged biologically important ions, in particular for the bosonic ions ca++, mg++ and fe++. the consumption of metabolic energy would correspond to a deionization of dark ion ca++ and this might make it possible to test the proposal. for instance, ca++ could accompany ciliary waves. where could the energy for ionization come from? 1. this question is also encountered in the chemistry of electrolytes [32]. it is very difficult to understand how the external electromagnetic potentials, which give rise to extremely weak electric fields in atomic scales, could lead to ionization. the acceleration of electrons in the electric field along dark flux tubes involves very small dissipation and can easily give rise to electron energies making ionization possible. 2. mts have a longitudinal electric field which by the generalization of maxwell’s equations to manysheeted space-time (in stationary situation potential difference is same for paths along different issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://cutt.ly/wdkyzzx https://cutt.ly/edkw2bu https://cutt.ly/5dkygb2 dna decipher journal | july 2022 | volume 12 | issue 1 | pp. 37-50 46 pitkänen, m., the hen & egg problems of biology from tgd viewpoint space-time sheets) gives rise to an electric field along the magnetic flux tubes. these flux tubes need not be gravitational. by darkness, the dissipation rate is low. could the acceleration along flux tubes, in particular mt flux tubes, lead to the ionization? could the electret property of linear biomolecules quite generally serve for the purpose of generating electronic metabolic energy storages in this manner? 3. assuming opposite charges ±zmt at the ends of dark magnetic flux tube associated with the mt, one obtains a rough estimate. the length of the cilium is l ≤ .5 × 10−4 m and its radius is r ∼ 2 × 10−7 m. the estimate for the energy gained by a unit charge e as it travels through the ciliary mt is e ∼ zmt e 2l/r2 ' zmt × 2.85 ev. the valence electron energy for atomic number z with principal quantum number n (giving the row of the periodic table) is e ' (z/n)2 × 13.6 ev. the ionization condition would be zmt ≥ (z2/n2) × 13.6/2.85. for the double ionization in the case of ca++ with z = 20 and n = 3 this would give zmt ≥ 212. 2.7 quantum gravitation in tgd inspired quantum biology the theory of penrose and hameroff [15] assigns to microtubules quantum gravity in planck length scale. in the tgd universe, one does just the opposite. the hierarchy of effective planck constants assigns to quantum gravitation quantum coherence scale even in the scales of astrophysical objects. 2.7.1 the notion of gravitational magnetic body the prpoposed picture allows us to reconsider a long-standing question relating to the notion of mb with an onion-like layered structure. what could this sentence mean quantitatively? 1. the gravitational magnetic body could be a layered structure containing the bohr orbits with bohr radii rn ∝ n2 of particles in the gravitational field of earth. particles with different masses would concentrate at the same orbits. one would have the shell structure of the ordinary atom. 2. flux sheets with a cylindrical rotational symmetry containing the orbits can be considered. these surfaces should be realized as preferred extremals of the action and should be minimal surfaces in h = m4 × cp2. as closed surfaces they cannot define minimal surfaces of the euclidean 3space e3. indeed, soap bubbles are not minimal surfaces but require a constant pressure difference between interior and exterior. the analog of pressure difference would be non-trivial and dynamic 1-d projection of 4-d surface to cp2 [44]. the liberation of metabolic energy quantum would be analogous to a transition of hydrogen atom to a lower energy state. 2.7.2 nerve pulse and quantum gravitation the proposed picture allows us to reconsider a long-standing question relating to the notion of mb with an onion-like layered structure. what could this sentence mean quantitatively? 1. the 4-surfaces x4 with 1-d cp2 projection and 3-d m4 projection having 2-d membrane as e3 projection are good candidates for various membrane objects in tgd universe [44]. the e3 projection is not a minimal surface although x4 is, and this possible if the 1-d cp2 projection is dynamical. the flux tubes of mb should be assignable to kind of membrane-like surface. 2. the gravitational magnetic body could be a layered structure containing the bohr orbits with bohr radii rn ∝ n2 of particles in the gravitational field of earth. particles with different masses would concentrate at the same orbits. one would have the shell structure of the ordinary atom. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 1 | pp. 37-50 47 pitkänen, m., the hen & egg problems of biology from tgd viewpoint 3. flux sheets with a cylindrical rotational symmetry containing the orbits can be considered. these surfaces should be realized as preferred extremals of the action and should be minimal surfaces in h = m4 × cp2. as closed surfaces they cannot define minimal surfaces of the euclidean 3space e3. indeed, soap bubbles are not minimal surfaces but require a constant pressure difference between interior and exterior. the analog of pressure difference would be non-trivial and dynamic 1-d projection of 4-d surface to cp2 [44]. the liberation of metabolic energy quantum would be analogous to a transition of hydrogen atom to a lower energy state. this picture makes it possible to formulate a more precise view about the model of cell membrane as a generalized josephson junction for which the generalized josephson energy for charge ze is the sum ej = zev + ∆ec of ordinary josephson energy zev and difference ∆ec of dark cyclotron energies for the flux tubes at the two sides of the cell membrane having in general different strengths of magnetic field. the model requires large heff in order that josephson frequencies can correspond to frequencies in the eeg range. this justifies the assumption that dark ions have heff = hgr . the ionization would be effective and caused by the transformation of protons of hydrogen bonds and valence electrons to dark charge carriers at the gravitational flux tubes. the physical meaning of the criticality against the generation of nerve pulse for a critical membrane potential evcr ' .05 ev has remained open. 1. since voltage gives rise to negative potential energy, it seems clear that there must be positive contribution to the energy and this could come from the reduction ∆egr of the gravitational potential energy due to the positive resp. effective ionization of atoms of metal atoms resp. electronegative atoms with hydrogen bonds. the reduction of the gravitational potential energy for electrons is fraction me/mp from that for protons so that protonic contribution should dominate in the reduction of gravitational potential energy if dark electrons and protons correspond to the same shell of gravitational atom. the first guess is that the energy shell and thus the distance from the earth’s surface is the same. the parametrization of the reduction of the gravitational energy per atom and for the difference ∆ec of cyclotron energies should in the standard picture correspond to a thermo-dynamical formulation using chemical potentials to fix the ion concentrations. the water has very special thermodynamic properties in the range between freezing and boiling points and anomalies are largest near physiological temperatures. this would be due to the presence of dark hydrogen bonds, which supports the view that the number of dark protons and electrons depends on temperature. 2. in the first approximation the negative coulombic interaction energy for the cell membrane is given by ecoul = −qtotev = − ∑ ini(out)ziev , where ni is the number effective ions with charge zie. the contribution of positive charges is negative since v corresponds to a negative net charge for the cell. the situation is stable for |ecoul| ≥ |ecoul,cr| = np∆egr. the system becomes critical at qtotevcr = np∆egr. the value of the critical potential energy is given by evcr = np∆egr/qtot and is roughly constant for a given neuron. this suggests that the ratio np/qtot characterizes the cell. neurons and ordinary cells could differ in that ordinary cells are either subcritical or so overcritical that nerve pulses do not occur. subcriticality looks the more plausible option. the emergence of the nervous system would mean the discovery of quantum criticality as a control tool of mb. 3. in the generation of the nerve pulse the dark protons and electrons become ordinary ones in the reduction hgr → heff ≤≤ hgr for them and the membrane potential changes sign. in zeo this transition could correspond to bsfr inducing time reversal and change of membrane potential. the second bsfr would bring back the original situation and membrane potential would return to the over-critical value. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 1 | pp. 37-50 48 pitkänen, m., the hen & egg problems of biology from tgd viewpoint 2.7.3 microtubules and quantum gravitation in the tgd universe quantum gravitation would be associated with the cell membrane, in particular neuronal membrane. quantum gravitation has been speculatively assigned with microtubules (mts) rather than cellular or neuronal membranes. what is the situation in tgd? 1. axonal mtss are highly critical systems, which continually change their lengths. the surface of mts has one gdp per tubulin dimer and the ends of mt has gtps so that there is a constant negative charge per unit length. the number of gtps is larger at the second end so that there is an electric field along mt. 2. gtp↔ gdp process accompanies the variation of the length of the mt. the transformation of the protons assignable to the phosphate hydrogen bonds to gravitationally dark protons could be an essential element of the mt dynamics. the periods of increasing/decreasing mt length could be initiated by bsfr and would correspond to different arrows of time. the effective ionization affects the effective charge of the axonal interior and therefore of membrane potential. this suggests a strong correlation with the variation of axonal mt lengths and nerve pulse propagation. the propagation of nerve pulse through the myelinated sections of the axons, where ion transfer with cell exterior is not possible, is a mystery in the standard model. without axonal mts the nerve pulse propagation would not be possible. this could allow us to understand why various neuronal diseases involve a reduced mt stability [16] (https://cutt.ly/4daf6qc). received april 4, 2022; revised april 19, 2022; accepted july 22, 2022 references [1] nottale l da rocha d. gravitational structure formation in scale relativity, 2003. available at: http://arxiv.org/abs/astro-ph/0310036. 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[44] pitkänen m. what could 2-d minimal surfaces teach about tgd? https://tgdtheory.fi/ public_html/articles/minimal.pdf., 2021. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://link.springer.com/chapter/10.1007/978-3-319-55612-3_11 https://link.springer.com/chapter/10.1007/978-3-319-55612-3_11 https:/tgdtheory.fi/public_html/articles/adelephysics.pdf https:/tgdtheory.fi/public_html/articles/adelephysics.pdf https://tgdtheory.fi/public_html/articles/mseeg.pdf https://tgdtheory.fi/public_html/articles/mseeg.pdf https:/tgdtheory.fi/public_html/articles/harmonytheory.pdf https:/tgdtheory.fi/public_html/articles/harmonytheory.pdf https:/tgdtheory.fi/public_html/articles/pollackyoutube.pdf https:/tgdtheory.fi/public_html/articles/pollackyoutube.pdf https:/tgdtheory.fi/public_html/articles/valenceheff.pdf https:/tgdtheory.fi/public_html/articles/philosophic.pdf https:/tgdtheory.fi/public_html/articles/gcharm.pdf 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dark biomolecules, and resonance mechanism did the dx-x pairing occur simultaneously for all basic biomolecules? did proto-cell and peptides emerge first? empirical and experimental support for the model of peptide formation how did lipids, small organic molecules, and dna and rna polymers emerge? what can one say about pre-trna? what could the prebiotic metabolic machinery be? could the metabolism of cilia and flagella rely on gravitationally dark electrons? quantum gravitation in tgd inspired quantum biology the notion of gravitational magnetic body nerve pulse and quantum gravitation microtubules and quantum gravitation unraveling the tree of life dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 01-35 king, c., biocosmology: part i issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 1 article biocosmology: part i chris king * abstract twenty years ago (king 1978) i proposed the biocosmological thesis that the form of life's origin and evolution is a cosmological interactive process defined in the cosmic symmetry-breaking at the origin of the universe. with the passage of time, the pendulum has shifted from the improbability of life as a random molecular accident to an awareness that central biomolecules may be cosmologically abundant products of the clouds forming young stars leading to an rna-era in which both catalysis and replication emerged from one cosmologically dervied molecule rna. . this paper unveils the non-linear quantum foundations of biocosmology as the founding science of life. part i of this paper covers the following topics: 1. paradise on the cosmic equator; 2. generating a complex twisted universe; 3. the abudantly fecund universe; 4. quantum chemistry as non-linear complexity; 5. the non-recurrent table and the elementary bifurcation tree; 6. structural dynamics of core polymerization pathways; 7. rna and cosmology; 8. diverse horizons of the rna epoch; 9. universal stability structures in molecular biology; 10. the last universal common ancestor; and 11. the precocious origins of life on earth. key words: cosmology symmetry-breaking, molecular evolution, chaos, complex system, neurodynamics, quantum non-locality, transaction, consciousness. 1. paradise on the cosmic equator could biological structures such as tissues, and organisms be cosmological interactive structures as fundamental as stars and galaxies to the cosmic design? the conventional objections are obvious. life is a fragile insignificance among the immense energies of black holes, galaxy formation and the big-bang. its tiny entropy-reducing photosynthetic energy budget and fragile chemical bonds are insignificant on the cosmic scale. biological structures are genetically coded in a vast variety of ways by specific nucleic acid sequences. biological evolution is a stochastic process combining random mutation and selective advantage, many of whose manifestations are opportunistic. nevertheless many features of life as we know it on earth may be the product of cosmic factors determining the laws of nature which make life possible. although traditional chemistry, despite its quantum foundations, treats molecules as arbitrary building blocks which can be arranged in almost any combination using suitable reagents and conditions, there is clear evidence for optimality of many prebiotic and biological molecules, giving life as we know it a cosmological basis as a culminating interactive structure. * correspondence: chris king http://www.dhushara.com e-mail: chris@sexualparadox.org http://www.dhushara.com/ mailto:chris@sexualparadox.org dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 01-35 king, c., biocosmology: part i issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 2 fig 1: paradise on the cosmic equator: darwin, the serpent and the hoopoe in eden: biological systems form a central cosmological manifestation of interactive complexity in the universe. when space-time is considered as a 4-manifold, biology's 'equatorial' position is as fundamental in cosmological terms, even though biological energetics are too weak to withstand either the polar big-bang at the origin nor the possible final fates, whether they are heat death by attrition in an ever-expanding universe, a big crunch, or fractal inflation, as shown at the left. this paper explains how and why the origins of chemical life, major aspects of biological evolution and the elaborate emergent structures of tissues, from biomolecules up to cellular organelles and even to the doors of perception of the conscious brain, are a fractal interactive consequence of the non-linear laws of nature established at the cosmic origin. this reverses the copernican revolution, putting life and with it ourselves back to centre stage in the cosmic arena. biology is a product of the twisted laws of nature dervied from cosmic symmetry-breaking. the rich diversity of structure in molecular systems is made possible by the profound asymmetries developing at the cosmic origin, between the nuclear forces, gravity and electromagnetism. the diversity of the elements and their asymmetric charge structure, with clusters of negatively charged electrons orbiting a massive nucleus containing all the positive charges in a concentrated nuclear 'droplet', is made possible only through the divergence of symmetry of the four fundamental forces. without these asymmetries there would be only one or two simple atoms and none of the richness of the almost unlimited variety of molecular structures which can be generated by the over one hundred complex atoms occurring in nature as we know it. chemical bonding is a consequence of the non-linear inverse square law of electromagnetic charge interaction in space-time. this non-linearity also gives rise to a succession of weak bonding interactions, generating the complex non-periodic secondary and tertiary structures of proteins and nucleic acids. dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 01-35 king, c., biocosmology: part i issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 3 fig 2: galaxies and galaxy clusters illustrate the fractal self-similar nature of large scale fluctuations in the universe. according to some versions of inflation theory these may be inflated quantum fluctuations. left: galaxy mc 100. right: a distant gravitationally-lensed red galaxy beyond a closer cluster, including blue galaxy lover right. top right inset large scale structure of the universe including the 'great wall'. 2. generating a complex twisted universe the four fundamental forces of nature the strong and weak forces mediating nuclear binding and neutron decay respectively, along with electromagnetism and gravity are believed to have emerged from a single superforce, perhaps a form of higher-dimensional string, or membrane theory, in twelve, or so dimensions, immediately after the big bang, fig 3(a). the higher-dimensional space, containing a single generalized superforce compactified most of its dimensions to sub-particulate scales, leaving the four dimensions of space-time and broke symmetry to form the different forces we see today, in much the way a ferromagnet is polarized at minimum energy, breaking symmetry in space, so that at the lowest energy, all domains point in one direction. the forces nevertheless do appear to converge at extremely high energies the unification temperature. the strong force is a secondary effect of the colour force between the three red, green and blue quarks comprising a proton or neurtron in much the same way that molecular bonding is a secondary consequence of the formation of atoms. the colour force has three colours and three anti-colours instead of two charges. it also comes in two ground flavours so that the proton and neutron are a composite of up and down flavours uud and udd as well as three different colours. the quarks' charges of u = +2/3 and d = -1/3 thus generate precisely the integral charges of the proton and neutron. the weak force has become very short range because it is mediated by massive particles, which are believed to gain the required extra degree of freedom by assimilating another concealed particle, the mysterious higg's boson (georgi 1981, t'hooft 1980, veltman 1986). dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 01-35 king, c., biocosmology: part i issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 4 complementing this picture at the quantum field theory level is a description on the cosmic scale in which a central theme is inflation. although recently questioned by difficulties finding enough dark matter to halt the universe's slide towards hyperbolic expansion (krauss 1999, bucher and spergel 1999), inflation concepts remain central to understanding how symmetry-breaking of the forces may have generated the expanding universe we know. in summary, a seed universe in the symmetrical state, below the unification temperature is in an unstable high-energy false vacuum, like a super-cooled liquid which could freeze to form a polarized magnet. the false vacuum in the higg's field causes a gravitational repulsion representing the negative energy difference between temperature and that required to maintain the higgs field. under this 'antigravity', the empty universe, expands exponentially, smoothing quantum irregularities to structures on the scale of galaxies (guth & steinhardt 1984). the breakdown of the false vacuum (in 10 -39 sec) halts this inflationary phase, releasing a shower of highenergy particles as latent heat, forming the hot expanding universe under attractive gravitation we are familiar with. the gravitational potential energy gained almost exactly equals the kinetic energy of the particles, making the generation of the universe possible from a quantum fluctuation. indications are that the universe will continue to expand suggesting a hyperbolic inflation or fractal cosmic inflation (linde 1992), in which the active tips of the universe are permanently inflating, to leave behind non-inflating bubble universes such as ours. fig 3 (a) divergence of the four forces from a single superforce. (b) the three non-gravity forces converge in strength at the unification temperature. what interests us here are the interactive consequences of this symmetry-breaking differentiation, because it leads to all the complex structures we see around us today. cosmology is traditionally preoccupied with alpha and omega initial and final causes the origin and fate of the universe. but there is another perspective in which life and its complexity is as central to cosmology, fomring the central nonlinear interactive processes that make the universe the complex one we know and exist within, during the vast epochs of its mature evolution. although life may be created and annihilated during the evolution of the universe from alpha to omega, just as the creation and anihilation of virtual particles are essential to quantum field theory, the biological forms and processes can have a cosmic origin as generic structures and a cosmic significance as culminating interactive complexity (fig 1). although fragile, on the cosmic scale of energies, the complexity of life is the supreme culmination in complexity of the interactive quantum process initiated in the quantum symmetry-breaking. dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 01-35 king, c., biocosmology: part i issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 5 fig 4: the standard model of particle physics involves half-integer spin fermions which obey the pauli exclusion principle and form matter and integer spin bosons which mediate force and radiation. right: the composite structure of symmetry-broken fermionic mattter is molecular. the interaction between the wave-particles emerging from the cosmic origin results in distinct effects on microscopic and cosmic scales. on the cosmic scale we find fractal structures galaxy clusters, star and planetary formation, mediated by gravity, through contraction, heating and the ignition of the strong nuclear force, producing the energy of stars and the secondary photosynthetic energy of visible light. on the quantum scale we find integration of quarks to protons and neutrons then atomic nuclei in stars, then supernovas in the formation of chemical elements, and finally molecules, in the lower energetics of second generation sun-like stars. quantum interaction of fermions reaches its full interactive complexity only in the molecular assemblies of biochemistry and finally, in tissues, organs and organisms, the brain being the most complex global expression of chemical non-linearities so far known, forming "the threepound universe" (hooper ad teresi). the hierarchical process leading to molecular complexity involves all the forces in sequence. quarks are bound by colour force gluons into composite particles, such as the proton p+ and neutron n. these then interact by the strong force, via the nucleosynthesis pathway, to form the elementary nuclei. the nucleosynthesis pathway generates over a hundred atomic nuclei from the already composite proton and neutron. parity between protons and neutrons is mediated by weak decay and is slightly broken at lowest energies to balance filling nuclear quantum levels with increasing electromagnetic repulsion of the positive protons, fig 6(b). nucleosynthesis is a complex process catalytically moderated by several of the isotopes of lighter elements such as carbon and oxygen. subsequently the weaker electromagnetic force interacts, firstly by formation of atoms through aggregation of electrons around nuclei and then by secondary interaction of complete atoms to form molecules. molecular bonding is a non-linear quantum interaction, which is never fully resolved and thus perpetuates in a sequence of stages through successive strong and weak bonding interactions, making possible the complex tertiary structures of biomolecules. dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 01-35 king, c., biocosmology: part i issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 6 fig 5: the extreme variety of conditions on our own planets and between the moons of jupiter and saturn are only a foretaste of the bizarre variety of planets detected around other neighbouring stars. this extreme variety is consistent with the non-linear nature of gravity under inverse square law attraction in four-dimensional space-time and the resulting capacity of the universe to explore its own space of possibilities through chaotic dynamical interaction. super-earth discovered in a habitable zone 2011 impacts 'more likely' to have spread life from earth 2011 comets may be creating oceans on alien planet 2011 fifty new exoplanets discovered 2011 exoplanet near gliese 581 star 'could host life' may 2011 exoplanet hunt turns up 54 potentially habitable worlds feb 11 'trillions' of earths orbit red stars in older galaxies dec 10 new exoplanet like 'one of ours' mar 10 first life-friendly exoplanet may not exist oct 10 not too hot, not too cold: new earth-like planet could sustain life sept 10 billions of earths in our galaxy and 32 discovered in 2009 cool find in hunt for exoplanets dec09 'super-earths' orbit nearby stars dec09 keeping the young earth cozy 09 generation of the chemical nuclei requires a cosmic cycle through the supernova explosion of a shortlived hot star, generation of heavier elements like gold possibly involving the collapse of twin neutron stars after supernova formation (rosswog). in the second phase, these elements are drawn into a lower energy long-lived sun-like star, the lighter elements associated with terrestrial biology occur in relatively high abundance as a result of nucelosynthesis dynamics, fig6(a), and can become concentrated on midrange planets. the final re-entry of the forces occurs through irradiation of molecular systems from photons emitted by stellar thermal radiation, representing the final re-interaction of the residual lower energy electromagnetic bosons with their fermionic counterparts in the electromagnetic orbitals of molecules. the typical coupling of the 5000 o c surface temperature of sun-like stars provides photonic energy suitable for energizing weak-bonded molecular structures, without destroying them. a pivotal environment in which this final negentropic low-energy re-entry occurs in abundance are the surfaces of rocky planets in the temperature belt where water is liquid. the variety of planetary systems so-far discovered demonstrates the capacity of the universe to explore through chatoic non-linearities in gravitational orbits, a diverse array of planetary surfaces, ensuring the phase space of potential molecular environments is well explored on a cosmic scale (fig 5). http://www.dhushara.com/biocrisis/11/oct/superhabitable.pdf http://www.dhushara.com/biocrisis/11/oct/lifespread.pdf http://www.dhushara.com/biocrisis/11/oct/cometplanet.pdf http://www.dhushara.com/biocrisis/11/oct/50exopl.pdf http://www.dhushara.com/biocrisis/11/jun/murky_planet.pdf http://www.dhushara.com/biocrisis/11/apr/rocky.pdf http://www.dhushara.com/biocrisis/10/dec/trilions_earths.pdf http://www.dhushara.com/biocrisis/10/apr/exoplanet.pdf http://www.dhushara.com/biocrisis/10/dec/no_planet.pdf http://www.dhushara.com/biocrisis/10/sept/goldilocksplanet.pdf http://www.dhushara.com/book/quantcos/planets/billions_of_earths.pdf http://www.dhushara.com/biocrisis/10/feb/cool_find.pdf http://www.dhushara.com/biocrisis/10/feb/super-earths.pdf http://www.dhushara.com/biocrisis/10/feb/sexy_young_earth.pdf dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 01-35 king, c., biocosmology: part i issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 7 fig 6: (a) cosmic abundances of the bioelements. (b) the neutron excess of the stable nuclei reflects the interaction between the strong and electromagnetic forces via the weak force the anthropic cosmological principle introduces the existence of observers as a boundary condition, effectively imposing the existence of life as a cosmological constraint. it asserts that fundamental properties of the universe may have been selected by the fact that only with such constraints on the laws of nature would there be a (complex biological) observer to witness the universe and examine its laws (barrow and tipler). forms of many-universes or many-histories cosmology likewise allow for a spectrum of possible universes, only some of which would have laws of nature which would permit the complex interactive states we associate with living systems. some cosmologies suggest selection principles may regenerate the universe as a whole, and predispose it to the complexity we find evident (smolin). a key approach which seeks to define the laws of nature uniquely derives from super-symmetric string theories. in supersymmetry, each half-integer spin matter-forming fermion (e.g. electron, proton, neutrino, fig 4) is matched by a force/radiation-generating integer spin boson (e.g. higgs, photon, zo, gluon, graviton, fig 4). in string theories point particles become resonant loops, strings or membranes in higher dimensional space as distance shrinks, avoiding the infinite singularity of point particles. consistent super-'brane' theories (green 1985, 1986, mukerjee 1996, duff 1998) require a large number of dimensions, between 10 and 26 in which all but four dimensions (space-time) curl up on microscopic scales. despite millions of possible compactifications, none has so far been defined which matches our particles and forces. regardless of the fine details of the ultimate theory resolving the origins of the universe in unification, the formof the forces as we know them is consistently described as a conseuqence of symmetry-breaking. dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 01-35 king, c., biocosmology: part i issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 8 fig 7: the orion nebula contains newly forming stellar systems possibly including the propylid (tiny black dot centre) with a dark 'planetary' disc (top and centre right) (buhl). some of these newly forming stars are also surrounded by clouds of hcn and hcho (inset bottom-left) (hubble telescope image). stars concoct complex molecules 2011 3. the abudantly fecund universe as time passes, more and more evidence is accumulating that, the universe and its galactic gas clouds are abundant in organic chemicals, from the simplest molecules to sugars, amino acids and nucleic acid bases. since fred hoyle coined the term "wooden universe" based on infra-red spectral data indicative of carbohydrate emission, there has been an awareness of the potential of galactic gas clouds to be cosmically abundant sources of prebiotic molecules. radio-telescope data as early as 1974 (buhl) demonstrated clouds of multiple-bonded hcn and h2c=o spanning the region in the orion nebula where several new stars are forming, fig 7. these are key precursors of complex polymerization pathways discussed below. glycine has also been found in interstellar gas and adenine is an abundant product in simulations of collapsing interstellar gas clouds containing a dozen elements including hydrogen, carbon, oxygen and nitrogen (chakrabadi 2000). along with amino-acids, all of a, u, g, and c have been detected in carbonaceous chondrites (hua et. al. 1986), such as the murchison meteorite. these also contain amphophilic membrane forming products (deamer and pashley 1989). cometary impacts are believed to have coated the earth in a rich endowment of organics from the earliest stages of solar system evolution when impact rates were high. http://www.dhushara.com/biocrisis/11/oct/complexmols.pdf dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 01-35 king, c., biocosmology: part i issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 9 fig 8: left: the cloud from which glycoaldehyde has been detected right droplets made by harsh radiation under interstellar conditions (dworkin et. al.) glycolaldehyde has recently been detected by jan hollis (2000) in a cloud of gas and dust 2 light years across of a type from which new stars are formed. he notes "interstellar clouds are spread throughout the galaxy and you often find the same molecule in many different clouds. since these organic molecules are so widespread, it may mean that pre-biotic chemical evolution is an ongoing process." glycoaldehyde can combine with other carbohydrate molecules to produce ribose. a team led by david deamer, jason dworkin, scott sandford and louis allamandola has also formed complex organic molecules under the harsh condition sof outer space. the main ingredients of interstellar ices are simple chemicals frozen together. mostly water, some ammonia, carbon monoxide, carbon dioxide and methanol. the team froze a mixture of these chemicals into a thin solid ice at temperatures close to absolute zero (-441â°f/ -263â°c) under extreme vacuum and exposed this to harsh ultraviolet radiation that mimics the radiation in space produced by neighboring stars. instead of finding a handful of molecules only slightly more complicated than the starting compounds, hundreds of new compounds were produced in every mixed ice studied. the types of compounds produced are strikingly similar to many infalling meteorites and interplanetary dust particles. thus much of the organic material found on the earth in its earliest years probably had an interstellar heritage." (dworkin et. al. 2001). the capacity of complex organic molecules generated in space to enter earth's atmosphere intact has also been confirmed. jeffrey bada has found evidence that "mother lodes' of buckyballs, football-shaped molecules made up of carbon atoms, have fallen intact to earth from outside the solar system from sudbtlry, ontario, where a meteoroid the size of mount everest crashed 2 billion years ago. they were loaded with helium, an element rare on earth, but abundant in inter-stellar space. the single impact site contained about 1 million tons of extra-terrestrial buckyballs. if complex buckyballs could fall on earth without burning up so could complex organic molecules (cohen 1996). dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 01-35 king, c., biocosmology: part i issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 10 4. quantum chemistry as non-linear complexity the complex expressions of chemistry particularly in biology are manifest as a final non-linear interactive consequence of cosmological quantum symmetry-breaking. the stability of the nucleus with increasing nuclear mass number and charge permits an unparalleled richness and complexity of quantum bonding structures around the diverse chemical elements. electron-electron repulsions, spin-obit coupling, delocalized orbitals and other effects perturb the periodicity of orbital properties and lead to the development of higher-order molecular structures. although quanta obey linear wave amplitude superposition, chemistry inherits an inverse quadtaic non-linearity in the form of the attractive and repulsive charge interactions caused by re-distributing electrons between orbital systems. such nonlinear interaction, combined with pauli exclusion, is responsible for the diversity of chemical interaction, from the covalent bond to the secondary and tertiary effects manifest in the complex structures of proteins and nucleic acids. the quadratic nature of charge interaction, leads to a situation in polymeric chemistry akin to the mandelbrot set, (fig 22a) and which is central in making complex molecules (fig 10) and the scale-dependent structures of tissues possible (fig 22b). fig 9: although all wave functions obey quantum superposition, the non-linear nature of electronic charge distribution and its resulting occupancy energetics, the pauli exclusion principle and additional electromagnetic effects results in the non-linear energetics of chemical bonding. this non-linear interaction is never fully resolved by any single bonding step and gives rise through subsidiary weak-bonding interactions to the global interactivity of complex biomolecules and cellular organelles. the source of this non-linear interaction is the foundation of all chemical bonding, the electric inverse square law of charge interaction. although the state vector of a quantum-mechanical system is a linear combination of base states, exemplified by the formation of linear combinations of s and p wave functions to form the four sp 3 hybrid orbitals, the electrostatic charge of the electron causes orbital interaction to have fundamentally non-linear energetics. the total energy is represented by the resonance integral of the hamiltonian composed with the wave function, divided by the normalizing overlap integral s. dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 01-35 king, c., biocosmology: part i issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 11 in the case of the one-electron hydrogen molecule ion, with saa= sbb normalized to 1, we have 2 solutions , as indicated: the capacity of orbitals, including unoccupied orbitals, to cause successive perturbations of bonding energetics results in an interaction bonding sequence, from strong covalent and ionic bond types, through to their residual effects in the variety of weaker h-bonding, polar, hydrophobic, and van der waals interactions, merging into the average kinetic energies at biological temperatures (watson et. al. 1988). these are responsible for secondary structures such as the a-helix of proteins and base-pairing and stacking of nucleic acids, and result in the tertiary and quaternary sturctures determining the global form of large biomolecules and the globally-induced active-site effects central to enzyme action. by contrast with the periodic crystalline or random amorphous structures of most minerals, the nonperiodic scale-dependent primary, scondary and tertiary structures in proteins and rna that are critical to establishing the richness of their forms and their bio-activity, fig 10. the almost unlimited variety of monomeric primary sequences induce higher-order secondary and tertiary structures through subsequent folding of the polymer. these are possible only because the non-linearity of charge interaction which causes chemical bonding also gives rise to further residual interactions at lower energies which are resolved by cooperative weak bonding. proteins are powerful catalysts because the global coherence of action arising from cooperative weak bonding makes for very powerful and responsive active sites. despite being genetically coded, such molecules form fractal structures both in their geometry and their dynamics, fig 31(e, f) (ansari et. al. 1985, liebovitch et. al. 1987, 1991). fig 10: global t-rna and protein [enzyme] tertiary structures are the result of hierarchy of strong and weaker chemical bonding interactions operating on a non-periodic secondary structure. both derive their structures in association with water. dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 01-35 king, c., biocosmology: part i issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 12 non-equilibrium thermodynamics (glansdorff and prigogine 1971) and the associated oscillating chemical systems such as the beloushov-zhabotinskii reaction (epstein et. al. 1983) demonstrate the capacity of auto-catalytic chemical systems, and membrane electrochemistry (chay & rinzel 1985), to enter into non-linear dynamics and chaos (epstein et. al. 1983, agladze et. al. 1984). quantum chaos and its suppression is also an emergent issue (gutzwiller 1992). the prebiotic polymerizations leading to the chemical origins of life share an informational paradox in which a small number of simple reactant lead to a large array of complex interacting products with many potential catalytic interactions. the initial conditions are thus insufficient to causally determine the products, except for a few predominant products such as adenine, leading to a huge variety of possible end states with increasing complexity. this allows for a high degree of polymeric variability which can be influenced both by auto-catalytic feedback and stochastic effects. 5. the non-recurrent table and the elementary bifurcation tree although the discrete quantum aspects of orbital occupancy are periodic, (fig 11 b, c) the properties of successive atoms in the same periods in the table are not exactly, or even approximately, periodic. successive members of the same group differ significantly in nuclear charge, atomic radius and electron repulsion, resulting in trends which permit interactive bifurcations between their properties. for example the properties of sulphur are significantly different from oxygen, although they are a period apart. the same goes for sodium and potassium through to fluorine and chlorine. when this non-linear nonperiodicity complicating the underlying periodicity of the s, p, d and forbitals is further extended to molecular systems, the parameter space of possible interactions resembles a quantum mandelbrot set (fig 22) forming an atlas of configurations in which the atomic interactions fig 11(a) and resulting molecular species supporting biogenesis (fig 14, 15) play a pivotal generic role. such trends are illustrated in polar and h-bonding properties of hydrides for which h2o is optimal (fig 11(b)), atomic and ionic radii in which the properties of elements like na and k differ sufficiently to induce distinct h2o bonding structures, and electronegativity, fig 11(c) in which o is even more electronegative than cl. such partial, or quasi-periodicity is also illustrated by the intrusion of the transition element d-orbital series between the subsequent s and p series (moeller et. al.). dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 01-35 king, c., biocosmology: part i issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 13 fig 11: (a) symmetry-breaking model of selection of bioelements, as an interference interaction between h and cno, followed by secondary ionic, covalent and catalytic interactions. (b) boiling points of hydrides illustrate the optimality of h2o as a polar h-bonding medium. (c) electronegativities illustrate optimality of o and water as a hydride and emphasize the unique role of first row covalent elements c, n, o demonstrated in primitive polymerizations. atomic and ionic radii also result in a two-way bifurcation of the properties of k, na, ca and mg. transition elements introduce unique catalytic activities partly through bringing the d-orbital into play. the stable aspects of quantum orbital interaction in biochemical evolution can be classified into a tree of fundamental bifurcations which distinguish the elements structurally and cause divisions between their properties in interaction. this forms a generative sequence in which the bioelements have key roles (fig 11(a)). each bifurcation gives rise to a reaction phase with added degrees of freedom and consequently greater interactive complexity. describing the evolution of interactive chemical quantum structures in terms of funadamental force bifurcations sheds constructive light on the broad categories into which molecular free interaction differentiates and determines both the degrees of freedom and the constraints for development of interactive complexity in bio-molecules. successive bifurcations are as follows: principal bifurcation : the covalent interaction of h with c, n, o. the central covalent quantum interaction in the table of the elements is between the two-electron 1s orbital and the eight-electron 2sp 3 hybrid. this is the fundamental covalent 1-2 shell quantum interaction and the bifurcation through which biocosmology comes into existence. all the members of the cno group have tetrahedral sp3 bonding geometry and form a graded sequence in electronegativity, from carbon in rough parity with hydrogen to electronegative oxygen, with one and two lone pair orbitals appearing successively in n and o. the resulting 3-d covalent bonds give c, n and o optimal capacity to form complex, diverse polymeric structures. symmetry is split, because the 1s has only one binding electron state, while the 2sp 3 has a series from 4 to 7 with differing energies and varied occupancy, as the nuclear charge increases. the 1s orbital is unique in the generation of the hydrogen bond through the capacity of the bare proton to interact with a lone pair orbital. some of the strongest covalent bonds known to chemistry are the multiple-bonds such as -cc-, -cn, and >c=o. these can be generated by applying any one of several high-energy sources such as u.v. light, high temperatures (900 o c), or spark discharge to the respective atoms. because of the higher energy of the resulting p-orbitals, these bonds possess a specific type of structural instability, in which one or two p-bonds can open to form lower energy partially s-bonded heterocyclic and other oligomeric structures. most of the prebiotic molecular complexity generated by such energy sources can be derived from mutual polymerizations of hcch, hcn, and h2c=o, and realated hybrids in association with 'sister' molecules such as urea h2n-co-nh2. these include purines such as nucleic acid bases adenine and guanine, their pyrimidine complements uracil and cytosine, key sugar types such as glucose and ribose, amino acids, polypeptides, porphyrins etc. they form a core pathway from high energy stability to structurally unstable polymerization, and to complexity, which we will elucidate. the formation of conjugated double and single bonds in these reactions results is delocalized p-orbitals (pullman and pullman 1962). such orbitals in heterocyclic (n-c) rings with conjugated resonance configurations also enable lone pair n > &pi* and &pi > &pi* transitions (rich and rajbandry 1976), dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 01-35 king, c., biocosmology: part i issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 14 resulting in photon absorption and electron transfer. these two effects in combination play a key role in many biological processes including photosynthesis, electron transport and bioluminescence. secondary splitting between c, n, and o: electronegativity bifurcation in addition to varying covalent valencies, lone pairs etc., the 8-electron 2sp3 hybrid generates a sequence of elements with increasing electronegativity, fig 11(c), arising from the increasing nuclear charge. this results in a variety of secondary effects in addition to the oxidation parameter, from the polarity bifurcation discussed below, to more subtle effects such as the complementation of -co2h and nh2 as generalized organic acidic and basic moieties. differential electronegativity results in several coincident bifurcations associated with water structure. a symmetry-breaking occurs between the relatively non-polar c-h bond and the increasingly polar n-h and o-h. this results in phase bifurcation dividing the medium into polar (aqueous) and non-polar phases in association with low-entropy water bonding structures induced around non-polar molecules. this is directly responsible for the development a variety of structures from the membrane in the context of lipid molecules fig 20, to the globular enzyme form and base-stacking of nucleic acids fig 10. critical in this process are the optimal properties of water h2o among all molecules, making possible in turn polarity interactions, aqueous acid-base bifurcation, ionic solubility and hydrogen bonding. the optimal nature of water as a hydride is illustrated in boiling points fig 11(b). water provides several other secondary bifurcations besides polarity. the dissociation h2o &harr h + + oh lays the foundation for the acid-base bifurcation, while ionic solubility generates anion-cation. many key properties of proteins and nucleic acids, are derived from water bonding structures in which a counterpoint of hbonding and phase bifurcation effects occu, determining the form of the alpha helix and nucleotide base pairing. hydrophilic-non-polar bifurcation is central to the tertiary structures of globular proteins as 'micelles' and hairpins of rnas, fig 10. the solubility or otherwise of a variety of molecules and ions is derived from the energies and entropies of their induced water-bonding structures. the large diversity of quantum modes in water is demonstrated by its very high specific heat, contrasting with that of proteins (cochran 1971). polymerization of nucleotides, amino-acids and sugars all involve dehydration elimination of h2o, giving water a central role in polymer formation. it has also been suggested water is a two phase medium containing quantum-coherent domains, in association with boundaries such as macromoleculaes and membranes (mae-wan ho isis report). http://www.i-sis.org.uk/quantum_coherent_water_life.php dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 01-35 king, c., biocosmology: part i issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 15 fig 12: the diversity of snow crystals illustrates the complexity of water bonding structures and their diversity under very slight perturbation of initial conditions (bentley and humphries). ionic bifurcation the cations bifurcate in two phases : monovalent-divalent, and series (na-k, mg-ca). although ions such as k + and na + are chemically very similar, their radii of hydration differ significantly enough to result in a bifurcation between their properties in relation to water structures and the membrane. smaller na + and h3o + require water structures to resolve their more intense electric fields. larger k + is soluble with less hydration, making it smaller in solution and more permeable to the membrane (king 1978) . ca 2+ and mg 2+ have a similar divergence, ca 2+ having stronger chelating properties. this causes a crossed bifurcation between the two series in which k + and mg 2+ are intracellular, mg 2+ having a pivotal role in rna transesterifications. cl remains the central anion along with organic groups. these bifurcations are the basis of membrane excitability and the maintenance of concentration gradients in the intracellular medium which distinguish the living medium from the environment at large. p and s as low-energy covalent modifiers the second-row covalent elements are sub-optimal in their mutual covalent interactions and their interaction with h. their size is more compatible with interaction with o, forming e.g. sio3 2, po4 3 and so4 2 ions including crystalline minerals. the silicones are notable for their o content by comparison with hydrocarbons. however in the context of the primary h-cno interaction, two new generic properties are introduced. po43is unique in its capacity to form a series of moderate energy dehydration polymers, both in the form of pyroand poly-phosphates, and in interaction with other molecules such as sugars. the energy of phosphorylation falls neatly into the weak bond range (30-60 kj/mole) making it suitable for conformational changes. the universality of dehydration as a polymerization mechanism in polynucleotides, polypeptides, polysaccharides and lipids, the involvement of phosphate in adenosine dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 01-35 king, c., biocosmology: part i issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 16 triphosphate (atp) energetics, ribonucleic acid (rna) and membrane structure, and the fact that the dehydration mechanism easily recycles, unlike the organic condensing agents, give phosphate optimality as a dehydrating salt. the function of s in biosystems highlights a second optimality. the lowered energy of oxidation transitions in s particularly s-s > s-h , by comparison with first row elements, gives s a unique role as a mediating mild covalent linkage both in terms of tertiary bonding and low energy respiration and photosynthesis pathways. transition element catalysis transition elements add key d-orbital effects, forming a catalytic group. almost all of the transition elements e.g. mn, fe, co, cu, zn are essential biological trace elements (frieden 1972), promote prebiotic syntheses (kobayashi and ponnamperuma 1985) and are optimal in their catalytic ligandforming capacity and valency transitions. zn2+ for example, by coupling to the po43backbone, catalyses rna polymerization in prebiotic syntheses and occurs both in polymerases and dna binding proteins. both the fe 2+ -fe 3+ transition, and spin-orbit coupling conversion of electrons into the tripletstate in fe-s complexes occur in electron and oxygen transport (mcglynn et. al. 1964). other metal atoms such as mo, mn have similar optimal functions, e.g. in n2 fixation. these five processes between them constitute the major quantum bifurcations in the free interaction of the elements. they are also the central processes operating in biogenesis. put together this says the following: the central biogenesis pathways are themselves results of the central interactive quantum bifurcations of symmetry-breaking and its resulting non-linear interactions. while life may be possible from other combinations of elements and other temperatures and pressures, life as we know it has taken the sang raal or blood-royal route of quantum cosmology. fig 13: (a) the perturbing effect of the neutral weak force results in violation of chiral symmetry in electron orbits. without perturbation (i) the orbits are non-chiral, but the action of zo results in a perturbing chiral rotation. (b) autocatalytic symmetry-breaking causes random chiral bifurcation (i).weak perturbation breaks stability to one chiral form (iii) dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 01-35 king, c., biocosmology: part i issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 17 kenso soai (1998) and his team have demonstrated the autocatalytic bifurcation framework as well they took a mixture of compounds containing a small excess of one enantiomer of the amino acid leucine. in the presence of this imbalance, the components of the solution reacted to form a compound called a pyrimidyl alkanol, also with a small excess of one enantiomer. but this molecule then acted as a catalyst in its own formation, and soon almost all the pyrimidyl alkanol in the solution was of this sort. (see also new sci 12 dec 98 16) did exploding stars shatter life's mirror? may 10 tertiary interaction of mineral interface both silicates such as kaolinite clays (strigunkova et. al. 1986) and volcanic magmas (lavrentiev et. al. 1984) have been the subject of intensive interest as catalytic or information organizing adjuncts to prebiotic evolution. clays have been proposed as a primitive genetic system and both include adsorbent and catalytic sites (cairns-smith 1982, weiss 1981). clays also appear to play a key role in stabilizing ribonucleotide polymerization (ferris 1996). the mineral interface involves crucial processes of selective adsorption, chromatographic migration, and fractional concentration, which may be essential to explain how rich concentrations of nucleotide monomers could have occurred over geologic time scales. 6. structural dynamics of core polymerization pathways the initial polymerizations of energetic multiple-bonded monomers in the reaction in figs 14 and 15 form a particularly interesting problem from a quantum-mechanical point of view, because they provide some of the richest examples of growth in quantum-mechanical complexity, in which a relatively small number of simpler entities give rise to increasingly complex structures whose properties cannot be fully predicted from the initial conditions. h2c=o in aqueous solution gives rise to 4 to 7 carbon sugars, including ribose, as well as branched polysaccharides. hcn gives rise to heterocyclic purine and pyrimidine nucleic acid bases, and in addition several amino acids, polypeptides, porphyrins, and many other types of biomolecule (lowe et. al. 1963, calvin 1969, mizutani et. al. 1975). a similar array of products arises from hybrids such as cyanogen nc-cn (schwartz et. al. 1975) and cyanoacetaldehyde nc-ch2-h2c=o. although several of these products, such as the ring polymers adenine (hcn)5 and ribose (h2co)5 are stable product structures, many of the more complex products, such as particular oligopeptides are metastable or stochastic products of the reaction. these conditions differ markedly from the current biochemical regime in which structurallystable metabolic pathways are maintained through genetically-coded enzyme catalysis except where recombinational stochasticity is specifically initated as in generation of antibody immuno-diversity. http://www.dhushara.com/biocrisis/10/sept/life'smirror.pdf dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 01-35 king, c., biocosmology: part i issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 18 fig 14: known product structures and pathways in hcn polymerization. since the initial conditions do not contain sufficient information to determine the final products, the system contains many potential outcomes. the lower energy configuration of key products, such as adenine's resonance stabilization, leads to some stable conformations based on free energy. stochastic indeterminacies in the interaction of simpler molecules lead to multiple branching pathways. products of increasing complexity such as polypeptides possess increasingly active catalytic potential, which may alter the structural-stability of polymerization to favour certain types of product. the dynamics may trigger a sequence of autocatalytic bifurcations, some of which may result in the formation of attracting molecular products. these reaction pathways are capable of producing a vast variety of complex molecules with generic relationships to key biomolecules, including amino acids, polypeptides, hcn polymers, purines, pyrimidines and porphyrins. both hcn and hcho polymerizations have prominent cyclic products which act as spontaneous end points of polymerization, because cyclization mutually neutralizes reactive moieties. the purines, pyrimidines, ribose and porphyrins all display structure consistent with being cyclic terminators. the capacity of polymers for non-periodic primary sequencing gives rise to complex tertiary structures, which are fractal as a result of structure on several overlapping scales from the atom, through local groups, to structures such as a-helices through to global conformation changes. this fractal nature is reflected both in the geometry and the quantum energetics of molecular transformations (ansari et.al. 1985, liebovitch & toth 1991). substrate form is dependent firstly on local active sites, and in turn on the global tertiary structure of catalytic molecules. dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 01-35 king, c., biocosmology: part i issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 19 fig 15: (a) one of several synthesis pathways for pyrimidines. (b) sample hcho polymerization routes. phosphorylation of the oligo-aldehydes causes the reaction to favour ribose. (eschenmoser 1992). although the first syntheses produced the purines adenine and guanine readily, cytosine and uracil, the complementary pyrimidine bases making up the other half of the pair a-u and g-c, however stanley miller, forty three years after his original pioneering experiment in spark synthesis, with michael robertson, discovered a way for the primordial pond to make them in high yield. although urea is produced in miller's original experimental setup, it never reaches a high enough concentration. when he added more urea, it reacted with cyanoacetaldehyde, another by-product of the spark synthesis, churning out vast amounts of the two bases. urea would have been able to reach high enough concentrations as shallow pools of water on the earth's surface evaporated. (cohen 1996, horgan 1996). eschenmoser (1992) has found that glyceraldehyde phosphate in the presence of hcho will produce 5carbon sugars with up to 33% ribose. in the absence of hcho the reaction tends to produce 6-carbon sugars. the phosphate-induced reaction is key here because rna, atp and glycolysis all involve phosphate dehydration energy. this indicates a specific link to phosphate energy primordial to the formation of oligonucleotides and even ribose. fig 16: (a) mgatp-complex illustrates linkage between primal stability structures. cyclic pentamers of hcn (adenine) and hcho (ribose) are linked by phosphate dehydration, stabilized by cation and water structures. (b) heterocyclic form of heme. porphyrins have also been detected in primal syntheses. (c) nucleophilic attack of adenine n9 on ribose. dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 01-35 king, c., biocosmology: part i issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 20 7. rna and cosmology in 1981 francis crick commented that 'the origin of life appears to be almost a miracle, so many are the conditions which would have to be satisfied to get it going." (horgan 1996) now, several findings bolster the dominant theory of genesis that life began in an era in which rna was both the genetic and catalytic basis the rna era (gilbert 1986, benner et.al.) in which simple replication and 'enzymatic' process based purely on rna catalysis established evolutionary biochemistry. the general outlines are clear. ribose, unlike the deoxyribose in dna, has plausible prebiotic syntheses. rna's capacity to both form double-helices, like dna and to also three-dimensional tertiary structures similar to proteins through base-backbone bonding to ribose fig 10(a), causes rna to have both genetic and catalytic capacity. simple biological rnas have been demonstrated to have autocatalytic selfassembling capacity. the catalytic activity of polynucleotides, hinges on various forms of proton transfer fig 17(a,b,c) (pace and marsh 1985), in particular transesterification. the essential core of the protein-assembling ribosome remains rna as does the signal recognition particle which shepherds nascent proteins through the membrane. the ancient fossil nucleotide coenzymes including atp, nad, coenzyme-a and vitamin b12 are all ribonucleotides. eucaryote organisms continue to have a massive commitment to rna processing within the nucleus, including the use of many small small nuclear ribonucleotides or snurps involved in rna splicing. this suggests eucaryotes have never fully transferred from an rna-based metabolism. reverse transcriptases also remain ubiquitous and essential for such basic functions as telomere extension, and have a common evolutionary tree, giving retrotransposons and retroviruses a potentially ancient origin in the commonality of the rna era. there is still debate about whether rna was actually the primordial genetic molecule and other hybrid molecules such as peptide-nucleic acids which use peptide rather than sugar linkages also have genetic potential and plausible prebiotic status (nelson et. al.), however it is clear rna itself has generic status as a cosmological molecular structure on several grounds. adenine is a principal thermodynamic product of hcn polymerization in industrial yields. all of a, g, u and c now have prebiotice status as favoured products of such reactions. ribose is an optimal sugar conformationally in terms of permitting complementary double helix formation, and has a synthesis route from glyceraldehyde phosphate. the complementations of a-u and g-c posses a type of structural optimality among the bases. the heterocyclic polymers are restricted in their variety by the positions of n atoms required by the polymerization process. the tautomeric states of a, u, g and c indicate au and gc may be optimal for base-pairing among close prebiotic variants. the nucleotide unit, as exemplified in atp consists of a direct concatenation of key products of hcn and hcho polymerizations. adenine and ribose are the cyclic pentamers of hcn and hcho linked via dehydration to a dehydrating oligo-phosphate giving it the statues of a generic structure, fig 16(a) stabilized by water and mg 2+ , positive ions also play an important role in stabilizing monoand oligonucleotides. it was originaly synthesized under primitive conditions by ponnamperuma et. al. (1963). mg 2+ ions are also bound to transfer rna and play a critical role in transesterification, balancing the negative phosphates. the fact that the polymerizing phosphodiester bond results from the removal of h2o from phosphate suggests that phosphate was the active moiety linking of the base-sugar-phosphate complex, fig 16(c) and thus drove the entire formation of nucliec acids. dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 01-35 king, c., biocosmology: part i issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 21 rna proved difficult for a time to induce into complementary replication in enzyme-free systems, but its relative difficulty of synthesis may be essential to its function. it is necessary that rna be thermodynamically unstable, or life could not exist dynamically but would 'crystalize' all the way to non-genetic polymers. a variety of partial model systems of complementary replication have been realized by orgel and his coworkers, however instabilities in polymerization have hindered experimental enzyme-free complementary polymerization of rnas (orgel 1992). it is clear that a regime of polynucleotide chemistry would have to have occurred stably over evolutionary time scales for an rnabased form of life to evolve to the point where it had established translation and captured metabolic synthetic pathways. ferris reported (1996) that he had found a means by which the first large chains could have been forged. when his team added montmorillonite, a positively charged clay believed to be plentiful on the young earth, to a solution of negatively charged adenine nucleotides, it spawned rna 10-15 nucleotides long. if these chains, which cling to the surface of the clay, were then repeatedly 'fed" more nucleotides by washing them with the solution, they grew up to 55 nucleotides long. ferris notes the clay gets rna off the hook of having to take on the tasks of information storage and catalysis in one fell swoop. it would catalyse rna synthesis, stocking pools with a large range of rna strands that, as szostak and others have shown, would evolve a catalytic capacity of their own. (horgan 1996). thus complementary replication can come into existence after a phase of single-stranded polymerization has given rise to a fractal rna environment with a diverse array of oligomeric and polymeric structures, which in turn feedback autocatalytically on replication and monomer synthesis. dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 01-35 king, c., biocosmology: part i issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 22 in 2009 sutherland discovered that pyrimidine nucleotides can be readily synthesized from simple prebiotic molecules bypassing the more difficult routes depending on synthesizing ribose, bases independently and trying to then attach them to phosphate. in fact phosphate was pivotal in producing new intermediates which would then in good yield polymerize to nucleotides. chemist shows how rna can be the starting point for life may 14, 2009 since then he and his colleagues have proposed one-pot pathways to both purine and pyrimidine nucleotides (powner, sutherland and szostack 2010 chemoselective multicomponent one-pot assembly of purine precursors in water j. am. chem. soc. 2010, 132, 16677â€“16688). hypothetical pathways to both purine and pyrimidine nucleotides fro the above paper powner and sutherland have also investigated interconversion of sugar bases between ribo and arabino nucleotide intermediates (powner mw, sutherland jd. 2010phosphate-mediated interconversion of riboand arabino-configured prebiotic nucleotide intermediates. angew chem int ed engl. 49(27):4641-3). a central scenario out of many, including volcanic hot pools, and hydrothermal vents, is the three-phase boundary of a phosphate-rich, clay shore line under tidal or weather-related variations in a pool in which the margin is reversibly dehydrated e.g. by sun-drying. both clays and volcanic basalts have been cited as possible mineral interfaces. precipitated phosphate at 37 o , leads to pyrophosphate formation and hence phosphate bond energy (hermes-lima 1990). since the energy for nucleotide polymerization is driven by h2o removal, reversible dehydration of a medium containing phosphate, bases and sugars provides one of the most direct and simple routes to polynucleotide formation. http://www.dhushara.com/book/bchtm/suth/sutherland.htm http://www.dhushara.com/book/bchtm/suth/sutherland.htm http://www.dhushara.com/book/bchtm/suth2.jpg dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 01-35 king, c., biocosmology: part i issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 23 8. diverse horizons of the rna epoch a whole new field of rna research has developed from the discovery of spontaneous splicing of rnas in living systems by tom cech and the demonstrated capacity of such rnas to function as catalysts in transesterifications and the work of jack szostack's teams in selective rna catalysis (cech 1986a). this immediately made the idea of the rna world before proteins a natural hypothesis. this work has grown with artificial selective evolutionary studies, culminating with the development of a ribozyme which is capable of high fidelity complementary replication of short rna oligomers of arbitrary sequence (johnston et.al. 2001). this has become a turning point in the credibility and maturity of the rna world as a precursor to dna-based life which can develop as an autonomous molecular system. the model has been extended to others for rna-based error-correction, synthetases and the ribosome (bass and cech 1984, cech 1986b, zany and cech 1986, garriga et. al. 1986, weiner and maizels 1987). modified ribozymes are capable of acting as polymerases which can replicate complements to subsections of themselves (green et. al. 1990, doudna et. al. 1991). the discovery that rna appears to be the agent of peptide-bond synthesis in the modern ribosome (guthrie 1992, pace 1992, noller et. al. 1992) and the capacity of modified ribozymes to act as aminoacyl esterases (picarilli et.al. 1992), the first step of ribosomal action in protein synthesis, establish rna has the potential to act as synthetase as well as transfer, messenger and ribosomal functions. this gives rna the capacity to act on its own to catalyse both its own replication and the ordered polymerization of proteins. simpler model systems have also been advanced of the stereospecific capacity of dnucleotides to act as a catalyst of l-amino acid polymerization (lacey et. al. 1990). these results enable rna to be the key prebiotic molecule generating ordered polynucleotide and polypeptide structures. fig 17: the ribozyme world: (a) phospho-imidazole. proton transfers in (a) imidazole, (b) in base tautomerization, (c) in tetrahymena intron. (d) the first effective ribozyme rna polymerase (iii) a 172 unit molecule bred by molecular selection from a ligase ribozyme (i) through selcctive evolution of a pool of other intermediates (ii). this ribo-rnapolymerase will faithfully perform complementary replication of oligo-ribonucleotides of arbitrary sequence up to 14 units long with accuracies of up to 98% per base pair. (e) the rna polymerase ribozyme tc19z, that was able to synthesize a spectrum of rna sequences, including the accurate synthesis of an enzymatically active rna dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 01-35 king, c., biocosmology: part i issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 24 szostak and wilson (1996, wilson and szostak 1995) have evolved ribozymes capable of a broad class of catalytic reactions. the catalysis of previous ribozymes tended to involve only the molecules' sugarphosphate "backbone," but these could also promote the formation of peptide bonds (which link amino acids together to form proteins) and between carbon and nitrogen. (horgan). david bartel a former member of szostak's team, has evolved rnas that are as efficient as some modern protein enzymes. the problem with most ribozymes is that they are as likely to snip an rna molecule apart as stitch one together which makes copying a molecule fifty nucleotides long (the minimum size necessary to catalyse a chemical reaction) difficult or impossible. bartel's new ribozymes, on the other hand, can stitch small pieces of rna together without breaking larger molecules apart. these ribozymes use highenergy tri-phosphate bonds similar to atp as their fuel, speeding the reaction up several million-fold. "we've got ribozymes doing the right kind of chemistry to copy long molecules" says szostak "we haven't achieved self-replication from single nucleotides yet, but it is definitely within sight". (cohen) zhang and cech have reported a step towards the goal of linking amino-acids. they isolated rnas that could efficiently link specific amino acids together (zhang and cech 1997). these pseudo-ribosomes were selected from a random pool of 1015 synthetic rnas. they then elicited a trans-acting by coupling one of the amino acids to a short rna with complementary sequence to the ribozyme achieving a ribozyme which whould join a ribosynthetase-amino acid to form a peptide bond with another thus relicating even more closely ribosomal function. they also found that a small region of many of the rnas they selected was 70 per cent identical to some regions of the ribosomal rna. "we not only copied ribosome function, we seemed to have recapitulated its evolution," says cech. the two researchers then removed or mutated these sequences in the synthetic rnas (zhang and cech 1998) any change to this region cut the activity of the rna by a factor of between 20 and 600. this suggests this region in both the modern ribosome and the synthetic rna may have the same role in the fusion reaction, such as holding the amino acids in the correct position and that they may have converged on the same molecular solution. in 2011 a breakthrough has been made by recombining traits evolved separately in different ribozyme lineages in combination with in-vitro evolution and engineering producing an rna polymerase ribozyme (tc19z in fig 17), capable of synthesizing rnas of up to 95 nucleotides in length, that was able to synthesize a spectrum of rna sequences, including the accurate synthesis of an enzymatically active rna, a hammerhead endonuclease ribozyme (wochner a, attwater j, coulson a, holliger p 2011ribozyme-catalyzed transcription of an active ribozyme science 332 209-212). the alternative hypothesis is that life may have begun as a molecular hybrid, pna or peptide nucleic acid. pna has a similar structure to rna except for having a peptide backbone based on prebiotically abundant glycine and can co-instruct complementary rna sequences and vice versa (bohler, nielsen and orgel). the bases of pna are joined together with peptide links like those in proteins which may not present the instabilities which sugars may have faced on the early earth. matthew levy and his colleagues (nelson, levy and miller) persuaded up to 78 per cent of plausible prebiotic chemicals to transform into pna backbone subunits amino-ethyl glycine or aeg. the acetic acid derivatives of the bases a, g u and c can likewise be generated from prebitotic reagents including nh4cn with glycine and cyanoglyceraldehyde. aeg units link up readily at 100 deg c, which may have been common temperature four billion years ago when our planet was rich in volcanic activity. pna is clearly an alternative route to establishing the rna era which also has a good cosmological foundation. however researchers concede that there is no evidence such alternative molecules have existed in earth's history dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 01-35 king, c., biocosmology: part i issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 25 "you don't see a smoking gun," says gerald joyce, of the scripps research institute. (marshall m 2011 first life: the search for the first replicator new scientist 15 aug). 9. universal stability structures in molecular biology the previous discussion of the rna era can unravel a double-bind that is central to biogenesis how did the core biochemical pathways become generated? the traditional viewpoint is that they were successively created starting from a simple chemical-feeding heterotroph, through mutational evolution, building one-by-one the protein components necessary to make a working whole. this however does not explain how integrated systems such as electron transport and the citric acid cycle could have functioned at all with only a vestigial complement of enzymes. this suggests that many of the major features of molecular biology are generic structures which can come into existence under suitable conditions, through bifurcation, independently of the emergence of genetic rna, and that these were subsequently captured by genetic takeover as genetic complexity permitted. such generic structures include the polymeric structure of proteins and nucleic acids, nucleotide coenzymes, bilayer membrane structure and the topological closure of the cell, ion transport and membrane excitability, membrane-bound electron transport, glycolysis and the citric acid cycle. such a perspective has far-reaching consequences for molecular biology in cosmological terms, for while the details of mutational evolution will be unique to each environment, the major features underlying biology could be universal. (a) nucleotides and the nucleotide coenzymes. the nucleotide co-enzymes are widely regarded as ancient molecular fossils retained from the rna-era. in addition to the key role of adp and atp as energy currency in the bio-metabolism, gtp is used in protein synthesis, and the nucleotides udp and cdp are carriers of glucose and choline and other membrane components. model prebiotic reactions have successfully coupled udp and cdp to glucose dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 01-35 king, c., biocosmology: part i issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 26 and choline (mar et. al. 1986). both nad, and fad function as carriers of redox energy. coenzyme a consists of adenosine coupled to pantothenic acid and functions as a carrier of acyl and other groups via the terminal sh bond (reanney 1977). vitamin b12 also illustrates how a di-nucleotide can bind a metallic porphyrin ring. eschenmoser (1988) has also discovered a plausible prebiotic pathway generating the more complex b12 molecule which involves two nucleotides and a coporphyrin.prebiotically such a molecule could have also utilized a lowered fe 2+ fe 3+ activation energy as a carrier of electrons. (b) translation. according to the genetic takeover hypothesis, evolution of rna captured existing stability structures in the prebiotic medium. the most central of these is clearly the use of proteins as coded enzyme catalysts. such a process could only have occurred in an environment in which rnas coexisted with amino-acids and in which a very small additional genetic advantage could capitalize on simple coding of existing structures to good effect. a variety of amino acids and oligopeptides are common products of prebiotic syntheses. the polymerization of amino acids and the development of peptide backbones with cyanide side chains from the linear hcn oligomer fig 14, provide alternative routes to oligopeptide structure. a natural propensity for -nh2 and -co2h moieties as basic and acidic groups arises directly from the electronegativity bifurcation. the discovery that ribosomal, synthetase, messenger and transfer functions of protein synthesis can all in principle be carried out by rnas alone leads to a natural interpretation of the development of the genetic code from a protein-free translation system. the major partitions of the genetic code have structural features consistent with an origin in underlying chemical bifurcations. the fundamental bifurcation sequence, fig 18 is as follows: (1) polarity bifurcation: there is a major bifurcation in polarity between amino acids with anticodons having centre bases u & a. uracil is correspondingly more hydrophilic than adenine, as reflected in their dominant split in hydrophobicity a(3.86)>g(2.3)>c(1.5)>u(1.45) and water solubilities a=1/1086, u=1/280. this leads to the idea that the polarity bifurcation was a principal symmetrybreaking factor in the origin of the nucleic acid code (king 1982). (2) abundance and gc: the initial base g also codes the most abundant amino acids, consistent with a gxy code starting with gay=polar (anticodon u), guy=non-polar (anticodon a) providing binding strength of gc and frame shift suppression (y=pyrimidine). (3) four-fold code: extending to include ggy, gcy, provides a fourfold specificity for polar (asp/glu), non-polar (val and larger), along with gly, and ala as most abundant. (4) eightand twelvefold codes: this could have then doubled to and 8-word code by including cay, cuy, cgy, and ccy coding for non-polar and basic groups, and then a similar series based on aay, auy, agy, and acy wong (1975) originally noted a correspondence between the first codon base and biosynthetic pathways in primitive organisms such as sulphur bacteria with pro, arg, gln leu, his derived from glu and having first codon base c and ser, thr, ile, asn, met, lys being derived from dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 01-35 king, c., biocosmology: part i issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 27 asp having first codon base a (knight, freeland and landweber 1999). ohand sh-containing amino acids also form a single additional block (ua)(gc)y, suggesting a third bifurcation for h-bonding, with uay reading stop. notably these is significant stereospecific affinity between certain amino acids such as ile and arg and their codons (ibid). (5) evolutionary takeover: from this point evolutionary selection begins to optimize the bifurcations caused by stereospecificity and the growth of these interactions into synthesis pathways, based on error minimization and the incorporation of the last of the amino acids. later assignments such as trp are consistent with evolutionary adaptions. freeland and hurst (1998), have shown that strong selective pressures must have acted on the code during its evolution. hurst found that single-letter changes to a codon, inserting the wrong amino acid into a protein, tended to specify amino acids that were very similar chemically to the correct ones, minimising the impact on the protein. freeland then reasoned that the code should minimise chemical differences most between the correct and incorrect amino acid at the third base in the codon since translation misreads this base 10 times as often as the second. in an analysis that gave extra mathematical weight to the vulnerable sites most likely to be mistranslated, freeland showed that no more than one in a million random codes was better at reducing the impact of errors than the natural code. the possibility of evolutionarty change in the code is affirmed by both mitochondrial and nuclear variants (knight, freeland and landweber 1999). following on from this freeland et. al. (2000) have analysed other work showing that more optimal global solutions do exist to propose that stereochemical and synthesis path constraints fixated the code ealy on into one which was later evolutionarily optimized on error minimization constraints, the modern code being optimal under these constraining conditions. this analysis gives strong weight to the idea that the form of the code is derived from chemical, historical and selective factors rather than being a frozen accident which happened to the predecessors of the last common ancestor of living cell lines. fig 19: left and centre: microcellular formations generated by the author from hcn and hcho. right: spores of a psilocybe species at the same magnification for size comparison (king 1991b). (c) the membrane, excitability and ion transport dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 01-35 king, c., biocosmology: part i issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 28 all life as we know it is dependent on maintaining a distinct internal micro-environment as an open farfrom-equilibrium thermodynamic system (glansdorff and prigogine), through the topological closure of the cell. viruses for example all depend on cellular life. the structure of the bilayer membrane is a direct consequence of the polarity bifurcation. the formation of amphophilic lipid-like molecules, joining a linear non-polar hydrocarbon section to an ionic or h-bonding polar terminal, leaves 2 degrees of freedom for layer formation. backing of the non-polar moeties to one another, fig 20(b), completes the bilayer. cell structure can then arise directly from budding of the bilayer, as illustrated in budding in several types of prebiotic reaction medium. microcellular structures are abundant in many origin of life syntheses, fig 19. the use of cdp associated with choline, inisotol & lipids in membrane construction is consistent with membrane formation in the rna era. the structure of typical biological lipids such as phosphatidyl choline display a modular structure similar to atp, consisting of fatty acid, glycerol, and substituted amine again linked by dehydration and involving phosphate, fig 20(e). the existence of the membrane as a non-polar structure leads to segregation into ionic and non-polar reaction phases. ion transport is essential in maintaining the concentration gradients that distinguish the cytoplasm from the external environment and thus must develop in the earliest cellular systems (macelroy et. al. 1989). ion transport is a source of significant electronic effects, because the membrane under polarization is piezo-electric and is capable of excitation in the presence of suitable ions. model systems using the simple 19 unit oligopeptide na-ionopore alamethicin and artificial membranes display action potentials (mueller and rudin 1968). similar results have been reported for microcells produced by prebiotic techniques containing light irradiated chromophores (przybylski and fox 1986), demonstrating that such effects are fundamental to the quantum architecture of lipid membranes (king 1990). four groups of non-polypeptide neurotransmitters: acetyl-choline, catecholamines, serotonin and histamine are amines, the latter three being derived from amino acids tyrosine, tryptophan and histidine by decarboxylation. two others are amino acids and thus also contain amine groups. notably alamethicin also has glutamine amides located in the core of the pore (fox & richards 1982). the catecholamines are linked to indoles such as serotonin by a prebiotic pathway, fig 20(c). fig 20: (a) nad structure permits linkage of other energies to a redox bifurcation. (b) h+ and e transport linked by h2 in membrane due to insolubility of eand solubility of h+. (c) prebiotic link between catecholamines and indole via quinone-type photoreduction. (d) hypothetical form of primitive electron transport as a non-equilibrium limit cycle. (e) acetyl-choline and phosphatidyl choline compared. phosphatidyl choline lipid stacks tail to tail as shown in the clothes pegs (b). dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 01-35 king, c., biocosmology: part i issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 29 (d) electron transport the fact that the proton is soluble in water to form the hydrogen ion, but the electron is not, unless attached to another group such as a protein, causes a physical linkage to exist between the polarity bifurcation and the charge bifurcations associated with electron and proton transfer, fig 20(b) mediated by h transport through quinone reduction, (c). despite the complexity of modern electron transport in photosynthesis and respiration, there is considerable evidence that membrane electrochemistry could have arisen before translation could produce coded enzymes. firstly there is a consistent basis for the existence of many of the components of electron transport during the rna era, since the nucleotide coenzymes nad, fad, a nucleotide-bound mg & fe-porphyrin ring similar to b12, a cysteine-bound fes group (hall et. al. 1974), possibly based on glutathione (g-glutamyl-cysteinyl-glycine) and quinones provide all the key components of electron transport in an rna dependent but protein-free form, fig 20(d) (king 1990). both porphyrins and quinones have obvious prebiotic syntheses and the primal role of nucleotide coenzymes has already been discussed. secondly, membrane structure and the solubility differences between the electron and proton guarantee a link between electron and hydrogen ion transport fundamental to quantum symmetry-breaking. electron transfer does not require the complex coded active sites required to catalyse specific molecular transformations. model systems using feporphyrins and imidazole can couple oxidative electron transport to phosphorylation (brinigar et. al. 1966) and photo activated mg-porphyrin to phosphate link (goncharova and goldfelt 1990, lozovaya et. al. 1990). fig 21: (a) di-phosphorylation of sugars leads to glycolysis through interaction of charged phosphates. (b) generic examples of group transfer in the tricarboxylic acid cycle. (e) glycolysis glycolysis forms a bridge between six and three carbon sugars, reversing the structural pathway from h2co, glycoaldehyde and glycderaldehyde to cyclic sugars, fig 15(b). glycolysis is made energetically possible by phosphorylation, and releases high energy phosphate capable of driving other phosphorylations (hermes-lima and vieyra 1989), fig 21(a). it is notable that glycolytic diphosphorylation of fructose is homologous with the route for nucleotide formation of fig 16(c). the high phosphate environment leading to rnas would then naturally lead to similar phosphorylation of other sugars, and release of the high-energy phosphate bond through cleavage of the sugar. mineral catalysis associated with phosphate gives the glycolytic pathway a natural basis for lysis of sugars as a dissipative dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 01-35 king, c., biocosmology: part i issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 30 structure. biological udp-glucose coupling is consistent with nucleotide-dependent glycolysis in the rna era. (f) the tricarboxylic acid cycle forms a pool of multiply carboxylated molecules which carry co2 in various states of energy, and result in reducing energy via nucleotide coenzymes nad and fad, which coupled with the use coenzyme a provide a basis for the tricarboxylic acid cycle in the rna era. this could have existed as a limit cycle of diand tri-carboxylated molecules acting both as an acceptor of acetate (a carbohydrate-equivalent i.e. (h2co)2) and as an emitter of molecular co2 and reducing h, thus bifurcating carbohydrate level redox potential into reduced and oxidized components. the linkage to nucleotide coenzymes such as nad would have served to create a bifurcation of redox potential in the molecular milieu contributing to the diversity of reacting species. the cycle may have been hypercyclic (eigen et. al. 1981) or chaotic, consisting of a population of molecules undergoing various generic transformations with net inflow of carboxylic acids and net emission of co2 and transfer of h, due to generic transformations as illustrated in fig 21(b). isomerization would have been catalysed by fe 2+ . several steps may have been driven by sunlight photolysis (waddell et. al. 1989). the probability that the the central structures of molecular biology existed in the rna era is consistent with their being chemical stability structures utilized by catalytic rnas. the small genomes during the rna era and limited catalytic capacity of rnas by comparison with protein makes it likely that the emerging rna-based system had to capitalize on existing chemical stability structures becase it lacked enzyme-based biosynthetic pathways. genetic takeover also places these stability structures in a category determined by the cosmological milieu, thus giving evolutionary biology a cosmological foundation. fig 22: modern stromatolites (left), structures built of cyanobacteria (blue-green algae) grace shark bay, australia. j. william schopf has found remnants of 3.6 billion-year-old stromatolites lying near fossils of 3.5 billion-year-old cells that resemble modern cyanobacteria,. resembling strings of microscopic cells (right). life thus arose within the first billion years of earth's formation from the planetary disc (scientific american feb 1991). dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 01-35 king, c., biocosmology: part i issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 31 10. the last universal common ancestor recent research suggests that the last universal common ancestor (luca) of all life on the planet may have arisen from a phase interface between alkaline hydrogen-emitting undersea vents and the archaic acidified iron-rich ocean (martin and russel 2003), giving rise to an active iron-sulphur reaction phase still present in living cells and associated with electron transport and some of the most ancent proteins, such as ferredoxin, in which differential dynamics in membranous micropores in the vents managed to concentrate polypeptides and polynucleotides to biologically sustainable levels (baaske et. al. 2007, budin et. al. 2009), giving rise to the rna era, while at the same time providing a free energy source based on proton transport across membranous microcellular interfaces resulting from fatty acids also being concentrated above their critical aggregate concentration. fig 1a: proposed scheme for the universal common ancestor (martin and russel 2003) http://www.dhushara.com/book/bchtm/biocos.htm#anchor-martin-47857 http://www.dhushara.com/book/bchtm/biocos.htm#anchor-baaske-11481 http://www.dhushara.com/book/bchtm/biocos.htm#anchor-baaske-11481 http://www.dhushara.com/book/bchtm/biocos.htm#anchor-budin-35882 http://www.dhushara.com/book/bchtm/biocos.htm#anchor-martin-47857 dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 01-35 king, c., biocosmology: part i issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 32 the universal common ancestor of the three domains of life may have thus been a proton-pumping membranous interface from which archaea and bacteria emerged as free-living adaptions. this is suggested by fundemantal differences in their cell walls and other details of evolutionary relationships among some of the oldest genes. 1. biocosmology an overview of how the origin of life may arise from cosmic symmetry-breaking. 2. chemist shows how rna can be the starting point for life may 14, 2009 a pivotal article showing how nucleotides can be synthesized from simple molecules. 3. first cells, proton-pumping and undersea rock pores (lane 2009 with abstracts pdf password "model") oct 19, 2009 a breakthrough in understanding how the first living cells could have been created at an undersea rock-pore interface. it has also been proposed, on the basis of the highly-conserved commonality of transcription and translation proteins to all life, but the apparently independent emergence of distinct dna replication enzymes in archaea/eucaryotes and eubacteria, that the last universal common ancestor had a mixed rna-dna metabolism based on reverse transcriptase, pinpointing it to the latter phases of the rna era (leipe et. al.1999). fig 1b: hypothetical branching and evolution of rna and dna replication machinery (leipe et. al. 1999). 11. the precocious origins of life on earth far from being an improbable accident taking billions of years to find the right conditions, life appears to have become established on earth as soon as the conditions permitted a liquid water ocean, suggesting either that earth was richly bombarded with complex organic molecules which quickly found within the diversity of microclimates on earth some which were directly conducive to the processes leading the to the genetic epoch, or that life's had already begun in the gas and dust cloud initially forming the solar system. gustaf arrhenius, (mojzsis et. al.) studying tiny apatite grains in the isua http://www.dhushara.com/book/bchtm/biocos.htm#anchor-three-47857 http://www.dhushara.com/book/bchtm/biocos.htm#anchor1540797 http://www.dhushara.com/book/bchtm/suth/sutherland.htm http://www.dhushara.com/book/bchtm/origins_of_life_proton.pdf http://www.dhushara.com/book/bchtm/biocos.htm#anchor-lane-23240 http://www.dhushara.com/book/bchtm/biocos.htm#anchor-leipe-14210 http://www.dhushara.com/book/bchtm/biocos.htm#anchor-leipe-14210 http://www.dhushara.com/book/bchtm/biocos.htm#anchor-leipe-14210 dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 01-35 king, c., biocosmology: part i issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 33 formation of greenland, has found carbon 12 to 13 ratios consistent with the grains originating from living matter. the isua rocks date from 3.85 billion years ago. although indications from zircon crystals indicate a solid crust 4.2 billion years ago, no intact rocks have been discovered older than 3.96 billion years. the moon and probably the earth likewise was heavily bombarded with meteors up to 3.8 billion years ago, suggesting that life evolved on earth as soon as environmental conditions allowed. there is continuing debate about whether these chemical and 'fossil' traces, now further studied with raman spectroscopy to give carbon isotope evidence, really represent early cyanobacterial life, prebiotic 'soup' or volcanic or meteorite material [schopf et. al. 2002, brazier et. al. 2002, mojzsis 2002]. however some researchers contend on the basis of inorganic simulations that these microfossils are purely mineral [hogan 2003]. jacques touret [2003] has found that methane as well as high salt water trapped in pillow lava from isua suggesting the involvement of hydrothermal vents beside an undersea volcano. however these findings are questioned by david vanko [necht 2003]. john parnell has also suggested radioactivity trapped in oily grains may have had a role [lawton 2003]. in any case there is consensus agreement that life was under way by 3.5 billion years the age of the fossil stromatolite in fig 22, although the nature of these is also debated. these fossils could be the earliest evidence of life on earth, yet these relics, with names like chromoccoceae and oscdlotorioceoe, are morphologically identical to modern cyanobacteria that cover the globe from antarctica to the sahara [cohen 1996]. in july 2011 brazier who had questioned the biological nature of the earliest fossils, himself claims to have discovered a genuine biological fossil of sulphur bacteria dating to 3.43 billion years. a,b,e, clusters of cells, some showing cell wall rupturing (arrows in a,b), folding or invagination (arrow in e). c,d,h, chains of cells with cellular divisions (arrows). f., cells attached to detrital quartz grains, exhibiting cell wall. oldest fossils show early life was a beach august 2011 new sceintist the oldest compelling fossil evidence for cellular life has been discovered on a 3.43-billion-yearold beach in western http://www.dhushara.com/book/bchtm/fossil_earliest.pdf dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 01-35 king, c., biocosmology: part i issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 34 australia. its grains of sand provided a home for cells that dined on sulphur in a largely oxygenfree world. the first breath (pdf password="model") ongoing debate about the first origins of life-driven oxidation the origins of the first fossil life forms including the stromatolites in fig 23, likewise lie at the limits of the geological record. at 3.5 billion years old, fossilised bacteria are the earliest evidence of life on earth, and yet these relics, with names like chromoccoceae and oscdlotorioceoe, are identical to the sophisticated modern cyano-bacteria that cover the globe from antarctica to the sahara (let there be life new scientist 6 july 96). the emergence of the eucaryotes that lead to the higher organisms is also almost as ancient as the geological record. traces of oil extracted from australian shale have pushed the date for the origin of complex cells back another half a billion years. compounds in the oil suggest that eucaryotic cells, which make up all life on earth except for bacteria, had evolved as early as 2.7 billion years ago. it is not until about 2.1 billion years ago that fossil imprints appear in the geological record that are so large that they can only be eucaryotes. a team of researchers in australia has found steranes, molecules with 26 to 30 carbon atoms arranged in four rings, in droplets of oil extracted from rock 700 metres below the surface in the pilbara region of north-western australia. these are produced by the decay of cholesterol and other steroids found in the membranes of eukaryotes, but not bacteria (brocks et. al.). genetic analysis of the base of the tree of life indicates the oldest branches of both archaea and (eu)bacteria are thermophilic suggesting a period in hot pools or significant meteoric impact leaving only the thermophiles as survivors. the copernican principle asserts that the earth is a typical rocky planet in a typical planetary system, located in an unexceptional region of a common barred-spiral galaxy, hence it is probable that the universe teems with complex life. this is supported to a reasonable extent by the discovery of an increasing number of planets including some putative "goldilocks" zone planets where water would be liquid and life as we know it could potentially exist. set against this, the rare earth hypothesis argues that the emergence of complex life requires a host of fortuitous circumstances including a galactic habitable zone, a central star and planetary system having the requisite character, the circumstellar habitable zone, the size of the planet, the advantage of a large satellite, conditions needed to assure the planet has a magnetosphere and plate tectonics, the chemistry of the lithosphere, atmosphere, and oceans, the role of "evolutionary pumps" such as massive glaciation and rare bolide impacts, and whatever led to the still mysterious cambrian explosion of animal phyla. this might mean that planets able to support a bacterial level of life are not so uncommon, but those supporting complex multicellular life might be. bringing this question to a pivotal crux in our context, the emergence of mitochondria as endosymbionts has been proposed to be a critical bottleneck which allowed complex life to evolve only once, because, only in this effectively fractal cellular architecture, can the membrane surface areas necessary to support the chemical reactions enabling the vastly larger number of genes in a complex organism's genome to maintain metabolic stability (lane and martin the energetics of genome complexity 2010 doi:10.1038doi:10.1038/nature09486). whether such endo-symbiosis is rare. or a common extreme of parasitic relationships would then determine how likely or unlikely complex life might be. http://www.dhushara.com/book/bchtm/first_breath.pdf http://en.wikipedia.org/wiki/rare_earth_hypothesis http://www.newscientist.com/article/dn18734-why-complex-life-probably-evolved-only-once.html http://www.newscientist.com/article/dn18734-why-complex-life-probably-evolved-only-once.html dna decipher journal | january 2012 | vol. 2 | issue 1 | pp. 01-35 king, c., biocosmology: part i issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 35 offset against both the uniqueness of the mitochondrial endo-symbiosis and the closely linked, but independent question of the origin of the nucleus and nuclear envelope, has been the discovery of mimiviruses and mamaviruses infecting amoeba (raoult et, al. the 1.2-mb genome sequence of mimivirus doi: 10.1126/science.1101485) and related very large aquatic viruses such as crov infecting single celled plankton species, which despite their recent discovery, appear from ocean gene analyses to be potentially ubiquitous and widespread in the oceans and possibly playing a crucial role in regulating the atmospheric-oceanic pathways, such as carbon sequestration (fisher, allen, wilson and suttle 2010 giant virus with a remarkable complement of genes infects marine zooplankton pnas doi: 10.1073/pnas.1007615107). these form an intermediate genetic position between viruses and cells, having the largest genomes, with extensive cellular machinery and larger than the smallest completely autonomous bacterial and archaeal genomes. mimiviruses also host parasitic virophages, affectionately named sputnik as viral satellites, which piggy back on the metabolism of the large viral factories set up by these giant viral genomes causing the mimiviruses to sicken, and these virophages also contains genes that are linked to viruses infecting each of the three domains of life eukarya, archaea and bacteria (la scola et. al. the virophage as a unique parasite of the giant mimivirus nature doi:10.1038/nature07218). it has thus been suggested that they have a primary role in the establishment of cellular life and that they may have been instrumental in the emergence of the nuclear envelope. fig 23: a quadratic iteration compared with the interactive effects of inverse quadratic charge interaction. the fractal structures of tissues have features similar to the mandelbrot set on changes of scale. the fractal effects reach from the molecular (a) in which individual proteins are illustrated embedded in the lipid membrane, through cell organelles (b) to the intercellular structure of whole organs as illustrated by skin (c). such scale-dependent coherence of structure is possible only because of the highly non-linear nature of the electromagnetic force in quantum charge interactions of fermionic matter (campbell). http://www.k8science.org/news/news.cfm?art=1288 http://en.wikipedia.org/wiki/mimivirus http://en.wikipedia.org/wiki/mamavirus http://www.newscientist.com/article/dn19625-giant-virus-with-tiny-victims-carries-a-monster-genome.html http://www.nature.com/news/2008/080806/full/454677a.html login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x dna decipher journal | september 2018 | volume 8 | issue 2 | pp. 102-118 102 pitkänen, m., new results in the model of bioharmony article new results in the model of bioharmony matti pitkänen 1 abstract this article describes some new results and considerations related to music harmony. for some years ago i developed a model of music harmony. as a surprising side product a model of genetic code predicting correctly the number of codons coding given amino-acid emerged. since music expresses and creates emotions, one can ask whether genes could have moods characterized by these bio-harmonies. the fundamental realization could be in terms of dark photon triplets replacing phonon triplets for ordinary music. the model relies on the geometries of icosahedron and tetrahedron and representation of 12-note scale as so called hamiltonian cycle at icosahedron going through all 12 vertices of icosahedron. the 20 faces correspond to allowed 3-chords for harmony defined by given hamiltonian cycle. this brings in mind 20 amino-acids (aas). one has three basic types of harmonies depending on whether the symmetries of icosahedron leaving the shape of the hamiltonian cycle is z6, z4 or z2. for z2 there are two options: z2,rot is generated by rotation of π and z2,refl by reflection with respect to a median of equilateral triangle. combining together one harmony from each type one obtains union of 3 harmonies and if there are no common chords between the harmonies, one has 20+20+20 3chords and a strong resemblance with the code table. to given aa one assigns the orbit of given face under icosahedral isometries so that codons correspond to the points of the orbit and orbit to the corresponding aa. 4 chords are however missing from 64. these one obtains by adding tetrahedron. one can glue it to icosahedron along chosen face or keep is disjoint. the model in its original form predicts 256 different harmonies with 64 3-chords defining the harmony. dna codon sequences would be analogous to sequences of chords, pieces of music. same applies to mrna. music expresses and creates emotions and the natural proposal is that these bio-harmonies correlate with moods that would appear already at molecular level. they could be realized in terms of dark photon triplets realized in terms of light and perhaps even music (living matter is full of piezo-electrets). in fact, also the emotions generated by other art forms could be realized using music of dark light. the model of music harmony is separate from the model of genetic code based on dark proton triplets and one of the challenges has been to demonstrate that they are equivalent. this inspires several questions. could the number of harmonies be actually larger than 256 as the original model predicts? one could rotate the 3 fused hamilton’s cycles with respect to each by icosahedral rotations other leaving the face shared by icosahedron and tetrahedron invariant. there are however conditions to be satisfied. there is purely mathematical restriction. if the fused 3 harmonies have no common 3-chords the number of coded aas is 20. can one give up the condition of having no common 3-chords and only require that the number of coded aas is 20? there is also the question about the chemical realizability of the harmony. is it possible to have dna and rna molecules to which the 3-chords of several harmonies couple resonantly? this could leave only very few realizable harmonies. the model predicts the representation of dna and rna codons as 3-chords. melody is also an important aspect of music. could amino-acids couple resonantly to the sums of the frequencies (modulo octave equivalence) of the 3-chords for codons coding for given aa? could coding by the sum of frequencies appear in the coupling of trna with mrna by codewords and coding by separate frequencies to the letterwise coupling of dna and rna nucleotides to dna during replication and transcription? what about trna. could trna correspond to pairs of harmonies with 20+20+444 codons? what about single 20+4=24 codon representation as kind of pre-trna? what is the origin of 12-note scale? does genetic code force it? the affirmative answer to this question relies on the observation that 1-1 correspondence between codons and triplets of photons requires that the frequency assignable to the letter must depend on its position. this gives just 12 notes altogether. simple symmetry arguments 1correspondence: matti pitkänen http://tgdtheory.com/. address: rinnekatu 2-4 a8, 03620, karkkila, finland. email: matpitka6@gamail.com. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.com/ mailto:matpitka6@gmail.com dna decipher journal | september 2018 | volume 8 | issue 2 | pp. 102-118 103 pitkänen, m., new results in the model of bioharmony fix the correspondence between codons and 3-chords highly uniquely: only 4 alternatives are possible so that it would be possible to listen what dna sequences sounds in given mood characterized by the harmony. what disharmony could mean? a possible answer comes from 6 hamiltonian cycles having no symmetries. these disharmonies could express ”negative” emotions. keywords: bioharmony, model, music harmony, genetic code, tgd framework. 1 introduction this article describes some new results and considerations related to music harmony. most of them have emerged during 2018. remark: in the sequel i will use the shorthand aa for amino-acids and shorthands ddna, drna, dtrna, daa for the dark analogs of dna, rna, trna, and aa realizes as dark proton sequences with codon represented as dark proton triplet. 1.1 some background for some years ago i developed a model of music harmony [17] (see http://tinyurl.com/yad4tqwl), which should define map of dark codons to 3-chords represented as dark photon triplets and defining allowed 3-chords of music harmony (music of light and perhaps also of sound). the appendix provides the tables describing the details of the harmonies. 1. the model relies on the geometries of icosahedron and tetrahedron and a representation of 12note scale as so called hamiltonian cycle at icosahedron going through all 12 vertices of icosahedron [5, 2, 4, 1, 3]. the 20 faces correspond to allowed 3-chords for harmony defined by given hamiltonian cycle. this brings in mind 20 aas. single step of hamiltonian cycle connecting vertices of a face of icosahedron (triangle) is assume to correspond to a scaling of the frequency by factor 3/2. this leads to a problem since 12 scalings of this kind does not quite given 7 octaves which reduced octave equivalence to the basic octave would give 12-note scale. the solution is to add single note slightly differing from 7 octaves and represented as vertex p of a tetrahedron glued to icosahedron along face. the hamilton cycles are deformed so that they begin and end from this vertex. this also gives the missing 4 dna codons realized as 3-chords and also defines unique ground note for the scales. 2. one obtains 3 basic types of harmonies depending on whether the symmetries of icosahedron leaving the shape of the hamiltonian cycle is z6, z4 or z2. for z2 there are two options: z2,rot is generated by rotation of π and z2,refl by reflection with respect to a median of equilateral triangle. combining together one harmony from each type one obtains union of 3 harmonies and if there are no common chords between the harmonies, one has 20+20+20 3-chords and a strong resemblance with the code table. to given aa one assigns the orbit of given face under icosahedral isometries so that codons correspond to the points of the orbit and orbit to the corresponding aa. 4 chords are however missing from 64. these one obtains by adding tetrahedron. one can glue it to icosahedron along chosen face or keep is disjoint. the model predicts a highly unique and realistic model for numbers of dna codons coding for a given aa. the model in its original form predicts two codes and also explains the fact that there are two additional aas pyl and sec that appear as end-products. 3. aas correspond to single 20-codon code, dna and rna to a union of 3 20-codon codes with symmetries z6, z4 or z2: here z2 would correspond to z2,rot or z2,refl and this would give to two two different codes. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/yad4tqwl dna decipher journal | september 2018 | volume 8 | issue 2 | pp. 102-118 104 pitkänen, m., new results in the model of bioharmony 4. the model in its original form predicts 256 different harmonies with 64 3-chords defining the harmony. dna codon sequences would be analogous to sequences of chords, pieces of music. same applies to mrna. music expresses and creates emotions and the natural proposal is that these bio-harmonies correlate with moods that would appear already at molecular level. they could be realized in terms of dark photon triplets realized in terms of light and perhaps even music (living matter is full of piezoelectrets). in fact, also the emotions generated by other art forms could be realized using music of dark light. [23]. dark photons in various wavelength ranges and correspond to various values of heff would correspond to various sensory qualia and are represented at pineal gland (”third eye”) as imagined sensory percepts [20]. they can be transformed to real sensory percepts at sensory organs by using dmt molecules as bridges allowing the propagation of dark photons (or the bio-photons resulting in their energy conserving transformation to ordinary photons) to sensory organs, where they generate genuine sensory experience identified as dream, psychedelic experience, hallucination, etc... this summarizes the original article about geometric model of harmony [17] and contributions in online books [12, 10]. this chapter contains besides this article also some new results and considerations related to music harmony. most of them have emerged during 2018. 1.2 questions emerged during 2018 the model of music harmony is separate from the model of genetic code based on dark proton triplets [18] and one of the challenges has been to demonstrate that they are equivalent. one can raise several questions. 1. could the number of harmonies be actually larger than 256 as the original model predicts? one could rotate the 3 fused hamilton’s cycles with respect to each by icosahedral rotations other leaving the face shared by icosahedron and tetrahedron invariant. there are however conditions to be satisfied. (a) there is purely mathematical restriction. if the fused 3 harmonies have no common 3-chords the number of coded aas is 20. can one give up the condition of having no common 3-chords and only require that the number of coded aas is 20? (b) there is also the question about the chemical realizability of the harmony. is it possible to have dna and rna molecules to which the 3-chords of several harmonies couple resonantly? this could leave only very few realizable harmonies. 2. the model predicts the representation of dna and rna codons as 3-chords. melody is also an important aspect of music. could aas couple resonantly to the sums of the frequencies (modulo octave equivalence) of the 3-chords for codons coding for given aa? could coding by the sum of frequencies appear in the coupling of trna with mrna by codewords and coding by separate frequencies to the letterwise coupling of dna and rna nucleotides to dna during replication and transcription? could the emergence of dna be interpreted as an evolutionary step from a holistic picture using codons as basic units (dark codons cannot be decomposed to letters) to more analytic picture in which letters are treated separately? 3. as i developed the model of bio-harmony [17] (see http://tinyurl.com/yad4tqwl) it did not occur to me that also the trna part of the dark code should have counterpart in the icosahedral model. could trna correspond to pairs of harmonies with 20+20+4=44 codons? what about single 20+4=24 codon representation as kind of pre-trna? could trna correspond to a union of 2 20-codon codes? combining only 2 20-codon codes with 40 codons and tetrahedral code with issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/yad4tqwl dna decipher journal | september 2018 | volume 8 | issue 2 | pp. 102-118 105 pitkänen, m., new results in the model of bioharmony 4 codons would give maximally 44-letter code and the upper bound for trnas is according to wikipedia 45! dark proton model predicts 40 dtrnas suggesting that only the 40 isosahedral codons contribute to dtrna code. the additional trnas could result from homonymy. the code sequences could be seen as a hierarchical sequence 3→ 2→ 1 in this framework. an important implication is that there are many realizations of dtrna and trna harmony: (z6, z4), (z6, z2), (z4, z2) and z2 could be either z2,rot or z2,refl. this could explain the homonymy of mrna-trna pairing via difference in the chords in turn affecting biochemical counterparts. note however that the chords for trna must be a subset of chords for mrna so that rna harmony determines trna harmony apart from the three choices (z6, z4), (z6, z2) or (z4, z2) giving rise to 3 different contexts. if daas code by 3-chords the aas then this choice does not affect aas. 4. what is the origin of 12-note scale? does genetic code force it? the affirmative answer to this question relies on the observation that 1-1 correspondence between codons and triplets of photons requires that the frequency assignable to the letter must depend on its position. this gives just 12 notes altogether. simple symmetry arguments fix the correspondence between codons and 3-chords highly uniquely: only 4 alternatives are possible. hence it would be possible to listen what dna sequences sounds in given mood characterized by the bio-harmony: the allowed 3-chords of harmonies with symmetries are given in [17] and i can provide the basic python modules allowing to transform dna sequences for given harmony to audible form using garage band program. 5. what disharmony could mean? a possible answer comes from 6 hamiltonian cycles having no symmetries. these disharmonies could express ”negative” emotions. 2 some questions about the realization of the bio-harmony in the sequel by i will proceed by posing questions related to the relationship between the 3 representations of genetic code [12] in terms of bio-molecules, their dark analogs represented as sequences dark proton triplets, and as 3-3-chords of bio-harmony. 2.1 what conditions pairings pose on the frequency triplets? the realization of ddna-dtrna and ddna-daa pairings in terms of frequencies must involve a loss of information since the correspondence is many-to-one. 1. for dna-mrna pairing information is not lost and the pairing must be of form (f1, f2, f3) → (f1, f2, f3). note that the frequencies cannot be associated with the letters. it is however possible to consider the assignment of (f1, f2) to the first letter pair xy as a whole and f3 to the third letter z. 2. for ddna-daa and dmrna-daa pairing the natural hypothesis is (f1, f2, f3)→ f1+f2+f3. aa couples to the sum of the frequencies of the triplet. the simplest possibility is that the f1 + f2 + f3 is same for all codons codin for given aa. one might say that aa sequence defines melody and mrna sequence the accompaniment.if the sums for codons coding given aa are different they must couple resonantly to it. if there are several harmonies the sum must same for all realizable 3-harmonies or all chords of 3-chord harmonies coding for same aa couple to it resonantly. since one has linear 1-d structures one might ask whether frequency differences coming as multiples of lattice frequencies are allowed. second natural possibility is octave equivalence. mrna-aa pairing would take place directly rather than with the mediation of of trna. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | september 2018 | volume 8 | issue 2 | pp. 102-118 106 pitkänen, m., new results in the model of bioharmony 3. in the case of dmrna-dtrna pairing one one does not lose so much information since the number of dark dnas is 40 (as also the 3-chords if tetrahedron does not contribute). one must remember that trnas are pairs of rna like codons call them rnat, and aas. therefore there pairing involves also the pairing mrna-aa give by (f1, f2, f3) → f1 + f2 + f3 and guaranteeing that the code is realized by this pairing alone irrespective of mrna-rnat pairing. at chemical level the first to mrna codons pair with trna anticodons according to the standard rules. could rnat have completely passive role in carrying the aa? this cannot be the case since the last two letters of rnat couple in standard manner to the first two letters of mrna. remark: trna is analogous to melody + accompaniment using one of the 3 possible 2-harmonies for a given 3-harmony. suppose that mrna-rnat pairing corresponds to 3 possible choices of 2-harmonies as sub-harmonies of 3-harmony. this would suggest these different sub-harmonies define maps (f1, f2, f3)→ (f1, f2, f3) such that rnat pairs only with two sub-harmonies. for each choice rnat would correspond effectively to 40 sub-codons of the entire code (forgetting the tetrahedral part giving 4 additional codons). the three different realizations of the projection would give rise to the homonymy. also the aa-trna coupling would come out correctly. daas would be different in the sense that they couple only to the sum of the frequencies. this is in accordance with bio-harmony in which aas correspond to orbits of 3-chords for dna under isometries rather than single 20-chord harmony. the coupling to the sum of frequencies is in accordance with the quantal interpretation as 3-dark-photon state whose energy is e = heff (f1 + f2 + f3) and couples to aa chemically via the transition to ordinary photons with the same energy. this leaves some questions. 1. could one consider the possibility that the chords of one of the 20-chord harmonies corresponds to aas? there would be 3 basic types of aas. this does not look plausible and the association of aas with the orbits of 20-note chords is more natural and fits nicely with f = fxy z picture. 2. it would be nice to assign notes to the individual letters of codons. this is not possible since codons with 2 or 3 identical letters would reduce to 2-chords or 1-chords. it is also impossible to assign frequencies with letters at dark level since letter decomposition does not exist. thus the 3-chord has resonant interaction with the entire codon. 3. the symmetries of the genetic code however suggest that it might make sense to treat the first two letters xy of the codon as a single unit and the third letter as separate single unit. could one assign to xy a 2-chord not reducible to frequencies for the letters x and y, and to letter z its own frequency. the frequencies of a,g, t,c as third letter must be different. four 32 codons of standard code the aa would not be sensitive to the frequency of z: this is possible if these frequencies are resonance frequencies of the same aa. for the remaining 32 codons the aa would not distinguish between frequencies of t and c resp. a and g so that the two frequencies would be both resonance frequencies of the corresponding aa. 2.2 probabilistic estimates for single 20-chord harmony one can make first some naive probabilistic estimates about single 20-chord harmony. 1. given 20-chord harmony makes 20/220 = 1/11 ' 9 per cent about al possible 3-chords. three 20 chord harmonies would make 3×9 = 27 per cent about all possible 3-chords if there are no common chords so that the optimistic expectation might make sense. of course, one cannot exclude the possibility that there are also triplets of 20-codon codes which gives smaller number of codons. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | september 2018 | volume 8 | issue 2 | pp. 102-118 107 pitkänen, m., new results in the model of bioharmony 2. the total number of chords with different notes is 12× 11× /3! = 220. bio-harmony has 64 chords corresponding to faces of icosahedron: this is about 64/220 making 29 per cent of all possible 3chords with different notes. given bio-harmony thus throws out roughly 2/3 of all possible codons. this should be easy to test. for instance, does given gene correspond to a fixed bioharmony? or does even entire genome do so. if bio-harmony is realized for non-nuclear genomes, it must satisfy rather strong constraints. 3. given 20-chord harmony corresponds to 12 edges. each edge is shared by two adjacent triangles. if all 20 triangles would contain just single face, there would be 24 triangles altogether. therefore there must be triangles containing two subsequent edges of the cycle. each triangle of this kind reduces the number of 24 neighbours by 2 units. hence it seems that one must have at least 2 triangles with 2 edges at the cycle (two quints in the 3-chord). if there are more than 2 triangles of this kind, there must be triangles having no edges along the path. each vertex of icosahedron is shared by 5 triangles and there are 5 edges starting from it. 4. the notion of hamilton cycle generalizes to any graph and magnetic flux tube networks define such graphs as tensor networks. why only icosahedron? could one consider the possibility that any tensor network is characterized by harmonies characterize by hamiltonian cycles and that one could assign some kind of codes with the combinations of these cycles? in the general case symmetries would be absent so that the notion of code in the proposed sense would fail: one could not identified codons as points at orbits of symmetry group. rather, one can imagine that the notion of code could be defined quite generally in terms of orbits as aas and points at them as dnas coding them. for regular polygons in any dimension the symmetries are present and one could define the notion of code and also fuse the codes. for arbitrary tensor network the faces need not be symmetry related and one can also have faces that can be interpreted as higher-dimensional polytopes. one can also ask whether the icosahedron is realized physically. icosahedral geometry is indeed very common in biology. could the fusion of icosahedral and tetrahedral geometries have some concrete realization at molecular level? 2.3 is the maximal number of codons for the fusion of 3 20-codon codes possible? it has not earlier occurred to me to wonder whether the chords associated with the 3-different icosahedral harmonies giving 20 codons each correspond to 20+20+20=60 different chords as assumed. could there be common 3-chords? this question could be answered by studying the hamiltonian cycles at icosahedron. remark: perhaps more important constraint than absence of common chords is the chemical realizability of the codes. if same mrnas and dnas realized different bio-harmonies then they must be able to respond resonantly to several 3-chords. one can make naive probability estimates for a pair of codes to allow the maximal number of 60 codons. it seems natural to assume that the isometries of icosahedron (or their subgroup) can be applied separately and only the isometries acting on both in similar manner are symmetries. the situation would be the same as in the case of many-particle system: only the translations acting on all particles simultaneously remain symmetries and relative translations cease to be symmetries. with this assumption the icosahedral group gives a large number of code pairs. for the fusion of 3 20-codon codes giving dna/rna the number is even higher. by choosing suitably the relative isometries it might be possible to obtain the maximal number of 60 different codons for the icosahedral genetic code. on the other hand, by a suitably choice of relative isometries one might have undesired common 3-chords. in any case, the earlier estimate 256 for the number of bio-harmonies [17] suggested to correlate with ”emotional” states of the basic biomolecules is expected to change. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | september 2018 | volume 8 | issue 2 | pp. 102-118 108 pitkänen, m., new results in the model of bioharmony before going to estimates one must consider some delicacies related to the notion of 12-note scale as hamiltonian cycle. 1. one can regard the cycles as purely geometric objects without orientation or assign to them orientation. for two different orientations the scales would run in opposite directions as scalings by 3/2 along single edge of the cycle. if two codes have common edge, the scaling must be same along it. if the orientation of the second cycle is changed, the common edge ceases to be common. 2. the basic note of the 12-note scale at cycle can be chosen arbitrarily: this corresponds to the choice of the key in music (one could of course argue that the key does not make sense in 12-note scale if one has tempered scale with notes comes as powers of 21/2 scaling of ground note rather than pythagorean scale with rational ratios of notes). the fusion of tetrahedron to icosahedron selects one particular triangular face and brings in one additional vertex outside the icosahedron, call it p . it would be natural to assign the ground note as p . the isometries not affecting p would correspond to those of icosahedron leaving the common face invariant and isometries of tetrahedron leaving p un-affected and continuable to icosahedral isometries. one would have subgroup of icosahedral group as allowed isometries acting on the cycles to be fused. 3. if one assigns note sequences to the cycle by quint rule, cycles c1 and c2 can have common triangle in geometric sense but if the distances of the vertices a,b,c of the triangles from p measured as the number of edges of cycle portion connecting them are not same along c1 and c2, the triangles correspond to different chords and are thus orthogonal in the proposed description as many-fermion states. 4. to sum up, the states associated with triangles would be characterize by the position of triangle (20 values), by the notes of the triangle characterized by the distances from p , and the number 0, 1, 2 of the edges belonging to the cycle and should make easier to find ortogonal basis. again one can make probabilistic estimates: cycles are treated as purely geometric entities without orientation and without assignment of notes to the triangles. 1. given cycles c1 and c2 what is the probability that they have at least one common edge as purely geometric entities without the sequence of notes? there are 30 edges so that given edge is shared with probability 1/30. if the edges of cycles were chosen randomly (certainly not true), the probability of having a common edge for two cycles would be p (1) = 12/30. the assumption of note sequence reduces this probability dramatically. 2. by the above estimate each cycle contains at least two triangles with 2 edges at the cycle with minimal angle between them. one can call these these edge pairs v-corners. assume that for cycle c1 one has v-corner abc at vertex a, call it v1,a. what is the probability that one one of the v-corners of c2 is located at a co-incides with abc. the probability of v-corner of c2 to locate at a is 1/12 and the probability that the edge of c2 from b is bc is is 1/4 so that the probability of having common v-corner is 1/48. if c2 contains n v-edges the probability is naively n/48. this estimate takes into account only geometry. the situation changes if one assumes that the cycles are oriented. in this case one can have common v-corner if the local orientations of c1 and c2 are opposite at the v-corner. if one assumes that the external vertex p of the tetrahedron defines the ground note then the number of edges connecting p to a defining distance d(p,a) must be same for c1 and c2. 3. given c1 and c2 (and vertices a with same distance d(p,a)) it might be possible to perform suitable isometry for c2 that there is common v-corner. therefore not all possible combinations of three code types allowing relative isometries need not maximal number of 3-chords. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | september 2018 | volume 8 | issue 2 | pp. 102-118 109 pitkänen, m., new results in the model of bioharmony remark: an interesting question is whether these can be allowed meaning that some codons are missing in the chemical realization of the dark codons in terms of ordinary dna codons. also the 1-1 pairing between dark dna and and dark rna would not be 1-1 if mediated by 3-chord resonance and one would have homonymy. this suggests that only codes without common chords can be allowed. 4. what about chords having 1 edge at cycle for two cycles c1 and c2? let the edge be ab. as found, the naive probability for this is p (1) = 12/30. both cycles must go through the third vertex c of the triangular face. the subsequent notes along cycle differ by a quint that is scaling of the frequency by factor 3/2. notes are same if the numbers of the needed quints are same for c1 and c2 for c1 the number nb > 1 of quints is known. in the approximation that possible portions of c1 represent n-step non-self-intersecting random walks from b to c, one must estimate the number of all non-self-intersecting n-step-paths from b to c and find what is the number of the paths leading to c. one can go from a to c with na steps and similar estimate applies. 5. the third possibility is that the one has 3 common vertices a, b, c forming a triangular face such that neither cycle contains any of its edges. the cautious conclusion is that it is plausible that one can find 3 cycles having no common chords if one allows relative rotations of the cycles and that this condition is necessary for realizing the absence of homonymies at dark level. the automatic orthogonality of the hamiltonian cycles cannot be excluded but would allow also codes with codons containing more than 3 letters so that one could have kind of superdna. whether they can be realized chemically depends on whether there are biomolecules resonating with the the n frequency triplets involved. octave equivalence for frequencies might give hopes about chemical realization of several harmonies. therefore the evolution might be seen as gradual emergence of molecules able to pair with ddna and one can even imagine artificial evolution by tailoring the frequencies involved (maybe cyclotron frequencies). 2.4 how the symmetries of the model of harmony could relate to those of the genetic code? genetic code has surprisingly strong symmetries. i have discussed a possible interpretation of these symmetries using analogies with particle physics and considered also a mechanism explaining their emergence earlier [8, 9]. the proposal was that 3-letter code emerged as a fusion of 2-letter code with 16 codons and 1-letter coded with 4 codons. in the recent framework, a more natural option is that the third codon of 3-letter code was originally passive and became active via symmetry breaking distinguishing first between uc and ag pairs and later between u and c resp. a and g. note that for the standard code the breaking is minimal and caused by odd number of start and stop codons. 1. for vertebrate code one half of codons has very high symmetry in the sense that the two first letters dictate the aa for 32 cases. exception is uuu, which codes for phe or leu for some modifications of the standard code. uuu → leu means breaking of maximal symmetry. 2. there is also a second symmetry, which i have referred to as isospin symmetry. it is only slightly broken. for general codons xyu and xyc code for same aa as also xya and ad xyg. for the standard code this symmetry is broken only in columns containing initiation codon or stop. the start codon aug codes also for met. uga and ugg code for stop and trp. for the remaining codons one has slightly broken ”isospin symmetry”. the breaking of isospin symmetry is minimal for vertebrate code. the modifications of the code tend to break the isospin symmetry and even the maximal symmetry of 32 codons. this must be important. if the model of genetic code based on music harmony [17] is correct, the symmetries for the model of music harmony should relate to those of genetic code. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | september 2018 | volume 8 | issue 2 | pp. 102-118 110 pitkänen, m., new results in the model of bioharmony 1. how the symmetries of the genetic code relate to the symmetries of icosahedron (60-element group) and tetrahedron (permutation group s4 with 24 elements) in the model of bio-harmony? icosahedral symmetry group has 60 elements and has sub-groups z2, z4, z5, z6 = z2z3. note that there are two z2:s having rotation by π and reflection as generators. the gluing of tetrahedron to icosahedral along single face reduces its group of symmetries to s3 leaving the point p not belonging to icosahedron invariant. s3 has as subgroups reflection group z2,refl and z4 consisting of rotations. 2. what is the counterpart for maximal symmetry in icosahedral and tetrahedral groups? do the 3-chords for codon xyz decompose to two-chord characterizing xy and a note characteriing z= a,u,c,g, which can depend on xy. the symmetry relating uc pair and ac pair could correspond to z2,refl reflection symmetry, which is shared by icosahedral and tetrahedral groups. for 32 icosahedral codons the action of z2,refl × z2,rot would be trivial so that aa would not depend on the third letter at all. for most of the remaining codons the action of the symmetry group on icosahedral codons would reduce to z2,rot permuting the third letters u and c resp. a and g. at the level of frequencies the sums of frequencies for codons coding for the same aa sould be same modulo octave equivalence. the addition of tetrahedron brings in 4 tetrahedral codons with one of them shared with icosahedron. icosahedral z2,rot does not make sense for these codons. intriguingly, there are 4 codons in vertebrate code which break isospin symmetry aua and aug coding for i and met/start and uga and ugg coding for stop and trp. if these codons correspond to the tetrahedral codons which cannot have z2,rot as isospin symmetry, the breaking of z2,rot would follow from the breaking of symmetry induced by the attachment of tetrahedron to icosahedron. 2.5 what is the origin of 12-note scale? one fundamental question is why dark photon realization of genetic code should involve 12-note scale as icosahedral model requires. remark: the gluing of tetrahedral codons gives 4 additional codons but if tetrahedron is glued to icosahedron along one of its faces, the additional vertex gives only one additional note, which should be very near to the 12:th one. this could relate to the basic problem observed already by pythagoras that 12-note pythagorean scale with rational valued frequency ratios does not quite close. a popular article in spacedaily with title ”scientists crack how primordial life on earth might have replicated itself” (see http://tinyurl.com/y92ng5vd) led to a possible answer to the above question. the research paper [7] is titled ”ribozyme-catalysed rna synthesis using triplet building blocks” and published in elife (see http://tinyurl.com/ya5qyjfn). it is possible to replicate unfolded rna strands in lab by using enzymes known as ribozymes, which are rna counterparts of enzymes, which are amino-adic sequences. in the presence of folding the replication is however impossible. since ribozymes are in general folded, they cannot thus catalyze their own replication in this manner. the researchers however discovered that the replication using rna triplets genetic codons as basic unit can be carried out in laboratory even for the folded rna strands and with rather low error rate. also the ribozyme involved can thus replicate in codon-wise manner. for units longer than 3 nucleotides the replication becomes prone to errors. these findings are highly interesting in tgd framework. in tgd the chemical realization of genetic code is not fundamental. rather, dark matter level would provide the fundamental realizations of analogs of dna, rna, trna, and aas as dark proton sequences giving rise to dark nuclei at magnetic flux tubes [21] (see http://tinyurl.com/yalny39x). also ordinary nuclei correspond in tgd universe to sequences of protons and neutrons forming string like entities assignable to magnetic flux tubes. the basic unit representing dna, rna and trna codon and aa would consist of 3 entangled dark protons. the essential aspect is that by entanglement the dark codons do not decompose to products of letters. this is like words of some languages, which do not allow decomposition to letters. this issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/y92ng5vd http://tinyurl.com/ya5qyjfn http://tinyurl.com/yalny39x dna decipher journal | september 2018 | volume 8 | issue 2 | pp. 102-118 111 pitkänen, m., new results in the model of bioharmony representation is holistic. as we learn to read and write, we learn the more analytic western view about words as letter sequences. could the same hold true in evolution so that rna triplets would have come first as entities pairing with dark rna codons from from dark proton triplets as a whole? later dna codons would have emerged and paired with dark dna codons. now the coupling would have have been letter by letter in dna replication and transcription to mrna. it is intriguing that trna consists of rna triplets combined from aas and analogs of mrna triplets! the translation of mrna to aas having no 3-letter decomposition alone forces the holistic view but one can ask whether something deeper is involved. this might be the case. i have been wondering whether during rna era rna replicated using a prebiotic form of translational machinery, which replicated mrna rather than translated rna to protein formed from aas (aas) with aa serving as a catalyst. 1. during rna era aas associated with pre-trna molecules would served as catalysts for replication of rna codons. the linguistic mode would have been ”holistic” during rna era in accordance with the findings of the above experiments. rna codon would have been the basic unit. 2. this would have led to a smaller number of rnas since rna and rna like molecules in trna are not in 1-1 correspondence. a more realistic option could have been replication of subset of rna molecules appearing in trna in this manner. 3. then a great evolutionary leap leading from rna era to dna era would have occurred. aa catalyzed replication of rna would have transformed to a translation of rna to proteins and the roles of rna and aa in trna would have changed. [perhaps the increase of heff in some relevant structure as quantum criticality was reached led to the revolution] 4. at this step also (subset of) dna and its transcription to (a subset of) mrna corresponding to trna had to emerge to produce mrna in transcription. in the recent biology dna replicates and is transcribed nucleotide by nucleotide rather than using codon as a unit so that helicases and dna and rna polymerases catalyzing replication and transcription should have emerged at this step. the ability of dna to unwind with the help of helicase enzyme helping dna to unwind is essential for the transcription and translation of dna. therefore helicase must have emerged together with the ”analytic linguistic mode” as an analog of written language (dna) decomposing codons to triplets of letters. this would been a crucial step in evolution comparable to the emergence of written language based on letters. also the counterpart of rna polymerase and separate rna nucleotides for transcription should have emerged if not already present. an alternative option would involve ”tdna” as the analog of trna and the emergence of helicase and polymerases later as the transition from holistic to analytic mode took place. the minimal picture would be emergence of a subset of dna codons corresponding to rnas associated with pre-trna and the emergence of the analogs of helicase and dna and rna polymerases as the roles of aa and rna codon in trna were changed. 5. how dna could have emerged from rna? the chemical change would have been essentially the replacement of ribose with de-oxiribose to get dna from rna and u→ t. single o-h in ribose was replaced with h. o forms hydrogen bonds with water and this had to change the hydrogen bonding characteristics of rna. if the change of heff = n × h0 was involved, could it have led to stabilization of dna? did cell membrane emerge and allow to achieve this? i have proposed [21] (see http://tinyurl.com/ yalny39x) that the emergence of cell membrane meant the emergence of new representation of dark genetic code based on dark nuclei with larger value of heff . remark: one has h = 6 × h0 in the most plausible scenario [19, 22] (see http://tinyurl.com/ goruuzm and http://tinyurl.com/y9jxyjns). issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/yalny39x http://tinyurl.com/yalny39x http://tinyurl.com/goruuzm http://tinyurl.com/goruuzm http://tinyurl.com/y9jxyjns dna decipher journal | september 2018 | volume 8 | issue 2 | pp. 102-118 112 pitkänen, m., new results in the model of bioharmony one can of course ask whether something simpler could be imagined by utilizing the potential provided by dark variants of bio-molecules present already from beginning and providing both genes and metabolism simultaneously. 1. viruses are probable predecessors of cellular life. so called positive sense single stranded rna (ssrna) associated with viruses can form temporarily double strands and in this state replicate just like dna (see http://tinyurl.com/yc5f8b3t). the resulting single stranded rna can in turn be translated to proteins by using ribosomal machinery. rna replication takes place in so called viral replication complexes associated with internal cell membranes, and is catalyzed by proteins produced by both virus and host cell. could ribozyme molecules have catalyzed rna replication during rna era? for this option aa translation would have emerged later and the storage of genetic information to dna only after that. there is however the question about the emergence of aas and of course, dna and rna. which selected just them from enormous variety of options. 2. lipid membranes are formed by self-organization process from lipids and emerge spontaneously without the help of genetic machinery. it would be surprising if prebiotic life would not have utilized this possibility. this idea leads to the notion of lipid life as a predecessor of rna life. in this scenario metabolism would have preceded genes (see http://tinyurl.com/y7ehv8cq and http://tinyurl.com/y8nltb9e). the basic objection against both genes-first and metabolism-first options is that they need each other! 3. in tgd framework the dark variants of dna, rna, aa, and trna would provide the analogs of genes and all basic biomolecules. they would also provide a mechanism of metabolism in which energy feed by (say) solar radiation creates so called exclusion zones (ezs) of pollack [6] in water bounded by a hydrophilic substance. ezs are negatively charged regions of water giving rise to a potential gradient (analog of battery) storing chemically the energy provided by sunlight and the formation of these regions gives rise to dark nuclei at magnetic flux tubes with scaled down binding energy. when the p-adic length scale of these dark nuclei is liberated binding energy is liberated as metabolic energy so that metabolic energy feed giving basically rise to states with non-standard value heff/h = n of planck constant is possible. for instance, processes like protein folding and muscle contraction could correspond to this kind of reduction of heff liberating energy and also a transformation of dark protons to ordinary protons and disappearance of ezs. the cell interiors are negatively charged and this is presumably true for the interiors of lipid membranes in general and they would therefore correspond to ezs with part of protons at magnetic flux tubes as dark nuclei representing dark variants of basic biomolecules. already this could have made possible metabolism, the chemical storage of metabolic energy to a potential gradient over the lipid membrane, and also the storing of the genetic information to dark variants of biomolecules at the magnetic flux tubes formed in pollack effect. 4. in tgd framework biochemistry would have gradually learned to mimic dark variants of basic processes as a kind of shadow dynamics. lipid membranes could have formed spontaneously in water already during prebiotic phase when only dark variants of dna, rna, aas and trna, water, and lipids and some simple bio-molecules could have been present. the dark variants of replication, transcription and translation would have been present from the beginning and would still provide the templates for these processes at the level of biochemistry. dark-dark pairing would rely on resonant frequency pairing by dark photons and dark-ordinary pairing to resonant energy pairing involving transformation of dark photon to ordinary photon. the direct pairing of basic biomolecules with their dark variants by resonance mechanism could have led to their selection explaining the puzzle of why so few biomolecules survived. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/yc5f8b3t http://tinyurl.com/y7ehv8cq http://tinyurl.com/y8nltb9e dna decipher journal | september 2018 | volume 8 | issue 2 | pp. 102-118 113 pitkänen, m., new results in the model of bioharmony this is in contrast with the usual view in which the emergence of proteins would have required the emergence of translation machinery in turn requiring enzymes as catalyzers so that one ends up with hen-or-egg question: which came first, the translation machinery or proteins. in rna life option similar problem emerges since rna replication must be catalyzed by ribozymes. 5. gradually dna, rna, trna, and aa would have emerged by pairing with their dark variants by resonance mechanism. the presence of lipid membranes could have been crucial in catalyzing this pairing. later ribozymes could have catalyzed rna replication by the above mentioned mechanism during rna era: note however that the process could be only a shadow of much simpler replication for dark dna. one can even imagine membrane rnas as analogs of membrane proteins serving as receptors giving rise to ionic channels. note however that in tgd framework membrane proteins could have emerged very early via their pairing with dark aa associated with the membrane. these membrane proteins and their rna counterparts could have evolved into transcription and translation machineries. dna molecules would have emerged through pairing with dark dna molecules. the difference between deoxi-ribose and ribose would correspond to the difference between dark rna and dark dna manifesting as different cyclotron frequencies and energies making possible the resonant pairing for frequencies and energies. proteins would have emerged as those proteins able to pair resonantly with dark variants of amino-acid sequences without any pre-existing translational machinery. it is difficult to say in which order the basic biomolecules would have emerged. they could have emerged even simultaneously by resonant pairing with their dark variants. the communication between dark ordinary variants of biomolecules involves resonance mechanism and would also involve genetic code represented as 3-chords, music of light, and it is interesting to see whether this model provides additional insights. 1. the proposal is that 3-chords assignable to nucleotides as music of light with allowed 64 chords defining what i have called bio-harmony is essential for the resonance [23, 24, 22](see http:// tinyurl.com/ydhxen4g, http://tinyurl.com/yd5t82gq, and http://tinyurl.com/y9jxyjns). the 3 frequencies must be identical in the resonance: this is like turning 3 knobs in radio. this 3-fold resonance would correspond to the analytic mode. the second mode could be holistic in the sense that it would involve only the sum only the sum of the 3 frequencies modulo octave equivalence assigning a melody to a sequence of 3-chords. 2. the proposal is that aas having no triplet decomposition are holistic and couple to the sum of 3 frequencies assignable to trna and mrna in this manner. also the rnas in trna could couple to mrna in this manner. one could perhaps say that trna, mrna and aas codons sing whereas dna provides the accompaniment proceeding as 3-chords. the couplings of dna nucleotides to rna nucleotides would rely on the frequencies assignable to nucleotides. 3. if the sum of any 3 frequencies associated with mrna codons is not the same except when the codons code for the same aas, the representation of 3-chords with the sum of the notes is faithful. the frequencies to dna and rna nucleotides cannot be however independent of codons since the codons differing only by a permutation of letters would correspond to the same frequency and therefore code for the same aa. hence the information about the entire codon would be needed also in transcription and translation and could be provided either by dark dna strand associated with dna strand or by the interactions between the nucleotides of the dna codon. 4. the dna codon itself would know that it is associated with dark codon and the frequencies assignable to nucleotides could be determined by the dark dna codon. it would be enough that the frequency of the letter depends on its position in the codon so that there would be 3 frequencies for every letter: 12 frequencies altogether. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/ydhxen4g http://tinyurl.com/ydhxen4g http://tinyurl.com/yd5t82gq http://tinyurl.com/y9jxyjns dna decipher journal | september 2018 | volume 8 | issue 2 | pp. 102-118 114 pitkänen, m., new results in the model of bioharmony what puts bells ringing is that this the number of notes in 12-note scale for which the model of bio-harmony [17, 23] (see http://tinyurl.com/yad4tqwl and http://tinyurl.com/ydhxen4g) based on the fusion of icosahedral (12 vertices and 20 triangular faces) and tetrahedral geometries by gluing icosahedron and tetrahedron along one face, provides a model as hamiltonian cycle and produces genetic code as a by-product. different hamiltonian cycles define different harmonies identified as correlates for molecular moods. does each dna nucleotide respond to 3 different frequencies coding for its position in the codon and do the 4 nucleotides give rise to the 12 notes of 12-note scale? there are many choices for the triplets but a good guess is that the intervals between the notes of triplet are same and that fourth note added to the triplet would be the first one to realize octave equivalence. this gives uniquely ceg], c]fa,df]b[, and dg]b as the triplets assignable to the nucleotides. the emergence of 12-note scale in this manner would be a new element in the model of bio-harmony. there are 4!=24 options for the correspondence between {a, t,c,g} as the first letter and {c,c],d,d]}. one can reduce this number by a simple argument. (a) letters and their conjugates form pyrimidine-purine pairs t,a and c,g. the square of conjugation is identity transformation. the replacement of note with note defining at distance of half-octave satisfies this condition (half-octave tritonus was a cursed interval in ancient music and the sound of ambulance realizes it). conjugation could correspond to a transformation of 3-chords defined as ceg]↔ df]b[ , c]fa↔ d]gb . (b) one could have {t,c} ↔ {ceg],c]fa} , {a,g} ↔ {df]b[,d]gb} , or {t,c} ↔ {df]b[,d]gb} , {a,g} ↔ {ceg],c]fa} . . (c) one can permute t and c and a and g in these correspondences. this leaves 8 alternative options. fixing the order of the image of (t,c) to say (c,c]) fixes the order of the image of (a,g) to (d,d]) by the half-octave conjugation. this leaves 4 choices. given the bio-harmony and having chosen one of these 4 options one could therefore check what given dna sequence sounds as a sequence of 3-chords [17]. that the position the frequency associated with the nucleotide depends on its position in the codon would also reflect the biochemistry of the codon and this kind of dependence would be natural. in particular, different frequencies associated with the first and third codon would reflect the parity breaking defining orientation for dna. 2.6 what disharmony could mean? harmonies also those, which are sad (consider only passions of bach) are usually thought of as something beautiful. could negative emotions really correspond to any bio-harmonies characterized by symmetries. in a discussion with sini kunnas i realized that also the notion of disharmony could make sense. there are indeed 6 hamiltonian cycles without any symmetries [5, 2, 4, 1, 3]. i neglected them in the model of harmony because they would represent which one might call disharmony. could one of the contributing 3 hamiltonian cycles in bio-harmony correspond to this kind of dis-harmony and bring in 20 3-chords without any symmetries? if so the relationship between geometry and aesthetics would become very concrete. the alternative view would be that there are several harmonies realized simultaneously and thi creates disharmony. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/yad4tqwl http://tinyurl.com/ydhxen4g dna decipher journal | september 2018 | volume 8 | issue 2 | pp. 102-118 115 pitkänen, m., new results in the model of bioharmony the faces of the icosahedron belonging to the orbits of the symmetries of the harmony correspond to dna codons coding for the same aa assignable to the orbit. the fact that there are no symmetries for these 6 bio-disharmonies, suggests one-to-one correspondence between dna and aas if also stop codon corresponds to ordinary aa. 2.7 how to concretely realize emotions as music of light? music expresses emotions and also create higher level emotions. as all art, it also induces experience of beauty. since heff/h = n [15, 16] serves as a kind of iq in the evolutionary hierarchy, there are good reasons to expect that the emotions/feelings induced by music and other art forms are assignable to mb. the dynamics of mb involves oscillations characterized by frequencies and in eeg frequencies are of key importance for the part of mb outside biological body. the communications from cell membrane to mb involve modulation of eeg frequencies identified as generalized josephson frequencies by nerve pulse patterns [11] and would define a coding of sensory data to higher level emotions. the control signals from mb via dna inducing gene expression would use dark photons at cyclotron frequencies to control bb. how to realize the music of genes represented as sequences of 3-chords of dark light as a communication tool between dark and ordinary dna/rna and possibly even dark and ordinary variants of trna and aas? 1. communication between ordinary and dark matter levels must be possible. this is guaranteed if the transition energy spectra at different levels of heff/h = n hierarchy contain common transition energies so that a resonant interaction by exchange of dark photons becomes possible. this condition is extremely demanding and could explain why basic bio-molecules are selected amongst numerous alternatives [21] this is indeed one of the hen-egg problems of pre-biotic evolution. 2. a hypothesis worth of studying is that the cyclotron transition energies of both ordinary dna and rna nucleotides and their dark variants represented as dark proton sequences are same [21]. cyclotron transition energies should cover several octaves and the natural proposal is that magnetic field strength associated with the flux tube codes for the notes. in music experience roughly 10 octaves are needed corresponding to the range of audible sounds. 3. the cyclotron frequencies of dna nucleotides a, t, c, g are very nearly the same and near 1 hz for b = bend = .2 gauss since their masses do not differ much. since the nucleotides are negatively charged, also the cyclotron energies for codons and codon sequences are around 1 hz. heff = hgr hypothesis states that the cyclotron energies of dna are in the energy range of bio-photons in visible and uv [16, 13, 14, 22]. there should be correspondences between a) the 64 ordinary dna codons and allowed 3-chords and b) 64 dark variants of dna codons and allowed 3-chords. these correspondences fix that between ordinary and dark codons. one would have triality. 1. to realize music of genes one the value of b must have values in a range of several octaves. the magnetic field strengths b associated with the flux tubes accompanying dna strand should have a spectrum given by 12-note scale. both 64 dark dna codons and 43 = 64 ordinary dna codons should correspond to 20 + 20 + 20 + 4 = 64 allowed 3-chords formed from the notes of 12-note scale. 2. dark codons correspond to entangled states of 3 dark protons. the positions of dark protons are different so that ermutations of the positions of dark protons are involved. the invariance of 3-chord under permutations of notes would correspond to fermionic statistics. these permutations are lifted to braidings if dark protons are connected by flux tubes to some other system, for instance ordinary dna. if the dark protons are ordered linearly along flux tube, it would seem that these these positions correspond to those of ordinary code letters. this does not make sense. if the letters of codon are issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | september 2018 | volume 8 | issue 2 | pp. 102-118 116 pitkänen, m., new results in the model of bioharmony connected to the dark protons by flux tubes, the permutations of dark codons induce braiding of the flux tubes but do not affect the order of the letters of the ordinary codon. braiding would become an essential part of the correspondence between ordinary and dark codons. 3. one should understand the correspondence of dark codons with the allowed 3-chords of a given harmony and also with the ordinary dna codons. bio-harmony is defined as a composite of 3 harmonies with 20 allowed 3-chords and having symmetries z6, z4, and z2 and of tetrahedral harmony with 4 chords. tetrahedron can be regarded as disjoint object or attached to dna, and this gives two variants of code. how could these the icosa-tetra-hedral hamilton cycles relate to the physical realization of dark proton triplets? each icosahedral cycle should give rise to 20 dark proton triplets. why the icosahedral geometry with hamiltonian cycle should make itself manifest in the quantum physics of dark proton triplet? 4. could icosahedral geometry quite concretely correspond to a tensor network? the vertices of the icosahedron would be connected by a sequence of flux tubes connecting nearest neighbors to form a hamiltonian cycle. dark proton triplets would quite concretely be localized at the triangular faces of the icosahedron. braided triplet of flux tubes would emerge from the vertices of an icosahedral triangle defining 3chord and would connect it to the nucleotides of the corresponding ordinary dna codon. magnetic field strengths at these flux tubes would correspond to the notes of 12-note scale as defined by the hamiltonian cycle in question. the permutations of the dark proton states at the vertices of the triangle would induce braidings of the flux tube triplet actually defining minimal braid in topological quantum computation (sic!) the braiding accompanying the states of 3 dark protons would make the correspondence with ordinary ordered dna codons possible. note that each dark proton triplet could be also connected (without braiding) to its conjugate dark proton triplet by a triplet of flux tubes so that one would obtain closed flux loops and one could speak of knots instead of braids. remark: braiding brings strongly in mind the many tgd inspired proposals for dna as topological quantum computer [8, 12]: maybe dna as topological quantum computer could be (also?) realized in this manner. what physical objects could the 20 vertices of icosahedron correspond to? hydrogen bonded water clusters give rise to both tetrahedral and icosahedral structures. could one associate dark proton triplets to the dark parts of these structures? could one try to experimentally identity possible sequence of icosahedral water molecule clusters with vertices connected by hydrogen bonds associated with the dna sequence? if the hydrogen bonds correspond to flux loops as suggested, they can be rather long (proportional to heff/h = n) so that even distant water molecules can become hydrogen bonds and one could have a fractal hierarchy of icosahedra. 5. resonance condition suggests that at the level of ordinary dna double strand the cyclotron energies of dark protons associated with the hydrogen bonds connecting dna nucleotides correspond to those of flux tube triplets connecting ordinary and dark dna codons. the magnetic field strengths associated with the dark flux tubes accompanying hydrogen bonds would correspond to those associated with the triangles of icosahedral triangle. this would make possible communication between the two dark sectors by dark-photon triplets as music of genes. this leaves unanswered questions. 1. why the 20+20+20=60 3-chords from 3 harmonies with different icosahedral symmetries (z6, z4, z2) and 4 chords from tetrahedral harmony would combine to form single bio-harmony with 64 chords? this requires the presence of 3 hamiltonian cycles with different symmetries. why all three different issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | september 2018 | volume 8 | issue 2 | pp. 102-118 117 pitkänen, m., new results in the model of bioharmony symmetry types for dna and rna? could the 20 aas correspond to single symmetry type? could trna codons correspond to two symmetry types? 2. how the 3-chords of dark photons could be played? 3-chord should be a collective effect affecting both dark and ordinary codon by inducing emission of 3-photon state like like playing a chord by string instrument. the notes of the light chord need not emerge simultaneously but as arpeggios. could there be a pulse travelling along the hamiltonian cycle and picking all the cyclotron notes at the vertices containing dark proton and sending a cyclotron signal along flux tubes to ordinary dna codon. this pulse would travel along dark dna and play the music defined by dark dna sequence. references [1] hamiltonian cycles on icosahedron? available at: http://cs.smith.edu/~orourke/ mathoverflow/hpaths.html. [2] icosahedral graph. wolfram mathworld. available at: http://mathworld.wolfram.com/ icosahedralgraph.html. [3] symmetrical icosahedral hamiltonians. available at: https://www.flickr.com/photos/edwynn/ sets/72157625709580605/. [4] why are there 1024 hamiltonian cycles on an icosahedron? available at: http://tinyurl.com/ pmghcwd. [5] hopkins b. hamiltonian paths on platonic graphs. ijmms. available at: http://tinyurl.com/ o84ahk6, 30:1613–1616, 2004. [6] the fourth phase of water : dr. gerald pollack at tedxguelphu. available at: https://www. youtube.com/watch?v=i-t7tcmudxu, 2014. [7] holliger p et al. ribozyme-catalysed rna synthesis using triplet building blocks. elife. available at: https://elifesciences.org/articles/35255, 2018. [8] pitkänen m. dna as topological quantum computer. in genes and memes. online book. available at: http://tgdtheory.fi/public_html/genememe/genememe.html#dnatqc, 2006. [9] pitkänen m. evolution in many-sheeted space-time. in genes and memes. online book. available at: http://tgdtheory.fi/public_html/genememe/genememe.html#prebio, 2006. [10] pitkänen m. quantum model for hearing. in tgd and eeg. online book. available at: http: //tgdtheory.fi/public_html/tgdeeg/tgdeeg.html#hearing, 2006. [11] pitkänen m. quantum model for nerve pulse. in tgd and eeg. online book. available at: http://tgdtheory.fi/public_html/tgdeeg/tgdeeg.html#pulse, 2006. [12] pitkänen m. three new physics realizations of the genetic code and the role of dark matter in biosystems. in genes and memes. online book. available at: http://tgdtheory.fi/public_html/ genememe/genememe.html#dnatqccodes, 2006. [13] pitkänen m. are dark photons behind biophotons. in tgd based view about living matter and remote mental interactions. online book. available at: http://tgdtheory.fi/public_html/tgdlian/ tgdlian.html#biophotonslian, 2013. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://cs.smith.edu/~orourke/mathoverflow/hpaths.html http://cs.smith.edu/~orourke/mathoverflow/hpaths.html http://mathworld.wolfram.com/icosahedralgraph.html http://mathworld.wolfram.com/icosahedralgraph.html https://www.flickr.com/photos/edwynn/sets/72157625709580605/ https://www.flickr.com/photos/edwynn/sets/72157625709580605/ http://tinyurl.com/pmghcwd http://tinyurl.com/pmghcwd http://tinyurl.com/o84ahk6 http://tinyurl.com/o84ahk6 https://www.youtube.com/watch?v=i-t7tcmudxu https://www.youtube.com/watch?v=i-t7tcmudxu https://elifesciences.org/articles/35255 http://tgdtheory.fi/public_html/genememe/genememe.html#dnatqc http://tgdtheory.fi/public_html/genememe/genememe.html#prebio http://tgdtheory.fi/public_html/tgdeeg/tgdeeg.html#hearing http://tgdtheory.fi/public_html/tgdeeg/tgdeeg.html#hearing http://tgdtheory.fi/public_html/tgdeeg/tgdeeg.html#pulse http://tgdtheory.fi/public_html/genememe/genememe.html#dnatqccodes http://tgdtheory.fi/public_html/genememe/genememe.html#dnatqccodes http://tgdtheory.fi/public_html/tgdlian/tgdlian.html#biophotonslian http://tgdtheory.fi/public_html/tgdlian/tgdlian.html#biophotonslian dna decipher journal | september 2018 | volume 8 | issue 2 | pp. 102-118 118 pitkänen, m., new results in the model of bioharmony [14] pitkänen m. comments on the recent experiments by the group of michael persinger. in tgd based view about living matter and remote mental interactions. online book. available at: http: //tgdtheory.fi/public_html/tgdlian/tgdlian.html#persconsc, 2013. [15] pitkänen m. criticality and dark matter. in hyper-finite factors and dark matter hierarchy. online book. available at: http://tgdtheory.fi/public_html/neuplanck/neuplanck.html#qcritdark, 2014. [16] pitkänen m. quantum gravity, dark matter, and prebiotic evolution. in genes and memes. online book. available at: http://tgdtheory.fi/public_html/genememe/genememe.html#hgrprebio, 2014. [17] pitkänen m. geometric theory of harmony. available at: http://tgdtheory.fi/public_html/ articles/harmonytheory.pdf, 2014. [18] pitkänen m. about physical representations of genetic code in terms of dark nuclear strings. available at: http://tgdtheory.fi/public_html/articles/genecodemodels.pdf, 2016. [19] pitkänen m. hydrinos again. available at: http://tgdtheory.fi/public_html/articles/ millsagain.pdf, 2016. [20] pitkänen m. dmt, pineal gland, and the new view about sensory perception. available at: http: //tgdtheory.fi/public_html/articles/dmtpineal.pdf, 2017. [21] pitkänen m. about the correspondence of dark nuclear genetic code and ordinary genetic code. available at: http://tgdtheory.fi/public_html/articles/codedarkcode.pdf, 2018. [22] pitkänen m. dark valence electrons and color vision. available at: http://tgdtheory.fi/public_ html/articles/colorvision.pdf, 2018. [23] pitkänen m. emotions as sensory percepts about the state of magnetic body? available at: http: //tgdtheory.fi/public_html/articles/emotions.pdf, 2018. [24] pitkänen m. homonymy of the genetic code from tgd point of view. available at: http:// tgdtheory.fi/public_html/articles/homonymy.pdf, 2018. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.fi/public_html/tgdlian/tgdlian.html#persconsc http://tgdtheory.fi/public_html/tgdlian/tgdlian.html#persconsc http://tgdtheory.fi/public_html/neuplanck/neuplanck.html#qcritdark http://tgdtheory.fi/public_html/genememe/genememe.html#hgrprebio http://tgdtheory.fi/public_html/articles/harmonytheory.pdf http://tgdtheory.fi/public_html/articles/harmonytheory.pdf http://tgdtheory.fi/public_html/articles/genecodemodels.pdf http://tgdtheory.fi/public_html/articles/millsagain.pdf http://tgdtheory.fi/public_html/articles/millsagain.pdf http://tgdtheory.fi/public_html/articles/dmtpineal.pdf http://tgdtheory.fi/public_html/articles/dmtpineal.pdf http://tgdtheory.fi/public_html/articles/codedarkcode.pdf http://tgdtheory.fi/public_html/articles/colorvision.pdf http://tgdtheory.fi/public_html/articles/colorvision.pdf http://tgdtheory.fi/public_html/articles/emotions.pdf http://tgdtheory.fi/public_html/articles/emotions.pdf http://tgdtheory.fi/public_html/articles/homonymy.pdf http://tgdtheory.fi/public_html/articles/homonymy.pdf introduction some background questions emerged during 2018 some questions about the realization of the bio-harmony what conditions pairings pose on the frequency triplets? probabilistic estimates for single 20-chord harmony is the maximal number of codons for the fusion of 3 20-codon codes possible? how the symmetries of the model of harmony could relate to those of the genetic code? what is the origin of 12-note scale? what disharmony could mean? how to concretely realize emotions as music of light? login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 140-142 king, c., what is resplendence? issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 140 guest editorial what is resplendence? chris king * abstract resplendence is an innovative concept and nascent social movement, complementing science and transcending religion, with the wisdom of conscious insight and motivation, to reflower the planet as a living paradise, abundantly resilient over evolutionary time, and ultimately, to reach to the stars. keywords: resplendence, social movement, science, religion, transcendence, paradise. resplendence is both a revolutionary, world-transforming concept and a nascent social movement to reflower the planet. if you like this presentation, you are invited to make contact at the e-mail address below. resplendence complements the knowledge of nature and the universe provided by science and the powers provided by advanced technology with the wisdom of what to do for the future, so that all the living generations of humanity and the diversity of life can continue to prosper, and in the process we will discover our true calling as guardians of all conscious life in the universe. the discoveries of science have unveiled a story of our origin and future far more challenging and exciting than any archaic tales of god's creation. we know the universe is vastly more inscrutable and confounding than simple ideas of creation by god's breath, manufacture, or verbal command. we also know the universe is capable of supporting stars and planets and that the gas clouds around young solar systems contain the very molecules of life that we find have spawned life on our planet. we now know beyond all doubt from molecular genetics that life has evolved from single celled organisms to bootstrap itself into conscious organisms, who in our case can ponder our fates and wonder at the enormity and sheer depth in complexity of the universe of which we are a part. science deals with the discovery process of how nature and the universe work, resplendence provides the wisdom to enable us to creatively express this knowledge, in reflowering paradise on earth the ultimate manifestation of wisdom in action. resplendence is both an attitude of mind and a social dynamic attuned to bringing earth back to a state of full and abundant resplendence, sustainable and resilient over evolutionary time scales, to ensure our own survival and the survival of the diversity of life. since the dawn of history, we have needed to develop both practical knowledge of the natural world which plants are safe to eat, or medicinal and which are poisonous, how to make arrow poisons, to master fire and toolmaking. we also have a deep need to make sense of our conscious * correspondence: chris king http://resplendence.org e-mail: dhushara@gmail.com dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 140-142 king, c., what is resplendence? issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 141 existence to give us the confidence to approach the world with a sense of meaning and purpose a sense of "having to believe". the practical knowledge, which we have to treat sceptically, to make sure we get it right and survive, became science. traditional religion has sought to complement our practical knowledge in human history with a sense of meaning and moral purpose, but has done so at the cost of a heritage of enforced doctrines, moral imperatives, subjugation of women and scorched-earth attitudes, in which nature can be discarded for the false promises of celestial realms, amid dire threats of hellfire for disobedience to the religious path. subjective conscious experiences, both of the world around us, and of the inner realities of dreaming and visionary states. are integral to the spiritual quest of who and what we are as sentient beings, but religion has tended to distort this discovery process, by asserting fearful and incorrect descriptions of our existential condition, designed to make us subject to the religious imperative. resplendence transcends religion, by providing untramelled direct first-person avenues towards enlightenment, complementing the objective science of the physical world with the subjective science of consciousness research a true discovery process of conscious meaning and existence, so that human society can discover the deeper inner dimensions of conscious experience, fully exploring the conscious realms that religions aspire to in a way we can verify in the first person, through our own discoveries, engaging meditative and contemplative vigils and the agency of entheogenic species to make a voyage of discovery together, complementing scientific discovery of the physical world, with a living account of our evolving collective experience, without depending on second or third-hand religious doctrines to distort the nature and integrity of the first-person contemplative condition. in this process we shall come to fulfill the central hope of the true religious quest, in the flowering and deepening of sentient consciousness in the universe. just as the scientific world view has shown us a vastly more complex and challenging view of the universe than religious creation myths, so the collective exploration of the conscious condition unfettered by social taboo is likely to lead to conscious experiences, utterly different from, and vastly transcending, those of traditional religious doctrines. the word resplendence means many things. we usually think of it as a state of glorious natural splendour, but its root meaning re-splendere is to "shine brightly" or "shine again". it is thus both the overflowing abundance of paradise shining forth in splendour, and as a global consciousness, it is the illumination of our conscious discoveries into an enlightenment gained in the regeneration of the living world. but it has a deeper meaning, as the immortal condition of humanity and is hence the natural paradigm successor to religion, whose name re-ligio means to bind together, thus inducing social compliance with bondage to the established order and its obedience to doctrine. instead of leading to the social dominion and physically unrealizable imaginary scenarios of religions, such as heaven, hell and a triage in the the day of judgment, resplendence leads to a real and positively awesome outcome the reflowering of earth in natural abundance, through a dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 140-142 king, c., what is resplendence? issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 142 democratic culture empowered by climax technology, medicine and science based on principles of ecosystemic diversity. we all want to find meaning in life and want it to have a meaning that extends beyond our own lifetime. we also want the security that we are living in a world that has a viable future for our offspring and the future generations. the critical source of our angst that many of us turn to religion to alleviate, is that we are living in a world which is not only teeming with injustice, violent conflicts and weapons of mass destruction, but is lurching towards an uncertain future as a result of human impacts on the world's living habitats, climate and resources which could take us to an irreversible tipping point, undermining the future of unborn generations. these are problems we need to deal with and heal in this life to have a sense of fulfillment, not just pass them on to future generations, or to an imagined afterlife. we already have a good understanding of how the universe comes into being, of how the forces of nature are shaped, how they can produce atoms and molecules and the complex structures making up cell organelles and the tissues of living organisms. we are discovering the neuroscience of consciousness. but this is not the end of the road. we urgently need to act as good guardians of the planet, so that consciousness can continue to flower and new horizons can be discovered by future generations, so that the consciousness of human culture becomes a great tapestry a living brocade over space time. the key meaningful contribution we can make to the future comes through several avenues the good life we bequest to our offspring, our own first-person vision quest into the mystical depths of the conscious condition, our contributions to deeper understanding in culture and society, in the humanities, science, technology, art and music, through innovations we bring to society which produce lasting benefit, though compassionate social justice, and through actually protecting the living planet through our actions to guard the diversity of life. this way we become a true perennial expression of intelligent planetary life, which over time can reach to the stars and find our place in the consciousness life permeating the galaxies. you can find a more detailed explanation of the whole inspiration and thrust of resplendence as a game-changing world view in the keynote articles below. "conscious existence and the fate of the universe" provides an explanation of how resplendence fulfils the existential quest in a primary exploration of the conscious condition that transcends religion and complements scientific discovery. "the origin of sex" shows how evolution has given rise firstly to sex, then multicelled organisms and conscious brains, explaining why female reproductive choice is key to the emergence of our super-intelligence. "planetary ecocrisis" is a real time research reference overview of damage being done to biodiversity and the biosphere as a direct evidential call to action. it speaks for itself. science, resplendence and existence gives the previous overview, with a poster and video introduction. together these articles account how and why consciousness, sexuality and biodiversity are the three keys to the survival of the living planet. "resplendence: a cosmological theory of knowing" looks at resplendence as a subjective theory and method complementing objective science. http://resplendence.org/conscuniv/conscuniv3.htm http://resplendence.org/conscuniv/conscuniv3.htm http://dhushara.com/origsex/origsex.htmhttp:/dhushara.com/origsex/origsex.htm http://dhushara.com/biocrisis/biocrisis.htm http://resplendence.org/resplendence/srr.htm http://resplendence.org/conscuniv/gnosis.htm unraveling the tree of life dna decipher journal | october 2014 | volume 4 | issue 2 | pp. 57-73 king, c., the tree of life: tracing the genetic pathway from the last universal common ancestor to homo sapiens (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 57 article the tree of life: tracing the genetic pathway from the last universal common ancestor to homo sapiens (part i) chris king * abstract this series of articles are fully referenced research reviews to overview progress in unraveling the details of the evolutionary tree of life, from life's first occurrence in the hypothetical rna-era, to humanity's own emergence and diversification, through migration and intermarriage, using research diagrams and brief discussion of the current state of the art. the tree of life, in biological terms, has come to be identified with the evolutionary tree of biological diversity. it is this tree which represents the climax fruitfulness of the biosphere and the genetic foundation of our existence, embracing not just higher eucaryotes, plants, animals and fungi, but protista, eubacteria and archaea, the realm, including the extreme heat and salt-loving organisms, which appears to lie almost at the root of life itself. to a certain extent the notion of a tree based on generational evolution has become complicated by a variety of compounding factors. gene transfer is not just vertical carried down the generations. there is also evidence for promiscuous incidences of horizontal gene transfer, genetic symbiosis, hybridization and even the formation of chimeras. this review will cover all these aspects, from the first life on earth to homo sapiens. part i of this article includes: 1. introduction; 2. luca: the universal common ancestor; and 3.two or three domains of life? key words: tree of life, genetic pathway, common ancestor, homo sapiens, biological diversity. 1. introduction the tree of life, in biological terms, has come to be identified with the evolutionary tree of biological diversity. it is this tree which represents the climax fruitfulness of the biosphere and the genetic foundation of our existence, embracing not just higher eucaryotes, plants, animals and fungi, but protista, eubacteria and archaea, the realm, including the extreme heat and salt-loving organisms, which appears to lie almost at the root of life itself. to a certain extent the notion of a tree based on generational evolution has become complicated by a variety of compounding factors. gene transfer is not just vertical carried down the generations. there is also evidence for promiscuous incidences of horizontal gene transfer, genetic symbiosis, hybridization and even the formation of chimeras. this review will cover all these aspects, from the first life on earth to homo sapiens. this series of articles are fully referenced research reviews to overview progress in unraveling the details of the evolutionary tree of life, from life's first occurrence in the hypothetical rna-era, to humanity's own emergence and diversification, through migration and intermarriage, using research diagrams and brief discussion of the current state of the art. * correspondence: chris king http://www.dhushara.com e-mail: chris@sexualparadox.org http://www.dhushara.com/ mailto:chris@sexualparadox.org dna decipher journal | october 2014 | volume 4 | issue 2 | pp. 57-73 king, c., the tree of life: tracing the genetic pathway from the last universal common ancestor to homo sapiens (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 58 fig 1: the tree of life dna decipher journal | october 2014 | volume 4 | issue 2 | pp. 57-73 king, c., the tree of life: tracing the genetic pathway from the last universal common ancestor to homo sapiens (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 59 2. luca: the last universal common ancestor following a phase of biogenesis possibly based on cosmic symmetry-breaking (king 1978, 2004), based on spontaneous prebiotic rna synthesis (powner et. al. 2009, 2010) recent research suggests that the last universal common ancestor (luca) of all life on the planet may have arisen before the first cells, from a phase interface between alkaline hydrogen-emitting undersea vents and the archaic acidified iron-rich ocean (martin and russel 2003) in which differential dynamics in membranous micropores in the vents managed to concentrate polypeptides and polynucleotides to biologically sustainable levels (baaske et. al. 2007, budin et. al. 2009), giving rise to the rna era, while at the same time providing a free energy source based on proton transport across membranous microcellular interfaces resulting from fatty acids also being concentrated above their critical aggregate concentration. the transition to enclosed cells is likely to have been in an active iron-sulphur reaction phase still present in living cells and associated with sodium-proton anti-porters activating atp (lane and martin 2012, lane 2009b), leading in turn to electron transport and some of the most ancient proteins, such as ferredoxin, fig 1a: proposed scheme for the universal common ancestor (martin and russel 2003) http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-king-30815 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-king-11481 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-powner-14210 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-powner-11481 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-martin-47857 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-baaske-11481 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-budin-35882 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-lane-35882 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-lane-23240 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-martin-47857 dna decipher journal | october 2014 | volume 4 | issue 2 | pp. 57-73 king, c., the tree of life: tracing the genetic pathway from the last universal common ancestor to homo sapiens (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 60 the universal common ancestor of the three domains of life may have thus been a proton-pumping membranous interface from which archaea and bacteria emerged as free-living adaptions. this is suggested by fundamental differences in their cell walls and other details of evolutionary relationships among some of the oldest genes. among the archaea, halobacteria still use a form of photosynthesis generating atp from h + gradients generated by a rhodopsin protein and those in hydrothermal vents rely on na + -h + antiporters to generate ion gradients, and their membrane proteins, such as the atp synthase, are compatible with gradients of sodium ions or protons (lane and martin 2012, yong 2012). fig 1b: (above) founding metabolism based on na + -h + anti-transported, atp synthetase and fesnis containing vents (lane and martin 2012). the extremely ancient origin of the rhodopsin family of heptahelical receptors can be seen from the ultra-primitive archael photosynthesis in halobacteria, which relies on direct coupling between photo-stimulated chemiosmotic h + pumping and h + generated atp formation, based on bacteriorhodopsin, which is heptahelical, uses a form of retinal and whose helices share a distant sequence homology with vertebrate rhodopsin (ihara et al 1999). http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-three-47857 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-lane-35882 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-yong-49575 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-lane-35882 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-ihara-47857 dna decipher journal | october 2014 | volume 4 | issue 2 | pp. 57-73 king, c., the tree of life: tracing the genetic pathway from the last universal common ancestor to homo sapiens (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 61 it has also been proposed, on the basis of the highly-conserved commonality of transcription and translation proteins to all life, but the apparently independent emergence of distinct dna replication enzymes in archaea/eucaryotes and eubacteria, that the last universal common ancestor had a mixed rna-dna metabolism based on reverse transcriptase, pinpointing it to the latter phases of the rna era (leipe et. al. 1999). fig 1c: hypothetical branching and evolution of rna and dna replication machinery (leipe et. al. 1999) suggests viruses were pivotal in the transition from rna to dna (see below) to get a characterization of luca at the point it diversified into the three domains of life archaea, eucaryotes and bacteria, one cannot rely on nucleotide gene sequences because these would have mutated beyond recognition, but amino acid sequences mutate more slowly because neutral mutations leave the amino acid sequence fixed and the tertiary folded structure of a protein is even more strongly conserved. we offer best quality cas-001 test papers and pass4sure materials. you can get our 100% guaranteed testking 156-215.75 questions & actualtests 1y0-200 to help you in passing the real exam of pmi training. the validity of the rna-era concept and the capacity for rnas to be both replicating informational and active ribo-enzymes is emphasized by the continuing dependence of the ribosome on rrna rather than the protein components demonstrated by the 3-dimensional realizations of the two subunits in fig 4, which show that the rrna molecules are still carrying out the central task of protein assembly with only minor modification due to the 'chaperoning' proteins, despite 3.8 billion years of evolution. http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-leipe-14210 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-leipe-14210 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-leipe-14210 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-viral-14210 http://www.braindumps.com/cas-001.htm http://www.pass4sure.co.uk/350-029.html http://www.test-king.com/exams/156-215-75.htm http://www.actualtests.com/exam-1y0-200.htm http://www.pmi.org/ dna decipher journal | october 2014 | volume 4 | issue 2 | pp. 57-73 king, c., the tree of life: tracing the genetic pathway from the last universal common ancestor to homo sapiens (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 62 fig 4: small and large rrna subunits of the eubacteia thermus thermophilus and the archaeon haloarcula marismortui. rna orange and yellow, protein blue and active site green. (wikipedia ribosome). brooks et al. (2002) have found that the amino acids used in sections of genes common to life which are believed to originate with luca show amino acid distributions reflecting the relative abundance of such amino acids in primitive synthesis, indicating that the first translational genes used the amino acids which were spontaneously available. one intriguing indication of the state of genetic translation in luca is the incorporation of selenocysteine into the genetic code. selenoenzymes which contain selenocysteine as a genetically translated amino acid are essential to the three domains of life and source back to luca, despite the fact that the 21st coded amino acid selenocysteine could not be fitted into the genetic code. an ingenious piece of genetic software engineering evolved in which the amber stop codon uag is overridden if the m-rna possessses a motif called secis (selenocysteine insertion sequence) and selenocysteine is then inserted instead of termination and translation continues. http://en.wikipedia.org/wiki/ribosome http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-brooks-35882 dna decipher journal | october 2014 | volume 4 | issue 2 | pp. 57-73 king, c., the tree of life: tracing the genetic pathway from the last universal common ancestor to homo sapiens (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 63 fig 1c2: left: evolutionary tree of selenophosphate synthetase (romero et al. 2005) spans the three domains of life. centre: secis hairpins of archaea (a), bacteria (b) and corresponding eukaryote variants (c, d) (moldave ed 2006). top right: tertiary structure of secis showing highly conserved regions (hot) (walczak et al. 1996). lower right: secis acts as an rnaenzyme to attach the selenocysteine t-rna to the nascent protein. secis is an unusual hairpin loop structure which has varying forms in archaea and prokaryotes with both forms appearing in eucaryotes, but they have a common feature of a highly conserved hairpin loop forming an rna translational catalyst, which literally takes over some of the ribosomal rna function, binding to the selenocysteine t-rna and coupling selenocysteine to the nascent protein chain, as shown in the above figure. it is clear that this unique piece of genetic software engineering evolved in luca because the wobble positions of three other essential amino acid t-rnas, lysine, glutamine and glutamic acid (those with two wobble positions xaa-xag, the fourth set being amber and ochre stop codons), all depend on a modified 2-seleno-uridine base to function and this has to be generated from selenophosphate, which in turn is generated by selenophosphate synthetase. as shown above left, this enzyme has an evolutionary tree extending back to luca confirming the obvious that the genetic code cannot exist without the 21st software engineered amino acid selenocysteine! http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-romero-49575 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-moldave-11481 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-walczak-47857 dna decipher journal | october 2014 | volume 4 | issue 2 | pp. 57-73 king, c., the tree of life: tracing the genetic pathway from the last universal common ancestor to homo sapiens (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 64 to reconstruct the set of proteins luca could make, kim and caetano-anollés (direct link) searched a database of proteins from 420 modern organisms, looking for structures that were common to all. of the structures he found, just 5 to 11 per cent were universal, meaning they were conserved enough to have originated in luca. by looking at their function, they conclude that luca had enzymes to break down and extract energy from nutrients, and some protein-making equipment, but it lacked the enzymes for making and reading dna molecules. fig 1d: phylogenomic tree of proteomes describing the evolution of 420 fl organisms. phylogenomic study of protein domain structure in the proteomes of 420 free-living fully sequenced organisms. domains were defined at the highly conserved fold superfamily (fsf) level of structural classification (kim and caetano-anollés). http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-kim-49575 http://www.biomedcentral.com/1471-2148/11/140 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-kim-49575 dna decipher journal | october 2014 | volume 4 | issue 2 | pp. 57-73 king, c., the tree of life: tracing the genetic pathway from the last universal common ancestor to homo sapiens (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 65 organelles were thought to be the preserve of eukaryotes, but in 2003 researchers found an organelle called the acidocalcisome also occurred in bacteria. caetano-anollés' team has now found that tiny granules in some archaea are also acidocalcisomes, or at least their precursors. that means acidocalcisomes are found in all three domains of life, and date back to luca (seufferheld et al. direct link). fig 1e: tangled web linking acidocalcisomes in existent archaea, bacteria and eucaryote species (seufferheld et al.), overlaying electron micrographs of acidocalcisomes in agrobacterium tumefaciens(a, b) and methanosarcina acetivorans (c, d). http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-seufferheld-47857 http://www.biology-direct.com/content/6/1/50 http://www.biology-direct.com/content/6/1/50 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-seufferheld-47857 dna decipher journal | october 2014 | volume 4 | issue 2 | pp. 57-73 king, c., the tree of life: tracing the genetic pathway from the last universal common ancestor to homo sapiens (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 66 acidocalcisomes were originally discovered in trypanosomes (sleeping sickness and chagas disease) but have since been found in toxoplasma gondii (toxoplasmosis), plasmodium (malaria), chlamydomonas reinhardtii (a green alga), dictyostelium discoideum (a slime mould), bacteria and human platelets. their membranes contain a number of protein pumps and antiporters, including aquaporins, atpases and ca 2+ /h + and na + /h + antiporters. acidocalcisomes have been implied in osmoregulation. they were detected in vicinity of the contractile vacuole in trypanosoma cruzi and were shown to fuse with the vacuole when the cells were exposed to osmotic stress. presumably the acidocalcisomes empty their ion contents into the contractile vacuole, thereby increasing the vacuole's osmolarity. this then causes water from the cytoplasm to enter the vacuole, until the latter gathers a certain amount of water and expels it out of the cell. luca may have used rna rather than dna, as there is no evidence luca possessed ribonucleotide reductases, which create the deoxy versions of ribonucleotides the building blocks of dna (lundin et al direct link). rather it appears these functions have been transferred from bacteria back to archaea by horizontal transfer on at least two separate occasions (arrows in fig 1e). eucaryotes (mid green) would also have received theirs after luca diversification. fig 1f: ribonucleotide reductase trees showing bacterial, eucaryote and archaeal branches, with evidence of two events of horizontal transfer from bacteria to archaea (arrows) after the diversification of luca (lundin et al). luca was a "progenote". progenotes can make proteins using genes as a template, but the process is so error-prone that the proteins can be quite unlike what the gene specified. both di giulio and caetanoanollés have found evidence that systems that make protein synthesis accurate appear long after luca. in order to cope, the early cells must have shared their genes and proteins with each other. caetanoanollés says the free exchange and lack of competition mean this living primordial ocean essentially functioned as a single mega-organism. http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-lundin-11481 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-lundin-11481 http://www.biomedcentral.com/1471-2148/10/383 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-lundin-11481 dna decipher journal | october 2014 | volume 4 | issue 2 | pp. 57-73 king, c., the tree of life: tracing the genetic pathway from the last universal common ancestor to homo sapiens (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 67 3. two or three domains of life? life today is informationally based on the sequences of the four bases a, g, t and c in dna, with messenger copies of the genetic sequence in mrna (with u replacing t) forming intermediates in the assembly of proteins, as the cell's primary active chemical and structural agents. this is achieved through a process of translation at the ribosome a supra-molecular complex composed of some 50 chaperoning proteins surrounding a core composed of three rrna units, fed by amino-acid coupled trnas. the rnas carry out the essential function, supporting the idea that translation was at first a purely rna-based process of protein construction. in line with this and other rna fossils found particularly in eukaryotes, it is widely believed that life began based on rna, which shares both the capacity for complementary replication of dna and the formation of 3-dimensional chemically reactive conformations, similar to proteins, after which the ribosome evolved, transferring the reactive burden on to proteins sequenced through the genetic code. some time later, the informational genome was consolidated into more stable dna. fig 2: the initial tree of rrnas shows three distinct founding domains originally the bacteria and archaea were thought to be one large diverse family of prokaryotes until carl woese (1977, 1978, 1987, 1990) and others investigated the evolutionary tree of ribosomal rnas and found that there were three distinct founding evolutionary domains, then named eubacteria, archaebacteria along with the eukaryotes. this gave the eukaryotes a closer founding status as well, by contrast with the idea that the procaryotic bacteria came first and then, somehow the higher eukaryote organisms with their complex cellular http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-woese-6296 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-woese-48213 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-woese-33869 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-woese-37516 dna decipher journal | october 2014 | volume 4 | issue 2 | pp. 57-73 king, c., the tree of life: tracing the genetic pathway from the last universal common ancestor to homo sapiens (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 68 structures, including among others the endoplasmic reticulum, along with the nuclear envelope and golgi apparatus all parts of a common complex of internal membranous partitions and the architecture of microtubules, including centrioles, and the eukaryote flagellum, as well as the eukaryotes endosymbiont mitochondria and chloroplasts. fig 3: key structural differences separating the larger rrna units of the three domains (woese 1987) in addition to their evolutionary sequence divergence, the smaller 30s ribosomal rnas of each domain, show distinct structural features characteristic of their own domain, but also emphasizing structural links between bacteria and archaea on the one hand and archaea and eukaryotes on the other, qualitatively confirming the central place of the archaea in the divergence. dna decipher journal | october 2014 | volume 4 | issue 2 | pp. 57-73 king, c., the tree of life: tracing the genetic pathway from the last universal common ancestor to homo sapiens (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 69 fig 5: (a) further elaboration of the rrna tree (pace 1997) (b) a third rrna tree which suggests archaea lie very close to the root is contrasted with that for the enzyme hmgcoa reductase (c), which also shows evidence of horizontal transfer to an archaean (ex doolittle 2000). norman pace subsequently enlarged the scope and accuracy of the rrna tree, including a greater diversity of organisms. this tree has become the basis of several other studies (see e.g. fig 11). fig 5b: three domains (a) is contrasted with a recent version of the "eocyte" hypothesis (b) showing the eucaryotes emerging from the wider crenarcheota grouping (tack) after divergence from euryarcheota, implying the amoeboid ancestor of the eucaryotes was an "eocyte" (williams et al. 2013). however james lake (1988) had already challenged the notion of three domains, with an analysis claiming that the eucaryotes instead branched off form only one line of the archaea, the eocytes or chrenarcheota. this view has been confirmed by accumulating genetic studies (williams & embley 2014, williams et al.2013, foster, cox & embley 2009, cox et al. 2008). the copernican principle asserts that the earth is a typical rocky planet in a typical planetary system, located in an unexceptional region of a common barred-spiral galaxy, hence it is probable that the universe teems with complex life. this is supported to a reasonable extent by the discovery of an increasing number of planets including some putative "goldilocks" zone planets where water would be liquid and life as we know it could potentially exist. set against this, the "rare earth" hypothesis argues that the emergence of complex life requires a host of fortuitous circumstances, including a galactic habitable zone, a central star and planetary system having the requisite character, the circumstellar habitable zone, the size of the planet, the advantage of a large satellite, conditions needed to assure the planet has a magnetosphere and plate tectonics, the chemistry of the lithosphere, atmosphere, and oceans, the role of "evolutionary pumps" such as massive glaciation and rare bolide impacts, and whatever led to the still mysterious cambrian explosion of animal phyla. this might mean that planets able to support a bacterial level of life are not so uncommon, but those supporting complex multicellular life might be. http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-pace-60133 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-doolittle-46919 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-fig-21683 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-williams-14210 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-lake-11481 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-williams-35882 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-williams-14210 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-foster-23240 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-cox-3800 dna decipher journal | october 2014 | volume 4 | issue 2 | pp. 57-73 king, c., the tree of life: tracing the genetic pathway from the last universal common ancestor to homo sapiens (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 70 fig 6: metabolic power of eucarote cells per haploid genome and hence the capacity for genomic complexity depends on the rspiraqtory power of mitochondria (lane and martin). bringing this question to a pivotal crux in our context, the emergence of mitochondria as endosymbionts has been proposed to be a critical bottleneck which allowed complex life to evolve only once on earth, because, only in this effectively fractal cellular architecture, can the membrane surface areas necessary to support the chemical reactions enabling the vastly larger number of genes in a complex organism's genome to maintain metabolic stability (lane and martin). lane and martin note "the cornerstone of eukaryotic complexity is a vastly expanded repertoire of novel protein folds, protein interactions and regulatory cascades. the eukaryote common ancestor increased its genetic repertoire by some 3,000 novel gene families. the invention of new protein folds in the eukaryotes was the most intense phase of gene invention since the origin of life. eukaryotes invented five times as many protein folds as eubacteria, and ten times as many as archaea. even median protein length is 30% greater in eukaryotes than in prokaryotes". whether such endo-symbiosis is rare. or a common extreme of parasitic or predatory relationships would then determine how likely or unlikely complex life might be. this massive increase in complexity remains obscure in the genetic and fossil records and requires some ingenious model construction to envisage how mitosis, meiosis, sexuality, the nuclear envelope, endoplasmic reticulum, cytoskeleton, and all the complexities of eucaryote regulation evolved. for a seminal work on this see (cavalier-smith 2010). regardless of this, lane and martin's metabolic approach explains neatly why there is little sign of any of these structures in any existing prokaryote. in effect endo-synbiosis created a completely new http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-lane-35882 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-lane-35882 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-cavalier-smith-35882 dna decipher journal | october 2014 | volume 4 | issue 2 | pp. 57-73 king, c., the tree of life: tracing the genetic pathway from the last universal common ancestor to homo sapiens (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 71 energetic regime, in which the only niche players were the newly formed endo-symbiotic chimeras themselves, who then underwent a massive adaptive radiation to form ever more complex forms of cellular machinery and ultimately leca and the diversity of eucaryotes as we now know them. there are echoes in this metabolic shangri-la of the conditions in lost city vents that we are coming to understand may have likewise given rise much earier to luca. fig 6b: left: bacterium gemmata obscuriglobus with internal nuclear envelope and vaccuoles (rachel melwig & christine panagiotidis / embl). right: ultrathin em section of a mimivirus in amoeba (jean-michel claverie) inset: mamavirus infected by sputnik phage. offset against both the uniqueness of the mitochondrial endo-symbiosis and the closely linked, but independent question of the origin of the nucleus and nuclear envelope, has been the discovery of mimi-, mama-, megaand pandora-viruses infecting amoeba (raoult et, al., philippe et al) and related very large aquatic viruses such as crov infecting single celled plankton species (fisher et. al.), which despite their recent discovery, appear from ocean gene analyses to be potentially ubiquitous and widespread in the oceans and possibly playing a crucial role in regulating the atmospheric-oceanic pathways, such as carbon sequestration. these form an intermediate genetic position between viruses and cells, having the largest genomes, with extensive cellular machinery and larger than the smallest completely autonomous bacterial and archaeal genomes. megavirus chilensis, for example is 10 to 20 times wider than the average virus. the particle measures about 0.7 micrometres (thousandths of a millimetre) in diameter. it just beats the previous record holder, mimivirus, which was found in a water cooling tower in the uk in 1992. a study of the megavirus's dna shows it to have more than a thousand genes. the mimivirus genome is a linear, double-stranded molecule of dna with 1.18 mbp in length. megavirus has 1.25 mbp. like mimivirus, megavirus has hair-like structures, or fibrils, on the exterior of its shell, or capsid, that probably attract unsuspecting amoebas looking to prey on bacteria displaying similar features. these viruses show many characteristics at the boundary of living and non-living. they are as large as several bacterial species, such as rickettsia conorii and tropheryma whipplei, possess a genome of comparable size to several bacteria, including those above, and code for products previously not thought to be encoded by viruses. mimivirus has genes coding for nucleotide and amino acid synthesis, which even some small obligate http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-raoult-47857 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-philippe-49575 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-fisher-11481 dna decipher journal | october 2014 | volume 4 | issue 2 | pp. 57-73 king, c., the tree of life: tracing the genetic pathway from the last universal common ancestor to homo sapiens (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 72 intracellular bacteria lack. however, it lacks genes for ribosomal proteins, making it dependent on a host cell for protein translation and energy metabolism. as of mid-2013, an even larger virus with a 2.5 mb genome without morphological or genomic resemblance to any previously defined virus families has been discovered by the same researchers that found mimivirus, in both the same ocean sample off peru and in a freshwater pond in australia. named pandoravirus reflecting their lack of similarity with previously described microorganisms and the surprises expected from their future study. the researchers suspect that giant viruses evolved from cells. they think that at some point, the dynasty on earth was much bigger than the three domains of bacteria, archaea and eukaryotes. some cells gave rise to modern life, and others survived by parasitizing them and evolving into viruses. pandora might thus provide a complementary relic of the genomes of this wider founding group (philippe et al). using the global ocean sampling (gos) expedition data to explore variants of reca (the universal dna repair enzyme) and rpob (the beta subunit of bacterial rna polymerase) a team associated with craig venter have discovered branches which may also point to a fourth domain (wu et al). fig 6c: evolutionary tree of b-family dna polymerase showing relationship of pandoravirus to other viruses and eucaryotes. inset is shown pandoraviruses invading acanthamoeba (philippe et al). http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-philippe-49575 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-wu-49575 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-philippe-49575 dna decipher journal | october 2014 | volume 4 | issue 2 | pp. 57-73 king, c., the tree of life: tracing the genetic pathway from the last universal common ancestor to homo sapiens (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 73 as an illustration of genes in mimivirus normally appearing only in cellular genomes, the mimivirus has genes for central protein-translation components, including four amino-acyl transfer rna synthetases, peptide release factor 1, translation elongation factor ef-tu, and translation initiation factor 1. the genome also exhibits six trnas. other notable features include the presence of both type i and type ii topoisomerases, components of all dna repair pathways, although the topoisomerase 1b has a different header structure from the eucaryote form (brochier-armanet, gribaldo & forterre 2008), many polysaccharide synthesis enzymes, and one intein-containing gene. inteins are protein-splicing domains encoded by mobile intervening sequences (ivss). they self-catalyze their excision from the host protein, ligating their former flanks by a peptide bond. they have been found in all domains of life (eukaria, archaea, and eubacteria), but their distribution is highly sporadic. only a few instances of viral inteins have been described. self-splicing type i introns are a different type of mobile ivs, selfexcising at the mrna level. they are rare in viruses. mimivirus exhibits four instances of self-excising intron, all in rna polymerase genes. fig 6d: evolutionary diversification of mimiviruses from nucleocytoplasmic large dna viruses (fisher et. al.) and in relation to the three domains of cellular life based on the concatenated sequences of seven universally conserved protein sequences (raoult et. al.) mamaviruses also host parasitic virophages, affectionately named sputnik (pearson 2008) as viral satellites, which piggy back on the metabolism of the large viral factories set up by these giant viral genomes causing the mimiviruses to sicken, and these virophages also contains genes that are linked to viruses infecting each of the three domains of life eukarya, archaea and bacteria (la scola et. al.). it has thus been suggested that they have a primary role in the establishment of cellular life and that they may have been instrumental in the emergence of the nuclear envelope. (continued on part ii) http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-brochier-armanet-47857 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-pearson-49575 http://www.dhushara.com/book/unraveltree/unravel.htm#anchor-la-14210 microsoft word stephensmith_v8n3 dna decipher journal | november 2018 | volume 8 | issue 3 | pp 166-180 smith, s. p., time, life & the emotive source issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 166 article time, life & the emotive source stephen p. smith* abstract a panpsychism, or neo-vitalism, is presented having to do with the penetration of time in living organism. time is described having bifurcated or polarized into two windows: one that looks forward in time and follows a chain of determinism, and one that looks backward in time to frequencies and past habits. the emotive source is described as a singularity, the timeless middle-term holding the two windows together. this view is related to the laws of physics, the second law of thermodynamics, genetics and epigenetic switches. warm-body quantum mechanics is implicated broadly, and in particular with the creation of adaptive mutations that are coxed by epigenetic cues. keywords: time, life, emotive force, panpsychism, neo-vitalism, living organism, determinism, bifurcation, thermodynamics, genetics, epigenetics, quantum mechanics, creation. 1. introduction the visionary and counter-culture proponent1, terence mckenna (1946-2000), defined life as something that time got into.2 saw the legs off a chair, and throw the pieces on the ground, and nothing will happen, he noted. come back the next day, and the pieces are still there where you left them, unchanged. do that with something living, he noted, and it will bleed and die as time unfolds. cutting body parts off of something living, he concluded, is to interrupt time and its connection to life. in this paper, mckenna’s hypophysis is taken serious, but without any intended cruelty of animals. surprisingly so, his view is found very compelling, that time has gotten into life. the view sees time bifurcated in life into two windows. from life emerged mind and the view see time bifurcated in our psychology. the two-sided time implies a timeless middle-term, hinting of a panpsychism or the emotive source. the philosophical proposal of panpsychism, as well as scientific accounts of consciousness based on quantum mechanics, are becoming more acceptable today as serious endeavors. to these we can add the emerging field of quantum biology. regarding biology, its reasonable to assume that panpsychism becomes a neo-vitalism if there is any truth to panpsychism. to proceed, this paper reissues the second law of thermodynamics in section 2 in terms that are friendly to neo-vitalism, without diminishing the law-like drive that increases entropy with time correspondence: stephen p. smith, ph.d., independent researcher. e-mail: hucklebird@aol.com note: this article was first published in journal of consciousness exploration & research 9(8): pp. 707-721 (2018). 1 this paper makes no endorsement of mckenna’s advocacy of psychedelics. 2 by comparison, immanuel kant viewed time as an internal intuition. dna decipher journal | november 2018 | volume 8 | issue 3 | pp 166-180 smith, s. p., time, life & the emotive source issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 167 passage. genetics is described in section 3, but in summary form. an account of time-impacted life based only on genetics, while missing epigenetics, is stilted at best. therefore, section 4 describes epigenetics, but in summary form. to relate neo-vitalism to what known about physics, including the 2nd law, it is necessary to reissue all these laws in section 5. an account of how time possibly leaves its mark on epigenetic switching is presented in section 6, including a universal grammar that engages proto-emotion and hinting of a necessary warm-body quantum mechanics. this leads to the possibility of some testable science, and a discussion of such possibilities are presented in section 7. 2. second law of thermodynamics the second law of thermodynamics describes the fall of energy from an ordered state (low entropy) to a disordered state (high entropy), in a universe where energy is otherwise conserved. the 2nd law is irreversible, in that energy has never been observed to flow in the opposite direction, from a disordered state to an ordered state that’s more that just a minor occurrence. a good example is a ball that is perfectly balanced on top of a hill (figure 1). the balanced state represents a perfect symmetry, where the path to be taken in the down-hill role is still not determined. this symmetry represents an impartiality in the future possibilities, but its highly unstable. the slightest wind will tip the balance and break the symmetry, causing the ball to start rolling in some particular direction. initially, the ball has high potential energy representing the a-prior order. as the ball starts rolling, the potential energy deceases and is transformed into some waste heat and kinetic energy when the ball accelerates. eventually that ball will come to rest in one of four valleys, and at that point all of the incremental change in potential energy is transformed into waste heat. the one-way flow has never been observed to go in reverse, where the ball absorbs waste heat from the surroundings and rolls up hill, and then finds itself perfectly balance at the apex of the hill. figure 1. energy landscaped showing black ball balanced on top of a hill, ever-ready to be tipped and to roll into one of four possible gullies before coming to rest in one of the respective valleys. statistical mechanics can represent the 2nd law as the behavior of free bodies inside a closed dna decipher journal | november 2018 | volume 8 | issue 3 | pp 166-180 smith, s. p., time, life & the emotive source issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 168 ensemble.3 the free bodies can float around unrestricted, in random directions, bouncing off each other like newtonian billiard balls. the migrations are restricted by transitions that are determined by probability. if all the free bodies are located in one corner of the ensemble initially, neatly stacked side by side, then that would represent a highly ordered state. with time passage the ordered state would decay and fall into a disordered state where the free bodies are smeared out in any such direction, almost uniformly over the space of the ensemble but deeply haphazardly. the 2nd law dictates that energy transitions from low entropy to high entropy, and never in reverse, and if you believe statistical mechanics this one-way flow is a matter of probability. when the probabilistic version of the 2nd law is interpreted as a universal law, however, what is discovered are deep contradictions having to do with the low entropy of the initial conditions (price 1996, chapter 2). this made boltzmann and others rethink the probabilistic law as a universal. if thermodynamic equilibrium is the normal state of affairs when the universe began boltzmann figured, then statistical mechanic paradoxically predicts that entropy was much higher at some time in the distant past than today and coming with high probability, a direct contradiction of the 2nd law (price, page 30). or we can assume that the initial conditions, now given as the birth of the universe, came with low entropy (albert 2000, chapter 4). where did that initial high order come from? smith (2008) described the 2nd law as two-sided, and holding the fatal equivocation of the meaning of “representation” given by statistical mechanics and the meaning of “recognition” given by a space that dissipates waste heat. william james sidis (1925) made similar observations, and predicted a new principle that works in reverse of the 2nd law and existed in some pockets of the universe, and related this new principle to life and life’s teleology4. given that kauffman (2008) describes a “ceaseless creativity” emerging at the criticality separating order and disorder, the 2nd law described by statistical mechanics can only be a onesided interface showing the fall into disorder. the other side of the demarcation is where disorder is found uniting into order again, forming larger wholes, but agreeing with sidis (1925) this must necessary happen in reverse-time to maintain consistency with both sides. moreover, sidis found the 2nd law to be a psychological law that’s necessary to keep track of apparent forward causation. david hume believed that our understanding of causation came to us by regularities discovered with past experiences rather than by reason.5 time is found polarizing into two psychological windows, then. one side looks forward deductively and recognizes deterministic chains as sidis found, but the other side looks backward to find itself in inductive habits, generalities and past frequencies as hume believed. the two windows of time are necessarily unified by a middle-term that’s undeclared by law, a middle-term that’s necessarily timeless6 and 3 this formulation is due to ludwig boltzmann, coming from his address to a meeting of the imperial academy of science, 1886. 4 in a similar vein, price (1996) also considers causal asymmetries implied by the 2nd law and postulated a possible backward causation or advanced action that involves quantum mechanics. 5 an enquiry concerning human understanding. 6 in the sense that photos are timeless (russell 2003). photons act as messenger particles that communicate the electromagnetic force, and are also massless and spaceless. gluons and postulated gravitons are also massless and also act as messenger particles for the strong force and gravity, dna decipher journal | november 2018 | volume 8 | issue 3 | pp 166-180 smith, s. p., time, life & the emotive source issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 169 represents a deep singularity. the middle-term is also implicated as the emotive source7; i.e., if alfred north whitehead is correct in his belief that causality can be directly prehended by experiential occasions, however vague a feeling but an emotion laden feeling nevertheless.8 the 2nd law describes the behavior of mindless free-bodies that risk the heat death, and sidis’s psychological law translates into the emotional warning: remain mindful or bad things will happen. it’s the kind of advice that a father will give to his son to stay on the straight and narrow path. it’s the watchful eye of the shepherd that looks after the flock and plans ahead. hume’s version of the same law, but on the receiving side, is more feminine: we are all in this together; and harmony is preferable to strife. 3. genetics and the fitness landscape wright (1932) was the first to describe the fitness landscape for a population where its average fitness is given by a position on a topology that’s dependent on gene frequency. natural selection and genetic drift can both influence gene frequency changes that can occur in a population over time, from one point on the topology to the next, presumably climbing higher on the landscape. figure 2 provides an illustration of a simple fitness landscape that applies on the population level, but there are other varieties of fitness landscapes that have been studied (e.g., kauffman 1993). figure 2. hypothetical fitness landscape given by the height dimension and overlaying a twodimensional surface that depicts gene frequency at two independent loci. independent of how variation offers itself to natural selection, the fitness landscape drives evolution. it represents a genetic determinism that points to a possible future state of a population that is more adapted. however, the fitness landscape is just one possible driver of evolution respectively. 7 rather than describing this as a panpsychism, or a panexperientalism, preference is given to protoemotionality as the fundamental because this is arguable less anthropomorphic and yet it carries the essential meaning that preferred directions are sought non-passively. 8 process and reality, chapter vii. dna decipher journal | november 2018 | volume 8 | issue 3 | pp 166-180 smith, s. p., time, life & the emotive source issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 170 among genetic drift, genetic recombination, mutation and the survival instinct that’s innate in life. it’s a gross oversimplification to imply these processes are blind and indifferent, particularly if evolution is to now be connected to the mysterious 2nd law of thermodynamics (e.g., wicken 1987; brooks and wiley 1988; chaisson 2001), particularly if life’s adaptability is found relating to quantum mechanics and the collapse of the quantum wave function (goswami 2008; mcfadden 2000), and particular if mutations are found not random but life-directed and even adaptive (cairns, overbaugh and miller 1988; martincorena and luscombe 2013). mutations that are accidental, or haphazard, tend to be detrimental to such an extent that natural selection is unable to remove them in numbers that can improve the adaptation of living organisms (stanford 2008, chapter 4). it is necessary for cells to utilize error correcting capabilities when mutations, or copying errors, occur in dna (radman and wagner 1988). the fitness landscape joints the energy landscape (figure 1) in that both imply a direction in time. genes found in the zygote somehow predict heritable traits that may be selected in the adult by natural selection. in that evolution of novelty can emerge unexpectedly from darwinian pre-adaptions (kauffman 2008), the fitness landscape must be able to coax the novelty into existence as if the landscape carried a remarkable foresight. nevertheless, the fitness landscape is a tool of the one-sided rational mind that sees a chain of causation in a world well described by newtonian billiard balls that bounce off of each other. 4. epigenetics and the waddington landscape epigenetics controls developmental biology by way of switches that are actually put on the dna. the switches turn genes off with methylation (siegfreid and cedar 1997), or they slow or accelerate the gene with a connection using histones by acetalyzation (eberharter and becker 2002). in other words, the epigenetic switches act as frequency modulators on the dna by determining the frequency profile of protein production. the genetic material, or dna, was never well described as a blue print or program. epigenetics reveals that genetic determinism is better described by the metaphor provided by a fourier analysis of a time series that depicts gene function as an action in time, where the time series is described as a linear combination of a set of basis vectors (now the original dna backbone), and where the linear coefficients are spectral frequencies attached to each gene by epigenetics. after fertilization the zygote divides and becomes a blastocyst, differentiated only into an inner cell mass (icm) and the outer trophectoderm. the icm and the trophectoderm will differentiate further into the embryo and placenta, respectively. when icm cells go through differentiation they specialize into tissue types, liver, brain, blood, hair, etc. while each cell in the body has the same dna, they have a different combination of epigenetic switches. in the process of cell division, these switches are passed on to the daughter cells, i.e., the switches are more the less permanent. however, the daughter cells can have new switches added if the daughter cells differentiate further from the parent, in a process that is not reversible9; i.e., the new epigenetic 9 there are notable exceptions. when animals are cloned, or when stem cells are generated experimental dna decipher journal | november 2018 | volume 8 | issue 3 | pp 166-180 smith, s. p., time, life & the emotive source issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 171 switches are added during some of the steps of embryonic development where changes among cell types occur. the differentiation of cells during early development, starting with the zygote, resembles the irreversible fall into disorder having to do with the 2nd law of thermodynamics (figure 1), a pattern of future possibilities provided by the waddington landscape depicted in figure 3. this characterization of irreversible differentiation as a ball rolling down an epigenetic landscape is due to waddington (1957). ferrell (2012) relates the dynamics carried by the waddington landscape with an attractor, an observation that is not lost in section 6. figure 3. one cell (dark dot) from a blastocyst set to roll down the waddington landscape and undergo irreversible differentiation following one of three paths that are provided by the two forks shown here. when the cell undergoes division it then assumes the identity of one of the daughter cells artificially, thus permitting a logical passage down the entire landscape. cells in the blastocyst are possibly in some still unexplored quantum entangled state, particularly if differentiation is recognized as partially a collective process but admitting to possible degrees of entanglement. this implies that daughter cells remain quantum entangled after cell division. with this interpretation, the blastocyst represents a quantum supper-position of possible realizations, differentiation being the collapse of respective wave functions when epigenetic switches are added to dna (e.g., asano et al., 2017). jorgensen (2011) also implies that epigenetics involves quantum mechanics, even suggesting a backward in time flow of information from the environment. epigenetics is more complicated than presented in this summary, and a broad overview of the emerging subject is presented by carey (2012) that also includes a description of the following side notes: 1. some epigenetic switches can also be passed through sexual reproduction (e.g., migicovsky and kovalchuk 2013). a parent can acquire an epigenetic change that makes its way to the germ line, then past that change to a child that inherits the same characteristics in a lamarckian sense. 2. sperm and egg cells can also be imprinted differentially by epigenetic switches, in a way from non-stem cells, the epigenetic switches are removed somewhat where experimental methods are discovered how to reverse epigenetic changes. dna decipher journal | november 2018 | volume 8 | issue 3 | pp 166-180 smith, s. p., time, life & the emotive source issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 172 that’s essential for development. 3. there is epigenetic regulation having to due with the deactivation of one x-chromosome, a necessary regulation for females that carry two x chromosomes. 4. the non-protein coding dna, which is 98% of the dna, transcribes into rna that acts in epigenetic switching. these processes are not well understood. 5. two-sided laws and quantum mechanics einstein’s special and general relativity are symmetric in time. the action principles of unified field theory look identical under cpt inversion10, which includes time. in summary, all of the laws of physics are found symmetric in time as sidis (1925) noted, apart from the asymmetrical 2nd law that is arguably two-sided. that is, the laws that come as action principles look the same in reverse time as they do in forward time, and they even hint of a possible teleology (helrich 2007). teleology can be recovered from the two-sided 2nd law as hypothesized in section 2. something must also be said about symmetry breaking, because laws that look the same in both time directions, that look the same in their own specified symmetry so polarized to provide two views, say very little about how the laws themselves came into being by a process of symmetry breaking. in the grand unification epoch, the universe is thought to have expanded and cooled from a big bang (chaisson 2001, pp 242-247). during this expansion, the four forces of nature emerged in the order gravity, the strong force, weak force, electromagnetism. this process involved spontaneous symmetric breaking, leaving the laws behind but coming with selected constants that modulate and calibrate the action of the laws. in the wake of these breaks we find: the speed of light, the cosmological constant for a flat universe, the relative strengths of the four forces of nature, the masses and coupling constants, planck’s constant. these are the affinities that nature selected. most of these are thought fine-tuned for life (barrow and tipler 1986). the question comes, were these selections the result of random occurrences when symmetries broke, or were they innate preferences selected by the ground of being? the weak anthropic principle tries to enforce the belief that it is all accidental, because we would not be here to ask questions if the selections were different, we are just very lucky. the symmetrical laws themselves look to be taking part of a greater symmetry breaking once a boarder view is taken on how they act. the broader view changes with law-restrained action, but something remains that’s unchanged called the law. first understand, that from the point of view of agency that carries information, symmetry is when everything looks the same from all points of view. after symmetry breaks things stop looking the same as natures arrives at an affinity or preference, and this implies there needs to be some kind of polarity before symmetry breaking that holds the two sides together in an indistinguishable state. symmetry breaking leads to a state of natural discernment, where one side becomes visible while the other disappears. in this view, that part of reality that became invisible does not mean necessarily that the unselected part of reality stops existing. because the middle-term is beyond law and cannot be excluded from reason, it only means that the unselected part of reality becomes part of a shadow. for example, 10 cpt is an acronym for charge, parity and time. cpt inversion changes a particle into its anti-particle, changes an image into its mirror reflection, and changes forward time into reverse time. dna decipher journal | november 2018 | volume 8 | issue 3 | pp 166-180 smith, s. p., time, life & the emotive source issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 173 the existence of dark energy and dark matter may be the left-over shadow that followed in the wake of symmetry breaking occurring in the early universe. the broader view of symmetry breaking may very well be synonymous with the collapse of the quantum wave function, in these cases the collapse of the universe's own wave function by the action of gravity. this view is a restatement of john wheeler’s (1990) particpatory universe, where the constants of physics were selected by the ground of being because something was preferred to nothing; i.e., preferred by proto-emotion that connects time over a very wide duration. the collapse of the quantum wave function, more localized in brain tissues and involving microtubules in cells, has already been implicated as something fundamental to consciousness (hameroff and penrose 2014). strapp (2007) also implicates the quantum wave function and its collapse to the phenomenon of consciousness, but strapp points to the quantum zeno effect within synapses rather than microtubules, and strapp further relates his theory to whitehead’s process philosophy. perhaps unsurprisingly now, the collapse of the quantum wave function may be the real driver behind irreversibility and the 2nd law (albert 2000, chapter 7), implying that order and disorder relate directly to quantum coherence and decoherence. if our experience of free will is real, then it must be possible to transcend the apparent flow of forward causation, to reach back and set initial conditions by a reverse causation that is modulated by our emotions. otherwise, benjamin libet’s (1985) timing experiment will spell the end of our imagined freewill. freewill is saved by quantum mechanics again, because its quantum mechanics that permits a reverse causation over a time duration (wolf 1998). in summary, the laws of physics are found two-sided, and the middle-term that holds the sides together is undeclared by law and is possibly the source of proto-emotion. therefore, the historical and premature rejection of vitalism is now recognized as the fallacy of excluded middle. the possibility of reverse-mode causation necessarily implicates quantum mechanics, and the collapse of the wave function. for the same reasons, quantum mechanics is implicated in gene action and epigenetics, in all probability. 6. when time finds itself up to this point, a mechanism has not been described how proto-emotion that’s completely confounded with time is found relating to genetics and epigenetics. the proposed hypothesis is that the mechanism is part of a universal grammar given that time presents two windows. only with the universal grammar better described can evidence be gathered to support this hypothesis. the backward in time window relates to a signal sensitivity given by past frequencies that modulate the effect of dna. this modulation is precisely what is found with the epigenetic switches provided by methylzation and acetalyzation. epigenetics is not limited by the dna modulation, however, because something epigenetic may be on top of dna modulation, and something may be on top of that.11 at any rate, the backward in time window is closely matches 11 lipton (2005, chapter 3) describes proteins that are embedded in the cell membrane, and act as information gates that relate to the outside environment and also impact on epigenetic signals inside dna decipher journal | november 2018 | volume 8 | issue 3 | pp 166-180 smith, s. p., time, life & the emotive source issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 174 with the frequency domain that characterizes time series analysis. the other type of time series analysis is called the time domain which is characterize by a forward progression such as the markov chain. the time domain or the forward in time window has to do with the forward flux of cause and effect given by the genetic determinism that presents itself: be it a population that’s navigating the fitness landscape; or cells undergoing division and embryonic differentiation by navigating the waddington landscape; or it’s a cell involved with its mature metabolic function thereby following an energy landscape. the two time windows will permit negative feedback in forward time, where the chain of determinism may reach back and reset epigenetic switches. this is classically defined regulation that still represents something habitual. however, this is not the emotive balancing act described next that will actually carry a reverse-time connection. the more speculative part of the grammar has to do with the creation of new functions. this is described as the great centering of proto-emotion to arrive at the critical point separating order and chaos.12 it must be that the backward and forward windows come together as time finds itself in a process of targeted synchronisation, the two widows oscillate. this brings a tension leading to an emotive climax where something new erupts on time’s manifold and comes into being so targeted: a new mutation or an alteration in an epigenetic switch. this coming into being involves the collapse of the quantum wave function so hypothesized, with a time duration and quantum non-locality that is significant enough to likely enhance the utility of the targeted change that was sought by proto-emotion.13 strict or quasi genetic and epigenetic determinism14 is inadequate during periods of crisis by definition, leading to exhaustion, stress, and even proto-emotional surrender. the response that comes in the wake of the eventual release is hypothesized as part of the universal grammar, which is the aforementioned coming together and synchronisation of time’s windows, and this grammar is followed by the cell and by human psychology15. there is known genetic regulation that can kick into gear during periods of stress, inducing adaptive mutation (e.g., hopkins et al., 2013; chen, lowenfeld and cullis 2009; tadderi et al., 1997). but is this the result of relaxing the cell. moreover, pert (1997, chapter 9) postulates that peptides circulating in the body communicate emotions. 12 what vattay, kauffman and niiranen (2012) describes as the “poised realm”. 13 specifics are lacking, but particulars of warm-body quantum mechanics are better provided by future investigations. unknown are where on dna, rna or proteins are regions of quantum supperposition? is a quantum collapse limited to biochemicals inside one cell? or are there any non-locality and entanglement effects among cells, among organisms? 14 a strict-determinism is a one-sided set of entailments that enforce the principle of excluded middle as kauffman (2014) describes, whereas a quasi-determinism permits an emotive middle-term that has achieved a high level of fidelity in a learned route. given that all physical laws are context dependent and are two-sided with undeclared middle-terms, this distinction is probably moot. nevertheless, a learned route that involved something emergent (beyond known laws) is probably better characterized as a quasi-determinism. 15 benjamin franklin is quoted, “we must all hang together, or assuredly we shall all hang separately.” dna decipher journal | november 2018 | volume 8 | issue 3 | pp 166-180 smith, s. p., time, life & the emotive source issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 175 the error correcting capabilities of the cell as keller (2000, page 34) implies? where genetic stability and mutability are otherwise held in a delicate balance (e.g., chen et al., 2010) because they are complementary epigenetic effects that modulate the same genes? and what is “stress,” if not a non-preferred state from the point of view of proto-emotion? the mere fact that these serious questions can be raised in the face of the aforementioned references in primal facial evidence that supports the contention that mutability and genetic stability is the work of protoemotional centering and synchronisation leading to switching. if the delicate balance is broken because of an innate one-sidedness that has developed, then the emotive centering may fail. note that mothering of baby rats creates a mood disposition in adult rats, all related to epigenetic methylation found in the brain that impacts on how adult rats relate to stress (weaver et al., 2004). rats can either be calm and tranquil, or easily agitated, when reacting to a stressful situation. epigenetics is again found cultivating the hypothesized proto-emotion, but now to determine an emotional response in adult rats. the recurring balancing act implies that protoemotion is necessarily two-sided, corresponding to time’s two windows. this regulation reaches into human emotions. mindfulness meditation, that will necessarily bring with it emotive centering, can improve health by impacting on epigenetic switching (kaliman et al., 2014). not that the great centering is limited to periods of stress and new creations, rather once a route is explored the coming-together that led the way can give itself over to genetic and epigenetic quasi-determinism and become a learned route as part of the waddington landscape. gould (1977) describes how ontogeny recapitulates phylogeny, perhaps only as an approximation, but an approximation made possible because the proto-emotive centering that occurred in biological evolution also gave its self to the waddington landscape to be expressed as a quasi-determinism. mitosis describes chromosomes that double in number during interphase, and line up on the equatorial plane during metaphase, that is, they center. the cell divides as chromosomes are pulled by spindle fibers (aggregates of microtubules), this being the eruption on time’s manifold coming with the emotive climax. meiosis is more complicated, but also involves centering on the equatorial plane. arguably, mitosis and meiosis have become part of the genetic and epigenetic quasi-determinism, taking with them emotive centering. lastly, there is an issue that relates to how epigenetic layers may stack one on top of the other. perhaps the layers are all related by this syntax, an alternating pattern: frequency modulation leading to a localized determinism (more strict than quasi), on top is more frequency modulation and an additional implied layer of determinism, etc. this layering is open to experimental investigation and discovery, but somehow they must all be connected by warm-body quantum mechanics. furthermore, the layering cannot be replaced by an overlaying strict-form determinism that ignores the emotive middle-terms that represent jumps beyond one-sided entailments, because those bridges cannot be “pre-stated” as kauffman warns (2014); at best, the layers can only be united by a quasi-determinism. therefore, finding such a layering experimentally that is alternating (from frequency to determinism) hints of the deep singularity connecting to the timeless.16 a quantum system poised on the edge of order and chaos (and 16 critics may even concede such a layering, if only because frequency switches followed by an implied determinism is all that has ever been discovered. however, it is possibly difficult to experimentally differentiate between strict and quasi determinism. dna decipher journal | november 2018 | volume 8 | issue 3 | pp 166-180 smith, s. p., time, life & the emotive source issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 176 coincidentally between coherence and decoherence) can support warm-body coherence of quantum waves over an extended duration, by synchronizing an incoming wave-form to system frequencies that swing between regularity and chaos making a system resonance (vattay, kauffman and nirranen 2012). hameroff (2014) sees the vibrations found in microtubule supporting warm-body coherence, and permitting the reality of conscious experience. vibrations are needed in a “goldilocks zone” to maintain coherence, and re-coherence, a goal that is in reach of biological evolution (lloyd et al., 2011). to the extent that the eventual fall into decoherence represents an implied determinism, we find that frequency modulation does support a variety of determinism, even a sequence of restrained zeno effects representing transitions (mcfadden and al-khalili, 2016, pages 292-298). the entire system must necessarily be composed of multiple layers, however, assuming that warm-body coherence is more widespread in the body. this stacking of layers is agreeable with kauffman’s (2014) alternative quantum mechanics, where new “possibles” (i.e., new states of coherence) present themselves in the wake of “actuals” that form (when decoherence arrives). 7. discussion section 6 can be seen as an alternative interpretation of quantum mechanics having to do with the collapse of the quantum wave function as the synchronisation of time’s widows, when time looks back to find itself as an emotional interplay. however, the main fucus should remain on finding evidence, supporting the hypothesis or otherwise refuting it, and looking to alternative views of quantum mechanism may be less productive given all the varieties already described by herbert (1985). this is not to say that what is proposed is radically different or incompatible with goswami, reed and goswami’s (1993) monistic idealism, or even with kauffman’s (2014) understanding that admits to a possible preference-laden panpsychism. as with kauffman’s proposed theory that carries the very significant triad17, the hypothesis described in this paper is open to some testable science. warm-body quantum phenomena have already been found in biology (mcfadden and al-khalili 2014); i.e., beyond the enzymatic reactions that utilize electron and proton tunneling. photosynthesis is found involving coherent waves (rather than particles) that are able to efficiently reach reaction centers in green bacteria (engle et al., 2007). the migratory pattern in birds may relate to quantum entanglement (ritz et al., 2004). the sense of smell is possibly a quantum assisted phenomenon (brookes et al, 2007). microtubules have quantum properties enough to strongly implicate them in the orchestrated objective reduction model of consciousness (hameroff 2014; hameroff and penrose 1996). the fact that quantum biology has become an entrenched science indicates some support for the ideas in section 6. so there is general support for section 6 given that quantum biology is real, and given references already sited in section 6. specifics are missing that relate to the proposed quantum-level action, and those are a matter of future investigations. nevertheless, if consciousness is now so strongly implicated with quantum mechanics in the brain, implying even a preference-driven panpsychism, one has to wonder how such a system could evolve without a parallel neo-vitalism 17 actuals, possibles and mind represent a very important advance beyond scientific monism and cartesian dualism. dna decipher journal | november 2018 | volume 8 | issue 3 | pp 166-180 smith, s. p., time, life & the emotive source issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 177 of a kind hinted at in section 6? seems unlikely! the now vindicated terence mckenna believed that evolution was taking us to an endpoint. his “transcendental object at the end of time” was acting as a strange attractor and pulling us into the future and our end of days. he was possibly wrong about the attractor being stuck at the end of time, when proto-emotion is possibly timeless and no less a strange attractor. what’s nice about strange attractors is that they leave evidence behind in the substrate of evolution given as reflections, on all levels being a fractal pattern. therefore, we might look to the evidence coming as reflections of the timeless pull on time’s two windows, to support the view of section 6. remarkable so, we do find such evidence. the philosophy of taoism is remarkable on how it relates to our psychology, and how it relates to the more deductive yang and the more inductive yin,18 all agreeing more or less with section 6 as a universal grammar. this reflection is found impacting depth psychology of a kind promoted by peterson (1999). not merely is the reflection found in psychology, but also in the way our asymmetrical brain is wired together in a left and right hemisphere that specialized differently to look forward and backward in time, respectively. the brain’s asymmetrical hemispheres are well described in mcgilchrist (2009). religious traditions based on love19 relate well to the timeless pull of a proto-emotionality, that comes with a universal grammar turned golden rule, and comes with a relational view of the world that agrees more or less with whitehead’s process philosophy. a closing question: what came first, genetics or epigenetics? the possibility is that they coevolved together, in a grand centering near the criticality where time was able to find itself through a process of synchronization. if the middle-term is the pristine source of all that is emotive, then the centering of proto-emotion is part of a universal grammar and far from a cheap variety of post-modernism. this implies that evolution carried its own direction and was highly non-passive, far from indifferent and blind as implied by dawkins (1996). references albert, d.z., 2000, time and chance, harvard university press. asano, m., i. basieva, a. khrennikov and i. yamato, 2017, a model of differentiation in quantum bioinformatics, progress in biophysics and molecular biology, 130 (part a): 88-98. barrow, j.d., and f.j. tipler, 1986, the anthropic cosmological principle, oxford university press. brookes, j.c., f. hartoutsiou, a.p. horsfield and a.m. stoneham, 2007, could humans recognize odor by photon assisted tunneling?, physical review letters, 98 (3): 038101(1-4). brooks, d.r., and e.o. wiley, 1988, evolution as entropy: toward a unified theory of biology, 2nd edition, the university of chicago press. cairns, j., j. overbaugh and s. miller, 1988, the origin of mutants, nature, 335: 142-145. 18 the connection of deduction to the masculine, and of induction to the feminine, is better described in smith (2010). smith also described how the two tendencies 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self-organization and selection in evolution, new york, oxford university press. kauffman, s.a. , 2008, reinventing the sacred: a new view of science, reason and religion, basic books. kauffman, s.a., 2014, beyond the stalemate: conscious mind-body quantum mechanics free will dna decipher journal | november 2018 | volume 8 | issue 3 | pp 166-180 smith, s. p., time, life & the emotive source issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 179 possible panpsychism possible interpretation of quantum enigma, arxiv achieved, paper # 1410.2127. keller, e.f., 2000, the century of the gene, harvard university press. libet, b., 1985, unconscious cerebral initiative and the role of conscious will in voluntary action, the behavioral and brain sciences, 8: 529–566 lipton, b.h., 2005, the biology of belief: unleashing the power of consciousness, matter, and miracles, mountain of love/elite books. lloyd, s., m. mohseni, a. shabani, h. rabitz, 2011, the quantum goldilocks effect: on the convergence of timescales in quantum transport, arxiv achieved, paper # 1111.4982. martincorena, i., and n.m. luscombe, 2013, non-random mutation: the evolution of targeted hypermutation and hypomutation, bioessays, 35(2): 123-130. mcgilchrist, i., 2009, the master and his emissary: the divided brain and the making of the western world, yale university press. mcfadden, j., 2000, quantum evolution: the new science of life, w.w. norton & company. mcfadden, j., and j. al-khalili, 2014, life on the edge: the coming of age of quantum biology, broadway books. migicovsky, z., and i. kovalchuk, 2013, changes to dna methylation and homologous recombination frequency in the progeny of stressed plants, biochemistry and cell biology, 91 (1): 1-5. pert, c.b., 1997, molecules of emotion, scribner. peterson, j.b., 1999, maps of meaning: the architecture of belief, routledge. price, h., 1996, time’s arrow and archimedes’ point: new directions for the physics of time, oxford university press. radman, m., and r. wagner, 1988, the high fidelity of dna duplication, scientific american, 259 (2): 40-46. ritz, t., p. thalau, j.b. phillips, r. wiltschko and w. wiltschko, 2004, resonance effects indicate a radical-pair mechanism for avian magnetic compass, nature, 429 (may 3): 177-180. russell, p., 2003, from science to god, new world library. sidis, w.j., 1925, the animate and the inanimate, the gorham press. siegfreid, z., and h. cedar, 1997, dna methylation: a molecular lock, current biology, 7 (5): r305r307. smith, s.p. 2008, trinity: the scientific basis of vitalism and transcendentalism, iuniverse, inc. smith, s.p., 2010, the proclivities of particularity and generality, journal of consciousness exploration & research, 1 (4). 429-440. stanford, j.c., 2008, genetic entropy & the mystery of the genome, fms publications. strapp, h.p., 2007, mindful universe: quantum mechanics and the participating observer, springer. tadderi, f., m. vulić, m. radman and i. matić, 1997, genetic variability and adaptation to stress, in environmental stress, adaptation and evolution, editors r. bijlsma and v. loescheke, 271-290. vattay, g., s. kauffman and s. niiranen, 2012, quantum biology on the edge of quantum chaos, arxiv achieved, paper# 1202.6433. dna decipher journal | november 2018 | volume 8 | issue 3 | pp 166-180 smith, s. p., time, life & the emotive source issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 180 waddington, c.h., 1957, strategy of the genes, george allen & unwin. weaver, i.c., n. cervoni, f.a. champagne, a.c. d’alessio, s. sharma, j.r. seckl, s.i. dymov, m. szyf and m.j. meaney, 2004, epigenetic programming by maternal behavior, nature neuroscience, 7 (8): 847–854. wheeler, j.a., 1990, information, physics, quantum: the search for links, in complexity, entropy, and the physics of information, editor wojciech h. zurek, addison-wesley. wicken, j.s., 1987, evolution, thermodynamics, and information: extending the darwinian program, oxford university press. wolf, f.a., 1998, the timing of conscious experience: a causality-violating, two-valued, transactional interpretation of subjective antedating and spatial-temporal projections, journal of scientific exploration, 12 (4): 511-542. wright, s., 1932, the roles of mutation, inbreeding, crossbreeding and selection in evolution, proceedings of the 6th international congress of genetics, 1 (8): 355-366. login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase 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issn: 2159-046x untitled dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 280-290 campbell, r., part ii: an intelligent face to evolution: plant exploring the spatial forms of the eukaryotic cell issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 280 article part ii: an intelligent face to evolution: plants – exploring the spatial forms of the eukaryotic cell robert campbell * abstract biological evolution follows four levels of development that are progressively delegated toward the emergence of sentient awareness with an increasing step-like capacity to span and integrate events extended in space and time. plants store the suns energy in an increasing complexity and refinement of forms. invertebrates explore routines of sensitive response. vertebrates reflect patterns of behavior in conscious knowledge. humans can create new ideas while remaining anchored to lower levels in the four level hierarchy: idea, knowledge, routine and form. the four levels subsume four self-similar levels within each level such that they are evident within the context of plant evolution as shown in this article with interdependent interplay between all levels in the hierarchy as higher levels emerge. single celled and multi-celled plant forms were followed by plants with vascular routines that allowed them to reach for the sky. the appearance of seeds in gymnosperms demonstrated knowledge of processes extended in space and time and liberated them from a swampy environment. the flowering plants were essential to the idea of evolving more sentient life forms in the mammals and birds by providing concentrated food to support their higher metabolic rate. this self similar four level pattern pattern within each level of the hierarchy is explored in successive articles. key words: cosmic order, evolution, intelligence, historic integration, idea, knowledge, routine, form. form-form: this first level in the universal hierarchy includes primitive plants, consisting of the huge variety of algaes, from microscopic unicellular varieties to giant kelp (apart from the cyanobacteria, often called blue-green algae, but which are in fact photosynthetic bacteria). also included in this formform level of plants are the fungi, slime molds, and the lichens. fungi will be considered as an involutionary variant of early plants that subsequently evolved in parallel with them. fungi cannot photosynthesize the nutrients that they need so they are dependent on green plants for food. but their spores are everywhere, growing whenever they find a food source such as dead plant life, and they assist the decay of organic matter through their digestive processes that extract the energy they need. they provide a vital function in this involutionary process of decay. most fungi are thus benign saprotrophs utilizing the waste of evolutionary variants, but some are parasites on living plants and animals. * correspondence: rober campbell, independent researcher. website: http://www.cosmic-mindreach.com e-mail: bob@cosmic-mindreach.com note: the articles presented in this issue are based on my book “downsizing darwin: an intelligent face for evolution” self-published in 1996 [1]. more information is available at my website [2]. dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 280-290 campbell, r., part ii: an intelligent face to evolution: plant exploring the spatial forms of the eukaryotic cell issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 281 the algae, in parallel with the fungi, explored the eukaryotic format, predominantly in the sea and fresh water lakes and streams. small simple forms first began to pioneer on land about five hundred million years ago. the simplest unicellular forms of algae reproduce by cell division with more complex forms developing alternate sexual and asexual generations, called the gametophyte and the sporophyte both sexual and asexual reproduction of some kind generally occurs in algae. the reproductive processes of fungi are considerably more varied, especially since the mycellium or body of many fungi is not partitioned into separate cells, but consists of branching hyphae, or filaments. these filaments grow at their tips, like a maze of intertwined tributaries, to form the body of the fungus. the cytoplasm circulates nutrients through the mycellium which may have many nuclei containing different genetic material. two groups of higher fungi, the basidiomycotina, such as toadstools, coral fungi and fairy clubs, and the ascomycotina, such as morels and truffels, produce elaborate fruiting bodies made up of a mass of hyphae that rise like a crown above a base.. they pioneered the classic root-trunk-top structure that is so typical of terrestrial plants, but without highly differentiated cell types employed in their separate organs. fungi generally lack cellulose, a common component of cell walls in green plants, and many use chitin instead, a component also found in the exoskeleton of arthropods, such as insects. the algae store food in a variety of starches, polysacharides and oils, while fungi never use starch. as pointed out in the last chapter, biologists have difficulty clearly classifying some organisms, especially single-celled creatures. for example the unicelled euglenida photosynthesize energy from the sun, just as plants do, but they also swim with a tiny tail and have a mouth and gullet to ingest food. these tiny one-celled creatures cannot survive by photosynthesis alone. they also eat. cells of this general kind are often called protists, or protozoa, since they have characteristics that are both plant and animal. fungi are also sometimes classified as protists rather than plants, however they are considered as an involutionary variant of plants for our purposes here. for our purposes at present we may consider protists that use photosynthesis under the general umbrella of plants, even though they may swim, have a mouth, gullet and eat. they emerged at a point early in evolutionary history where animals began to diverge. sublevels of delegation such as these are comparatively limited in kind and they are generally associated with transitional stages between levels. we shall see that it is a common feature of evolution for higher levels to begin diverging in the early stages of a previous level, and only begin diversifying widely at some point considerably later. we shall point out examples of this pattern again and again. protists or protozoa that do not use photosynthesis and that are motile and ingest food will be considered animals. amoebas and most of the ciliates are examples. the common paramecium is a single-celled ciliate that uses the many hair-like cilia covering the cell surface to swim. the life cycles of algae generally show great variation and all algae types, except red algae, have flagellated motile cells at some stage in their life cycles that are much like some of the swimming protists. dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 280-290 campbell, r., part ii: an intelligent face to evolution: plant exploring the spatial forms of the eukaryotic cell issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 282 eukaryotes have explored an enormous range of size at the form-form level. some one-celled fungi are only about ten times larger than bacteria, while some algae produce giant cells. the mermaid’s wineglass is a single cell about 7 centimeters long with a single nucleus and some multi-nucleated cells may become much larger. brown, green and red algae have explored many diverse forms, including sheet like leaves, filaments, hollow tubes, bushy branched types, stalks with branchlets of many kinds, in a vast array of shapes and sizes. the largest seaweeds, brown algae and kelp, have highly developed multicellular structures, some that are fifty meters or more in length. a group called the diatoms, golden-brown and yellow-green algae types, have a rigid cell wall consisting of pectin impregnated with silica and they are generally restricted to single cells or loose colonies. lichens consist of two organisms in an intimate partnership, namely a higher fungus and an alga (sometimes a cyanobacteria takes the place of an alga). the alga is entrapped in the body of the fungus but is allowed enough light for photosynthesis. the fungus thus feeds on the alga and the two grow and reproduce together, although the algae can get along quite well on their own. slime molds are especially strange. they are unlike either fungi or algae, although they are closer to fungi. they come in two types. one type flows as a single mass of protoplasm over decaying plants and trees, devouring microorganisms and plant matter. this protoplasmic mass, called the plasmodium, resembles a single cell containing many nuclei. when conditions are right it produces a fruiting body that rises on a stem and releases spores. the other type of slime mold has no plasmodium and spends most of its life cycle as a proliferating collection of single cells just like amoebas, engulfing food and dividing. as food supplies dwindle the amoebae cells congregate into a mobile slug-like mass, called a pseudoplasmodium, that can respond to heat and light and move, just like an animal. once this slug-like collection has found a suitable place to its liking, the cells at the head end form into a stalk that rises from a base, to elevate cells at the top. the fruiting body at the top then develops into spores for dispersal, just as in the classic base-trunk-top structure of many plants. for our purposes here slime molds will be considered an involutionary variant of plants, similar in this respect to fungi, since they facilitate the process of decay. there is clearly a certain capacity at this level to span space and time in working out the spatial forms of the eukaryotic cell and its development in time, from swimming protists, to slime molds and fungi, to giant kelp. the evidence indicates that divergence to the animals took place from this most basic functional level of the eukaryotic cell, from the single-celled protozoa, and not from more highly evolved levels in the plant kingdom. we shall see repeatedly that each higher level tends to diverge from the early stages of a previous level. it is a recurrent pattern. the emphasis here is on the task cycles of plant cells rather than on product cycles of host plants with highly differentiated organs. it is apparent that this form-form level of plants explores a vast range of size, shape, and type of eukaryotic cell and its processes, including energy acquisition and storage, reproduction, and an immense array of multi-cellular forms. this level generally lacks a developed vascular system dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 280-290 campbell, r., part ii: an intelligent face to evolution: plant exploring the spatial forms of the eukaryotic cell issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 283 associated with integrated circulation routines for the whole plant. it requires an aquatic or very moist environment, apart from a comparatively few small algae, fungi, and lichens. form-routine: the routines essential to evolving higher plant forms on land required the development of vertical support with an efficient vascular system to transport nutrients between roots, trunk and top structure. this overall vascular integration of plant structure required convergence to common reproductive routines also. vascular systems were essential to the distribution of nutrients within land plants destined to rise fifty meters and more into the air. however, before vascular land plants could get started plants first had to colonize the land. the first true pioneers were probably the liverworts, hornworts and simple mosses that grew in moist shaded areas near water. they also developed rhizoid type structures to absorb nutrients from soil, short stalks with thickened cell walls for a degree of support, and leaf-like structures. the earliest vascular plants appeared over four hundred million years ago, during the silurian period, and they developed throughout the devonian period. the first forms were small leafless stems lacking real roots. ancestral mosses elaborated with root-like and leaf-like structures, while the club mosses, horse tails and ferns built on the scheme. these ancestral plants took their leap for the sky at the end of the devonian and during the carboniferous period, from three hundred and fifty to two hundred and eighty million years ago. tree sized versions, forty meters or more high, proliferated in abundance in extensive swamp lands before they became almost completely extinct, with only small modern versions remaining among the horsetails and club mosses. up until five hundred million years ago the earth had not yet been colonized to a significant extent by plants. it was essentially a vast desert during the first great convergence of the continents into a single super-continent. the first land pioneers near lakes, streams and bogs were probably little more than collections of algae-like cells with root-like projections beneath them and upright sporebearing structures protruding from their upper surfaces. the liverworts, hornworts and mosses that followed elaborated with similar features. the cells of the spore bearing structures are fundamentally different from the cells of the main body of the plant. the spores have only one set of chromosomes while the main cells of the body have two sets. the spores are said to be haploid rather than diploid. cell division of a type that produces four daughter cells, called meiosis, precedes spore production, as it does in algae. the spores then germinate asexually to produce a new haploid gametophyte generation of the plant with only one set of chomosomes. the sexual gametophyte generation of mosses and liverworts requires a sperm to swim to an egg, so these plants must stay close to the ground in moist habitats, to produce in turn the sporophyte generation again with a diploid set of chromsomes. haploid spores are then released from elevated stalks to promote dispersal in the wind. this alternation of two generations is a common feature of all terrestrial plants, although in the flowering plants the gametophyte generation completes its short life within the tissues of the sporophyte generation. the point is that all future variation in the reproductive routines of dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 280-290 campbell, r., part ii: an intelligent face to evolution: plant exploring the spatial forms of the eukaryotic cell issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 284 terrestrial plants became confined within these fixed constraints, allowing also for vegetative reproduction from new shoots in many cases. as plants colonized land by this reproductive pattern, they turned their focus to developing vertical support which required a vascular system to transport water and nutrients. one of the first pioneers over 400 million years ago, was a plant called cooksonia. it had developed specialized fiber-like elements in its stem, called xylem, which were the forerunners of wood. these tube-like elements contain lignen for support and can also be used to transport water through their capillaries, since they are dead and contained within a dense layer of protective outer cells. by 50 million years later, toward the end of the devonian period about 360 million years ago, this support and conducting system was reaching for the sky. the giant club mosses and horsetails proliferated in swamp forests to heights of 40 meters or more, forming the coal beds of the earth with their abundant remains. the present day descendants of horsetails reach heights of only three feet, the club mosses only one foot. the ferns, with compound fronds radiating from a stem or trunk, also evolved during devonian times. the tree ferns, up to sixty feet or more high, have survived to the present day, along with many smaller fern varieties. one species of surviving club moss, selaginella, produces both male and female spores from separate spore producing organs called sporangia. instead of germinating when they are shed, the female spores develop haploid tissue within the spore, where they produce egg cells. the smaller male spores release swimming sperm which must find and fertilize the eggs. this separation of male and female gametophytes, and their contraction in size and duration is a significant development for the reproductive routines of subsequent plant evolution. the reproductive and vascular routines of plants which developed together at this form-routine level in their history concerned the integrated organization of more specialized cell types within the whole plant. this emphasized product cycles of the host as opposed to the collective task cycles of cells. it focuses on product routines of the whole plant, rather than task cycles associated with basic cell forms. as we shall soon see, this development anticipated evolutionary events to follow that incorporated the knowledge gained by specific routines of plant growth in a more refined and coherent manner. it works much like the evolution of a company from the supervisory routine level to the administrative knowledge level. the focus at this routine level of form is on prioritizing the commitment of available resources to specific routines of reproduction, support and vascular circulation within the whole organism. this is similar to the supervisory level of work where available resources must be appropriately distributed for a variety of tasks. plants re-explored the limits to size within this context. form-knowledge: the collective knowledge gained by early vascular plants and their reproductive methods was reformulated into more refined versions that replaced them by the end of the carboniferous period. some two hundred and eighty million years ago the gymnosperms appeared, including the cycads, gingkos and conifers. dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 280-290 campbell, r., part ii: an intelligent face to evolution: plant exploring the spatial forms of the eukaryotic cell issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 285 the gymnosperms, especially the conifers, liberated plants from a dependence on wet swampy terrain in their gametophyte generation. they did this by developing the pollen grain and the seed. seeds took over the task of dispersal, in the fern as well as in the gymnosperms which eventually outpaced them. both had an ancient origin typically diverging comparatively early in the development of the previous level. the gymnosperms were thus slow to capitalize, replacing ancient forms only after a hundred million years. yet they integrated the knowledge accumulated by ancient giant forms of horsetails and club mosses and capitalized on it. they were thus able to incorporate features of the form-routine level that emerged subsequent to their divergence. it was not a gradual linear development of progressive dna survival according to darwinist rules. knowledge became manifest in more refined organs generally, not only in sexual reproduction but also in woody vascular systems, and a variety of hardy leaf structures in the conifers. more refined organs became more independently formed, such as highly structured needles, cones, bark and branches. these distinctively integrated plants of many species thrived for another two hundred million years, into the late cretaceous period. this includes many that have survived to the present day, such as the pine, spruce, cypress, hemlock, and so on that we are familiar with, especially in colder climates. the mosses, horsetails and ferns at the form-routine level depend upon a wet environment for sexual reproduction in their gametophyte generation. this seriously restricts them as land plants. the development of the pollen grain and the seed in the sporophyte generation integrated knowledge of many factors extended in space and time to overcome this restriction in a much broader context. the first step was the production of separate male and female spores, as in the club moss selaginella, producing separate male and female gametophytes. the gametophytes had to be protected from drying up, however, if they were to survive in drier terrain. this required protection which was provided for in the conifers by retaining the female on the sporophyte generation securely wrapped in tissue. this meant that the male gametophyte had to travel further, often in a horizontal direction. the male gamete also had to penetrate the sporophyte tissue protecting the female egg cells. the pollen grain constituting the male gametophyte thus had to be small enough to be carried on the wind, and likewise encased in a waterproof covering. so these modifications required knowledge of weather processes and how to exploit them by methods extended in space and time beyond the plant and its current environment. it can not be explained by random mutations since parallel mutations acting in concert are needed to meet many parallel needs. no process of selection pressure to promote gradual random changes can be demonstrated. conifers have male cones carrying microsporangia (pollen sacs) and female cones carrying megasporangia (nucelli), producing pollen and eggs respectively. many diverse and complex factors had to be biochemically incorporated for this to happen. could it really have happened gradually by a long series of accidental mutations? when a pollen grain is carried inside the female cone it is drawn to the nucellus by a drop of extruded fluid. one of the cells in the pollen grain grows through the nucellus to produce a pollen dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 280-290 campbell, r., part ii: an intelligent face to evolution: plant exploring the spatial forms of the eukaryotic cell issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 286 tube reaching down into the egg. the sperm cell from the pollen grain then passes through the tube to fertilize the egg. the fertilized egg develops into an embryo of a new sporophyte generation inside a covering of nutritional material provided by the gametophyte generation. this gives the new sporophyte a start when it is seeded in a new location. this whole process is slow, taking two years in some cases. the outer coat of this seed is derived from the old sporophyte generation. repeated complex sets of mutations are required for these developments to happen. since the task of dispersal now falls to the seed they sometimes develop wing-like appendages to help them travel on the breeze. how did a detailed wing structure happen by accident without some sort of feedback to inform the plant? in the junipers, the cone scales swell into an edible covering attractive to animals and birds which transport the seeds. again there is knowledge of animal needs and how to meet them implied, that is extended in space and time. some cycads still survive in tropical regions. the cycads produce swimming sperm, requiring a moist surface on the female cone to fertilize the egg cell. the gingko also produces swimming sperm released from pollen borne on the wind to the female sporangia. these female organs are naked at the tips of special shoots and not protected by cones. these ancient forms were outpaced by the conifers that still survive in great abundance today. the conifers are much more elaborate in their organization. many produce spreading crowns supported by huge trunks over 50 feet thick reaching heights of 300 feet, such as the giant redwoods that span a few thousand years in their life cycles. evergreen needles provide most conifers with a distinct advantage in the short growing season at higher latitudes. different root systems have been explored for varying conditions of moisture, frost, and need for support. the conifers have various other refinements of structure including a resin filled system of ducts in their stems and leaves to inhibit attack from microbes and insects. the resin produces spruce gum, amber and the familiar aroma of pine forests. all these developments of form incorporate knowledge of many very diverse factors that go beyond the prioritized commitment of resources to routines in the host plant. not only do they incorporate knowledge of biochemical properties but also a knowledge of complex environmental processes extended in space and time, from preventing the dehydration of eggs and sperm, to the flight characteristics of seeds, the feeding habits of animals, birds, and insects, and the climate of the new terrain to be colonized. these diverse factors must be brought together and integrated coherently into the facilities and infrastructure of the whole plant. to an impartial observer it should be unnecessary to numerate the number of false sets of trials by accidental mutations in concert that would be required before successful combinations of so many factors converged without benefit of intelligent feedback and input. this is especially so when the result is consistent with such an obvious self-similar pattern that clearly implies intelligence at work in the evolutionary order. the complete plant implicitly reflects the knowledge inherent in its living form. its various organs must relate to one another coherently and appropriately. the integration of space and time thus takes another major step forward at this form-knowledge level. dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 280-290 campbell, r., part ii: an intelligent face to evolution: plant exploring the spatial forms of the eukaryotic cell issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 287 form-idea: the idea level of the plant kingdom is not an isolated venture. as plants evolved at this level they also provided nutrients for species of animals higher up the ladder of sentience. without this food the animals could not have evolved in tandem. even the insects couldn’t have diversified. the higher sentient levels, especially the higher mammals and birds, needed more concentrated food provided by flowering plants. the seas were already teaming with many species of invertebrate and vertebrate animals in the carboniferous period, some three hundred million years ago. carboniferous bogs were crawling with amphibians and giant cockroaches, with giant insects droning overhead. it was only at the end of the cretaceous, with dinosaurs at their zenith, that the flowering plants, called angiosperms, began to diversify. a few species of magnolia and water lily had been around much longer, having diverged typically early in the previous level, but widespread diversification waited for the demise of the dinosaurs. it is as if the flowers came for the funeral. in the angiosperms the pollen grain germinates on the flower’s stigma, producing a pollen tube that grows down through it to the ovary, where the female gametophyte is housed. the male gamete then flows down the tube and fuses with the egg. as the seed matures, the carpel that surrounds it grows into a fruit. flowers are thus adapted to attract an insect pollinating vector, and their fruits are often designed for dispersal by animals by providing them food not essential to the seed. these plants also refined their vascular systems with more efficient water conducting vessels, and their foliage, stems and roots usually have concentrated nutritional value. the flowering plants thus exploit new ideas that integrate processes extended in space and time that are of critical value far beyond their own survival concerns. the angiosperms are essential to the progression of the whole evolutionary process, and they constitute two thirds of all living land plant species today. virtually all land mammals and birds are dependent on the more concentrated food supplies offered by flowering plants to support their higher metabolic rates. the earliest angiosperms were probably woody shrubs. although there has been some disagreement on whether the first angiosperms evolved from gymnosperms or seed ferns, they typically evolved from an early variety of seed plant, not from a highly evolved gymnosperm at the top of the form-knowledge level. so all that digitized information encoded in dna would again be lost to them if the darwinian theory is right. there is evidence that the magnolia is ancient and that the first flowers were probably upright cone-like structures with flower parts derived from leaves arranged in a spiral sequence. the uppermost leaves harbored female ovules, which they enclosed to form the carpel. the next set of leaves became modified into male stamens surrounding the carpel. next came the petals which became modified in color, many developing sugar secreting nectaries to attract insects. last came the green sepals that provide a protective covering for the bud and a base for the flower together with the receptacle. a great variety of floral types have evolved from this basic format. dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 280-290 campbell, r., part ii: an intelligent face to evolution: plant exploring the spatial forms of the eukaryotic cell issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 288 the carpel typically consists of a sticky stigma that receives the pollen, connected by a stalk (style) to the ovary that contains one or more ovules. in insect pollinated flowers the stigma is contained within a colorful flower, while in wind pollinated flowers, such as in grass and silver birch, they are exposed, with the petals and sepals reduced or absent. a few flowers fertilize themselves. upon fertilization the ovules develop into seeds and the ovary wall develops into a fruit containing the seed(s). the enclosing fruit distinguishes angiosperm seeds from naked gymnosperm seeds. fruits fall into two general types, dry or succulent. dry fruits are dispersed by mechanical means. the dandelion and thistle have a parachute to carry them on the wind, the sycamore and maple have wings attached, burrs hitch a ride on animals, peas and beans disperse from a pod. plums, mangoes, acorns, citrus fruits, almonds, coconuts, etc., are succulent fruits. they may contain one seed as in a cherry or many as in a berry. the fleshy succulent part of a fruit may also develop from the receptacle as in a strawberry and apple. sometimes seedless fruit can form without prior pollination of the flower, as in bananas and pineapples. fruits come in large variety and are often dependent on animal dispersal. some violet fruits are carried by ants back to their burrows, where just a small droplet of oil produced by the seed for the purpose is consumed by the ants, thus planting the seed intact. a clever idea, employing a knowledge of preferences in the ant’s diet and also of the complex biochemistry to produce it. the succulent fruits are not essential to the germination of the seeds they contain. and they are produced in such abundance with such a generous allotment of fleshy food stores, that it is hard to believe that they evolved solely by accident and selection pressure with such a large amount of wastage for self-serving seed dispersal. there is also a considerable variety of food storage in root systems such as the potato, turnip, beet, carrot, onion, peanut, yam, tapioca and so on. this allows some of them to reproduce vegetatively as well as by seed, in the process also providing abundant stores of food for animals. many flowers have developed fused floral parts, for instance tubular sheaths around nectar bearing organs that target only certain pollinators, such as humming birds with long curved beaks, and exclude others. honeysuckle and sweet tobacco flowers are adapted to the long proboscis of a pollinating moth, but excludes bees and flies. it’s hard to see any advantage to the plant here. the fig is completely dependent on a certain wasp for pollination, and in winter produces sterile fruit solely to ensure the survival of its wasp pollen vector. coryanthes orchids have a reservoir of fluid in the bottom of a deep chamber in the bloom that drugs bees, making them groggy so they fall in. there is only one possible exit from the chamber at the fluid level, directly beneath the stigma and stamens. on its first encounter two pollen sacs are glued to the bee’s back as it crawls out through this single long passageway to a higher exit, giving it time to regain its senses. on the next encounter another orchid’s stigma picks up the pollen from the bee. this is an extraordinary idea that could hardly have evolved by chance. of the millions of organic compounds possible, the flower must hit on a drug that is strong enough but not too strong, and yet not discourage the bee from trying again. its fluid consistency must allow the bee to swim for the exit, the dimensions of which must be precisely positioned with respect to stamens and stigma. many factors must be just right and evolve in concert to produce the result. otherwise there is no selection pressure. dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 280-290 campbell, r., part ii: an intelligent face to evolution: plant exploring the spatial forms of the eukaryotic cell issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 289 as soon as a pollen grain attaches to the stigma of the carpel during the pollination of a flower, it begins to grow a male gametophyte pollen tube down through the stigma and the style into the ovary at the base of the carpel. it grows very quickly, an inch an hour or more. once the pollen tube locates a female gametophyte embryo sac, not one but two male gametes flow down the tube. one fuses with the egg cell to begin producing the new embryo plant. the other fuses with two more haploid nuclei in the embryo sac, to begin producing the endosperm, a rich food reserve in endospermic seeds such as the cereal grains. in non-endospermic seeds the food is absorbed by the embryo, especially the seed leaves, called cotyldons, which are likewise designed to give a germinating seed a head start once it is dispersed. this provision of food stores for the germinating seed is a main feature of angiosperms, anticipating future needs and thus spanning space and time. angiosperms have a more highly differentiated vascular system than gymnosperms. they have continuous water conducting vessels formed of dead cells connected end to end by perforated plates to make a continuous duct, allowing for freer more organized flow. growth processes and vascular bundles consisting of xylem and phloem tissues are more intricately arranged. xylem vessels transport water and nutrients from the soil. phloem vessels transport food from production sites in leaves to growing points where they are needed. many angiosperm leaves have elaborate protective measures, as in poison ivy, nettles and thistles. some plant leaves and branches are sensitive with motor responses and fold up when touched. some leaves are thick and succulent for storage of food and moisture. the leaves of carnivorous plants trap and digest insects. again these ideas exploit knowledge of complex processes extended in space and time. the angiosperms have greater differentiation of organs and organ parts than do the gymnosperms, and they have developed into a much greater diversity of different plant forms, spanning space and time on a broader scale. these forms have implicitly re-assimilated the routines and knowledge explored by earlier plant species according to a host of new ideas that are extended in space and time, far beyond the plants themselves and even beyond their own survival needs. these developments came at a time when the continents were coming under compression forcing up new mountain ranges and plateaus throughout the planet. the dinosaur habitat rose and dried out, preparing the way for the next phase of vertebrate evolution in the mammals and birds, with major repercussions throughout the evolutionary hierarchy as it moved inexorably toward a new balance. the arrival of the flowers, together with the diversification of pollinating insects, signaled the departure of the dinosaurs, and heralded the coming of more refined and sentient creatures. *** commentary: from the above we can begin to see that there is a progression through the evolution of the plants that parallels higher levels in the animals and complements their needs on ascending levels in the sentient hierarchy, especially on land. the levels, described as successive levels of delegation apparent from the historical record, do not mean that flowers give explicit direction to conifers, which give direction to horsetails, which give dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 280-290 campbell, r., part ii: an intelligent face to evolution: plant exploring the spatial forms of the eukaryotic cell issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 290 direction to algae, any more than we should think that the president of general motors gives direction to a local restaurant. each species has a distinctive number of levels delegated within its own biological organization. we may think of it as a single-celled algae functioning like a one man company, whereas an apple tree or a rose functions like a larger more sophisticated four level company. within an apple tree the idea level integrates extended processes in space and time, from weather, to pollinating insects, to providing animal food. the integrating idea of the apple tree directs the accumulated knowledge essential to the development of its organs, which in turn directs its routines such as circulation through its vascular system, which in turn directs the formation of its cells in new growth consistent with available resources and needs. the direction is implicit in the plant’s organization. there is also a larger sense in which the higher species do give direction to the lower species, with feedback in the opposite direction, just as general motors has needs in order to make cars that are provided for by a host of interdependent industries. likewise every species is concerned with energy transformations up and down the evolutionary hierarchy, forever seeking a balance, so that major evolutionary developments at the top affect the whole hierarchy. the biosphere seeks dynamic balance within itself through biospheric resonance. the biosphere is in communication with itself and it seeks harmony. it is a resonating whole in which all life is interdependent. the whole hierarchy is humming in accord between levels, allowing members in each level to profit from the lessons of members on different levels. otherwise the digitized information of dna could only be progressively lost. progress could not be recognized in the evolutionary process. references 1. robert campbell, downsizing darwin: an intelligent face for evolution. mindreach library (1996). 2. http://cosmic-mindreach.com 3 robert campbell, fisherman’s guide: a systems approach to creativity & organization. boston: shambhala, 1985 dna decipher journal | june 2013 | volume 3 | issue 2 | pp. 188-210 188 pitkänen, m., evolution in many-sheeted space-time: big vision article evolution in many-sheeted space-time: big vision matti pitkänen 1 abstract this article is third part of an article consisting of four parts and devoted to evolution in manysheeted space-time. in the first part the basic facts believed to be known about pre-biotic evolution were discussed and the tgd inspired vision about prebiotic evolution was introduced. in the second part a physical model for the genetic code (not the only one) and its evolution was introduced and mcfadden’s views were compared with tgd views. in the third part a general vision about biological evolution, evolution of brain, and cultural evolution are discussed. in the fourth part quantum variant of expanding earth model and pre-cambrian evolution of continents, climate, and life will be developed. the considerations of all these articles rely heavily on the notion of magnetic body and dark matter identified as hierarchy of phases labelled by an effective value of planck constant coming as an integer multiple of ordinary planck constant. also the idea about hierarchy of josephson junctions (cell membrane would provide the basic realization) is central. in the proposed model for the evolution great leaps in evolution would correspond to phase transitions in which the effective value of planck constant ~eff assignable to an onion like layer of the magnetic body increases. this implies scaling up of quantum coherence lengths and times and therefore macroscopic quantum coherence in arbitrarily long length scales. ~eff serves as a kind of intelligence quotient. evolution would correspond to the emergence of new layers to the magnetic bodies of organisms. this would take place also for the magnetic bodies of populations making possible cultural evolution and the great differences between us and our ancestors and nearest species with almost the same genome might be due to the cultural evolution not reducible to the evolution of genome alone. coherent collective gene expression would be one of the implications. 1 introduction the idea about magnetic body carrying macroscopic quantum phases characterized by a hierachy of effective values of planck constants suggests that great leaps in evolution would correspond to phase transitions in which the effective value of planck constant ~eff assignable to an onion like layer of the magnetic body increases. this implies scaling up of quantum coherence lengths and times and therefore macroscopic quantum coherence in arbitrarily long length scales. ~eff serves as a kind of intelligence quotient. evolution would correspond to the emergence of new layers to the magnetic bodies of organisms. this would take place also for the magnetic bodies of populations making possible cultural evolution and the great differences between us and our ancestors and nearest species with almost the same genome might be due to the cultural evolution not reducible to the evolution of genome alone. coherent collective gene expression would be one of the implications. when i started to develop the idea, several obvious questions popped up. the preferred values of (effective) planck constant are assumed to be integer multiples of ordinary planck constant: does this integer have preferred values? for eight years later i take the original speculative answer to this question with a grain of salt. can one distinguish between evolution of biological and magnetic body and identify cultural evolution as evolution of magnetic body? eeg and its variants (and the predicted scaled variants of these) are expected to characterize living organisms, even super organisms like ant nest, bee hive, and bacterial colony: is this really the case? does bee hive possess a long term memory and what is the role of the queen? one can also ask questions about the evolution of nervous system in the same conceptual 1correspondence: matti pitkänen http://tgdtheory.com/. address: köydenpunojankatu 2 d 11 10940, hanko, finland. email: matpitka@luukku.com. issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.com/ mailto:matpitka@luukku.com dna decipher journal | june 2013 | volume 3 | issue 2 | pp. 188-210 189 pitkänen, m., evolution in many-sheeted space-time: big vision framework. are the magnetic bodies of neurons and larger structures characterized by ~eff? what about collective and transpersonal levels of consciousness? sheldrake’s vision [23] about species memory is also highly interesting from tgd point of view but is not considered in the article series about prebiotic evolution. the interested reader can however consult the article at [23]. the latest view about tgd inspired theory of consciousness justifying sheldrake’s vision in terms of negentropically entangled states defining representations invariant under quantum jump sequence and in this manner giving rise to ”akashi records” defining sensory , memory , etc. representations can be found at [22]. dark photons characterized by the value of ~eff and transforming to ordinary photons with the same energy identified as biophotons are becoming a central element of tgd inspired quantum biology [21]: in particular the non-destructive conscious reading of the memories represented in terms of negentropically entangled states by interaction free measurement is very attractive idea [22]. the communications by dark photons might have been present already during the prebiotic era before the emergence of biochemical signalling and neural communications. the role of dark photons is not discussed in the vision as it was formulated for more than five years ago. 2 great vision about biological evolution and evolution of brain the following great vision about evolution is not perhaps strictly about hierarchy of eegs. the hierarchy of dark matter and eegs however leads to this vision naturally. the first part of vision relates to biological evolution. second part is about the evolution of brain. here the key thread is evolution of two kinds of intelligences, the ordinary fast intelligence evolving via the emergence of fast computation type activities and emotional slow intelligence developing via the emergence of higher levels of dark matter hierarchy. the latter intelligence is what distinguishes us from animals. 2.1 basic assumptions the great vision about evolution and brain relies on two several new notions and ideas. 1. life as something in the intersection of real and p-adic worlds making possible negentropic entanglementboth space-like and time-like. this makes possible to understand what conscious intelligence is and nmp reduces evolution to a generation of negentropic entanglement. dna as topological quantum computer hypothesis [15] finds also a justification. 2. the notion of many-sheeted space-time implying a universal hierarchy of metabolic energy quanta, and the notion of magnetic body. 3. communication and control based on josephson radiation and cyclotron transitions crucial for understanding biophotons and eeg and its fractal generalization as a key element of bio-communications. 4. zero energy ontology and the closely related notion of causal diamond (cd) assigning a hierarchy of macroscopic time scales to elementary particles coming as octaves of the basic time scale and justifying p-adic length scale hypothesis. zero energy energy ontology also justifies the vision about memory and intentional action and the idea that motor action can be seen as time reversal of sensory perception. 5. the hierarchy of planck constants and the identification of the fundamental evolutionary step as an increase of planck constant. evolutionary steps mean migration to the pages of the big book labeled by larger values of planck constant and living system can be regarded as a collection of pages of the big book such that a transfer of matter and energy between the pages is taking place all the time. the change of the planck constant implies either reduction or increase of the quantum scales-this leads to a model for biocatalysis and a model of cognitive representations as scaled down or scaled up ”stories” mimicking the real time evolution. issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | june 2013 | volume 3 | issue 2 | pp. 188-210 190 pitkänen, m., evolution in many-sheeted space-time: big vision 6. a resonant like interaction between hierarchy of planck constants and p-adic length scale hierarchy favoring the values of planck constant proportional to powers of two, and idea that weak and color interactions are especially important in the length scales which correspond to mersenne primes and gaussian mersennes. the simplest option is that weak bosons have their standard masses but appear as massless below their compton length which scales up like ~ and preferred p-adic length scales correspond to mersenne primes. also copies of weak bosons and gluons with ordinary value of planck constant and reduced mass scale can (and will) be considered. 2.1.1 how to identify the preferred values of planck constant? the basic problem is to identify the preferred values of planck constant and here one can only make theoretical experimentation and all what follows must be taken in this spirit. one can consider assumptions which become increasingly stronger. 1. if only singular coverings of cd and cp2 are possible planck constant is a product of integers. algebraic simplicity of algebraic extensions of rationals favors ruler and compass integers (appendix). this includes powers of two. 2. a resonant interaction between the dark length scales and p-adic length scales with ordinary value of planck constant favors planck constants coming as powers of two. 3. an even stronger assumption would be that p-adic length scales coming as mersennes and gaussian mersennes are especially interesting. (a) if weak bosons can appear with the ordinary value of planck constant only in the p-adic length scale k = 89, one obtains the condition kd = k − 89 , k ∈ {89, 107, 113, 127, 151, 157, 163, 167} (2.1) for the values of of r = 2kd allowing dark weak bosons in p-adic length scales assignable to mersennes. these values of kd assign to electrons and quarks dark p-adic length scales l(keff ) = √ rl(k), r ≡ ~/~0 = 2kd . the scales could correspond to size scales of basic units of living systems. (b) if weak bosons and possibily also gluons with ordinary value of planck constant are possible in all p-adic length scales l(k), k ∈ {89, 107, 113, 127, 151, 157, 163, 167}, one obtains much richer structure. this hierarchy defines defines secondary dark matter hierarchies from the condition that the scaling the p-adic length scale l(k1) in this set by √ r, r ≡ ~/~0 = 2kd , gives a p-adic length scale equal to another p-adic length scale l(k2) in this set. this requires kd + k1 = k2 so that the values kd = k2 − k1 (2.2) are favored for the scaling of ~. in this case the hierarchy of dark scales assignable to quarks and leptons is much richer. the tables below demonstrate that electron appears as its dark variant for all mersennes and also in atomic length scales k = 137, 139 so that this option puts electron in a completely unique position. 4. also other scales are possible. for instance, r = 247 required by 5 hz josephson frequency gives dark weak scale which corresponds k = 136 as a p-adic scale. the stages of sleep can be understood in terms of scaling of ~ by factor 2 and 4 so that also the atomic length scale k = 137 and the scale k = 138 are involved. issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | june 2013 | volume 3 | issue 2 | pp. 188-210 191 pitkänen, m., evolution in many-sheeted space-time: big vision since the experimental input is rather meager, one is forced to do theoretical experimentation with various hypothesis. the quantitative experimental tests are rather primitive but basically quantal. 1. the time scales assignable to cds of leptons and quarks and their scaled up counterparts for the preferred values of planck constant should define biologically important time scales. one might even speak about evolutionary level of electron. these time scales could define fundamental biorhythms and also time scales of long term memory and planned action. 2. josephson frequencies and cyclotron frequencies scaling like 1/~ (if magnetic field scales down like 1/~) charactering biologically important ions and elementary particles. with inspiration coming from the quantum criticality of living matter one can ask whether cell membrane can also correspond to almost vacuum extremal so that besides classical em force also the classical z0 force would be an essential element of the model [16]. also corresponding cyclotron and josephson frequencies should define fundamental bio-rhythms and characterize the evolutionary level of cell. experimentally of special importance are the cyclotron frequencies assignable to ca++ ions. 3. the amplitude windows for electric field scaling like ~ for a particular cyclotron frequency define a basic prediction. 2.1.2 tables about predicted time and length scales the following tables summarize various predictions for time scales and length scales. they correspond to the most general assumption that exotic bosons with the ordinary value of planck constant are possible in all length scales associated with mersennes and gaussian mersennes. kd p1 p2 kd p1 p2 4 163 167 38 89 127 6 107 113 38 113 151 6 151 157 40 127 167 6 157 163 44 107 151 10 157 167 44 113 157 12 151 163 50 107 157 14 113 127 50 113 163 16 151 167 54 113 167 18 89 107 56 107 163 20 107 127 60 107 167 24 89 113 62 89 151 24 127 151 68 89 157 30 127 157 74 89 163 36 127 163 78 89 167 table 5. the integers kd characterizing the preferred values of r = ~/~0 = 2kd identified from the condition that the dark variant of p-adic length scale l(p1) corresponding to some ordinary p-adic length scale defined by mersenne prime mp or gaussian mersenne mg,p, p ∈ {89, 107, 113, 127, 151, 157, 163, 167} corresponds to similar p-adic length scale l(p2). if one assumes that weak bosons can appear with ordinary value of planck constant only in the p-adic length scale k = 89, only the rows with p1 = 89 of the table are possible: in these cases p1 is in boldface and the row has double underline. the corresponding values of kd are in the set {18, 24, 38, 62, 68, 74, 78}. note that the table above include only the dark length scales associated with k = 89 gauge bosons. issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | june 2013 | volume 3 | issue 2 | pp. 188-210 192 pitkänen, m., evolution in many-sheeted space-time: big vision z,w d u e kd 89 120 124 127 0 93 124 127 131 4 95 126 129 133 6 99 130 133 137 10 101 132 135 139 12 103 134 137 141 14 105 136 139 143 16 107 138 141 145 18 109 140 143 147 20 113 144 147 151 24 119 150 153 157 30 125 156 159 163 36 127 158 161 165 38 129 160 163 167 40 133 164 167 171 44 139 170 173 177 50 143 174 177 181 54 145 176 179 183 56 149 180 183 187 60 151 182 185 189 62 157 188 191 195 68 163 194 197 201 74 167 198 201 205 78 table 6. the dark p-adic length scales √ rl(k) = l(keff ), keff = k + kd, of intermediate gauge bosons z,w , d and u quarks, and electron for the values r = 2kd of planck constant defined in table 5. the uppermost row gives the integers characterizing the p-adic length scales of the particles for the standard value of planck constant. keff characterizes also the cd times scale through the formula t (cd, keff ) = 2keff−127 × .1 seconds. the rows which correspond to the less general option for which only m89 corresponds to weak bosons with ordinary value of planck constants have double underline and the corresponding values of kd are in boldface. issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | june 2013 | volume 3 | issue 2 | pp. 188-210 193 pitkänen, m., evolution in many-sheeted space-time: big vision k1 km k1 km k1 km k1 km 113 89 113 107 163 127 163 157 127 89 119 107 167 127 169 157 151 89 123 107 133 127 173 157 157 89 113 107 139 127 163 157 163 89 117 107 143 127 167 157 167 89 111 107 133 127 161 157 95 89 175 113 137 127 169 163 109 89 181 113 131 127 183 163 133 89 187 113 225 151 207 163 139 89 191 113 229 151 213 163 145 89 119 113 157 151 219 163 149 89 133 113 171 151 223 163 103 89 157 113 195 151 177 163 127 89 163 113 201 151 201 163 133 89 169 113 207 151 207 163 139 89 173 113 211 151 213 163 143 89 127 113 165 151 217 163 113 89 151 113 189 151 187 163 119 89 157 113 195 151 193 163 125 89 163 113 201 151 199 163 129 89 167 113 205 151 203 163 95 89 137 113 175 151 169 163 101 89 143 113 181 151 175 163 105 89 149 113 187 151 179 163 95 89 153 113 191 151 169 163 99 89 119 113 157 151 173 163 93 89 125 113 163 151 167 163 145 107 129 113 167 151 187 167 169 107 119 113 157 151 211 167 175 107 123 113 161 151 217 167 181 107 117 113 155 151 223 167 185 107 195 127 235 157 227 167 113 107 201 127 163 157 181 167 127 107 205 127 177 157 205 167 151 107 133 127 201 157 211 167 157 107 147 127 207 157 217 167 163 107 171 127 213 157 221 167 167 107 177 127 217 157 191 167 121 107 183 127 171 157 197 167 145 107 187 127 195 157 203 167 151 107 141 127 201 157 207 167 157 107 165 127 207 157 173 167 161 107 171 127 211 157 179 167 131 107 177 127 181 157 183 167 137 107 181 127 187 157 173 167 143 107 151 127 193 157 177 167 147 107 157 127 197 157 171 167 issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | june 2013 | volume 3 | issue 2 | pp. 188-210 194 pitkänen, m., evolution in many-sheeted space-time: big vision ľ table 9. the table gives all weak boson length scales -both non-dark and dark implied by the assumption that all mersennes primes and their gaussian counterparts and their dark counterparts defined kd = ki − kj them are possible. particle z,w d u e k 89 120 123 127 f(cd)/hz 2.7488× 1012 1280 160 10 table 8. the fundamental frequencies associated with the cds of intermediate gauge bosons z,w , d and u quarks, and electron. note that for intermediate gauge bosons the frequency of cds corresponds to energy e = 1.13× 10−2 ev and wavelength λ = 1.01× 10−4 m (size of a large neuron). z,w d u e kd 3.64e-13 7.81e-04 6.25e-03 1.00e-01 0 5.821e-12 1.25e-02 1.00e-01 1.60e+00 4 2.31e-11 5.00e-02 4.00e-01 6.40e+00 6 3.73e-10 8.00e-01 6.40e+00 1.02e+02 10 1.49e-09 3.20e+00 2.56e+01 4.10e+02 12 5.97e-09 1.28e+01 1.02e+02 1.65e+03 14 2.38e-08 5.12e+01 4.10e+02 6.55e+03 16 9.54e-08 2.05e+02 1.64e+03 2.62e+04 18 3.81e-07 8.19e+02 6.55e+03 1.05e+05 20 6.10e-06 1.31e+04 1.05e+05 1.68e+06 24 3.91e-04 8.39e+05 6.71e+06 1.07e+08 30 2.50e-02 5.37e+07 4.30e+08 6.87e+09 36 1.00e-01 2.15e+08 1.72e+09 2.75e+10 38 4.00e-01 8.59e+08 6.87e+09 1.10e+11 40 6.40e+00 1.37e+10 1.10e+11 1.76e+12 44 4.10e+02 8.80e+11 7.04e+12 1.12e+14 50 6.55e+03 1.41e+13 1.13e+14 1.80e+15 54 2.62e+04 5.63e+13 4.50e+14 7.21e+15 56 4.19e+05 9.01e+14 7.21e+15 1.15e+17 60 1.68e+06 3.60e+15 2.88e+16 4.61e+17 62 1.07e+08 2.31e+17 1.84e+18 2.95e+19 64 6.87e+09 1.48e+19 1.18e+20 1.89e+21 74 1.10e+11 2.36e+20 1.89e+21 3.02e+22 78 table 9. the ~-scaled fundamental time scales t (cd, keff ) = 2keff−127 × .1 seconds associated with the cds of intermediate gauge bosons z,w , d and u quarks, and electron for the values ~/~0 = 2kd of planck constant defined in table 5. the scales are expressed in seconds. the uppermost row gives the time scales of cds for the standard value of planck constant. the rows which correspond to the less general option for which only m89 corresponds to weak bosons with ordinary value of planck constants have double underline and the corresponding values of kd are in boldface. issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | june 2013 | volume 3 | issue 2 | pp. 188-210 195 pitkänen, m., evolution in many-sheeted space-time: big vision 2.1.3 electron and u quark are different before continuing an important observation is in order. electron is exceptional when compared to quarks. it appears as a dark particle in all p-adic length scales defined by biologically important gaussian mersennes and also in atomic length scales k = 137 and k = 139. the reason is trivial: by the basic assumptions electron must appear at same length scales as weak bosons above k = 127 since it corresponds to mersenne prime. also for the less general option (exotic intermediate gauge bosons are possible only as the dark variants of the standard ones) it appears at cell membrane length scale k = 151, which is due to the fact that one has 113− 89 = 151− 127 = 24. also u quark can appear with keff = 137, 139, 163, 167 and also this is an accident. the light invariants of intermediate gauge bosons appearing in long p-adic length scales would naturally correspond to almost vacuum extremals making possible the criticality as the basic aspect of life. one must of course be very cautious about the masses of exotic counterparts of u and d quark: one can also consider the possibility that masses are identical. 2.2 dark matter hierarchy and big leaps in evolution dark matter hierarchy leads to an amazingly concrete picture about evolutionary hierarchy allowing to identify the counterparts for concepts like mineral, plant, and animal kingdom that we learned during schooldays and ceased to take seriously as students of theoretical physics as we learned that other sciences are just taxonomy. even more, a view about what distinguishes between prokaryotes, eukaryotes, animal cells, neurons, eeg, and even about what makes cultural evolution, becomes possible. this view is also very useful when one tries to understand the role of microtubules. the appearance of cds scaled up in size by r = ~/~0 and space-time sheets scaled up in size by√ r means the emergence of new levels of structure and it is natural to identify big leaps in evolution in terms of emergence of new larger matter carrying space-time sheet magnetic flux sheets and corresponding magnetic bodies. if magnetic flux quanta are scaled by r magnetic flux quantization conditions remain unaffected if magnetic field strengths scale down by 1/r so that the energies of cyclotron photons are not affected. the thickness of flux tubes can remain unchanged if the currents running at the boundaries of the flux quantum cancel the magnetic flux. as already found, this mechanism must be at work inside living organisms wheras in far away region flux quanta are scaled up in size. the attractive hypothesis is that the leaps in evolution correspond to the emergence of dark variants of weak and possibly also color interactions in dark p-adic length scales which correspond to ordinary p-adic length scales characterized by mersenne primes. these leaps would be quantum leaps but in different sense as thought usually. the emergence of higher dark matter levels would basically mean the integration of existing structures to larger structures. a good metaphor are text lines at the pages of book formed by magnetic flux sheets whose width is scaled up by r as the new level of dark matter hierarchy emerges. the big leaps can occur both at the level of organism and population and organisms with rather low individual dark matter level can form societies with high dark matter levels and high collective intelligence (honeybees and ants are good example in this respect). certainly also other scalings of planck constant than those summarized in tables are possible but these scalings are of primary interest. this intuition is supported by the observation that electron is completely exceptional in this framework. electron’s dark p-adic length scales corresponds to p-adic length scales l(k), k = 167, 169, assignable to atomic and molecular physics and to the gaussian mersennes mg,k = (1 + i)k − 1, k ∈ {151, 157, 163, 167}, assignable to the length scale range between cell membrane thickness 10 nm and nucleus size 2.58 µm. the corresponding p-adic length scales, the number of which is 23, are excellent candidates for the scales of basic building brickes of living matter and vary from electron’s p-adic length scale up to 1.25 m (k = 167 defining the largest gaussian mersenne in cell length scale range) and defining the size scale of human body. the corresponding p-adic time scales are also highly interesting and vary from .1 seconds for electron defining the fundamental biorhythm to 9.6× 1014 years which is by 4-5 orders longer than the age of the observed universe. for k = 167 the time scale is 1.1× 1011 years and is by one order of magnitude longer than the age of the observed universe estimated issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | june 2013 | volume 3 | issue 2 | pp. 188-210 196 pitkänen, m., evolution in many-sheeted space-time: big vision to be 1.37× 1010 years [3] . this conceptual framework gives rather strong guidelines for the identification of the levels of evolutionary hierarchy in terms of dark matter hierarchy. the outcome is a more detailed vision about big evolutionary leaps. note that in the sequel only the general option is considered: the justification for this is that for this option electron appears as a dark particle for all length scales defined by gaussian mersennes as well as in atomic length scales. the basic vision in nutshell is that evolution means the emergence of dark weak and gluonic physics in both dark and ordinary length scales and that the size scales of the basic biostructures correspond to mersenne primes and their gaussian variants. 2.2.1 a sketch about basic steps in evolution the vision about evolution depends on what one assumes about the initial state. 1. if one assumes that weak bosons with ordinary value of planck constant were present in the begining, evolution would mean a steady growth of kd. the problem is that small values of kd = k1 − k2 correspond to the gaussian mersennes defining cellular length scales. if these exotic weak physics were present from the beginning, large parity breaking in cellular length scales would have been present all the time. 2. an alternative and perhaps more realistic view is that the evolution means the emergence of exotic weak physics corresponding almost vacuum extremals in increasingly longer length scales. a possible mechanism could have been the induction of exotic ~0 variant of weak physics at the nearest mersenne length scale knext by the dark variant of weak physics at level k so that one would have kd = knext−k. the simplest induction sequence would have been 89→ 107→ 113→ 127→ 151→ 157 → 163 → 167 corresponding to kd ∈ {18, 6, 14, 24, 6, 6, 4}. a possible interpretation of exotic ~0 physics is in terms of almost vacuum extremals and non-standard value of weinberg angle: also weak bosons of this physics would be light. this sequence defines the minimal values for kd but also larger values of kd are possible and would correspond to steps between neighbours which are not nearest ones. the following sketch about the basic steps of evolution relies on the latter option. 1. elementary particle level magnetic bodies with size scale defined by the sizes of cds assignable to quarks and leptons and possibly also weak bosons (already now the size of big neuron emerges) corresponds to the lowest level of hierarchy with the sizes of the basic material structures corresponding to the compton lengths of elementary particles. the fundamental bio-rhythms corresponding to frequencies 10, 160, and 1280 hz appear already at this level in zero energy ontology which suggests that elementary particles play a central and hitherto unkown role in the functioning of living matter. 2. 89→ 107 step with kd = 18 the first step would have been the emergence of keff = 107 weak bosons inducing ~0 weak physics in k = 107 length scale characterizing also ordinary hadrons. this in turn would have led to the emergence of exotic nucleons possibly corresponding to almost vacuum extremals. the reduction of the model for the vertebrate genetic code to dark hadron physics [20] is one of the most unexpected predictions of quantum tgd and assumes the existence of exoticpossibly darknucleons whose states with a given charge correspond to dna, rna, mrna, and trna. the ~0 variants of these nucleons would interact via weak bosons with hadronic mass scale. the exotic variants of the ordinary k = 113 nuclei would correspond to the nuclear strings consisting of exotic nucleons [14, 20] and define nuclear counterparts for dna sequences. their dark counterparts could define counterparts of dna sequences in atomic physics length scales. therefore a justification for the previous observation that genetic code could be realized at the level of hadron physics and that chemical realization would be higher level realization finds issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | june 2013 | volume 3 | issue 2 | pp. 188-210 197 pitkänen, m., evolution in many-sheeted space-time: big vision justification. the anomalous properties of water could be also partly due to the presence of dark nucleons and the proposal was that the presence of exotic nuclei is involved with water memory [17] . the possible existence of the the analog of dna-rna transcription between ordinary dna and its nuclear counterpart would have dramatic implications. for instance, one can imagine a mechanism of homeopathy based on this kind of transription process which would also allow a modification of genome by using dark nuclei to communicate the dna sequences through the cell membrane to the target nuclei. 3. 107→ 113 step with kd = 6 the next step would have been the emergence of keff = 113 weak bosons inducing ~0 weak physics in k = 113 length scale characterizing also ordinary hadrons. exotic variants of the ordinary nuclei possibly corresponding to almost vacuum extremals could have emerged interacting weakly (or actually relatively strongly!) via the exchange of weak bosons with mass scale of order 100 mev. also dark variants of the exotic k = 107 nucleons could have have emerged and formed exotic nuclei of size scale k = 119. 4. 113→ 127 step with kd = 14 at this step weak bosons in electron mass scale would have emerged. whether these weak bosons could have induced large parity breakings in atomic and molecular length scales is not clear. viruses, which do not yet possess cell membrane could correspond to this level of hierarchy. 5. 127→ 151 step with kd = 24 this step would have been fundamental since weak bosons in cell membrane length scale would have appeared. note that by 113 − 89 = 24 this step also leads from k = 89 weak bosons to k = 113 weak bosons. the weak bosons assignal to k = 151 could correspond to the weak interactions associated with almost vacuum extremals and sin2(θw ) = .0295 could correspond to the weak physics in question. kd = 24 step for k = 113 ~0 weak bosons would have produced them in keff = 137 atomic length scale with l(137) ' .78 angstrom this could have naturally led to large parity breaking effects and chiral selection. dark keff = 151 electrons appearing in the tgd inspired model of high tc super-conductivity would have been a by-product of this step. whether dark electrons could have transformed to light ~0 electrons (of mass .25 kev) with a common mass scale of order 102 ev with exotic weak bosons is an interesting question. the model of high tc super-conductivity predicts the presence of structures analogous to cell membrane. this would suggest that cell membranes emerged and chiral selection emerged at this step so that one could not distinguish the emergence of molecular life as a predecessor for the emergence of cell membrane like structures. this would conform with the fact that dna molecules are stable only inside cell nucleus. note that for keff = 151 electron’s cd has time scale 224 × .1 seconds -that is 19.419 days (day=24 hours). the smallest nanobes [6] appearing in rocks have size 20 nm and could have emerged at this step. the size of the viruses [7] is between 10-300 nm covers the entire reange of length scales assignable to gaussian mersennes, which suggests that smallest viruses could have emerged at this step. also the smallest [5] [5] , which by definition have size smaller than 300 nm could have appeared at this stage. 6. the remaining steps the remaining steps k = 151 → 157 → 163 → 167 could relate to the emergence of coiling structure dna and other structures inside cell nucleus. k = 167 would correspond to kd = 167 − 89 = 68 to be compared with the value kd = 47 required by 5 hz josephson frequency for the neuronal membrane for -70 mv resting potential. note that kd = 48 (state 1-2 of deep sleep) corresponds to k = 163. by their smallness also double and triple steps defined by kd = ki+n − ki, n > 1, are expected to be probable. as a consequence, electrons can appear as dark electrons at all the gaussian mersenne levels. at these steps the dark electrons corresponding to primes keff = 137, 139 would appear. for k = 137 dark electron appears with cd time scale equal to 128 secondsrather precisely two minutes. the model for eeg suggests that the exotic weak bosons appear in the scales keff = 136, 137, 138. issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | june 2013 | volume 3 | issue 2 | pp. 188-210 198 pitkänen, m., evolution in many-sheeted space-time: big vision further multisteps from the lower levels of hierarchy would give structures with size scales above the size of cell nucleus possibly assignable to organs and structural units of brain. the dark levels assignable to electron are expected to be of special interest. it is encouraging that the longest scale assignable to electron in this manner corresponds to k = 205 and length scale of 1.28 m defining body size. as a consequence dark electrons are predicted at levels k = 137, 139, 141, 143, 145, 147 coming as octaves. prokaryotic cells (bacteria, archea) without cell nucleus for which cell membrane is responsible for metabolic functions and genome is scattered around the cell could have emerged at this step. this would mean that the emergence of the cell membrane thickness as a fundamental scale is not enough: also the size scale of membrane must appear as p-adic length scale. the sizes of most prokaryotes vary between 1 µm and 10 µm: the lower bound would require k = 163. there also prokaryotes with sizes between .2 µm (k = 157 corresponds to .08 µm) and 750 µm. cell nuclei, mitochondria, and other membrane bounded cell nuclei would have evolved from prokaryotes in this framework. the sizes of eukaryote cells are above 10 µm and the fact that multicellular organisms are in question strongly suggests that the higher multisteps giving rise to weak bosons and dark electrons in length scales above l(167) are responsible for multi-cellular structures. this scenario leaves a lot of questions unanswered. in particular, one should understand in more detail the weak physics at various length scales as well as various exotic nuclear physics defined by dark nucleons and dark variants of nuclei. 2.2.2 division of the evolution to that of biological body and magnetic body electron’s mersenne prime m127 is the highest mersenne prime, which does not correspond to a completely super-astrophysical p-adic length scale. in the case of gaussian mersennes mg,k one has besides those defined by k in {113, 151, 157, 163, 167, } also the ones defined by k in {239, 241, 283, 353, 367, 379, 457, 997} [1] . the appropriately extended model for evolution allows to distinguish between three kinds of values of keff . 1. the values of keff for which electron can appear as dark particle and thus satisfying keff ≤ 205 (table 5). these levels would correspond to structures with size below 1.25 m defined roughly by human body size and it is natural to assign the evolution of super-nuclear structures to the levels 167 < keff ≤ 205. 2. the values of of keff for which dark gauge bosons are possible in the model. this gives the condition keff ≤ 235. these levels correspond to structures in the range 1.25 m-40 km. the identification as parts of the magnetic body can be considered. 3. the values of keff obtained by adding to the system also the gaussian mersenne pair k ∈ {239, 241} allowing also the dark electrons. the lower size scale for these structures is 640 km. 4. the higher levels corresponding to keff in {283, 353, 367, ...}. the lower size scale for these structures is 3 au (au is the distance from earth to sun). keff > 205 levels would correspond to the emergence of structures having typically size larger than that of the biological body and not directly visible as biological evolution. this evolution could be hidden neuronal evolution meaning the emergence of extremely low josephson frequencies of the neurons modulating higher frequency patterns and being also responsible for the communication of long term memories. 2.2.3 biological evolution in principle the proposed model allowing multisteps between hierarchy levels defined by mersenne primes and their gaussian counterparts could explain the size scales of the basic structures below the size scale 1.25 m identified in terms of the keff ≤ 205 levels of the hierarchy. issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | june 2013 | volume 3 | issue 2 | pp. 188-210 199 pitkänen, m., evolution in many-sheeted space-time: big vision 1. the emergence of cells having organelles the appearance of the structures with keff > 167 (possibly idetifiable as magnetic body parts) should correlate with the emergence of simple eukaryotic cells and organisms, in particular plant cells for which size is larger than 10 µm, which could correspond to keff = 171 for electron and dark variants of weak gauge bosons. keff = 177 is the next dark electron level and corresponds to 80 µm scale. it seems natural to assume that these dark weak bosons do not transform to their ~0 counterparts at these space-time sheets. cell nucleus would be the brain of the cell, mitochondria would be the energy plant, and centrioles generating microtubules would define the logistic system. also other organelles such as golgi apparatus, ribosomes, lysosomes, endoplasmic reticulum, and vacuoles would be present. these organelles would live in symbiosis by topologically condensing to keff ≥ 171 magnetic body controlling their collective behavior. centrosomes associated with animal cells would not be present yet but microtubule organizing centers would already be there. the recent observations show that centrioles are not always in the characteristic t shaped conformation. daughter centrioles resulting during the replication of mother centriole use first ours of their lifetime to roam around the cell before becoming mature to replicate. a possible interpretation is that they are also life forms and that magnetic body utilizes daughter centrioles to perform some control functions crucial for the future development of the cell. for instance, centrioles visit the place where axonal growth in neurons starts. cytoskeleton would act as a counterpart of a central nervous system besides being responsible for various logistic functions such as transfer of proteins along microtobuli. centrioles give also rise to basal bodies and corresponding cilia/flagella used by simple cells to move or control movement of air or liquid past them. centriole pair would be also used by the magnetic body to control cell division. the logistic functions are the most obvious functions of microtubules. magnetic body would control cell membrane via signals sent through the cell nucleus and communicated to the cell membrane along microtubuli. basal bodies below the cell membrane and corresponding cilia/flagella would serve as motor organs making possible cell motion. tubulin conformations representing bits would allow microtubule surface to represent the instructions of the magnetic body communicated via via cell nucleus to various proteins moving along the microtubular surface so that they could perform their functions. tgd based view about long memory recall as communication with geometric past allows also the realization of cellular declarative memories in terms of the conformational patterns. memory recall corresponds to a communication with geometric past using phase conjugate bosons with negative energies reflected back as positive energy bosons and thus representing an ”image” of microtubular conformation just like ordinary reflected light represents ordinary physical object. there would be no need for a static memory storage which in tgd framework would mean taking again and again a new copy of the same file. receptor proteins would communicate cell level sensory input to the magnetic body via mes parallel to magnetic flux tubes connecting them to the magnetic body. we ourselves would be in an abstract sense fractally scaled up counterparts of receptor proteins and associated with dark matter iono-lito josephson junction connecting the parts of magnetosphere below litosphere and above magnetosphere. the communication would be based on josephson radiation consisting of photons, weak bosons, and gluons defining the counterpart of eeg associated with the level of the dark matter hierarchy in question. 3. the emergence of organs and animals the emergence of magnetic bodies with keff in the range (177, 181, 183, 187, 189, 195, 201, 205) allowing both dark electron and weak bosons could accompany the emergence of multicellular animals. magnetic body at this level could give rise to super-genome making possible genetic coding of organs not yet possessed by plant cells separated by walls from each other. the super structures formed from centrosomes and corresponding microtubuli make possible complex patterns of motion requiring quantum coherence in the scale of organs as well as memories about them at the level of organs. issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | june 2013 | volume 3 | issue 2 | pp. 188-210 200 pitkänen, m., evolution in many-sheeted space-time: big vision 4. the emergence of nervous system keff in the range (187, 189, 195, 201, 205) allowing dark electrons and weak bosons gives size scales (.25, .5, 4, 32, 128) cm, which could correspond to the scales of basic units of central nervous system. what would be of special interest would be the possibility of charged entanglement based on classical w fields in macroscopic length scales. the emergence of the new level means also the integration of axonal microtobuli to ”text lines” at the magnetic flux sheets making possible logistic control at the multineuronal level. the conformational patterns of the microtubular surface would code nerve pulse patterns to bit patterns representing declarative long term memories. an interesting question is whether the reverse coding occurs during memory recall. 2.2.4 the evolution of magnetic body for mammals with body size below 1.25 m the levels keff > 205 cannot correspond to biological body and the identification in terms of magnetic body is suggestive. the identification of eeg in terms of josephson frequencies suggests the assignment of eeg with these levels. 1. the emergence of eeg eeg in the standard sense of the word is possessed only by vertebrates and one should understand why this is the case. the value of josephson frequency equal to 5 hz requires only kd = 47 so that something else must be involved. a possible explanation in the framework of the proposed model comes from the following observations. 1. besides the maximal p-adic scale k = 205 for which electron and weak bosons appears as dark variants the model allows also levels at which only gauge bosons appear as dark particles. from table 9 one finds that levels k ∈ {207, 211, 213, 217, 219, 221, 223, 225, 229, 235} are allowed. could it be that these levels and possibly some highest levels containing both electrons and gauge bosons as dark particles are a prerequisite for eeg as we define it. its variants at higher frequency scales would be present also for invertebrates. the lowest josephson frequency coded by the largest value of ~ in the cell membrane system determins the josephson frequency. 2. the membrane potentials -55 mv (criticality against firing) correspond to ionic josephson energies somewhat above 2 ev energy ((2.20,2.74,3.07,2.31) ev, see table 1). for 2 ev the wavelength 620 nm is near to l(163) = 640 nm. therefore the josephson energies of ions can correspond to the p-adic length scale k = 163 if one assumes that a given p-adic mass scale corresponds to masses half octave above the p-adic mass scale so that the opposite would hold true at space-time level by uncertainty principle. josephson frequencies fj ∈ {5, 10, 20, 40, 80, 160} hz correspond to kd ∈ {47, 46, 45, 44, 43, 42} giving keff ∈ {210, 209, 208, 207, 206, 205}. (a) cerebellar resonance frequency 160 hz would correspond to k = 205 -the highest level for for which model allows dark electrons (also 200 hz resonance frequency can be understood since several ions are involved and membrane potential can vary). (b) the 80 hz resonance frequency of retina would correspond to keff = 206 -for this level dark electrons would not be present anymore. (c) 40 hz thalamocortical frequency would correspond to keff = 207. (d) for ekg frequencies are eeg frequencies below 20 hz 12.5 and heart beat corresponds to .6-1.2 second cycle (the average .8 s corresponds to keff = 212). 3. even values of keff are not predicted by the model based on mersenne primes allowing only odd values of keff so that the model does not seem to be the the whole truth. the conclusion which however suggests itself strongly is that eeg and its variants identified as something in the range 1100 hz, are associated with the levels in at which only dark weak bosons are possible in the proposed issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | june 2013 | volume 3 | issue 2 | pp. 188-210 201 pitkänen, m., evolution in many-sheeted space-time: big vision model. note that the size scales involved with eeg would be above the size scale of human body so that we would have some kind of continuation of the biological body to be distinguished from the magnetic body. the time scales assignable to the dark cds would be huge: for instance, k = 205 would correspond to t = 242 × .1s making about 1395 years for electron. 2. does magnetic body correspond to the space-time sheets carrying dark weak bosons? the layers of the magnetic body relevant for eeg have have size of order earth size. natural time scale for the moment of sensory consciousness is measured as a fraction of second and the basic building blocks of our sensory experience corresponds to a fundamental period of .1 seconds. this scale appears already at ~0 level for electron cd. the natural question concerns the relationship of the magnetic body to the k > 205 space-time sheets carrying only gauge bosons in the model and having size scale larger than that of biological body. do they correspond to an extension of biological body or should they be regarded as parts of the magnetic body? the following observations suggest that they could correspond to layers of the magnetic body responsible for the fractal variant of eeg. 1. the primary p-adic time scales (compton times) t (239) and t (241) correspond to frequencies, which are 2±1/2 khz. the geometric average k = 240 corresponds to khz frequency. is the appearance of khz scale a mere accident or do the frequencies assignable to the quark cds correspond to compton times ∝ √ 2keff/2? 2. one can apply scalings by 2kd to the triplet (239, 240, 241) to get a triplet (239+kd, 240+kd, 241+kd). the results are summarized in table 10. clearly the frequencies in question cover also the eeg range. note that these frequencies scale as √ 1/r whereas josephson frequencies scale as 1/r. kd f1/hz f2/hz f3/hz 0 707 1000 1412 4 177 250 354 6 89 1250 177 10 22.1 31.3 44.2 12 11.1 15.6 22.1 14 5.5 7.8 11.1 16 2.8 3.9 5.5 18 1.4 2.0 2.8 20 0.7 1.0 1.4 24 0.2 0.2 0.3 table 10. the compton frequencies obtained by scaling 2kd/2 from the basic triplet keff = (239, 240, 241). the values of kd correspond to those predicted by the model based on mersenne primes. also zeg and weg would appear but in much shorter scales dictated by keff and might accompany eeg. somehow it seems that the effective masslessness of weak bosons below given scale is highly relevant for life. one can of course ask whether some larger gaussian mersenne could change the situation. there is a large gap in the distribution of gaussian mersennes after k = 167 and the next ones correspond to mg,k, with k in (239, 241, 283, 353, 367, 379, 457, 997) [1] . the twin pair k = (239, 241) corresponds to a length scales (1.6, 3.2)× 102 km and the minimum value for kd are (72,74) (167→ (239, 241) transition). 3. long term memory and ultralow josephson frequencies what determines the time scale associated with long term memory is a crucial question if one really wants to understand the basic aspects of consciousness. issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | june 2013 | volume 3 | issue 2 | pp. 188-210 202 pitkänen, m., evolution in many-sheeted space-time: big vision 1. does the time scale correspond to the size scale of cd assignable to electron scaled by r = ~/~0? in this case relatively small values of r would be enough and r = 247 would give time scale of 1013 s for for electron’s cd, which is about 3× 105 years. this does not make sense. 2. does josephson frequency define the relevant time scale? in this case the long term memory would require the analog of eeg in the time scale of memory span. keff = 205 would give 6 ms time scale for memory from the assigment of keff = 163 to the josephson photons at v=-50 mv implying kd = 42. minute scale would require keff = 217. the highest level keff = 235 allowed by the model involving only gaussian mersennes with k ≤ 167 would correspond to a time scale of 77.67 days (day is 24 hours). for gaussian mersennes defined by keff = (239, 241) the time scales become about (41.4,82.8) months (3.4 and 6.8 years). these scales should also define important biorhythms. the claimed 7 years rhythm of human life could relate to the latter rhythm: note that the precise value of the period depends on the membrane potential and thus varies. the presence of the scaled up variants of the by kd ≤ 78 allows longer time spans of long term memory and the scaling defined by kd = 167− 163 = 4 scales up the span of long term memories to (54.4,108.8) years. 4. cultural evolution higher levels in the hierarchy would correspond mostly to the evolution of hyper-genome coding for culture and social structures. introns are good candidate for the nucleodes involved. the development of speech faculty is certainly a necessary prerequisite for this breakthrough. already eeg seems to correspond to dark layers of biological body larger than biological body so that one can cask whether the weak bosons and dark electrons in the length scales k = 239, 241, 283, 353, 367, ... could be relevant for the collective aspect of consciousness and cultural evolution. maybe the size scales (175, 330) km and their scaled up variants by kd ≤ 78 might have something to do with the spatial scale of some typical social structure (not city: the area of new york is only 790 km2). 2.3 could insect colonies have ”eeg”? only vertebrates can have eeg in 1-100 hz range. according to the proposed model this means the presence of the k > 205 levels which can be regardd as a continuation of the biological body carrying dark weak bosons and having size scales larger than 1.25 m. that only vertebrates have eeg conforms with the empirical findings about the effects of elf em fields on vertebrate brain. this does not however imply that one could not assign eeg to the collective levels of consciousness. for instance, in the case of social insects forming colonies some kind of collective eeg might exist and explain the ability of the colony to behave like single organism. indeed, elf magnetic field and magnetic fields affect the behavior of honeybees just as elf em fields affect the behavior of vertebrates [12] : the model for this findings led to a model for the fractal hierarchy of eegs. one could argue that insect brain is so simple (in the case of honeybee the number of neurons 1/1000 of number of neurons in human retina) that it is not possible to assign ”personal” eeg to honeybee. the fact that a honeybee isolated from colony dies just as does the cell separated from organism, suggests that the relationship of insect to colony is like that of a cell to organism. hence one could test whether colonies of social insects or their sub-colonies might possess an analog of ordinary eeg. what this would mean that ant colonies have sufficiently complex hyper-genome making possible collective variants of memory, sensory input, and intelligence, as well as the ability to realize collective motor actions. even bacterium colonies have intricate social structures [13] so that one must remain open minded. an objection against this line of thinking is that even in the case of collective eeg the proposed model assigns the josephson frequencies with neurons. one might imagine josephson frequencies at eeg range even in case of insectssay the queen of the nest. since dark photons are in question the fields are very weak. i do not know whether any-one has got the crazy idea about checking whether beehive has eeg -certainly not any routine measurement! one an also imagine a fractal counterpart of eeg at the level of some individualssay queen of the nestat very low frequencies making possible long term memory. issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | june 2013 | volume 3 | issue 2 | pp. 188-210 203 pitkänen, m., evolution in many-sheeted space-time: big vision 2.3.1 do honeybees have long term memory? the realization that insect colonies rather than insects might correspond to higher keff > 205 levels of the dark matter hierarchy came via an indirect route. the article ”why honeybees never forget a face?” of new scientist [8] described evidence supporting the view that that honeybees might possess long term memory in the time scale of days. adrian dyer of the university of cambridge and colleagues trained honeybees to associate a sucrose drink with a photograph of a particular face. the insects were then tested on their memory and recognition skills by being presented with the picture of this face and the pictures of three other faces not associated with any reward. of the seven bees tested, two lost interest in the trial and flew away. but the five remaining bees correctly identified the target face in more than 80 per cent of trials, even though the reward had been removed. moreover, some bees remembered the face two days later, indicating that they had formed a long-term memory of it. 1. the conservative explanation is that the achievement is due to keeping the face-honey association intact in the absence of the stimulus which created it in a time scale of days. for this option the ability of honeybee to express the distance and orientation to the food source could be hardwired involving no conscious memory about the flight. also the interpretation of the honeybee dance telling the distance and orientation of food source to advices where to fly would be completely ”instinctive”whatever this means. 2. a more radical option is that honeybee hive rather than honeybee has long term memories in the sense as long term memories are interpreted in tgd framework: that is as communications with the geometric past. in this case the span of long term memories is determined by the level of dark matter hierarchy as time scale defined by josephson frequency assignable to level of dark matter hierarchy in question and a span of few days for long term memories forces the conclusion kd ≥ 63: the upper bound is kd = 78 (see table 5), when one allows only k ≤ 167 mersennes and this corresponds to 87.6 years. one can ask whether the ability of honey bee queen to found a new honeybee colony could involve long term memory in the time scale of year. if this were the case, the queen would not face her formidable challenge alone: the former colony in the geometric past still exists as a conscious entity and could communicate advices to the queen. the magnetic body of the former colony could exist also in the geometric now, being physically associated with the queen. this magnetic body could serve as the conscious entity communicating to the queen the advices and commands making possible to construct the beehive. a more conservative explanation is that these activities are genetically hardwired and instinctive (leaving open what ’instinctive’ really means if it actually means anything). the distinguished social position and anatomy of queen are consistent with the hypothesis that queen has more massive connections than other bees with the magnetic body of beehive. for instance, it is known that the new hive is oriented in exactly the similar manner as the old. either long term memory or passive magnetic coding of the orientation of the hive with respect to earth’s magnetic field made possible by the magnetite in the abdomen of queen could explain this. the neurons of queen could correspond to a very large value of ~ giving rise to the required low josephson frequencies. the colony would have sensory resolution in a time scale of a fraction of second and short term memory in minute time scale. the counterpart of eeg at the level of hive is highly suggestive and conforms with the finding that elf magnetic fields with strengths in the range .1-1 mt (2be − 20be affect honeybee dance [12] as does also the absence of earth’s magnetic field. interestingly, 1-2 mt dc field causes epileptiform activity in the case of humans [10] (the change of the dc field used seems to be more important that the period it is applied). could the beehive suffer a kind of epileptic seizure! the intentional actions of the honeybee colony would be realized via magnetic flux sheets traversing the super-genes of the insects participating to the action in question. workers, soldiers, etc.. would act issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | june 2013 | volume 3 | issue 2 | pp. 188-210 204 pitkänen, m., evolution in many-sheeted space-time: big vision to some extent as organs of the colony being connected by hyper-genes of hyper-genome to larger units. queen could act as the analog of a complex grand mother neuron in brain or a leader in human society. this view can be criticized. honeybee dance [4] is performed by forager bees and the dance represents among other things the angle between the lines connecting hive to the food source and sun as the angle between movement of bee and vertical direction (also other options are possible). the intricate pattern of the dance in turn codes for the distance to the food source. if beehive is a conscious entity using bees as its cells, why is honeybee dance needed at all? tgd based vision about the evolution of modern human society from a bicameral society in which individuals received advice and commands from ”god” [18, 19] , suggests an answer to this criticism. the society able to survive must be maximally flexible and allow maximal individual intelligence and maximal freedom of individual actions consistent with the overall goals. this requires delegation of simple tasks to lower levels meaning also that communications between individuals become necessary (the development of language and other communications parallels the transition from bicamerality to modern society in the case of humans). the communication itself might however involve also the beehive. foreagers could be like the prophets of the bicameral society communicating in semitrance the advices of god to the colony. it should be noticed in passing that honeybees have already earlier made a visit to tgd inspired theory of consciousness [16] . as discovered by topologist barbara shipman [2] , honeybee dance has a mathematical description in terms of a construct assignable to color group su(3) of gauge interactions between quarks and gluons. this led her to propose that color interactions might have some deep role in living matter. this is in a sharp contrast to the fact that color interactions as establishment knows them are completely invisible above the length scale of 10−15 meters. the tgd based prediction that there exists an entire hierarchy of scaled up copies of qcd, in particular qcds with confinement length scale of order cell size, changes completely the situation. 2.3.2 honeybees as magneto-receptors of the beehive or magnetic cells as magneto-receptors of bee? earth’s magnetic field has a crucial status in the model of living systems even at the lowest levels of dark matter hierarchy so that earth’s magnetic field is expected to play a role in the functioning of all cells, also bees and ants. this is indeed the case. it is known that that bees have two navigation systems. the first system is based on the direction of sun and polarization of solar light but does not work on cloudy days. the second navigation system uses earth’s magnetic field and is used in cloudy days. bees have in their abdomen magnetite (fe3o4) particles of size about 30 nm and iron storage protein ferritin which correspond 10 to nm sized super-paramagnetic particles [11] . magnetite particles and ferritin in principle make possible magneto-reception instead of a mere passive compass behavior. the minimum option is that honeybee itself does not receive any neural information about the magnetic field but acts as a passive magneto-receptor of the bee colony or sub-colony (such as workers flying to the food source) and that the information contained by the receptor grid allows the sub-colony to deduce its position in the varying magnetic field. ”beeg” would mediate this information to the magnetic body of the (sub-)colony and the general mechanism based on josephson currents does not require nerve pulse patterns to achieve this. since foreagers seem to act as individuals able to navigate in the magnetic field of earth, it would seem that some cells of the honeybee could act as magneto-receptors so that the reaction of the magnetic particles would be coded to a neural signal. it has been proposed that the changes in the shape of the configurations formed by magnetite particles in a varying magnetic field induce changes in the shape of neuron and in this manner can induce neural signal. this mechanism could also induce the voltage perturbations coding the information to the josephson current giving rise to the sensory part of eeg as a state of coherent elf photons. perhaps the genes expressing these neurons are activated only in foragers and ferritin makes possible the magneto-reception in this sense. issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | june 2013 | volume 3 | issue 2 | pp. 188-210 205 pitkänen, m., evolution in many-sheeted space-time: big vision 2.3.3 social bacteria and magneto-tactic bacteria magneto-tactic behavior of bacteria [9] was discovered for 30 years ago by microbiologist richard p. blakemore and means that certain motile, aquatic bacteria orient and migrate along magnetic field lines. this ability could be purely passive compass mechanism made possible by the magnetite detected in the bacteria. during last years we have learned that bacteria are not simple creatures having only single goal: to multiply and fill the earth. bacteria are able to communicate and act co-operatively [13] . this raises the question whether hyper-genes could appear already at this level and whether bacteria acting as a colony they individual bacteria could act as magneto-receptors of colony allowing it to detect even variations of the magnetic field much like individual cells in the brain of vertebrates or perhaps even in the abdomen of honeybee are believed to serve as magneto-receptors. 2.3.4 great leaps in evolution as emergence of higher levels of dark matter hierarchy at level of individuals the vision about great leaps in evolution led to the view that the emergence of eeg corresponds to the emergence of keff > 205 levels of dark matter hierarchy. on the other hand, the time scale of gene translation corresponds to that associated with the ordinary eeg, which forces to ask whether these levels are present already in the lowest life forms. perhaps a more plausible option is that the .1 second time scale of electronic cd defines the time scale of gene translation and corresponds therefore to the standard value of ~0. the findings about honeybees however support the view that keff > 205 levels are present but are associated with the honeybee colony rather than individuals. this however requires that the these levels have neuronal realization in terms of josephson frequencies. therefore a more precise formulation of the hypothesis about great leaps in evolution would be that great leaps in evolution correspond to the emergence of a new dark matter level at the level of individual organism. if this view is correct then keff > 205 levels would correspond to a collective level of consciousness in the case of invertebrates down to bacteria, which are indeed found to form societies [13] . this conforms also with the fact that the genome of invertebrates is too small to allow realization of keff > 205 flux sheets as genes or even super-genes. the somewhat unexpected conclusion would be that all activities of invertebrates involving gene expression would be controlled by collective levels of consciousness: invertebrates would not be individuals in this sense. viruses do not possess dna translation machinery which is consistent with the absence of also collective keff > 205 levels. one can of course ask whether the queen of honeybee could be an exception to this rule. if one believes that the time scale of gene expression corresponds to josephson frequency then the explanation for the universality of the genetic code could be that keff > 205 levels controls gene expression: for keff > 205 wave length scale indeed corresponds to the length scale assignable to the magnetosphere of earth. one could of course counter argue that it is more reasonable form magnetic mother gaia to delegate this kind of duties to the lower levels and that the cds of electron and quarks are ideal for this purpose. 2.4 dark matter hierarchy, hierarchical structure of nervous system, and hierarchy of emotions one can ask how the structural and functional hierarchy of cns and the hierarchy of emotions relates to the dark matter hierarchy. the basic picture wherefrom one can start is following. 1. the emergence of nervous system corresponds to the emergence of keff < 205 levels of dark matter hierarchy above keff < 167. for instance, worms and insects would correspond to this level. 2. vertebrates have eeg and thus the most primitive vertebrates (reptiles) should correspond to keff ≥ 205. issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | june 2013 | volume 3 | issue 2 | pp. 188-210 206 pitkänen, m., evolution in many-sheeted space-time: big vision 3. the emergence of new structures need not mean the emergence of new levels of dark matter hierarchy. rather, the most reasonable criterion for the presence of these levels is the emergence of behaviors involving long term goals and the magnetic bodies of the parts of brain assignable to the control of this kind of behaviors would correspond to higher values of keff . also the maximum span of memories at given level should be characterized by the value of keff associated with the brain structures involved (hippocampus, mammillary bodies). this picture conforms with the fact that already insects possess neurons, ganglia, and head containing the predecessor of cerebrum but correspond to keff ≤ 205 most naturally. for goal related emotions the maximal time scale assignable to the achievement of the goal might allow to identify the time scale characterizing corresponding level of dark matter hierarchy. the lowest level emotions would be ”primitive” emotions not related to any goal and one can as whether they could be assigned to organs consisting of ordinary cells and correspond to keff ≤ 205. 1. the time scale of planned behavior and of long term memories makes possible to estimate upper bounds for the values of keff assuming josephson frequency hypothesis. keff ≤ 205 would give the upper bound of 6 ms which corresponds to cerebellar resonance frequency 160 hz. this time scale looks too short even for the simplest vertebrates and one must be very cautious here. 2. an alternative interpretation is as the shortest possible span for short term memory whose time scale is known to vary. 3. cerebellar rhythm could be analogous to hippocampal theta rhythm and involved with the crebella memory storage and therefore would not tell anything about the span of the memory but would characterize the time resolution of memories and planned actions. the role of cerebellum in the fine coordination of motor actions indeed requires high time resolution. brain has anatomic division into midbrain, hindbrain, and forebrain [j5] . midbrain and hindbrain (sometimes both are included in brain stem) is possessed by even the most primitive vertebrates and its emergence could therefore correspond to the emergence of keff ≥ 205 levels and eeg. the emergence of these levels relates naturally to the emergence of long term planning of motor actions in motor areas. the emergence of limbic brain, which defines the most primitive forebrain, could mean the emergence of the gaussian mersenne defined by keff = 239 containing dark electron condensates level and goal related emotions. this conforms with the fact that for mammals forebrain and cerebral hemispheres dominate whereas for other vertebrates hindbrain and cerebellum are in the dominant role. 2.4.1 reptilian brain as keff ≤ 205 system? reptilian brain contains only the structures corresponding to brain stem (midbrain and hind brain, in particular cerebellum) and as far structures are considered would correspond to keff ≤ 205 levels of the hierarchy. cerebellum is not believed to contribute directly to our consciousness. the absence of higher looks however an unrealistic assumption since reptiles certainly have long term memories. simplest emotions correspond to emotions involving no goal. moods like excitement, feeling good/bad/tired/strong, etc.. could represent examples of such emotions and could be experienced already by reptilians. of course, the scaled up variants of these emotions could appear at higher levels of hierarchy and would relate to the states of magnetic bodies (degree of the quantum coherence of bose-einstein condensates!). 2.4.2 limbic system limbic system is not possessed by reptiles [j3] . it is responsible for emotions, control of emotions, and also emotional intelligence. limbic system corresponds to the brain of the most mammals. the limbic brain includes the amygdala, anterior thalamic nucleus, cingulate gyrus, fornix, hippocampus, hypothalamus, mammillary bodies, medial forebrain bundle, prefrontal lobes, septal nuclei, and other areas and pathways of the brain. issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | june 2013 | volume 3 | issue 2 | pp. 188-210 207 pitkänen, m., evolution in many-sheeted space-time: big vision 1. the sub-cortical part of the limbic system involves amygdalar and septal divisions. according to [j3] amygdalar division promotes feeding, food-search, angry, and defensive behaviors related to obtaining food. septal division promotes sexual pleasure, genital swelling, grooming, courtship, and maternal behavior. these divisions are emotional mirror images of each other hand could correspond to 205 < keff < 239. 2. the cortical part of the limbic system contains cingulate gyrus which is the newest part of the limbic system and belongs to thalamo-cingulate division which promotes play, vocalization (e.g., the separation cry), and maternal behavior. the time scale of memories would be shorter than 3.4 at this level. 3. frontal lobes [j2] are often regarded as the organ of volition. the frontal lobes are involved in motor function, problem solving, spontaneity, memory, language, initiation, judgement, impulse control, and social and sexual behavior. prefrontal lobes representing the extreme front part of frontal lobes belong also to the limbic system and are responsible for motivation and ability to pose long term goals. this ability distinguishes humans from other primates. for these reasons frontal lobes, in particular prefrontal lobes, could involve the highest levels of dark matter hierarchy in the case of humans. the gaussian mersenne levels keff = (239, 241) could be assigned as lowest level in this hierarchy. the time scale of long term memories would be longer than 3.4 years at these levels. cortico-striatal emotions like sadness, hate, fear anger, surprise, embarrassment, happiness, contentment, and joy involve goal structures and failure or success to achieve the goal in essential manner and would involve prefrontal lobes. these levels would naturally relate to collective levels of consciousness coded by hyper genes. hence these emotions could also relate to goals not directly related to the fate of biological body. mirror neurons are a crucial prerequisite of a social behavior (autistic children seem to lack them), which suggests that hyper genes are involved at least with them. social emotions (feeling embarrassed, ashamed, guilty, loved, accepted, ...) could be induced by the collective levels of dark matter hierarchy as punishments or rewards for social behavior very much like neurotransmitters are believed to provide rewards and punishments at neuronal level. 2.4.3 neocortex and two kinds of intelligences neocortex is often assumed to be superior (”neomammalian”) part of the brain and makes the majority of brain hemispheres. the species which are considered to be highly intelligent, such as humans and dolphins, tend to have large amounts of neocortex. the amount of neocortex is roughly proportional to the brain size for primates. neocortex cannot correspond to keff ≥ 239 (defining gaussian mersenne) as a whole. the decomposition of sensory areas to layers is consistent with the presence of lower levels since it is time resolution which matters in the case of sensory representations. same conclusion applies to sensory association areas. the fine tuning of the motor control performed by cerebellum is consistent with keff ≤ 205. intelligence understood in the conventional sense of the word is accurate, works fast, and is computer like. the part of neocortex responsible for ordinary intelligence would be a rapid and accurate processor of sensory and cognitive representations. hence keff < 239 would naturally characterize sensory areas, secondary and primary motor areas, to hippocampal representation of declarative memories, and all association areas except dorsolateral prefrontal sensory-motor association cortex where short term memories are represented. emotional intelligence works slowly and is responsible for visions and holistic views and would thus correspond to higher levels of dark matter hierarchy. limbic system is involved with emotions, motivation and long term planning and would thus be responsible for emotional intelligence. indeed, the damage to frontal lobes [j2] need not affect ordinary intelligence but affects emotional intelligence. issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | june 2013 | volume 3 | issue 2 | pp. 188-210 208 pitkänen, m., evolution in many-sheeted space-time: big vision 2.4.4 the levels of dark matter hierarchy associated with short and long term memory the first thing to ask is of course whether the notions of short and long term memory make sense in tgd framework. indeed, it would seem that it is more natural to speak about hierarchy of memories with characteristic time scales coming as selected powers of two. 1. according to [j4] , the span of other than visual short term memories is 30-45 seconds. this requires keff ∈ {217, 218}. 2. visual short term memories [j1] representing selected features of visual field are reported to have time span of few seconds. this suggests keff ∈ {213, 214, 215}. 3. iconic visual memories representing entire visual field have much shorter time span of order 1 s: keff ∈ {211, 212} would be appropriate for them, 4. long term memories would correspond to keff > 218. hippocampus and mammillary bodies involved with long term memory recall are part of the limbic system. the hippocampal theta rhythm 4-12 hz , which could corresponds roughly to keff ∈ {163, 162, 161} has nothing to do with the span of long term memories but would define the time resolution of the memories: the moment of sensory experience indeed corresponds to 10 hz frequency. the frequencies responsible for memory storage need not have anything to do with the ultralow frequencies characterizing the temporal distance of the past event associated with the memory recall and hippocampus could just build a kind of bit sequence which during memory recall is communicated from the geometric past to some part of the future brain or magnetic body. anterograde amnesia means an inability to restore long term memories. the damage of hippocampus or of mammillary bodies can induce anterograde amnesia. in the usual conceptual framework the explanation would be the inability to store new long memories. in tgd framework this would be inability to construct those cognitive representations which are communicated to the geometric future in long term memory recall. retrograde amnesia seems to involve almost always anterograde amnesia and means loss of memories for some time span before the injury. a possible explanation is that injury can propagate also to the geometric past of the brain quantum jump by quantum jump. during ageing memories tend to be lost but the memories of childhood are the most stable ones. a possible interpretation is that faster rhythms of the generalized eeg tend to disappear: kind of scaled up variant for the process of falling into sleep accompanied by silencing of higher eeg bands could be in question. 2.4.5 what about transpersonal levels of consciousness? keff > 245 levels of dark matter hierarchy correspond to time span longer than 109 years and cannot relate to the biological body alone. they could relate to higher collective levels of the dark matter hierarchy and evolution of social structures. the memories extending over personal life span claimed by meditators could have interpretation in terms of keff > 245 transpersonal levels of consciousness. also the ”god module” located to temporal lobes could correspond to this kind of levels of dark matter hierarchy. if it corresponds to gaussian mersenne with keff = 283 the time scale of memories becomes huge: about 1014 years so that the notion of ”god module” is indeed appropriate. references mathematics [1] gaussian mersenne. http://primes.utm.edu/glossary/xpage/gaussianmersenne.html. issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. http://primes.utm.edu/glossary/xpage/gaussianmersenne.html dna decipher journal | june 2013 | volume 3 | issue 2 | pp. 188-210 209 pitkänen, m., evolution in many-sheeted space-time: big vision [2] b. shipman. the geometry of momentum mappings on generalized flag manifolds, connections with a dynamical system, quantum mechanics and the dance of honeybee. http://math.cornell.edu/ ~oliver/shipman.gif, 1998. cosmology and astrophysics [3] age of the universe. http://en.wikipedia.org/wiki/age_of_the_universe. biology [4] magnetic bees. http://www.abc.net.au/science/k2/trek/4wd/over57.htm. [5] nanobacterium. http://en.wikipedia.org/wiki/nanobacterium. [6] nanobe. http://en.wikipedia.org/wiki/nanobe. [7] virus. http://en.wikipedia.org/wiki/virus. [8] why honeybees never forget a face? new scientist, page 22, december 2005. [9] s. clement. magnetic microbes. http://commtechlab.msu.edu/sites/dlc-me/curious/ caoc96sc.html, 1996. [10] j. p. dobson et al. evocation of epileptiform activity by weak dc magnetic fields. american geophysical union meeting, baltimore, maryland. eos, (16), 1993. [11] m. desoil et al. definitive identification of magnetite nanoparticles in the abdomen of the honeybee apis mellifera. journal of physics: conference series, 17, 2005. [12] j. l. kirschvink. constraints on biological effects of weak extremely-low-frequency electromagnetic fields’. phys. rev. a. http: // prola. aps. org/ abstract/ pra/ v46/ i4/ p2178_ 1 , 43(1991), 1992. [13] s. silberman. the bacteria whisperer. wired magazine. http: // www. wired. com/ wired/ archive/ 11. 04/ quorum. html , april 2003. neuroscience and consciousness [j1] visual short term memory. http://en.wikipedia.org/wiki/visual_short-term_memory. [j2] frontal lobes. http://en.wikipedia.org/wiki/frontal_lobes. [j3] limbic system. http://en.wikipedia.org/wiki/limbic_system. [j4] short term memory. http://en.wikipedia.org/wiki/short_term_memory. [j5] j. s. nicholis s. w. kuffler and a. r. martin. from neuron to brain. sinauer, massachusetts, 1984. issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. http://math.cornell.edu/~oliver/shipman.gif http://math.cornell.edu/~oliver/shipman.gif http://en.wikipedia.org/wiki/age_of_the_universe http://www.abc.net.au/science/k2/trek/4wd/over57.htm http://en.wikipedia.org/wiki/nanobacterium http://en.wikipedia.org/wiki/nanobe http://en.wikipedia.org/wiki/virus http://commtechlab.msu.edu/sites/dlc-me/curious/caoc96sc.html http://commtechlab.msu.edu/sites/dlc-me/curious/caoc96sc.html http://prola.aps.org/abstract/pra/v46/i4/p2178_1 http://www.wired.com/wired/archive/11.04/quorum.html http://www.wired.com/wired/archive/11.04/quorum.html http://en.wikipedia.org/wiki/visual_short-term_memory http://en.wikipedia.org/wiki/frontal_lobes http://en.wikipedia.org/wiki/limbic_system http://en.wikipedia.org/wiki/short_term_memory dna decipher journal | june 2013 | volume 3 | issue 2 | pp. 188-210 210 pitkänen, m., evolution in many-sheeted space-time: big vision books and articles related to tgd [14] m. pitkänen. cosmic strings. in physics in many-sheeted space-time. onlinebook. http:// tgdtheory.com/public_html/tgdclass/tgdclass.html#cstrings, 2006. [15] m. pitkänen. dna as topological quantum computer. in genes and memes. onlinebook. http: //tgdtheory.com/public_html/genememe/genememe.html#dnatqc, 2006. [16] m. pitkänen. general theory of qualia. in bio-systems as conscious holograms. onlinebook. http://tgdtheory.com/public_html/hologram/hologram.html#qualia, 2006. [17] m. pitkänen. homeopathy in many-sheeted space-time. in bio-systems as conscious holograms. onlinebook. http://tgdtheory.com/public_html/hologram/hologram.html#homeoc, 2006. [18] m. pitkänen. semi-trance, mental illness, and altered states of consciousness. in magnetospheric consciousness. onlinebook. http://tgdtheory.com/public_html/magnconsc/magnconsc. html#semitrancec, 2006. [19] m. pitkänen. semitrance, language, and development of civilization. in magnetospheric consciousness. onlinebook. http://tgdtheory.com/public_html/magnconsc/magnconsc.html# langsoc, 2006. [20] m. pitkänen. three new physics realizations of the genetic code and the role of dark matter in bio-systems. in genes and memes. onlinebook. http://tgdtheory.com/public_html/genememe/ genememe.html#dnatqccodes, 2006. [21] m. pitkänen. are dark photons behind biophotons. in tgd based view about living matter and remote mental interactions, 2013. [22] m. pitkänen. comparison of tgd inspired theory of consciousness with some other theories of consciousness. in tgd based view about living matter and remote mental interactions. onlinebook. http://tgdtheory.com/public_html/pdfpool/consccomparison.pdf, 2013. [23] m. pitkänen. sheldrakes morphic fields and tgd view about quantum biology. http:// tgdtheory.com/articles/sheldrake.pdf, 2011. issn: 2159-046x dna decipher journal june www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.com/public_html/tgdclass/tgdclass.html#cstrings http://tgdtheory.com/public_html/tgdclass/tgdclass.html#cstrings http://tgdtheory.com/public_html/genememe/genememe.html#dnatqc http://tgdtheory.com/public_html/genememe/genememe.html#dnatqc http://tgdtheory.com/public_html/hologram/hologram.html#qualia http://tgdtheory.com/public_html/hologram/hologram.html#homeoc http://tgdtheory.com/public_html/magnconsc/magnconsc.html#semitrancec http://tgdtheory.com/public_html/magnconsc/magnconsc.html#semitrancec http://tgdtheory.com/public_html/magnconsc/magnconsc.html#langsoc http://tgdtheory.com/public_html/magnconsc/magnconsc.html#langsoc http://tgdtheory.com/public_html/genememe/genememe.html#dnatqccodes http://tgdtheory.com/public_html/genememe/genememe.html#dnatqccodes http://tgdtheory.com/public_html/pdfpool/consccomparison.pdf http://tgdtheory.com/articles/sheldrake.pdf http://tgdtheory.com/articles/sheldrake.pdf introduction great vision about biological evolution and evolution of brain basic assumptions how to identify the preferred values of planck constant? tables about predicted time and length scales electron and u quark are different dark matter hierarchy and big leaps in evolution a sketch about basic steps in evolution division of the evolution to that of biological body and magnetic body biological evolution the evolution of magnetic body could insect colonies have "eeg"? do honeybees have long term memory? honeybees as magneto-receptors of the beehive or magnetic cells as magneto-receptors of bee? social bacteria and magneto-tactic bacteria great leaps in evolution as emergence of higher levels of dark matter hierarchy at level of individuals dark matter hierarchy, hierarchical structure of nervous system, and hierarchy of emotions reptilian brain as keff205 system? limbic system neocortex and two kinds of intelligences the levels of dark matter hierarchy associated with short and long term memory what about transpersonal levels of consciousness? dna decipher journal | july 2020 | volume 10 | issue 1 | pp 14-25 smith, s. p., pitch inverted songs as affirmation of panpsychism based on a theoretical mirror universe issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 14 article pitch inverted songs as affirmation of panpsychism based on a theoretical mirror universe stephen p. smith * abstract every song that carries a melody can be pitch inverted to uncover a dual song that is different to the original song and where the pitch-inverted melody also relates to our emotions. this is creating music for the minor cost of pitch inversion, and without a lot of creativity beyond technical skills. the principle is demonstrated on 50 songs, with 100% success. as a general principle this implicates a reflective property that is necessarily part of human psychology. moreover, this discovery affirms the belief in panpsychism where the reflexive property is active as part of a broader mirror universe. keywords: song, pitch inversion, panpsychism, mirror universe, reflective property. 1. introduction panpsychism is a philosophical theory of consciousness that is gaining acceptance today (skrbina 2017). this theory stipulates that consciousness is a fundamental property of matter. because matter cannot be disconnected from the entire universe, panpsychism also asserts that consciousness is a fundamental property of the universe. smith (2018, 2019) described a panpsychism that relates to a fundamental symmetry described by physics, the charge-parity-time symmetry (or cpt symmetry), and also connects it to a mirror universe theory described as a two-sided cpt inversion. as a logical necessity for a comprehensible universe, it must be that the universe holds a reflective properly that permits comprehension, otherwise the world would not be comprehendible (langan 2017). this logical necessity resembles photographic prints that are made from negative film, where the negative film equates to the reflective property in the universe as an analogy. moreover, while the negative film is found necessary, there remains an undeclared middle-term that takes the negatives and does the work of making the prints, agreeing with trinitarian philosophy (smith 2008). therefore, evidence that supports the belief in such a mirror universe comes in the form of discovering the negative film, or reflections, that are found after looking for them. this paper entertains the theoretical possibility that songs also carry a negative, or dual song, and these songs are represented by pitch-inversion. to the extent that every song that has ever been composed comes with such a dual song, that is also recognized to carry a distinct melody that evokes an emotional response to some degree, then this would constitute evidence of a mirror universe that encapsulates the emotive source. the theory predicts a 100% success rate in finding correspondence: stephen p. smith, ph.d., independent researcher. e-mail: hucklebird@aol.com dna decipher journal | july 2020 | volume 10 | issue 1 | pp 14-25 smith, s. p., pitch inverted songs as affirmation of panpsychism based on a theoretical mirror universe issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 15 a dual song that carries a melody, not that all such melodies will be found pleasing. this is a testable prediction that is reported in this paper on 50 different attempts to create dual songs. section 2 describes pitch inversion in music, and how to pitch-invert songs. appendix a provides more details on how to pitch-invert sheet music by hand. these instructions were used to pitch invert 50 popular songs, using a music note editor (cresceno, made by nch software). section 3 describes the information content in songs, and how songs carry a relativity that makes them invariant to transposition. section 4 explains how the relative information contained in a song pertains to panpsychism and the mirror universe. section 5 summarizes the results for 50 songs, including links to youtube videos where the songs can be heard. all 50 attempts were found successful in generating a distinct melody, most being very different from the initial song, and these findings support the belief in the mirror universe. concluding remarks are presented in section 6. 2. pitch inversion the pitch inversion of musical notes have been studied in musical set theory (forte 1977). pitch inversion is defined as the flipping, or reflecting, of a note around a second note that represents the center note. the center note is selected once 1 but can be selected anywhere, but various keys have natural center notes that do not complicate the notation. for example, using the note d as the center note returns notation in c major given that the original song is in c major, where the pitch-inverted notes will have accidentals only when the original notes have accidentals. like the transposition of notes, pitch inversion maps a song into a class without changing the tempo while making a second song. in the case of transposition, which is the raising or lowering of notes a specified number of chromatic steps, the same melody is returned. that is, melody is found invariant to transposition, even as the tone changes. pitch inversion changes the melody, but not necessarily to an extreme extent even as extreme changes are found in particular examples. therefore, the pitch-inverted song represents a dual song that shadows the original melody, and only when the melody and its dual are defined equivalent is a broader equivalence or invariance (representing a class) meaningful. when working with an audio file, it is possible to use software (e.g., patrick feaster‟s software described on griffonagedotcom.wordpress.com) to pitch-invert a song around a selected pitch (if not a note). the evolution of sound from notes played by a musical instrument are impacted by time creating a waveform signature that‟s asymmetrical in its presentation (changes in amplitude), and in any regard, pitch-inverting sound is not as pristine as pitch-inverting notes before they are played. the bigger challenge is that the chromatic scale is exponentially spaced, where frequency must be log transformed to make a linear scale for direct pitch inversion of sound. its more straightforward to invert notes before they are turned into sound, using the natural exponential chromatic spacing. c++ software (craig stuart‟s midi file parsing library, part of github) is available for pitch-inverting a midi file around a center note. if not careful, however, reflecting midi files can lock the process into making all notes on the bass clef high 1. when inverting notes in one staff. dna decipher journal | july 2020 | volume 10 | issue 1 | pp 14-25 smith, s. p., pitch inverted songs as affirmation of panpsychism based on a theoretical mirror universe issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 16 notes and while making all notes on the treble clef low notes, and this creates an inflexible method that is not desirable. it is preferable to break a song into multiple staffs (which is tantamount to making multiple midi files), pitch-invert each staff individually using a center note that‟s natural for the key but in the middle of the staff (more or less), then transpose each staff up or down one octave to present the most desired arrangement for all the staffs together. therefore, pitch-inversion of a song does not necessarily lock the process into a single center note. the added flexibility is actually preferred with a process that is otherwise highly automatic, and the process can now be done by hand using a good music note editor (see appendix a). the disadvantage of doing the inversion by hand with a note editor is that the operation can introduce errors. 3. information contained in a song and relativity the exponential spacing (given by the factor 12 √2) that typifies the chromatic scale is remarkable. the implication is that the human ear not only can distinguish among these notes, but actually prefers this arrangement when notes are set to music. because the normal scale with seven notes represent a subsequence of the 12 chromatic notes, the same preference given to exponentially spaced notes is again realized. its unclear how this preference can be explained in mathematical terms, but there is a vague hint that this preference connects to the probabilistic concept of entropy, or to the scale invariant prior and utility function of bayesian statistics, all of which incriminate multiplicative transitions. the fact that this preference connects to consciousness makes the spacing very mysterious. nevertheless, pitch inversion will be taken to pertain to this unusual spacing, which is not linear in pitch, it is multiplicative. the fact that a transposition of notes in a song leaves the melody intact while changing the tone, implies that the information that is recognized as a melody is contained in the relative changes of notes as time unfolds according to the tempo. only the tempo and transitions between notes define the melody, not the absolute frequency that defines any particular note. this represents a type of relativity given by the representation of melody as the transitions given in the exponential scale. this is not saying that the melody is relative, only the representation of melody is relative. the representation does not stand in isolation to its reception in mind, i.e., something must receive the representation, and something must hold the representation to its reception. the strict application of relativity only applies to the song‟s representation, and perhaps the song‟s reception, but not to the undeclared middle-term that holds the representation to its reception. imposing relativity on the middle-term is to imply that everything is relative, which is to confuse the thing-in-itself with appearance and is a mistake that kant recognized in the critique of pure reason. the observation that representation is relative, as is the representation‟s reception, is presumably a condition of consciousness. information showing the middle-term gets left out of appearance by necessity, and must be apprehended by something other than simple appearance. we cannot see the middle-term for the same reason that our eyes cannot see the back of our head without the aid of a mirror; i.e., the blind spot is caused by self-referral. a mirror, or frame of reference, must always be provided in order to detect something closer to the middle-term. likewise, a popular science turned folk philosophy might leap to the false conclusion that everything is relative (radical relativism) based on the findings of special and general relativity (if not postmodernism), dna decipher journal | july 2020 | volume 10 | issue 1 | pp 14-25 smith, s. p., pitch inverted songs as affirmation of panpsychism based on a theoretical mirror universe issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 17 but clear thinking shows that something fundamental and non-relative may go unnoticed in the possible eather that never finds experimental detection. it is not accidental that einstein‟s theories postulated a frame of reference as a first step in his thought experiments. however, a frame of reference (even those described in physics) implies a self-referral that carries its own blind spots. 4. panpsychism and the mirror universe information of any kind presupposes the existence of consciousness. or if consciousness is to be taken for granted, attempts to turn information into a one-sided measure (such as shannon‟s information given the thermodynamic quantity called entropy) pushes consciousness out of the window of appearance and into a metaphysics that may get completely ignored. in the worst case this is to confuse appearance with the thing-in-itself again, as kant warned. nevertheless, the push of consciousness out of the one-sided appearance leaves it fully in reality as the other side of appearance, consciousness carries the appearance that is reflected off the other side, and carries an undeclared middle-term again. consciousness becomes a fundamental substance in reality, something that is not a derivative of one-sided causation, and even if it is not admitted by those confused by appearances. this view of consciousness that connects to a fundamental is the definition of panpsychism, and because this view also carries a realty that is two-sided with an undeclared middle-term this view indicates a rediscovery of the logos that makes a particular type of panpsychism and implies a mirror universe. the logos that represents the absolute mover 2 of the universe acts now as a strange attactor, and forms a fractal pattern in evolution by leaving behind a reflection of itself on all levels. the mirror universe leaves behind lesser mirrors that may serve as evidence for the theory of the mirror universe. information that represents a melody, given as tempo and the relative spacing of notes, must somehow meet the representation‟s reception (the reflection). the hypothesis of this paper is that the organic reception, or the song‟s reflection, is none other than the pitch inversion of the melody. this is not to say that there are not deeper reflections, perhaps going all the way to cptinversion that‟s described in physics. however, its very ambitious to dig this deep, and a deeper reflection may be unintelligible to the human mind. the deeper search is unnecessary, however, as the proof in the mirror universe is the finding of lesser mirrors that are all necessary; we are permitted to make incremental discoveries. so finding ourselves sitting at a piano we may also find our self-looking into a near-by mirror. playing the piano while looking into the mirror we discover that the right hand is playing on the low-pitched keys while the left hand is playing on the high-pitched keys, the complete reverse of what normally happens, but matching perfectly the operation of pitch-inversion using the chromatic scale with its exponential spacing. the pitch-inverted song matches perfectly the mirror reflection of ourselves playing the piano that‟s unified through the unspecified middleterm. could this be the organic mirror we are looking for, a lesser mirror that‟s found necessary? 2. as in motivation and the source of all that is emotive. dna decipher journal | july 2020 | volume 10 | issue 1 | pp 14-25 smith, s. p., pitch inverted songs as affirmation of panpsychism based on a theoretical mirror universe issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 18 songs carry a remarkable connection to emotion, and less so to intellect. a possible panpsychism is better described as a vitalism because its emotion that we look for, not so much consciousness. to seek is to be motivated, and that‟s an emotional requirement. to seek is futile if there was no awareness of fulfilment, and so consciousness in some degree is also required and therefore goes hand in hand with emotion. a song is like a language that connects with emotion and takes us somewhere with a motivated direction. the mirror image of the song should also take us somewhere as it necessarily does if the original song is faithful to a direction representing the melody. therefore, all pitch-inverted songs should carry a hidden melody, the dual song, provided pitch-inversion is the actual organic mirror, a lesser mirror, that is necessary for the mirror universe where the middle-term represents the source of all that is emotive. this is a testable prediction, 100% of the inverted songs should carry a melody if the hypothesis is true. finding one song that is little more than random noise would indicated that the organic mirror is not yet discovered. 5. fifty pitch-inverted songs all the songs were pitch-inverted following the method in appendix a, for the present investigation, and are identified in table 1. the 50 remade songs are presented in a youtube play-list and are found with this internet link: https://www.youtube.com/playlist?list=pldhv1duzhj8-nhmv2wxevvuhpi-56bp5q simply match the video named in table 1 to the video in the play-list. table 1. list of pitch-inverted songs. video original song composers 1. beautiful dreamer beautiful dreamer stephen foster 2. southern swamps bonnie blue flag harry mccarthy 3. swan lake and its echo swan lake peter ilyich tchaikovsky 4. abducted by the mirror man in the mirror glen ballard and siedah garrett 5. wanderlust america paul simon 6. broken ties castles in the air don mclean 7. once upon a time in the mirror once upon a time in the west ennio morricone 8.brothers in repose brothers in arms mark knopfler 9. the big mirror the big country jerome moross 10. polished corn popcorn gershon kingsley 11. the magnificent mimic the magnificent seven elmer bernstein 12. do you know the way? do you know the way to san jose burt bacharach dna decipher journal | july 2020 | volume 10 | issue 1 | pp 14-25 smith, s. p., pitch inverted songs as affirmation of panpsychism based on a theoretical mirror universe issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 19 13. the reflection of love the look of love burt bacharach 14. don‟t wake in a dream don‟t sleep in the subway tony hatch and jackie trent 15. burning daylight the hustle van mccoy 16. hot death valley hot hot hot alphonsus cassell 17. ride the train locomotive breath ian anderson 18. ode to joy and its echo ode to joy ludwig van beethoven 19. ipanema the girl from ipanema antonio garlos jobim 20. gun fighters the man who shot liberty valance burt bacharach 21. sailor‟s dream daydream believer john stewart 22. painted desert this guy‟s in love with you burt bacharach 23. internet killed the shopping mall video killed the radio star bruce woolley, trevor horn and geoff downes 24. cover of darkness the sun ain‟t gonna shine anymore bob crewe and bob gaudio 25. saturday‟s travel come saturday morning fred karlin 26. everybody‟s leavin‟ town good time charlie‟s got the blues danny o‟keefe 27. new beginnings goodbye john lennon and paul mccartney 28. empty places brandy elliot lurie 29. dancing in the garden dancin‟ in the moonlight sherman kelly 30. baja california come monday jimmy buffett 31. god‟s will be done god only knows brian wilson and tony asher 32. empty streets downtown tony hatch 33. sweeter song than the birds my girl william “smokey” robinson and ronald white 34. wabash cannonball and its echo wabash cannonball a.p. carter 35. armidale by afternoon amarillo by morning terry stafford and paul frasier 36. the master‟s tapestry coat of many colors dolly parton 37. god‟s sanctuary amazing grace john newton 38. where have they gone abraham, martin and john richard holler 39. on straight and narrow the only daddy that will walk the line ivy j. bryant 40. the fast track lost highway leon payne 41. is anybody goin‟ to shangrila is anybody goin‟ to san antone dave kirby and glenn martin dna decipher journal | july 2020 | volume 10 | issue 1 | pp 14-25 smith, s. p., pitch inverted songs as affirmation of panpsychism based on a theoretical mirror universe issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 20 42. how „bout them memories how „bout them cowgirls casey beathard and ed hill 43. time reversal time passages al stewart and peter white 44. waiting for a sign waiting on a friend mick jagger and keith richards 45. my front pages my back pages bob dylan 46. ghost returning from other side wuthering heights kate bush 47. megaliths and geoglyphs no one to depend on gregg rolie, michael carabello and thomas escovedo 48. music from the other side both sides now joni mitchell 40. pyroclastic flow landslide stevie nicks 50. from flower to seed from hank to hendrix neil young all 50 remakes produced melodies, supporting the belief that pitch-inversion is more than just an interesting generation of musical notes. by comparison, playing notes backward can create interesting sounds sometimes, but these are unlikely to generate interesting melodies; playing notes backward may only generate uninteresting sounds. what has been demonstrated here is more of a general principle, a demonstration that all songs that have a defined melody also carry a hidden song by necessity, a dual song that can be recovered by pitch-inversion. this is not to say that the pitch-inverted songs are necessarily beautiful, or as beautiful as the originating song. its only that an emotion connecting melody is guaranteed by the principle that‟s now found validating the hypothesis of a mirror universe, as described. some of the pitch-inverted songs are quite beautiful, however. the author finds the songs (5, 21, 25, 27, 30, 41, 42, 48 and 50) very beautiful, and quite striking. other songs (4, 5, 8, 10, 15, 16, 20, 38, 39 and 46) are very interesting, and beautiful in an unconventional way. most of the pitch-inverted melodies bear little resemblance to the originals, but there are dual songs (9, 10, 12, 15, 19, 28, 30, 34, 46 and 47) that hold some minor similarities with the original song. these appraisals are likely to show subjective variation. when first investigating pitch-inversion, very simple songs were considered, limited to one staff showing mostly single notes, with few or no chords. but to avoid the selection bias of only showing interesting examples, these few simple songs (videos 1 and 2) have a listing in table 1. video 1 plays the original song followed by the pitch inversion, followed again by an improvisation that has little to do with pitch-inversion. video 2 also plays the original melody followed by the pitch inversion, but it also experiments with overlaying a two melodies which actually worked for that particular song. overlaying the song with its pitch-inversion, however, was in general found to generate dissonant sounding notes and was abandoned in the later productions. videos 3 and 34 also plays the original song and its pitch inversion. the remaining videos only play the pitch-inverted songs, but versions of the original melodies can easily be found on youtube if a comparison is needed. it was found that the method of appendix a was very robust, and worked best for more complicated songs that had several staffs. the staffs for a more complicated song can all be dna decipher journal | july 2020 | volume 10 | issue 1 | pp 14-25 smith, s. p., pitch inverted songs as affirmation of panpsychism based on a theoretical mirror universe issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 21 inverted independently, then transposed up or down to make a harmonious synthesis of all the inverted staffs. most of the 50 songs listed in table 1 came with four staffs: for a guitar; the chords, and the piano‟s bass and treble clef. these staffs were then borrowed by different musical instruments (by the computer synthesizer) to create more interesting productions. something must be strangely said about the very unusual experience of hearing a pitch-inverted song for the very first time. in some cases the music comes out as not sounding right, confusing, and more like a failure showing less than the expected 100% success rate now reported. some of this is due to small errors that end up getting corrected, and doing the inversion by hand can introduce errors. however, this can‟t be the only reason for the initial confusion. its like looking at the figure 1 below, and getting confused about seeing a vase or two opposing faces. figure 1. optical illusion. having recognized the melody for the very first time, then the confusion goes away like magic! the melody becomes a rote that‟s first learned, but this is where the experience becomes inexplicable because i doubt that any of my youtube viewers find an initial confusion while listening to these 50 songs! the implication is that the learned rote becomes part of the collective memory, a sort of mandela effect that rewrites history, or a type of morphic resonance that becomes available to the collective. extraordinary claims demand extraordinary evidence, and no one should adopt this speculation as certain. something unusual happened when listening to some (not all, but including 8, 13, 31, 40, 43, 45 and 46) of the pitch-inverted songs for the first time, that‟s all that is being claimed. fortunately, the experience can be repeated if its real. if any investigator wants to pitch invert different songs in the future, be looking for this experience. there is no shortage of songs that can be inverted, and so its possible to bring clarity to this issue. dna decipher journal | july 2020 | volume 10 | issue 1 | pp 14-25 smith, s. p., pitch inverted songs as affirmation of panpsychism based on a theoretical mirror universe issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 22 6. conclusion the attempts to make melodies by pitch inverting 50 songs was 100% successful. interesting songs of all types were generated using the robust method presented in appendix a, and most of the remade songs showed little resemblance to the originating song even when the tempo was maintained. this strongly implies the validity of a general principle, that all songs that carry an identifiable melody can be pitch inverted to make new melodies with 100% success. this conclusion is firm because the results are highly reproducible. doubters will find the identical melodies reported here following independent attempts at pitch inversion with any of the same 50 songs. moreover, new songs can be inverted to further test the general principle, but it is now doubtful that the conclusion will change. the only possible controversy is with what these findings mean, including the general principle that‟s now uncovered. as argued in this paper, these results affirm the belief that we live in a mirror universe that is a necessary adjunct of panpsychism of a sort that endorses trinitarian philosophy. the proof of the mirror universe is in the lesser mirrors that are discovered, and one such lesser mirror is the pitch-inverted song that equally brings the listener on an emotion laden journey like all songs. moreover, the middle-term that holds the song to its reflection is the emotive source that connects to the absolute mover or motivator for the entire universe. such a system act as a strange attractor that generates the lesser mirrors out of necessity and on all levels of a fractal pattern, and so finding these mirrors constitutes evidence that affirms this speculation. yes, this last paragraph is speculation, but it now falls into testable science because there are many kinds of mirrors beyond music that can be gathered as evidence. appendix: robust method to pitch invert songs with multiple staffs a.1 general protocol 1. rewrite the sheet music using c major notation. an attempt might be made to pitch invert a song directly in the key its written in (sheet music notation) by following the instructions given under section a.3. but this will lead to unwanted complexity for those notes that come with accidentals. therefore, its better to rewrite the sheet music into the key of c major (or a minor). music note editors may provide this operation as part of software, and a transposition of notes is also needed to minimize the creation of accidentals when going into c major. those required transpositions are presented in section a.2. 2. identify and separate out all the staffs, and transpose all the notes down making bass clefs. songs come with multiple staffs, and these will all have to be treated separately. in addition to the staffs that are explicitly represented with the sheet music, it is sometimes recommended to break a staff into sub-staffs when notes are found running over a few octave levels. these sub-staffs can all be inverted separately (jumping ahead to step 3), and brought back together after inversion by resetting them on preferred octave levels (jumping ahead to step 4) and this need not mimic pitch inversion of the originating staff and had the staff not been broken up. this lets the composer stir the process better based dna decipher journal | july 2020 | volume 10 | issue 1 | pp 14-25 smith, s. p., pitch inverted songs as affirmation of panpsychism based on a theoretical mirror universe issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 23 on preference rather than being locked into an automatic protocol. more generally, all the notes and staffs (and possible sub-staffs) will be in the key c major, where the note d is the reflective center as found in section a.3. the note d is right in the center of the bass clef, running longitudinally down the middle, making an ideal platform to pitch invert by hand. therefore, its preferable to transpose all staffs down by octave steps and express them as bass clefs. 3. pitch invert all the staffs around the note d that‟s in the middle of each bass clef. the precise instructions for pitch inversion are given in section a.3, with reference to music in the key of c major notation. however, it is now very easy to see pitch inversion in figure 2. figure 2. showing two staffs in c major notation, where the top staff is the pitch inversion of the bottom staff, and visa versa. the note d that serves as the center note, is indicated by the red line that runs through the middle of each staff. the notes are flipped around the red line making the pitch inversion. sharps are turned into flats, and flats into sharps, and the natural accidental is carried without adjustment. 4. transpose up and re-express the preferred key. transpose all the pitch-inverted staffs up by octave steps to reestablish treble clefs, perhaps leaving only one bass clef for the piano. by following section a.2, its also possible to change the music key (for all the staffs) into something other than c major, noting the further transpositions in table 2 that may be preferred. one uses preference to determine the octave levels for each staff, and the overall key for all staffs, and this is different than using a single center note across all staffs where a literal pitch inversion is found unnecessarily restricted. the recommended inversion described here provides for multiple center notes 3 that permit a harmonious union over all the staffs. a.2 instructions for changing sheet music notation rewrite the notation into the new notation; either c major or one of the other keys if starting from c major. this may introduce many accidentals. then transpose the notes up or down the prescribed steps as given by table 2. the transposition will remove all of the newly introduced accidentals. 3. that‟s suitable for the key. as an example, the note d can be found in several places and is suitable for the key of c major. dna decipher journal | july 2020 | volume 10 | issue 1 | pp 14-25 smith, s. p., pitch inverted songs as affirmation of panpsychism based on a theoretical mirror universe issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 24 table 2. transposition steps needed to change sheet music notation from a given key into c major (or a minor), or from c major into the key. transposition steps #‟s → c major ♭‟s → c major key in sharps c major → ♭‟s c major → #‟s key in flats # -7 or +5 +7 or -5 ♭ # # -2 or +10 +2 or -10 ♭♭ # # # -9 or +3 +9 or -3 ♭♭♭ # # # # -4 or +8 +4 or -8 ♭♭♭♭ # # # # # -11 or +1 +11 or -1 ♭♭♭♭♭ # # # # # # -6 or +6 +6 or -6 ♭♭♭♭♭♭ # # # # # # # -1 or +11 +1 or -11 ♭♭♭♭♭♭♭ a.3 instructions for manual pitch reflection of musical notes identify the key that the music is written in, thus finding the note representing the reflective center in table 3. locate one note position on the staff corresponding to the reflective center, selecting from suitable choices merely by preference. reflect all the notes in a measure around the reflective center, as if this center note represents a mirror going down the length of the measure. notes that happen to equal the reflective center are left unreflected. special treatment is given to notes that may rarely come with accidentals. first observe that if sharps (#) always increased the impacted note by one semitone, and if flats (♭) always decreased the impacted note by one semitone, and if the natural accidental (♮) always reset the impacted note to the default for the selected key, then pitch reflection would be an easy extension. however, these conditions are only satisfied for c major (or a minor) notation. these conditions are not stickily enforced for the other keys, a fact that is sometimes missing off introductory accounts of sheet music notation pertaining to accidentals. fortunately, table 2 permits a transformation of music into c major that‟s followed by the specified transposition to minimize accidentals, and this transformation can be made for music written in any of the keys. its in c major that pitch inversion is made following these straightforward instructions: first, it is recommended simplifying the notation by removing multiple expressions of enharmonic equivalence, so that each note inside one measure is represented only by one of the variants that come as the natural accidental (♮), sharp (#), flat (♭), or an adjacent scale note, making sure any ties are correctly indicated; accidentals are reflected like regular notes, but in the reflection show a flat if starting from a sharp, or show a sharp if starting from a flat, or show a natural accidental if starting from a natural accidental; ties are transferred automatically. this pitch reflection is made around a central note d that is well positioned in the staff. once this is completed for all the measures, the entire staff can be transposed up or down one octave to improve appearance. table 2 is also used to return the reflected notes back into the originating notation or key. table 3. center note that permits pitch reflection while maintaining the notation (without the need of accidentals) dna decipher journal | july 2020 | volume 10 | issue 1 | pp 14-25 smith, s. p., pitch inverted songs as affirmation of panpsychism based on a theoretical mirror universe issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 25 within a key. key sheet music notation reflective center c major or a minor default d g major or e minor # a d major or b minor 2 #‟s e a major or f# minor 3 #‟s b e major or c# minor 4 #‟s f b major of g# minor 5 #‟s c f# major or d# minor 6 #‟s g c# major or a# minor 7 #‟s c f major or d minor b g bb major or g minor 2 b‟s c eb major or c minor 3 b‟s f ab major or f minor 4 b‟s b db major or bb minor 5 b‟s e gb major or eb minor 6 b‟s a cb major or ab minor 7 b‟s e references forte, a., 1977, the structure of atonal music, yale university press. langan, c., 2017, an introduction to mathematical metaphysics, cosmos and history: the journal of natural and social philosophy, 13 (2), 313-330. skrbina, d., 2017, panpsychism in the west, 2 nd edition, the mit press. smith, s.p., 2008, trinity: the scientific basis of vitalism and transcendentalism, i-universe, inc. smith, s.p., 2018, time, life & the emotive source, journal of consciousness exploration & research, 9 (8), 707-721. smith, s.p., 2019, a possible holarchy representing morphic resonance as one side of the poised realm, journal of consciousness exploration & research, 10 (5), 371-379. dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 158-181 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 158 article the resplendence codex: reflowering apocalypse in the tree of life (part i) chris king * abstract this article was written in response to a life-and-death wake-up call, in which i realized i needed urgently to write down before it was too late and the threads became scattered and lost. resplendence is an innovative concept and nascent social movement, complementing science and transcending religion, with the wisdom of conscious insight and motivation, to reflower the planet as a living paradise, abundantly resilient over evolutionary time, and ultimately, to reach to the stars. part i of this four-part article includes: 1. the dilemma and healing of apocalypse; 2. planetary apocalypse now; 3. the deeper origins of apocalypse; 4. apocalypse in judaism, christianity and islam; and 5. paradoxes of parousia. keywords: resplendence, apocalypse, evolution, science, religion, reflowering, tree of life. 1. the dilemma and healing of apocalypse this work is a "rosetta stone", to unveil the entire phenomenon of apocalypse, so we can finally come to terms with it, in a reckoning that includes both the tortured religious history and the complex cosmological and biological science our world-view now encompasses. although it is daunting in its complexity, it has an outcome that is so world-transforming towards resplendent paradise on earth, that there is no other work in existence that can have such bounteous potential. the reader needs to have patience and persistence to seek to unfold its full ramifications, for it is the resplendence codex, reflowering the immortal tree of life. an apocalypse (ἀποκάλυψις apokálypsis, from ἀπό and καλύπτω meaning "uncovering" or more directly "unveiling"), translated literally from greek, is a disclosure of knowledge, i.e., a lifting of the veil, or revelation. in religious contexts it is usually a disclosure of something hidden. above: dimensions of planetary apocalypse. the 58 megaton tsar bomba equaling over 3800 hiroshima bombs and amazon deforestation by fire. below left: in nov 2015 russia revealed plans for a 100 megaton nuclear torpedo designed to cause a 500m tsunami, probably "salted" to form cobalt-60 emitting intense gamma radiation with a half-life of 5.27 years to kill everyone within 1500 km. the document was shown at a meeting where putin warned that "russia will take necessary retaliatory measures to strengthen the potential of our strategic nuclear forces". even as a defensive strategy, or merely cold war rhetoric, this is apocalyptic thinking. the world * correspondence: chris king http://resplendence.org e-mail: dhushara@gmail.com http://dhushara.com/book/sakina/fatwah/purdah.htm http://dhushara.com/book/sakina/fatwah/purdah.htm dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 158-181 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 159 is still at 15 times nuclear overkill, risking accidental holocaust. habitat destruction goes on unabated, precipitating the sixth great mass extinction of biological and genetic diversity in the history of earth. below right: amazon deforestation in brazil as of 2006 (nature). we are living in a world in which human impact on the living habitats and climate of the planet on a vast scale is becoming ever more severe, taking us towards a tipping point that could both threaten our long-term survival as a species and will certainly cause a mass extinction of the diversity of life. at the same time as the covers have well and truly been thrown off reality by the scientific and technological revolution that is sweeping the planet, religious forces with an avowed agenda of world domination are fomenting violence in the name of the one true god. in the name of islam, believers are committing genocide, mass beheadings, sexual slavery, and other inhuman actions taking us right back to the tribal law of the seventh century, while innocent people are being blown apart by islamic 'martyrs' in the vain hope of seeing the face of al-llah in paradise, with 72 black-eyed virgins at one's beck and call. in the christian sphere, in slavish adherence to the sabbatical creation, people continue to deny the natural evolution of life in anticipation of a "late planet earth" rapture in the heavens. amid this turmoil, we still have the insecurity of enough nuclear weapons of mass destruction to devastate the planet, should they become unleashed. whether we are religious and believe in a day of judgment, or are simply people trying to look to a sustainable world, where our offspring and those of society around us can have the confidence to survive, we have to acknowledge that we are living in a very troubled world, where the future remains uncertain and where potential violence and tumult burgeon. we thus need urgently to come to terms with why we are living in this state, in a world which would otherwise be capable of sustaining a perpetual paradise, how we got ourselves into this dire situation, and how to find the way through to a soft-landing outcome that does protect the generations of life from the tumultuous threats that humanity has wrought upon the world. the word apocalypse is both a beacon and a plague to the human consciousness. it is our destination in the final awakening in the end of days and it is the feverish fantasy that leads http://dhushara.com/biocrisis/biocrisis.htm http://dhushara.com/biocrisis/biocrisis.htm http://dhushara.com/fallacies/fallacies.htm http://dhushara.com/book/explod/explod.htm dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 158-181 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 160 countless people to commit violence and genocide in the name of the rule of god, from the muslim caliphate to the heavenly jerusalem, with the jewish mashiach, the parousia of the second coming of christ and the mahdi of the shi'ities playing the role of healing, or avenging, hero in the piece. we can love it and hate it. we can try to ignore it, but it keeps creeping up on us as a fascinating and terrifying vision, no matter how much, in the interests of common sense, protecting the sanctity of life, we try to set it aside, . so here follows a key unravelling to come to terms with it, to understand its roots in our existential condition and to discover how we can turn the tide of misfortune and the tumult of genocide into a new epoch of paradise under the banner of the tree of life. for all the negativities of gloom and doom the tumult of apocalypse entails there is a golden lining in the covers being thrown off reality in a win-win for the ongoing survival and flourishing of life and consciousness in resplendent abundance. 2. planetary apocalypse now apocalypse is only now coming to a high noon out of a wider, deeper backdrop in our existential condition over the last two thousand years, and extending into the next century. it is an expression of a sense of future-shock, of political domination by corrupt world powers, of military turbulence and genocide on a vast planetary scale. it is dealing to currents deep in our collective subconscious that we have brought about an epoch of tumultuous change in which the future looks like coming to a 'high noon' in which everything will be revealed in a final reckoning. a hard planetary landing. four global scenarios requiring urgent long-term solutions: (1) predicted world average july temperatures, indicating loss of crop production due to temperature and rainfall changes (nasa). (2) biodiversity zones surviving four different global warming scenarios (groombridge 1992 global biodiversity). (3) loss of land area in a 6m sea level rise (wikipedia). because of the long response time, it has been estimated that we are already committed to a sea-level rise of around 2.3m for each degree of temperature rise within the next http://dhushara.com/apoc/apocalypse_files/image003.jpg dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 158-181 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 161 2,000 years. a temperature rise of 3 degrees would lead to a 6.9m rise, but up to 50m if the antarctic ice sheets melted from below. (4) world gross national income per capita shows spread of world poverty and affluence. in many ways this has been a burgeoning reality ever since the agricultural revolution. it was certainly the case around the time revelation was written, when it is said that over a million people died in the siege of jerusalem in a world whose population was only around fifty million. jesus was aware of this and events shortly after his death led to a holocaust, resulting in the jewish diaspora, so it is very understandable that perspectives took an apocalyptic turn. but today we are facing a much huger planetary apocalyptic crisis, potentially eclipsing the whole of earth's cosmic history, in which we have gained the powers to effectively destroy much of life on earth and ourselves through nuclear holocaust and are having irreversible impacts which are leading to tipping points, in the climate, ocean levels, precipitating a mass extinction of biological and genetic diversity, diminishing our own survival prospects as a species in the process. as a marker in the sand of misadventure, a 2016 research report shows the rate of carbon emission is an order of magnitude higher than the last mass extinction event the petm some 56 million years ago, so the changes we are inducing go back not just to the origin of major religions some 4000 years ago, or human culture some 40,000 years ago, or the human species some 200,000 years ago, but a span of at least 50 million years to early in the mammalian radiation before the monkeys differentiated from the lemurs. this is hardly surprising since, in a century or two, we are releasing into the atmosphere much of the carbon in coal dating back to the carboniferous 300 million years ago and a good half of the oil accumulated from the ordovician 450 million years ago on through the permian to the demise of the dinosaurs. the image below shows a hard landing mass-extinction, which could threaten human survival, would set the world back on cosmological time scales. comparison of the evolution of the universe from the big bang and the evolution of life on earth shows that life has existed for a quarter of the universe's lifetime and can thus be considered a http://dhushara.com/book/explod/explod.htm http://dhushara.com/biocrisis/biocrisis.htm http://dhushara.com/biocrisis/16/mar/petm.pdf dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 158-181 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 162 long-term stable feature of cosmic evolution. astronomical events including impacts and nearby supernovae have always played a major role in causing mass extinctions accompanied by volcanism possibly as a secondary consequence of the impacts themselves. however the advent of so-called human civilization is threatening in the next century to cause a mass extinction more serious than the cretaceous-tertiary event that wiped out the dinosaurs. apocalypse is a motif in every person's existential consciousness in the sense that we seek to understand the ultimate mystery of existence and come face to face with it before we pass away into oblivion. this is a fundamental theme of eastern religion, which places its emphasis on an individual attaining enlightenment, in union with the cosmic self, albeit with varying degrees of moral responsibility for the welfare and enlightenment of all sentient beings, in the greater mahayana. the 'unveiling' of reality is also absolutely central to the scientific revolution. as we have progressed from the first wave of greek science through to the renaissance and the flowering of the western scientific tradition, the covers have well and truly been thrown off reality, from end to end of the description of nature, confounding all our preconceived notions and religious doctrines, from the flat earth and the centre of the cosmos, to the existence of the human ovum. we now have a model of the universe from the putative theories of everything through the standard model of particle physics, to molecular dynamics, biogenesis, and with the human genome project, the decoding of human genetic evolution and that of a rich diversity of our sister species, rendering the naïve endearingly quaint notion of the sabbatical creation of genesis 1 no more than a beautiful impossible poetic fantasy, where the plants are created before the sun and moon. nevertheless the grip of affirmative religion clings to the scriptures like a drowning man clings to life flashing before one's eyes, right up to the moment of death in the final tumultuous apocalyptic expose. we still find christians and muslims alike rationalizing that the revealed scripture is somehow truer than physical reality itself, that we are all destined for the day of judgment and that evolution is just some kind of corrupt sleight-of-hand invented by atheistic humanists to undermine our faith in the one true god. this again affirms to us that apocalypse is not just a figment of religious doctrine, but a deep current in our existential consciousness induced by the paradox of subjective existence in a biological body in a culture in a continual state of flux towards an endpoint, which has throughout been one of crisis on a grand scale. with our own generation "apocalypse now" has become an even more potent planetary reality. at their climax during the cold war nuclear weapons of mass destruction rose to 40 times overkill, with arsenals poised to a hair trigger. we have an exponentiating world population which is consuming vast areas of the planet's natural habitable systems for human production, causing the depletion of non-renewable resources such as oil which have taken hundreds of millions of years to accumulate, irreversible mass extinction of genetic and biological diversity and climate change which could submerge major areas of the planet and lead ultimately to a 50 metre ocean rise with the under-melting of the antarctica and greenland ice sheets, as well as catastrophic storms on a scale never previously recorded by humanity. we are thus literally facing planetary apocalypse if we don’t get a grip on our own folly and the impacts of businessas-usual on the planetary future. dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 158-181 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 163 into the middle of this toxic mix, we find that apocalyptic religions, and particularly islam, and its divided camps, are entering ever more feverishly into an end of days struggle, in which the entire middle east is now enmeshed in a religious war between sunni and shi'ite elements, amid calls from either side to the apocalyptic final solution in martyrdom and effective genocide driven by religious scripture. both of these have end of days assumptions, with shi'ites anticipating the return of the mahdi the figure of the end of days who jesus is believed to accompany to the ka'aba in the final judgment and the caliphate of islamic state which seeks to return the world to a totalitarian monolith of seventh century arabia, in which all who are perceived to have different views are taken into sexual slavery or summarily beheaded, or crucified, and minorities of other beliefs are committed to genocide, in the shadow of muhammad's own genocide of 700 jewish men in medina. again one can see this in even deeper time as an evolutionary phenomenon of humans developing language and culture over tens of thousands of years as gatherer-hunters, only to explode as we left africa and migrated to every "corner" of the globe. the culture of agricultural civilization then set the paradigm for reproductive expansion amid the rise and clash of cultures, amid genocidal wars of ascendency, accompanied by instances of natural disaster from flood and famine and the growth of epidemic plagues caused by human mobility and the density and marginal living conditions of urban populations. this became incorporated in turn into the religious dialogue as cultures sought more convincing and more universally cohesive ways of giving expression to moral and physical dystopia with a utopian expectation. apocalypse is in many ways a global archetype of the vision quest to find transformative meaning in an existence caught in the mortal coil, where there seems no alternative to the eventual decay of time and age and no respite from the ultimate fate of death we all face. the one way we could perhaps 'turn the tables' on reality is to discover the visionary roots of existence and convey it back to our fellow beings in a redemption of existence that includes us all in the fabric of meaning through love and the fertility of life itself. perhaps all conscious organisms in the universe experience the apocalyptic condition and the messiah is simply an archetype of the discovery process any one of us could take to the absolute limit and return illuminated with the wisdom to weave the threads of existence into a coherent bundle of life. 3. the deeper origins of apocalypse we are all conscious sentient beings and have a huge amount of trouble coming to terms with what the relationship is between our conscious experience, our biological mortality in the natural world around us, and the mystery of being itself, which remains enigmatic, even in the scientific era. belief in transcendent deities and spirits is an evolutionary feature of human consciousness that has existed for tens to hundreds of thousands of years. fulton cave drawing 1000 bc celebrating a san girl's menarche, drakensberg mountains, natal (van der post). dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 158-181 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 164 one of our oldest founding cultures, the san bushmen, whose genetic history dates back 130,000 years, have a creator deity, a lesser god of misfortune and notions of the afterlife not dissimilar from those in major world religions, although they regard these gods philosophically rather than in fear and supplication: ≠gao!na, the !kung great god, using one of his seven divine names, created himself: "i am hishe. i am unknown, a stranger. no one can command me. i am a 'bad' thing. i follow my own path." then ≠gao!na created a lesser god who lives in the western sky where the sun sets; and after this two wives for himself and for the lesser god. ≠gao!na, tallest of the bushmen, was in his earthly existence a great magician and trickster with supernatural powers, capable of assuming the form of an animal, a stone or anything else he wished, and who changed people into animals and brought the dead back to life. but as the great god who lives beside a huge tree in the eastern sky, he is the source and custodian of all things. he created the earth with holes in it where water could collect and water, the sky and rain both the gentle 'female' rain and the fierce 'male' rain thunder and lightning, the sun, moon, stars and wind. he created all the plants that grow on the earth. he created the animals and painted their individual colours and markings, and gave them all names. then came human beings, and he put life into them; and gave to them all the weapons and implements they now have, and he implanted in them the knowledge of how to take all these things for themselves. thus their hunting and gathering way of life was ordained from the very beginning and ≠gao!na ordained that when they died they should become spirits, //gerais, who would live in the sky with him and serve him. he set the pattern of life for all things, each in accordance with its own rules. http://dhushara.com/paradoxhtm/culture.htm#anchor-24819 dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 158-181 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 165 but the idea of apocalypse ultimately stems from the beginnings of agricultural civilization, as we emerged from the gatherer-hunter 'paradise', in the fall into the tumult of future shock, with ever more cycles of facing grim reality, as one civilization after another struggled for dominance. in a sense it is woven into our existential condition. a key feature of the apocalyptic epoch is the fact that the entire period has been one of patriarchal domination, in which woman was cursed and social patterns involving the matriarchy and female reproductive choice were violently repressed. we can see in the fall from eden the very origins of apocalypse in adam and eve being thrown out into a world of diaspora by the sweat of their labours, in an ongoing contratemps with god, evoking a dysphoric epoch lasting throughout biblical history. the shekhinah of jewish mythology, representing the indwelling feminine face of god's presence on earth in matrimonial concord, was said to have retreated in the fall, only to return in shards, or 'sparks', which will reunite in the end of days. although in genesis 1 woman and man are conceived in the likeness of the 'elohim god in the sexually dyadic plural, in eden, yahweh (jehovah) is now a lone (male) god, and eve is now blamed for parleying with the serpent and persuading adam to eat with her the fruit of the tree of knowledge of good and evil, becoming sexually shy, covering themselves with fig leaves, only to be cast out of eden with a flaming sword by god, for man to live by the sweat of his brow among thorns and thistles and woman to suffer the pain and travail of childbirth, to be ruled over by her husband and both to go as dust to dust and ashes to ashes in the round of mortal existence. woman is thus cast as the "devil's gateway" in the christian tradition, along with all the symbols of female reproductive choice as personified in the great whore of babylon ‚äì inanna-ishtar. woman is cast in christianity as the devil's gateway, cursed for her own desire to have reproductive choice and the sexual and sensual responses to enable her do so. here the world is divided between the frigidity of obedient female virtue and the heated lust of the cursed scarlet sinner. this current of patriarchy opposed to matriarchal traditions is also spelt out in the pentateuch, where jacob, the founder of the twelve tribes of israel spends seven years with the matriarchal family of laban for each of rachel and leah, before departing with his wives and cattle to found a patriarchal dynasty, with rachel hiding the teraphim, or house gods of laban's family, under her menstrual skirts, in a telling portrayal of the women conceding to be complicit in the transition to patriarchy. this is followed by a severe warning in judges, that matrilineal patterns were to be violently overthrown by a zealous patriliny. the concubine of bethlehem-judah is accused of 'whoring' by going back to live with her father-in-law for four months. when the levite returns to claim her, http://dhushara.com/paradoxhtm/fall.htm http://dhushara.com/paradoxhtm/jealous.htm#anchor-trouble-21683 http://dhushara.com/paradoxhtm/fall.htm#anchor-38219 http://dhushara.com/paradoxhtm/fall.htm#anchor-38219 http://dhushara.com/paradoxhtm/jealous.htm#anchor-there-49575 http://dhushara.com/apoc/apocalypse_files/pros.jpg dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 158-181 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 166 the father-in-law keeps saying to stay a little longer. when the couple leave and turn in at gibeath, and men of belial ask to 'know the man within', the levite offers his concubine, who is raped and dies on the doorstep. above: the hieros gamos from 10,000 bc through catal huyuk 7500 bc to inanna and dumuzi in sumeria 2500 bc represents conjugal fertility. middle: bottleneck in human ychromosome from 10,000 years ago with the spread of urban agricultural civilizations resulted from an ongoing sex ratio of 1 reproducing man for every 17 women the extreme polygyny of male elite power with a few high status males controlling female reproductive choice (doi:10.1101/gr.186684.114). below: the law codes of sumerian enmetena/urukagina, babylonian hammurabi and the assyrians each contain provisions for the repression of female power and reproductive choice. the first said "women speaking out of turn could have their teeth smashed by a brick", the second introduced the death penalty for adultery, and the third enforced veiling for women as well as far more violent punishments than the babylonians. to understand the extreme degree to which reproductive patriarchal dominance occurred across widespread cultures of the planet, from 10,000 years ago to the biblical era (fielder and king), we only need to turn to emerging genetic research from 2015. throughout human evolutionary emergence over the last hundred thousand years, some men have had two reproductive partners while others have had none, while every fertile woman can become pregnant leading to a reproductive sex ratio the number of reproducing females for each reproducing male of two. with the rise of agriculture this ratio rose to seventeen women for each reproducing man, due to the men with power and assets commandeering all the reproductive opportunities through extreme polygyny, supported by subject male military power. the fact that this is observed across a sample of the entire human genome from all continents shows patriarchal dominance became an extreme phenomenon and that monogamy, is a modern invention, although it has operated in mutual mate-choice between couples throughout human emergence, to provide protection and resources for pregnancy and enable human children to reach an age where they http://dhushara.com/paradoxhtm/fall.htm#anchor-hieros-59125 http://dhushara.com/paradoxhtm/fall.htm#anchor-diminishing-44867 http://dhushara.com/paradoxhtm/contents.htm http://dhushara.com/apoc/apocalypse_files/image007.jpg dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 158-181 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 167 can converse and fend for themselves in an extended family, or village community, around the age of four to five, as is increasingly becoming the case with serial monogamy. the entire apocalyptic paradigm has thus been distorted by motifs of male paternity uncertainty, made explicit in law codes from sumerian enmetena and urukagina, where women speaking out of turn were to have their teeth smashed out with a brick, through babylonian hammurabi to the assyrians, who both veiled their women and allowed all manner of oppression and violence to occur, leading to patriarchal religious traditions invoking the violent repression of female reproductive choice, including stoning in ancient deuteronomic and continuing islamic practice, to the subordination, sequestering and enforced veiling of women. it has also led to a highly imbalanced religious cosmology, in which male anxiety about mortality through not giving live birth to the continuity of life, has led to the condemnation of nature, the quest for eternal life, increasingly violent notions of moral punishment, and the notion of cosmological war between dark and light in the manner of a male reproductive contest, central to apocalyptic tumult. throughout the old testament, yahweh is described as a jealous god, jealous of the whoring of the bride israel, through the worship of other deities, casting the theme of paternity uncertainty into cosmological proportions. the whole phenomenon of apocalyptic tumult, from the pangs of the messiah to the return of the mahdi in the day of judgment, is thus a distorted product of the male sense of mortality and the endless conflict of male dominant societies upon one another in genocidal war and the rumours of war. marduk as civic order, battles the underworld chaos of the old mother goddess tiamat. joseph campbell in his works on mytho-poetry and comparative religion has expanded the horizon of founding themes shared by major religions into the diverse cultures that preceded them and subtended the collective doctrines they established. thus we can see precursors of figures such as jesus in the heroic quests of many earlier culture heroes and demi-gods, from tammuz, through adonis and dionysus to melkarth and the struggle of marduk with tiamat as an archetype of the war of dark and light. these comparisons are grounded in universals of the human condition awakening a sense of awe before the mystery of being, explaining the nature of the universe and world around us, validating and supporting the existing social order and guiding the individual through the stages of life. as religions evolved with the cultures that sustained them, a transition occurred from civic deities that stood fairly transparently for the national order, or agricultural deities related to the power of the weather and seasons to more abstract notions of a god acting in history, which wasn't simply represented in iconic form as statues or carvings, which ultimately became cursed http://dhushara.com/paradoxhtm/vale.htm http://dhushara.com/book/sakina/fatwah/purdah.htm http://dhushara.com/apoc/apocalypse_files/image009.jpg dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 158-181 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 168 as idolatry. ironically, christian and particularly catholic churches, display the most ornate iconography one could imagine. however idolatry was superseded by bibliolatry, which has plagued the three abrahamic religions ever since, so that today fundamentalists commit grievous crimes against humanity on the basis of ancient revealed scripture. ironically the old deities of founding cultures like the san already possessed many of the abstract features, augmented by later major world religions developing a form of transcendent 'protection racket' in which a punishing moral deity, who can see right into your very soul, but remains elusively invisible succeeds in frightening the faithful into more moral forms of behaviour that reduce intra-social strife and strengthen inter-social dominance. thus the principal power and sheer population size of major world religions stems not form transcendental insight but fearsome moral and frequently physical punishment. the christian view of history is an epoch of sinful rebellion against god, extending like a great bow across time, with the fall from eden at one end, and apocalypse in the end of days at the other. in the centre is jesus – the arrow of violence in the great bow, hanging from the cross and believed to return in power as the avenging lord of the second coming. although revelation portrays a tumult of genocide and the triage of all life, and the "rapture" of paul paints a picture of leaving the debased nature of the late planet earth for celestial space, the tree of life stands at both ends, protected in the garden of eden and entwined around the seat of god and the lamb in revelation. the apocalypse of revelation is also a bridal unveiling in a sacred marriage, in which the bride of the lamb is the heavenly jerusalem, just as israel was the whoring bride of jehovah, and as the song of songs is the mystical holy of holies of the same sacred marriage, more like the metaphorical complementarity of body and soul than a fertile sexual reunion of female and male. 4. apocalypse in judaism, christianity and islam judaism, christianity and islam all share to varying degrees the apocalyptic vision and sense of prophecy in terms of the day of judgment, promulgated by zoroaster in terms of the victory of ahura mazda light and wisdom over angra mainyu the source of ignorance and confusion. all of these three have adopted the central elements of zoroaster's cosmology of renovation, taking it for their own in claiming to be the one true religion of god and, in the cases of christianity and islam, turning into more inexorable forms of punishment without redemption. http://dhushara.com/fallacies/fallacies.htm#anchor-35882 http://dhushara.com/apoc/apocalypse_files/image011.jpg dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 158-181 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 169 apocalypticism arose gradually in hebrew history as a consequence of the cross-transference of ideas. the underworld of the dead of sheol, which we can still see in passages of the old testament, gave way to a heaven and hell and with the exile into babylon and then the takeover by cyrus the mede, who is regarded as a messiah anointed for his support of the jews' return to the 'holy land': thus said the lord to his anointed, to cyrus, whose right hand i have held, to subdue nations before him; and i will loose the loins of kings, to open before him the two leaved gates; and the gates shall not be shut (isaiah 45:5) the notion of the zoroastrian renovation became absorbed into jewish apocalypticism in works like the book of enoch and then into christian eschatology as well, culminating in the book of revelation. enoch's "apocalypse of weeks" (c 170bc) sets out such a world history with the future climax in the seventh part of the tenth week, but far less gratuitously violent than revelation: and after this, in the tenth week in the seventh part, there shall be the great eternal judgement, in which he will execute vengeance amongst the angels. and the first heaven shall depart and pass away, and a new heaven shall appear, and all the powers of the heavens shall give sevenfold light. and after that there will be many weeks without number for ever, and all shall be in goodness and righteousness, and sin shall no more be mentioned for ever. according to jewish tradition, the messianic era will be one of global harmony, a future era of universal peace and brotherhood on earth, and one conducive to the furtherment of the knowledge of god. although judaism concentrates on the importance of the earthly world, all of classical judaism posits an afterlife the "world to come", עולם eht ,nede nag ot detaler ,הבא heavenly garden of eden, and gehenna its dark opposite. according to religious judaism, any non-jew who lives according to the seven laws of noah is regarded as a righteous gentile, and is assured of a place in the world to come, the final reward of the righteous. resurrection of the dead, fresco from the dura-europos synagogue dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 158-181 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 170 in judaism, beliefs vary about a last day of judgment for all mankind. some rabbis hold that there will be such a day following the resurrection of the dead. others hold that this accounting and judgment happens when one dies. still others hold that the last judgment only applies to the nations and not the jewish people. in rabbinical literature for example we find the following: the messianic age is when the jews will regain their independence and all return to the land of israel. the messiah will be a very great king, he will achieve great fame, and his reputation among the gentile nations will be even greater than that of king solomon. his great righteousness and the wonders that he will bring about will cause all peoples to make peace with him and all lands to serve him.... nothing will change in the messianic age, however, except that jews will regain their independence. nevertheless zechariah (520-518 bc) does have an apocalyptic climax, anticipating the triages and tumults of revelation in the christian tradition: and it shall come to pass, that in all the land, saith the lord, two parts therein shall be cut off and die; but the third shall be left therein. and i will bring the third part through the fire, and will refine them as silver is refined, and will try them as gold is tried: they shall call on my name, and i will hear them: i will say, it is my people: and they shall say, the lord is my god. … and his feet shall stand in that day upon the mount of olives, which is before jerusalem on the east, and the mount of olives shall cleave in the midst thereof toward the east and toward the west, and there shall be a very great valley; and half of the mountain shall remove toward the north, and half of it toward the south (zech 13-14). christianity, cast in the apocalyptic traditions of john the baptist and the desert essenes, adopted a fully fledged end of days with jesus claiming in the synoptic gospels and john to challenge the devil in a final confrontation, through which he would come to return in power at the right hand of god. the siege of jerusalem, the jewish diaspora and the depravities of the roman emperors subsequently sublimed this picture into a view of world history in which christ would return as the lord and conqueror of evil in the millennium and the day of judgment. despite the failure of this entire concept over two millennia in the absence of the lord's return the spectre of apocalyptic victory remains in tumult and conflict remains integral to christian eschatology. pivotal to our concept of apocalypse is the revelation of john, the culminating chapter of the christian bible. it is the most extraordinary book of eschatological religious vision ever written. it is literally bursting with tumultuous battles and cataclysms, from the beasts of belial, to the avenging lord, amid tumult and destruction, resulting in the triage of all life and impossibly a triage of the sun, moon and stars: the first angel sounded, and there followed hail and fire mingled with blood, and they were cast upon the earth: and the third part of trees was burnt up, and all green grass was burnt up and the second angel sounded, and as it were a great mountain burning with fire was cast into the sea: and the third part of the creatures which were in the sea, and had life, died; and the third part of the ships were destroyed. … and the fourth angel sounded, and the third part of the sun was smitten, and the third part of the moon, and the third part of the stars; so as the third part of them was darkened, and the day shone not for a third part of it, and the night likewise. (rev 8). dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 158-181 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 171 and the four angels were loosed, which were prepared for an hour, and a day, and a month, and a year, for to slay the third part of men. by these three was the third part of men killed, by the fire, and by the smoke, and by the brimstone, which issued out of their mouths (rev 9). later we see the pregnant woman clothed with the sun standing on the moon, who is an apotheosis of the queen of heaven, inanna-ishtar but also identified by christians with mary. her boy-child, the warlord-to-come, is attacked by a dragon, and taken up to god, precipitating the war in heaven: and there appeared a great wonder in heaven; a woman clothed with the sun, and the moon under her feet, and upon her head a crown of twelve stars: and she being with child cried, travailing in birth, and pained to be delivered. and there appeared another wonder in heaven; and behold a great red dragon, having seven heads and ten horns, and seven crowns upon his heads. and his tail drew the third part of the stars of heaven, and did cast them to the earth: and the dragon stood before the woman which was ready to be delivered, for to devour her child as soon as it was born. and she brought forth a man child, who was to rule all nations with a rod of iron: and her child was caught up unto god, and to his throne (rev 12). the woman clothed with the sun and the dragon (william blake). on the other side of the cosmic battle we find the great whore of babylon, the dark manifestation of the same inanna-ishtar goddess figure: i saw a woman sit upon a scarlet coloured beast, full of names of blasphemy, having seven heads and ten horns. and the woman was arrayed in purple and scarlet colour, and decked with gold and precious stones and pearls, having a golden cup in her hand full of abominations and filthiness of her fornication: and upon her forehead was a name written, "mystery, babylon the great, the mother of harlots and abominations of the earth". and i saw the woman drunken with the blood of the saints, and with the blood of the martyrs of jesus: and when i saw her, i wondered with great admiration (rev 17). http://dhushara.com/apoc/apocalypse_files/image015.jpg dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 158-181 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 172 the cosmic christ appears as an utterly feudal dictator-lord of mass destruction: and i saw heaven opened, and behold a white horse; and he that sat upon him was called faithful and true, and in righteousness he doth judge and make war. his eyes were as a flame of fire, and on his head were many crowns; and he had a name written, that no man knew, but he himself. and he was clothed with a vesture dipped in blood: and his name is called the word of god. and the armies which were in heaven followed him upon white horses, clothed in fine linen, white and clean. and out of his mouth goeth a sharp sword, that with it he should smite the nations: and he shall rule them with a rod of iron: and he treadeth the winepress of the fierceness and wrath of almighty god (rev 19). unmitigated death and destruction is cast on the unbelievers: and i saw an angel standing in the sun; and he cried with a loud voice, saying to all the fowls that fly in the midst of heaven, come and gather yourselves together unto the supper of the great god; that ye may eat the flesh of kings, and the flesh of captains, and the flesh of mighty men, and the flesh of horses, and of them that sit on them, and the flesh of all men, both free and bond, both small and great. … and the beast was taken, and with him the false prophet that wrought miracles before him, with which he deceived them that had received the mark of the beast, and them that worshipped his image. these both were cast alive into a lake of fire burning with brimstone. … and the remnant were slain with the sword of him that sat upon the horse, which sword proceeded out of his mouth: and all the fowls were filled with their flesh (rev 19). as gratuitous violence, revelation reigns supreme, but as a model for planetary apocalypse, it is profoundly dangerous, deceptive and misleading an unmitigated disaster. yet it contains two pivotal elements – the tree of life entwined around the throne of the lamb, giving its twelve monthly fruit for the healing of the nations – and the notion of the sacred marriage, or hieros gamos. however the sacred marriage here is not that of the true fertility between woman and man that generates the passage of the living generations, but in the corrupted form of the lamb and the heavenly jerusalem, christ and his church, falling in the shadow of the dysfunctional marital relationship of jehovah and the whoring bride israel, whose ultimate holy of holies is sequestered in the metaphor of unrequited love in the song of songs: let us be glad and rejoice, and give honour to him: for the marriage of the lamb is come, and his wife hath made herself ready (rev 19). and i john saw the holy city, new jerusalem, coming down from god out of heaven, prepared as a bride adorned for her husband. … and there came unto me one of the seven angels … and talked with me, saying, come hither, i will shew thee the bride, the lamb's wife (rev 21). finally we come to the tree of life itself, hidden since the foundation of the world in eden, still beckoning to our living futures: and he shewed me a pure river of water of life, clear as crystal, proceeding out of the throne of god and of the lamb. in the midst of the street of it, and on either side of the river, was there the dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 158-181 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 173 tree of life, which bare twelve manner of fruits, and yielded her fruit every month: and the leaves of the tree were for the healing of the nations (rev 21). the feeling of the covers being thrown off reality is well-captured by paul of tarsus in 1 corinthians: βλέπομεν γὰρ ἄρτι δι' ἐσόπτρου ἐν αἰνίγματι "for now we see through a glass, darkly." when i was a child, i spake as a child, i understood as a child, i thought as a child: but when i became a man, i put away childish things. for now we see through a glass, darkly; but then face to face: now i know in part; but then shall i know even as also i am known. the implication is that in the current epoch we act like children and cannot see the essential nature of reality, but in the unveiling we will come of age and see reality intimately as it actually is. the zoroastrian and the muslim day of judgment derived from it contain the same motifs, including a razor-thin bridge the human souls have to cross and a welcoming heavenly maiden. although both contain fiery torments, the zoroastrian version has more emphasis on cleansing of ignorance rather than eternal damnation. despite absorbing the prophetic figures of the jewish tradition, from adam, through moses to solomon, and the deuteronomic diabolical punishments of stoning for adultery, discontinued centuries before by the jews, islam has taken up the christian and zoroastrian notions of the day of judgment as a moral punishment cosmology, central to the ideas of violent martyrdom, in which one will see the face of al-llah and be entertained by black eyed virgins made anew every day in paradise: surely those who guard (against evil) are in a secure place, in gardens and springs;  they shall wear of fine and thick silk, (sitting) face to face;  thus (shall it be), and we will wed them with houris pure, beautiful ones (44:51). conscious life is described as a mere shadow of the events on the day of judgment: http://dhushara.com/apoc/apocalypse_files/image017.jpg dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 158-181 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 174 o mankind! have fear of your lord and fear that day when no father shall avail his son nor a son his father. surely the promise of allah is true. let not the life of this world deceive you, nor let the deceiver (satan) deceive you concerning allah. surely allah alone has the knowledge of the hour (31:33). jesus is also a central actor in the day of resurrection: and there is not one of the followers of the book but most certainly believes in this before his death, and on the day of resurrection he (isa) shall be a witness against them (4:159). he (isa) is surely a knowledge of the hour. ... and when isa came with clear arguments he said: i have come to you indeed with wisdom, and that i may make clear to you part of what you differ in (43:61). there are also clear indications of the zoroastrian judgment woven into the quranic account. the chinvat bridge is likewise in the quran, and even more explicitly in the hadith, as the sirat bridge, which is sharper than the edge of sword and thinner than a hair: we will call them to account in the company of all their satans and set them on their knees around the fire of hell; then from every sect. we will certainly drag out its stoutest rebels against the compassionate (allah). certainly we know best who deserves most to be burned therein. there is not a single one of you, who shall not pass over it [the sirat bridge], this absolute decree of your lord is unavoidable; then we will deliver those who were pious and leave the wrongdoers therein humbled on their knees (19:68). in a description reminiscent of revelation, the angel israfil [the burning one] will sound the trumpet and all living creatures, mankind, angels and jinn then living, will die. another blast and all will be raised to life. allah's throne will appear in the clouds, carried by eight angels. believers will receive a book of their deeds in their right hand, and unbelievers their left hand. the books will be opened and men's works weighed on scales (mizan) as in the zoroastrian description. in fear, men will look for someone to plead with allah. they will go to adam, abraham, moses and jesus, but find no help. at last they will turn to muhammad and allah will judge, as in the earthquake: when the earth will be shaken to her utmost convulsion, and the earth shall bring out all her inner burdens, man shall say: "what is happening to her?" on that day she shall report whatever had happened on her, for your lord shall have commanded her to do so. on that day men shall proceed in sorted out groups to be shown their ‘book of deeds.’ then, whoever has done an atom’s weight of good shall see it there, and whoever has done an atom’s weight of evil shall see it there (99:1). the quranic day of resurrection also has signs in the form of an eclipse: "when will this day of resurrection be?" well, it will come when the sight shall be dazed, the moon becomes dark, and the sun and the moon are brought together (75:6). dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 158-181 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 175 consistent with revelation's astronomical triages we witness the splitting of the moon, although this supposed astronomical calamity has little enough effect on the earth for the unbelievers to think it a mere magic trick: the hour drew nigh and the moon did rend asunder. and if they see a miracle they turn aside and say: transient magic. and they call (it) a lie, and follow their low desires (54:1). this is consistent with an archaic view of the heavens in the quran as a firmament with lamps erected on it, as in the original sabbatical creation of genesis 1: blessed is the one who has decked the sky with constellations and placed in it a lamp and a shining moon (25:61). 5. paradoxes of parousia christians remain just as transfixed in their belief of the return of christ, despite the second millennium having passed without any signs of the four horsemen of revelation's apocalypse appearing. this itself is an unbelievable situation, because jesus, according to the gospels, made specific statements that his return would be in the lifetimes of those present during his own life, although he entreated them to be ever ready: jesus said unto them, 'verily i say unto you, that there be some of them that stand here, which shall not taste of death, till they have seen the kingdom of god come with power" (mark 9). and this know, that if the goodman of the house had known what hour the thief would come, he would have watched, and not have suffered his house to be broken through. be ye therefore ready also: for the son of man cometh at an hour when ye think not (luke 12). in luke jesus invokes a full apocalyptic spectacle of the pangs of the messiah, insisting it will come in the same generation: and there shall be signs in the sun, and in the moon, and in the stars; and upon the earth distress of nations, with perplexity; the sea and the waves roaring; men's hearts failing them for fear, and for looking after those things which are coming on the earth: for the powers of heaven shall be shaken. and then shall they see the son of man coming in a cloud with power and great glory. and when these things begin to come to pass, then look up, and lift up your heads; for your redemption draweth nigh. and he spake to them a parable; behold the fig tree, and all the trees; when they now shoot forth, ye see and know of your own selves that summer is now nigh at hand. so likewise ye, when ye see these things come to pass, know ye that the kingdom of god is nigh at hand. verily i say unto you, this generation shall not pass away, till all be fulfilled. heaven and earth shall pass away: but my words shall not pass away. and take heed to yourselves, lest at any time your hearts be overcharged with surfeiting, and drunkenness, and cares of this life, and so that day come upon you unawares. for as a snare shall it come on all them that dwell on the face of the whole earth (luke 21). dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 158-181 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 176 jesus was a unique creative genius who brought together the currents of pharisaic judaism of the time, with the more firebrand end-of-days vision of john the baptist's followers and the qumran community, complementing them with other more feminine elements of nature religion, reaching a cultural climax at the time in neighbouring nabatea, otherwise referred to as edom in the bible. moon and sun deities surmounted by the eagle. al-uzza as moon goddess commands the zodiac surmounted by the moon and carrying a moon staff. the temple of manatu at petra. dionysian tragic mask with dolphins. grape freeze (centre). coinage of aretas iv king of the nabataeans, friend of his people and shaqilat ii in joint reign in the time of jesus (glueck). nature religion motifs abound. jesus was anointed to his sacrificial doom by a woman who is variously claimed to be a sinner, or mary magdalene, out of whom he cast seven devils ‚äì the galla of inanna , whom gnostic tradition claims was also his lover. he was ministered unto by the women "out of their substance". john the baptist was likewise sacrificed in a beheading in a dance of the seven veils an enaction of the descent of inanna after which dumuzi (tammuz in the bible) is sacrificed at the behest of herodias when her daughter salome danced to delight the generals who were defending machaerus at the border, because herod antipas had insulted the nabateans by divorcing the princess of nabatea, who had had to flee in fear of her life. herod had then taken as wife herodias, his cousin and wife of his brother herod ii (philip), as decried by john, precipitating his ritual demise. this theme occurs likewise in the sacrifice of haman in esther (ishtar) in saving mordechai (marduk), having persuaded her husband king ahasuerus to offer 'half his kingdom', just as herod did at machaerus. jesus crying "eloi, eloi, lama sabachthanei" on the cross is likewise a reference to the cry of mot, the canaanite god of the sterile season to his father el, when defeated by ba'al the god of rain and fertility who has now become el's favourite in the spring, aided by anath. jesus adopts a miraculous style of faith healing characteristic of dionysus and his nabatean reincarnation dhushara, whose tragic mask gave the gift of immortal life. jesus' water into wine and nature miracles are classic dionysian fare, as was the carefully staged passion play, with the palm king and turning the tables, leading up to the crucifixion (schonfield). the talmud referred to jesus as "balaam the lame" specifically stating his acts as being in the traditions of edom. his lameness is indirectly acknowledged in his own statement " ye will surely say unto me this proverb, physician, heal thyself" at the synagogue, before he was nearly thrown off the cliffs for blasphemy. when one comes up close to his miraculous acts, they become harder to realize, indicating they thrived on distance and rumour, rather than the harsh light of day: dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 158-181 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 177 'a prophet is not without honour, but in his own country, and among his own kin, and in his own house.' and he could there do no mighty work, save that he laid his hands upon a few sick folk, and healed them. and he marvelled because of their unbelief" (mark 6). his brethren said: 'if thou do these things, shew thyself to the world.' for neither did his brethren believe in him. then jesus said unto them, 'my time is not yet come: but your time is alway ready. (john 7) the same applies to the vision of the disciples crossing genessaret, because it states clearly that they didn't believe in the 'miracle' of dividing the loaves, even though they were present: for they considered not the miracle of the loaves: for their heart was hardened (mark 6). the walking on water is again classic dionysian fare, as the miraculous god of storm and darkness. nevertheless jesus was a genius who presented two conflicting personalities in the gnostic and synoptic versions of his account. the synoptics have him saying "whom do men say that i am?", with peter replying that he is the (anointed) christ messiah: "whom do men say that i am?" and they answered, "john the baptist; but some say, elias; and others, one of the prophets". and he saith unto them, "but whom say ye that i am?" and peter answereth and saith unto him, "thou art the christ" (mark 18). but the gospel of thomas (pagels 2003), which contains several foundation sayings in older form than the synoptics, has jesus say he was not their master: "compare me to someone and tell me whom i am like." simon peter said to him, "you are like a righteous angel." matthew said to him, "you are like a wise philosopher." thomas said to him, "master, my mouth is wholly incapable of saying whom you are like." jesus said, "i am not your master. because you have drunk, you have become intoxicated from the bubbling spring which i have measured out" (thomas 13). likewise his vision of the kingdom in thomas is far from an apocalyptic late planet earth rapture: his disciples said to him, "when will the kingdom come?" jesus said, "it will not come by waiting for it. it will not be a matter of saying 'here it is' or 'there it is'. rather, the kingdom of the father is spread out upon the earth, and men do not see it" (thomas 113). dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 158-181 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 178 if those who lead you say to you, 'see, the kingdom is in the sky,' then the birds of the sky will precede you. if they say to you, 'it is in the sea,' then the fish will precede you. rather, the kingdom is inside of you, and it is outside of you (thomas 3). left: a figure believed to be one of the earliest representations of jesus discovered in 2014 in a buried underground crypt in the ancient egyptian city of oxyrhynchus. right: an oxyrhynchus papyrus of the gospel of thomas. the date of writing of the gospel of didymos judas thomas, is considered to be between 40 and 140 ad, with the core sayings coming earlier than the completed work. thomas didymos, meaning "twin" in aramaic, was considered to be a twin brother of jesus, so his word should hold good. the oxyrhynchus papyri date to between 130 and 250 ad. by comparison, mark was probably written around 66-70 ad, during nero's persecution of the christians in rome or the jewish revolt, as suggested by internal references to war in judea and to persecution, and a fragment found in a mummy is claimed to date before ad 90. luke dates to 80-100 ad and john reached its final form about 90-100 ad. this effectively dates thomas before john because the "doubting thomas" passage is a clear reference to the more firebrand gnostic position of the author of john disputing the more accommodating gnostic sayings of thomas and his following, which were already in circulation: but thomas, one of the twelve, called didymus, was not with them when jesus came… and after eight days again his disciples were within, and thomas with them: [then] came jesus … then saith he to thomas, reach hither thy finger, and behold my hands; and reach hither thy hand, and thrust [it] into my side: and be not faithless, but believing. and thomas answered and said unto him, my lord and my god (john 20). however saul of tarsus who on the road to damascus within a few years of the crucifixion had a born-again experience of the resurrected jesus, became blinded for three days and set out on a life-journey redefining the nature of christianity, from the narrow vehicle of the desposyni and the hebrew church of james the just, into a hellenistic religion of the risen christ that would sweep through and engulf the entire pagan world, unashamedly adopting many of its beliefs and practices in the process. one can see his huge influence on christian theology by the fact that fourteen of the twenty-seven books in the new testament are attributed to him. this religion is completely different from that of the mission of jesus in its diverse gnostic and synoptic emphases. as rosemary radford ruether in "gaia & god" notes: "new testament and early christian cosmological christology built on theologies of cosmogenesis in oriental hellenism, particularly as these had already been assimilated into hellenistic judaism. the http://dhushara.com/apoc/apocalypse_files/image021.jpg dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 158-181 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 179 mediation of these ideas through judaism allowed christians to assimilate ideas of hellenistic philosophy, while 'denying' their pagan origins. … christianity also took over from judaism an ideology of religious 'purism' over against paganism as 'false religion'. this dualism still shapes christian self-understanding causing it to obscure and deny its actual syncretistic reality". "the cosmos is seen as originating in a transcendent divine being, who is the source of all things. this divine being brings forth from 'himself', a perfect 'image' and self-expression, in which the intellectual essences of all things are contained. this second god is then identified with the demiurgos, who shapes the cosmos form the intellectual 'blueprint' contained in 'his' own mind. the world soul, in turn expresses this divine logos in immanent form as the sustaining power of the cosmos. human souls are seen as partaking in the substance of this world soul or immanent logos of the cosmos." this picture was used first in jewish wisdom literature as divine wisdom, a secondary manifestation of the creator god and in a more elaborate way by philo, in which each human soul reflects the divine logos. the term christ originally referred to the anointed one or messiah, appearing at the end of world history to destroy the forces of evil and renovate the epoch. in jewish thought there was no identification of the messiah with cosmogenesis, nor is it in the synpotic gospels, but when we come to the more speculative works of paul we this has been put together into a unified vision of the beginning and end of all things. in whom we have redemption through his blood, even the forgiveness of sins: who is the image of the invisible god, the firstborn of every creature: for by him were all things created, that are in heaven, and that are in earth, visible and invisible, whether they be thrones, or dominions, or principalities, or powers: all things were created by him, and for him: and he is before all things, and by him all things consist. and he is the head of the body, the church: who is the beginning, the firstborn from the dead; that in all things he might have the preeminence. for it pleased the father that in him should all fulness dwell; and, having made peace through the blood of his cross, by him to reconcile all things unto himself; by him, i say, whether they be things in earth, or things in heaven (coloss 1). the logos-christ is seen one unifying figure in both creation and redemption as the manifestation of god, the immanent presence of god that creates and sustains the universe and the divine power remanifest at the end of time, healing the enmity that has divided the cosmos and reconciling the cosmos to god. the divine person encountered in jesus is thereby identified with this logos-christ. his redemptive act 'through the blood of the cross' is seen as the paradigmatic manifestation of one and the same divine being of the beginning and end of all things. – "so that god may be all in all" (1 cor). jewish thought originally saw humans as essentially mortal. redemption was a fulfilled, blessed existence on earth within mortal limits. greek thought, by contrast saw the relation of god and cosmos as emanational. classical christianity presented several efforts to unify these disparate worldviews. in the hebrew view, the body was essential for the wholeness of existence and the resurrection of the body was intrinsic to salvation. at the same time in the platonic mould, the dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 158-181 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 180 transience and mortality of material existence was evil, leading to the notion of a pure immortal spiritual body created of the soul. christians shared the hellenistic view that the whole cosmos was alive. even animals and plants had animal and vegetative soul. while some gnostics saw nature and the material world as fundamentally evil and flawed and rejected the body, others, such as the valentinians saw gnosis as a state of knowing, or wisdom, in which simple moral imperatives became superfluous and ignorance rather than sin was the cause of the fall from grace. they adopted a complex partially inverted platonic model of the universe. elaine pagels in “the gnostic gospels” (1979 79) notes that some concluded that the god of israel ... was merely instrumental power whom the mother, or the father anthropos, had created. "they say that he believed that he had made everything by himself, but that, in reality, he had created the world because wisdom, his mother, 'infused him with energy' and implanted into him her own ideas. ... 'it was because he was foolish and ignorant of his mother that he said, 'i am god; there is none beside me'. according to another account, the creator caused his mother to grieve by creating inferior beings, so she left him alone and withdrew into the upper regions of the heavens". "according to the hypostasis of the archons, ... both the mother and her daughter objected when he [said], 'it is i who am god, and there is no other apart from me.' ... and a voice came forth from above the realm of absolute power, saying, 'you are wrong, samael' ['god of the blind']. and he said, 'if any other thing exists before me, let it appear to me!' and immediately, sophia ('wisdom') stretched forth her finger, and introduced light into matter, and she followed it down into the region of chaos.... and he again said to his offspring, 'it is i who am the god of all.' and life, the daughter of wisdom, cried out; she said to him, 'you are wrong, saklas!' " (pagels 1979 79). ildabaoth, becoming arrogant in spirit boasted himself above all those who were below him and explained "i am father and god and above me there is no one" his mother hearing him speak thus cried out against him 'do not lie ildabaoth for the father of all, the primal anthropos is above you and so is anthropos, the son of anthropos (pagels 1979 133). irenaeus, in his refutation of the gnostic rejection of the body, in favour of the resurrection, notes: but indeed vain are they who despise the entire dispensation of god and disallow the salvation of the flesh, and treat with contempt its regeneration, maintaining that it is not capable of incorruption. but if this indeed does not attain salvation, then neither did the lord redeem us with his blood, nor is the cup of the eucharist the communion of his blood, nor is the bread we break the communion of his body. but since salvation requires transcending mortality, the only way one can think about redemption is that by being infused with immortal life of the divine, it will overcome its mortality. this redemption of creation following the apocalyptic tradition involves firstly a millennium of paradise: and they shall come and rejoice in mount zion, and shall continue to come to what is good, and into a land of wheat and wine and fruits, of animals and of sheep that their soul shall dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 158-181 king, c., the resplendence codex: reflowering apocalypse in the tree of life (part i) issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 181 be as a tree bearing fruit and they shall hunger no more. then the whole cosmos will be transformed into a 'new heaven and earth' immortalized and united with the divine life of god, fulfilling the promise of the original creation. this effort to incorporate hebraic earthly blessedness into eternal salvation was dropped by mainline christianity after the third century. christ is seen as establishing his millennial reign through the political power of the church and christian rulers, but this has no effect on the renewal of nature nor does it bring forth a new era of justice between humans. the distance between god and humans could now only be bridged by divine revelation, not by any 'natural' speculative or mystical capacities of humans. we can also see that, since the fall, mortality has been inextricably connected with the moral notion of sin. although the renaissance brought about a revival of cosmological mysticism and idealism such as that of the jewish philosopher spinoza who conceived of god as natura naturans, the underlying from which arose the physical world and the human mind, along with others such as fichte and schelling, the wild pony of human inventiveness had by now escaped the confines of religious tradition. the christian church was originally conceived as a steward to guard the earth until the immanent return of the lord, not to assume perpetual power. for the first few centuries this remained a feverish belief, with christians such as perpetua, whose sad tale is recounted in elaine pagels' "adam and eve and the serpent", determined to face annihilation rather than repent their beliefs, in the conviction that they were facing an immanent end of days anyway. but the second coming never arrived. by 313 constantine had in one fell swoop converted a religion of refugee zealots into the state religion of rome and christianity continued a chequered career of domination through crusade and inquisition until the renaissance and age of enlightenment toppled it from exclusive temporal power in europe. the christian church now continues in perpetuity in violation of its founding principle. (continued on part ii) is reality really real dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 385-408 smetham, g. p., quantum genes[?]: bell’s theorem, quantum entanglement, consciousness & evolution issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 385 article quantum genes[?]: bell’s theorem, quantum entanglement, consciousness & evolution graham p. smetham * abstract the supporters of the hardcore materialist mud worldview tend to consider, without actually thinking too much (if at all), that anyone involved in scientifically investigating the nature of quantum reality and its relationship to the ‘observer’ as being so irredeemably infected with what these ‘rationalists’ call ‘woo’ that they should not be taken seriously. in this article we take a more in depth look at the crucial issues raised by the paper that tsakiris unsuccessfully attempted to draw to the unwilling attention of jerry coyne. for physicists such as bohm, planck, schrödinger, heisenberg and others, consciousness, or potential consciousness, is an innate and inseparable aspect of the quantum immaterial realm which underlies the apparently material realm. furthermore, as bohm states, “every part of the universe is related to every other part but in different degrees;” this interconnection accounts for a deep level of the evolutionary interrelationships between creatures and environments. because of the deeply connected nature of the quantum field there must be a quantum informational interconnection between environments and the creatures within them. keywords: materialist, nonlocality, quantum gene, bell’s theorem, quantum entanglement, consciousness, evolution, darwinism. in this article we take a more in depth look at the crucial issues raised by the paper that tsakiris unsuccessfully attempted to draw to the unwilling attention of jerry coyne. figure 1 shows the upper half of the first page of the paper ‘an experimental test of non-local realism.’ the paper, as can be seen, is written by seven physicists, physicists who make up a world renowned team of experimenters at the ‘erwin schrödinger international institute for mathematical physics’ based in vienna. given the credentials of these physicists i think it is beyond dispute that, as tsakiris says to coyne, the paper in question can be considered as not being “too out-there, woo-wooish, fringy.” unfortunately, however, the supporters of the hardcore materialist mud (materialist ultradarwinian) worldview tend to consider, without actually thinking too much (if at all), that anyone involved in scientifically investigating the nature of quantum reality and its relationship to the ‘observer’ as being so irredeemably infected with what these ‘rationalists’ call ‘woo’ that they should not be taken seriously. coyne, having managed to deflect any possibility of having to confront the evidence of ‘quantum woo’, posted to his blog associated with his wet (why evolution is true) book: * correspondence: graham smetham, http://www.quantumbuddhism.com e-mail: graham.smetham@gmail.com http://www.quantumbuddhism.com/ mailto:graham.smetham@gmail.com dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 385-408 smetham, g. p., quantum genes[?]: bell’s theorem, quantum entanglement, consciousness & evolution issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 386 figure 1 alex tsakiris: woomeister and coward well, after my fractious interview at skeptiko with alex tsakiris, in which he failed to get me to admit to the existence of any number of woo-ish phenomena, he got lambasted in the comments, something he’s not used to from his usual gaggle of espers, neardeath-experiencers, and quantum wowsers. what does he do when faced with an onslaught of rationalism? 1 the charge that tsakiris is a ‘coward’ is based on the claim that, according to coyne, he closed off the online discussion too early in order to avoid the massed ranks of ‘rationalists’ who wanted to give him what they mistakenly consider to be the ‘true’ facts. when i went to the site to have a look it appeared that this was not the case, there seemed to be a reasonable length of opinion. it might be the case however, that tsakiris reopened the discussion. one of the first comments from a coyne supporter is: one of the worst interviews i ever wasted my time listening to. it’s clear the host has an agenda and is only interested in forcing everything to fit it. you had as your guest one of the most renowned evolutionary biologists in the world, and all you can do is push your own wacky pet theories about consciousness? … what a disgrace. 2 tsakiris, of course, was actually asking coyne to take into account the possible implications of the quantum discoveries which have been made by zeilinger and his team, experimental results which confirm remarkable quantum metaphysical insights about the ultimately immaterial nature of reality. this is a conclusion that has been increasingly inescapable since the inception of quantum physics. so it seems appropriate to consider whether zeilinger might have been infected with the dreaded ‘woo’, whatever that might be. according to wikipedia anton zeilinger (fig.2): dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 385-408 smetham, g. p., quantum genes[?]: bell’s theorem, quantum entanglement, consciousness & evolution issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 387 …has held positions at the university of innsbruck, the technical university of munich, the technical university of vienna and at the massachusetts institute of technology (mit) and distinguished visiting positions at humboldt university in berlin, merton college of oxford university and the collège de france in paris. zeilinger received many awards for his scientific work, among the most recent being the king faisal prize (2005), and the first newton prize of the iop (2007). he is a member of six scientific academies. anton zeilinger is currently professor of physics at the university of vienna and scientific director of the institute of quantum optics and quantum information of the austrian academy of sciences. since 2006, zeilinger is the vice chairman of the board of trustees of the institute of science and technology austria, an ambitious project initiated by zeilinger's proposal. … in 2005 anton zeilinger was among the “10 people who could change the world”, elected by the british newspaper new statesman. in 2010 he received the wolf prize in physics. anton zeilinger’s achievements have been most succinctly described in his citation for the isaac newton medal of the institute of physics (uk): “for his pioneering conceptual and experimental contributions to the foundations of quantum physics, which have become the cornerstone for the rapidly-evolving field of quantum information.” 3 one would have thought, then, then zeilinger would be safe from being infected with ‘woo’! whatever that might be. figure 2 – zeilinger with some experimental apparatus. 4 the abstract to the ‘an experimental test of non-local realism’ paper begins: most working scientists hold fast to the concept of ‘realism’a viewpoint according to which an external reality exists independent of observation. but quantum physics has shattered some of our cornerstone beliefs. already we have an extraordinary and disturbing intimation. it seems that the most precise and delicate experiments carried out at the quantum level of reality, experiments which have been carried out in different variations over and over again, indicate that an “external reality” which is “independent of observation” does not exist! and, furthermore, if this should turn out to be correct then it must be the case that the consciousness or consciousnesses of ‘observers’ are interconnected in some way with the production of what appears to be an external reality. in fact dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 385-408 smetham, g. p., quantum genes[?]: bell’s theorem, quantum entanglement, consciousness & evolution issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 388 zeilinger has elsewhere referred, in his discussion of the importance of the work of the twentieth century physicist john wheeler, that we must appreciate wheeler’s: …realisation that the implications of quantum physics are so far-reaching that they require a completely novel approach in our view of reality and in the way we see our role in the universe. this distinguishes him from many others who in one way or another tried to save pre-quantum viewpoints, particularly the obviously wrong notion of a reality independent of us. 5 in other words we must now conclude that quantum theory, the most fundamental level of the physical investigation of the process of reality, has proved that there is no external reality which is entirely independent of consciousness. another important and highly regarded physicist and philosopher, bernard d’espagnat, has indicated the situation in clear terms: the doctrine that the world is made up of objects whose existence is independent of human consciousness turns out to be in conflict with quantum mechanics and with facts established by experiment. 6 the majority of significant physicists have reached similar conclusions. the paper tsakiris refers to concerns an experiment which sets out to test ‘non-local realism’, which means that it tests the notion that there are ‘real’ ‘hidden’ connections between every part of reality which are independent of mind and minds. in other words if we allow ‘reality’ to be such that all points of reality are instantaneously interconnected by ‘real’ external links we can then also assume that there is an external reality which is independent of observers. and the answer is that such an objectively ‘real’ external world, independent of observation, does not exist. this means accepting a thoroughly and spookily interconnected world and we must abandon “certain intuitive features of realism.” one aspect of this situation is that there are no definite properties of quantum systems prior to measurement. the experiment confirms spooky instantaneous quantum non-local interconnections, which may take place over cosmic distances, and it also confirms the fact that a reality which is entirely independent of consciousness does not exist. this conclusion, as tsakiris suggests and coyne willfully remains ignorant of, undermines the position of metaphysical materialism that is maintained by coyne by ignoring the evidence. how ironic it is that coyne in his wet blog claims that it is tsakiris who is “deeply and willfully ignorant.” 7 the phenomenon of quantum entanglement, which is the fact that quantum ‘particles’ can be interconnected as potentialities smeared out over large distances until an observation disentangles them, was first highlighted by schrödinger who wrote that: attention has recently been called to the obvious but very disconcerting fact that even though we restrict the disentangling measurements to one system, the representative obtained for the other system is by no means independent of the particular choice of observations which we select for that purpose and which by the way are entirely arbitrary. it is rather discomforting that the theory should allow a system to be steered or piloted into one or the other type of state at the experimenter's mercy in spite of his having no access to it. 8 dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 385-408 smetham, g. p., quantum genes[?]: bell’s theorem, quantum entanglement, consciousness & evolution issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 389 in other words when we have an ‘entangled’ quantum situation wherein two systems are part of the entanglement, observation of one system, which disentangles the system from its quantum state of potentiality, will instantaneously disentangle the other system, even though it may be vast distances away. quantum entanglement, then, occurs when two or more particles interact in a way that causes their fates to become linked. it becomes impossible to consider, or mathematically describe, each particle’s condition independently of the others. they constitute a single quantum state of potentiality, which means that there are no fully existent ‘particles’ but only potential particles. two entangled particles often must have opposite values for a property for example, if one is spinning in “up” direction, the other must be spinning in the “down” direction. if someone measures one of the entangled particles and, by doing so, measures it into an ‘up’ state, this causes the entangled partner to become spin ‘down.’ making the measurement ‘here’ affected the other particle ‘over there’ instantaneously, even if the other particle was a million miles away. and this observational effect involves a conscious decision to perform the observation. the questions which immediately become relevant are 1) how does the distant particle ‘know’ its partner has been measured, and 2) how does it ‘know’ what attribute its partner has adopted? a crucial debate which was raised in a famous paper written by einstein, podolsky and rosen, called the epr paper, ‘can quantum mechanical description of physical reality be considered complete?’ was as to whether entangled particles could be thought of as having, or indeed whether they did have, on board pieces of information which determined their behaviour. this is the way that einstien thought reality must be, it must consist, at some level, of definite entities, ‘elements of reality’ he called them, which are both independent of other entities and independent of the minds of the observers. as schrödinger had pointed out with his famous cat thought experiment which he outlined to einstein in a letter ( denotes the quantum mathematical wavefunction of quantum potentiality): confined in a steel chamber is a geiger counter prepared with a tiny amount of uranium, so small that in the next hour it is just as probable to expect one atomic decay as none. an amplified relay provides that the first atomic decay shatters a small bottle of prussic acid. this and – cruelly – a cat is also trapped in the steel chamber. according to the -function for the total system, after an hour … the living and dead cat are smeared out in equal measures. 9 in other words because the quantum world hovers in a state of undetermined potentialilty, when unobserved the macroscopic world should theoretically also hover in indeterminacy. it is only when a measuring ‘observation’ is made that the quantum ‘superposition’, which means a potentiality of both possibilities, of the live and dead cat can be disentangled to become one or the other. einstein was never happy with such a view which is why he considered quantum theory to be ‘incomplete.’ quantum theory, however, clearly suggested that einstein’s definite ‘elements of reality’, a concept sometimes referred to as ‘hidden variables,’ do not exist and therefore quantum entanglement is a fundamental aspect of reality. and if this turned out to be the way that unobserved reality really was it would mean that ‘reality’ would not fully exist but would be a kind of quantum soup of potentiality containing all possibilities, until, that is, it is ‘observed.’ dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 385-408 smetham, g. p., quantum genes[?]: bell’s theorem, quantum entanglement, consciousness & evolution issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 390 the influential high energy physicist john s. bell was dissatisfied with the fact that this situation seemed to be beyond resolution and he spent some time considering a method by which the issue could be resolved one way or another. in 1964 he published a paper entitled ‘on the einsteinpodolsky-rosen paradox’ 10 which transformed the study of the foundation of quantum mechanics. the paper showed that no “physical theory which is realistic and also local in a specified sense can agree with all of the statistical implications of quantum mechanics.” 11 this means that the implications of quantum theory contradicts a locally real world, which is a world wherein ‘elements of reality’ have definite properties independent of observation and there are no faster than the speed of light interconnections. from his assumptions about how a locally real world, which is a world without spooky interconnections, must function bell proved an inequality, later called “bell's inequality”, which is violated by the quantum mechanical predictions made from an entangled state of a composite system. figure 3 an inequality is a mathematical formulation which indicates that a certain sum on one side of the inequality musts be less than or equal to a certain number. consider the case of a source emitting entangled polarized photons, one to the right the other to the left (figure 3) towards two polarization filters, pd1 and pd2. in the experiment the filters can either be set to correspond with each other of turned to an offset of 30 degrees or -30 degrees. what bell showed was that if there were ‘hidden’ on board information, corresponding to einstein’s ‘elements of reality’, then the following inequality must be satisfied: n(pd1= -30, pd2=30) <= n(pd1= -30, pd2= 0) + n(pd1= 0, pd2= 30) where n(x) indicates the number of photons which pass with the detectors set in the configuration x. quantum theory (at the time it was called ‘quantum mechanics’) predicted that reality would fail this test, indicating that einstein’s belief in a local world of ‘real’ externally independent bits and pieces of reality, which were independent of the minds of observers, was false. in his book the dance of the photons zeilinger presents an intriguing derivation of bell’s inequality for polarization of entangled photons based on the notion of identical twins which are assumed to be carrying fully determinate ‘genes’. in this case the ‘genes’ are representative of einstein’s ‘elements of reality.’ we consider pairs of identical human twins instead of entangled quantum ‘particles.’ identical twins, of course, have ‘on board’ information; their features do not hover in potentiality prior to observation, so they stand in for quantum ‘particles’ which are considered to have definite features prior to observation. and we can derive a bell type inequality which must be obeyed by such an ‘inherently real’ situation. the three polarization measurements (0, -30, or 30) are identified with the observation of three features of the twins, their height, hair color, and eye color, and we set this up so that we use two dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 385-408 smetham, g. p., quantum genes[?]: bell’s theorem, quantum entanglement, consciousness & evolution issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 391 valued features: tall or short (we can set a height to divide our sample into two groups), blue eyes or brown eyes, blond hair or brunet hair. because the twins are identical we know that if one of the twins is tall, blue-eyed, and brunet, we also know that the other twin will be tall, blue eyed, and brunet. from the perspective of einstein, podolsky, and rosen, these three properties height, eye color, and hair color are ‘elements of reality’ that we predict with certainty for the second twin upon observation of the first twin. we also assume that the reason for these correlations is that the twins carry the same genes. these hypothetical ‘genes’ correspond to the ‘local hidden variables’ we postulate might be operational in the quantum situation. we can now look at all the possible combinations in a large sample of these twins:  tall, blue-eyed, brunet  tall, blue-eyed, blond  tall, brown-eyed, brunet  tall, brown-eyed, blond  short, blue-eyed, brunet  short, blue-eyed, blond  short, brown-eyed, brunet  short, brown-eyed, blond now we can make some very simple and obvious statements about the numbers involved. for instance: [exp 1] the equality (expression 1) should be obvious, as the hair colours blond and brunet cover all the twins there cannot be any tall, blue-eyed twins with another hair colour. from this equation we can derive the following inequality, the symbol ‘≤’ means that the number on the left hand side is less than or equal to the number on the right hand side: [exp 2] dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 385-408 smetham, g. p., quantum genes[?]: bell’s theorem, quantum entanglement, consciousness & evolution issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 392 the reason that this inequality must be true is because both of the bracketed sets on the right hand side of exp 2 must be larger than the corresponding bracketed sets in exp 1. this is because extra pairs of twins are added in. in the case of the first bracket on the right hand side pairs of twins who are tall, brunet with brown eyes are added in; and in the case of the second bracketed set on the right hand side we have added in pairs of twins with blue eyes, blond hair and are short. this is indicated in the diagram below: now we suppose that we can only observe one property on each twin, we can write down exp 2 as follows: [exp 3] why does this work? consider the set on the left hand side. the number of pairs of twins where one is tall and the other is blue eyed must be the same as the number of tall twins with blue eyes because they are twins. if the twin of a tall twin has blue eyes then the tall twin must have blue eyes also because they are twins. the same reasoning applies to the sets on the right hand side; dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 385-408 smetham, g. p., quantum genes[?]: bell’s theorem, quantum entanglement, consciousness & evolution issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 393 so exp 3 is equivalent to exp 2 but expressed in a different form. exp 3 is bell’s inequality for twins. now the point of this inequality is that it must be satisfied by a ‘reality’ which conforms to our everyday notions concerning reality, which is that ‘reality’ is made up of individual, separately existing things which have their features inherently attached to them independently of observations. in fact this inequality must be passed by reality if ‘genes’ can be considered to be independent and self-enclosed ‘elements of reality.’ zeilinger comments upon bell’s achievement in devising this possibility for performing ‘experimental metaphysics’: how is it possible that a statement as simple as bell’s inequality might not hold in nature? the problem we have is that the considerations that led us to bell’s inequality were extremely simple. i would argue that they are so simple that the greek philosopher aristotle could already have derived bell’s inequality had he known that this was an interesting and nontrivial problem. we did not have to use quantum mechanics for its derivation. but aristotle would never have expected that this could be an interesting problem. in contrast, he probably would have said that this is quite uninteresting, because nature obviously has to behave in a way so as not to violate the inequality. as daniel greenberger commented, to think that nature could possibly function in a manner to violate bell’s inequality is surely “crazy”. 12 this is because we are all conditioned by our dealings with our everyday world to simply believe that the apparently ‘external’ world and the objects within it must be independent of our minds, having absolutely no dependence on mind or minds in any way. also the notion that every piece of the apparent ‘matter’ within the universe might be quantumly connected through quantum entanglement is also hard to conceive of. we tend to believe the ‘classical’ view of reality is the way reality really is. zeilnger transform this ‘twins and genes’ analysis into the quantum situation and derives bell’ inequality for pairs of entangled quantum particles: in this version we can take: x = -30, y = 0, z = 30, ‘+’ indicates the photon passes through the filter, ‘-’ indicates it does not. bell’s inequality must be satisfied for a ‘locally real’ ‘reality’ to be functioning, which is a ‘reality’ with ‘real’ individuated and separate ‘things’, or ‘elements of reality,’ to ultimately exist independently of observations, and independently of all other apparent ‘things.’ this point is crucial and needs emphasizing. in a ‘classical’ type world, which is the type of world darwin dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 385-408 smetham, g. p., quantum genes[?]: bell’s theorem, quantum entanglement, consciousness & evolution issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 394 assumed he inhabited and coyne still thinks is essentially operative, a world wherein ‘matter’ is the straightforward ‘matter’ conceived of by newton and descartes, a ‘matter’ which is entirely independent of the minds of observers, bell’s inequality cannot be violated. quantum theory predicts that bell’s inequality must be violated; and it turns out that in all experiments (except an early one which certainly was defective) quantum physics has been validated and bell’s theorem violated. figure 5 (13) in his excellent book sneaking a look at god’s cards, physicist giancarlo ghirardi, in the final paragraph of his ’telepathy or cheap trick’ section, which discusses quantum entanglement and bell’s theorem, writes: i would like to conclude this section with a quotation from einstein that is particularly apt for the example just discussed, and shows how lucidly he intuited (even while refusing to accept) the deepest implications of the theory, long before bell’s own analysis: “it seems hard to sneak a look at god's cards. but that he plays dice and uses ‘telepathic’ methods (as present quantum theory requires of him) is something that i cannot believe for a single moment.” 14 indeed, it seems remarkable that einstein, who was the first to take the notion that ‘reality’ at its deepest physical level was quantum in nature, when he used the idea to solve the puzzle of the photoelectric effect, and was the person, of course, who overturned notions of absolute space and time with his relativity theories, simply could not, and would not accept that independent and completely separate ‘elements of reality’ ultimately do not exist. ghirardi, however, tells us that the evidence tells us that “the photons themselves must be telepathic.” 15 experiments of extraordinary delicacy and precision have been carried out, many of them by zeilinger and his team, to probe the phenomenon of the telepathic nature of quantum entanglement. ghirardi describes one carried out by alain aspect and collaborators, who carried dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 385-408 smetham, g. p., quantum genes[?]: bell’s theorem, quantum entanglement, consciousness & evolution issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 395 out one of the first precise demonstrations of the violation of bell’s inequality, that involved a system which precluded any form of hidden message being transmitted at the speed of light and he concludes: personally, i take the experiment of aspect and his collaborators as conclusive: photons really are telepathic, or to use more scientific terminology they cannot be considered as possessing any local characteristics that determine whether or not they will pass the test before the test is carried out. nevertheless, they still react the same way for the same test. 16 in other words they are instantaneously interconnected at the deep quantum level of reality. and this kind of deep interconnection applies to all kind of ‘particles’. zeilinger concludes that: quantum particles do not behave like identical twins. even though they always show the same results when they are measured for the same property, we are not allowed to explain this by saying that they carried that property before and independently of observations. 17 note the clear indication that the properties which are finally manifested are not independent of observation. the properties that the apparent particles adopt are in some way measured into existence by observation. this situation clearly indicates the fact that consciousness is in some way interconnected with the quantum realm. in their excellent book quantum enigma: physics encounters consciousness bruce rosenblum and fred kuttner give a summary of the implications of the bell violation: bell’s theorem in a nutshell: suppose our world to have physical real properties that are not created by their observation. further, suppose that objects can be separated from each other so that what happens to one cannot affect the other. (for short, we call these two suppositions “reality” and “separability”) from only these two premises – both assumed in classical physics but denied by quantum theory – bell deduced that certain observable quantities could not be larger than certain other observable quantities. this experimentally testable conclusion of bell’s theorem, which must be true in any world with reality and separability, is bell’s inequality. if bell’s theorem is shown to be false in any situation, one or both of the premises leading to it (reality and separability) must be false. … in what we will call a “reasonable” world, objects have physically real properties (not merely properties created by their observation). moreover, in such a reasonable world, objects are separable. that is they affect each other only by physical forces, which cannot travel faster than the speed of light (not by “spooky actions” traveling infinitely fast). the newtonian world described by classical physics is, in a sense, a reasonable one. the world described by quantum physics is not. bell’s theorem allows us to test to see whether perhaps it’s just quantum theory’s description of our world that’s unreasonable, and that our actual world is in fact a reasonable one. … when the experiments were done, bell’s inequality was violated. … our world therefore does not have both reality and separability. it’s, in this sense, an “unreasonable” world. 18 this means that the ultimate quantum nature of the ‘stuff’ of reality, what zurek calls “dreamstuff”, is not newtonian ‘classical’ type stuff. the term “unreasonable,” however, is slightly misleading, the quantum world is only “unreasonable” for someone, like coyne, who expects the dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 385-408 smetham, g. p., quantum genes[?]: bell’s theorem, quantum entanglement, consciousness & evolution issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 396 world to be comprised of tiny billiard balls. coyne wants to brush all this “unreasonableness” aside and pretend that he can carry on as if living in darwin’s ‘classical’ times. he says: it’s as if you’re saying we can’t play billiards and we can’t shoot rockets to the moon because of this stuff that happens on a micro level. the fact is that assuming that these phenomena apply on most of the levels of reality that we deal with renders everything wrong is simply incorrect. for most macro phenomenon, newtonian or classical mechanics works fine. for most micro-phenomenon you’re turning to quantum mechanics. it works fine. and in terms of evolution i don’t see how this quantum mechanics affects evolution at all. 19 and this is an extraordinary and ignorant statement because we are discussing biology at the micro level of genes and dna, not moon-shots. photosynthesis, a central mechanism for the maintenance of life, is now known to operate by a quantum ‘look-ahead’ mechanism. and this mechanism, described by feynman’s sum over histories approach to quantum phenomena, is fundamental to the quantum world. as physicist neil turok, director of the perimeter institute for theoretical physics, has pointed out: according to quantum theory, the world is constantly exploring all of its possible classical states all of the time, and is only appearing to us as any one of them with some probability. 20 it would be remarkable if this fundamental quantum mechanism was not an aspect of the process of evolution. it is at this point that it is important to be clear that the nature of this interconnection is an issue of controversy. this is why coyne is able to claim that the notion that consciousness is in some way involved at the quantum level is ‘controversial’. but this just indicates his ignorance. the fact that the disentanglement of properties depends in some way upon observation is not controversial, which is why zeilinger writes that the breakdown of local realism means: …the property of a particle observed in a specific experiment is not an element of physical reality before the measurement is performed. in the end this means that the reality depends upon the decision of the observer… 21 and yet at the same time a few pages earlier zeilinger also says that: it is dangerous – and not supported by the physics of the quantum measurement process – to claim, as is sometimes claimed, that it is the mind of the observer that influences the quantum state. 22 one can only conclude that even zeilinger is confused as to the actual nature of the dependence of the manifestation of quantum properties on the decisions of observers. as has been pointed out earlier zeilinger elsewhere has clearly indicated that the ‘classical’ notion that the material world is independent of observers is “obviously wrong.” the above quote, however, would suggest that zeilinger does not want to suggest that the mind of an individual observer can directly affect quantum reality, and therefore reality in general. or, perhaps zeilinger is worried about sticking his neck out too far on the issue of the interconnectedness of consciousness and the quantum realm. the problem is indicated by wojciech zurek, instigator of the ‘quantum darwinism’ paradigm, as follows: dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 385-408 smetham, g. p., quantum genes[?]: bell’s theorem, quantum entanglement, consciousness & evolution issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 397 …while the ultimate evidence for the choice of one alternative resides in our illusive “consciousness,” there is every indication that the choice occurs much before consciousness gets involved and that, once made, the choice is irrevocable. 23 in other words the ultimate evidence of quantum experimentation and theory indicates that consciousness is clearly implicated in the choices of which potentialities emerge from the quantum realm. and yet the mechanism through which this occurs is such that as time goes by these choices become solidified in a manner such that the functioning of the apparently external material world appears to be independent. zurek’s ‘quantum darwinism’ paradigm provides an insight into how this happens. according to zurek the ultimate ‘stuff’ of reality is ‘quantum dream-stuff’ which ‘epiontically’ created the appearance of the external world and its inhabitants. the term ‘epiontic’ indicates that perception creates ontology. this reiterates the quantum fact stated by zeilinger that the external world is not independent of observations. wheeler stated also stated this quantum fact: directly opposite to the concept of universe as machine built on law is the vision of a world self-synthesized. on this view, the notes struck out on a piano by the observer participants of all times and all places, bits though they are in and by themselves, constitute the great wide world of space and time and things. 24 in other words it is the internal ‘epiontic’ observing processes of the collective consciousness of the sentient beings within the universe that ‘chooses’, to use a word used by hawking and mlodinow, which potentialities to unfold. prior to the evolution of such observers the universe itself is clearly epiontically creating the conditions and paving the way for the emergence of such high level observers. the mechanism which underlies this process is the quantum amplificatory zeno effect, which is the implied quantum fact that the more often a particular quantum state is observed, or ‘registered’ to be a particular way the more likely it is to be observed in the same way in the future. zurek describes his view as follows: the main idea of quantum darwinism is that we almost never do any direct measurement on anything … the environment acts as a witness, or as a communication channel. … it is like a big advertising billboard, which floats multiple copies of the information about our universe all over the place. 25 but what he does not seem to home in on is the amplificatory aspect. the quantum advertising campaign for the classical world get more solidified the more it is ‘bought into.’ the ’quantum amplificatory zeno effect’ is an extension of the accepted quantum zeno effect. an amplificatory mechanism of this sort must be operational at the dream quantum level in order to account for the emergence of zurek’s ‘preferred states’ from the potentiality of the quantum field. in his discussion of the “axioms that provide a textbook summary of quantum foundations” zurek lists them as follows: 1) the state of a quantum system is represented by a vector in its hilbert space. 2) the evolution of the vector is unitary as generated by the schrödinger equation. 3) immediate repetition of a measurement yields the same result. dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 385-408 smetham, g. p., quantum genes[?]: bell’s theorem, quantum entanglement, consciousness & evolution issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 398 4) the measurement outcome is one of the orthonormal states – eigenstates of the measured observable. as zurek points out, it is the incompatibility of the first two with the second two which constitutes the “measurement problem” how is it that the many quantum alternatives ‘collapse’, apparently in interaction with consciousness, into one actuality. zurek considers that he has at least partially solved this problem with the notion of einselection (environment induced superselection): …einselection is caused by the transfer of information about selected observables. hence, the ontological features of the state vectors objective existence of the einselected states is acquired through the epistemological “information transfer”. 26 it is this ‘objective’ information transfer’ which zurek suggests takes place independently of observing consciousnesses. this seems to be the case. however, this does not rid the universe of some deeper level of consciousness which epiontically produces the preferred states which are imprinted into the quantum “advertising billboard” which is responsible for doing the ‘einselecting.’ it is this deeper level of non-individualized consciousness which eventually becomes embodied to various degrees in sentient beings. it is no surprise therefore that the manner in which the consciousnesses of human beings appear to interact with the quantum level of potentiality within quantum experiments at the micro level gives a clue to the way in which the “advertising billboard” of the quantum matrix of the ‘classical’ world came into being. the clue to this mechanism lies in the third quantum axiom, which is the quantum fact that immediate repetition of a measurement yields the same result. this is called the quantum zeno effect. given a superposition expressed in some basis: |ψ> = p1|b1> x p2|b2> x p3|b3> … x pn|bn> … when a measurement is performed this will ‘collapse’ into one of the eigenstates and all the other possibilities disappear. at the exact moment of collapse the state will be: |ψ> = px|bx> where px= 1 and |bx> is the resulting eigenstate. as time progresses this state will smear out into a spread of possibilities but if measured again immediately the same result will be obtained precisely because the probability is one. thus quickly repeated measurements can pin a quantum state into ontological stability. if, additionally, there is an amplificatory aspect then ontology would be solidified as time progressed. there is also an inverse zeno effect which was originally proposed by aharonov and vardi who showed that, by performing a dense sequence of measurements along a presumed path, a quantum system can be forced to follow an arbitrarily chosen path. johnjoe mcfadden has proposed that the inverse quantum effect may be a crucial factor in the evolutionary process: both the quantum zeno effect and the inverse zeno effect are really aspects of the same phenomenon: the ability of quantum measurement to interact with, and shape the dynamics of a system. the special relationship between quantum objects and quantum measuring devices draws out classical reality from the quantum world. … measurement of a quantum system draws out from the quantum superposition of all possible states, a dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 385-408 smetham, g. p., quantum genes[?]: bell’s theorem, quantum entanglement, consciousness & evolution issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 399 single reality for the physical world. as niels bohr said, ‘one must never forget that in the drama of existence we are ourselves both actors and spectators’. 27 this is consistent with hawking and mlodinow’s participatory account of the way the universe evolves: in this view, the universe appeared spontaneously, starting off in every possible way. most of these correspond to other universes …. some people make a great mystery of this idea, sometimes called the multiverse concept, but these are just different expressions of the feynman sum over histories. … the histories that contribute to the feynman sum don’t have an independent existence, but depend on what is being measured. we create history by our observations, rather than history creating us. 28 the actual spread of probabilities must change over time in an excruciatingly slow evolution of potentialities over vast time periods. there is no other way to account for the evolution of the universe. repeated ‘registrations’, ‘interactions’, correlations’ ‘observations’ within quantum dream stuff must make the potentiality for the same quantum possibility increase to an unimaginably tiny extent, and over vast time periods this mechanism builds up the quantum “advertising billboard” of classical reality. in this way the apparent solidity and immutability of the ‘external’ and ‘material’ world, as well as the beings inhabiting this world, is built up over time. in his final section ‘what could that mean?” of his book dance of the photons zeilinger further investigates what he considers to be the implications of the quantum violation of bell’s inequality. he begins by asserting that at least one of the assumptions about “reality” which were used to derive bell’s inequality must be wrong. these assumptions he lists as follows: 1) realism: this is the idea that an experimental result reflects in some way the ‘inherent’ features of the particles that we measure. 2) locality hypothesis: the assumption that the real physical situation of the measurement at apparatus b including particle b must be independent of the kind of measurement done at the same time to the distant particle a using measurement apparatus a. 3) counterfactual nature of reality: zeilinger writes: “there is a third assumption, which we used implicitly but did not express in detail. it is the assumption that it makes sense to consider what kind of experimental result would have been obtained if one had measured a different property than the one that was actually measured. for the case of twins the assumption means that it makes sense to assume that, for example, blue-eyed blond twins must be either tall or short, even if we do not check their height.” zeilinger then writes that: we now discuss some of the possible conceptual consequences of the breakdown of local realism. one possibility is that the reality assumption is not correct. this would mean in principle that the property of a particle observed in a specific experiment is not an element of physical reality before the measurement is performed. in the end, this means that reality depends on the decision of the observer of the experimentalist about which measurement to perform. the breakdown of realism would mean that the measured result does not reflect any kind of property that existed before and independently of observation. dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 385-408 smetham, g. p., quantum genes[?]: bell’s theorem, quantum entanglement, consciousness & evolution issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 400 another possibility would be that the locality hypothesis is not correct. such a breakdown of locality could, for example, mean that something is wrong with our picture of space and time. a quantum system that consists of two or more entangled particles remains an unseparated entity regardless of how far the individual components of the system are separated from each other. a breakdown of the third assumption would mean that one is only allowed to talk about the properties of systems when these properties are indeed measured. expressed very simply, the question “what if?” would be illegal. this would certainly contradict our everyday experience. we always consider different possible alternatives, and we base decisions on the possible consequences of these alternatives. for example, to know what will happen if we cross a superhighway during rush hour with our eyes closed, it is not really necessary for us to perform that experiment. at present, there is no agreement in the scientific community as to what the philosophical consequences of the violation of bell’s inequality really are. and there is even less agreement about what position one has to assume now. nearly all physicists agree that the experiments have shown that local realism is an untenable position. the viewpoint of most physicists is that the violation of bell's inequality shows us that quantum mechanics is nonlocal. this nonlocality is exactly what albert einstein called “spooky”; it seems eerie that the act of measuring one particle could instantly influence the other one. the other possibility would be for us to give up the picture of a world that exists in all its properties independent of us. that would mean that we have a very essential influence on reality just by deciding which measurement to perform. there are indeed hints that this might be the message we have to accept. 29 in the above quote zeilinger says that there “is no agreement in the scientific community as to what the philosophical consequences of the violation of bell's inequality really are.” the reason for this seems to be that there is a general desire to minimize as much as possible any ‘mystical’ implications. when one investigates the evidence of quantum theory and the metaphysical debates surrounding it, it is impossible not to notice that there is a tendency to try and produce what henry stapp calls ‘conservative’ accounts as a matter of principle. coherent ‘conservative’ accounts, however, are difficult to come by, which is why zeilinger indicates that we may need to accept the message that “we have a very essential influence on reality just by deciding which measurement to perform.” the violation of bell’s theorem, which has been experimentally verified over and over again with astonishing degrees of precision, indicates that the realm of what was once thought be independent ‘matter’ and the realm of mind are not separate but interpenetrate in a nonlocal quantum field of potentiality. one implication of bell’s theorem is the correctness of quantum field theory as the most fundamental physical and metaphysical account of ‘reality’. as the physicist and philosopher bernard d’espagnat, who has pondered, investigated and written about these issues over a long period, writes: …what, from a philosophical standpoint, is by far the most remarkable feature of quantum field theory is that it reduces the (scientifically unmanageable) notion dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 385-408 smetham, g. p., quantum genes[?]: bell’s theorem, quantum entanglement, consciousness & evolution issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 401 “creation” [of particles] to the (scientifically tractable) notion “state change.” and the point that is relevant to the here considered issue is that it succeeds in doing so by making primary some concepts of a general nature such as fields associated with types of particles and secondary the concept of individualized particles. consequently, if we are on the lookout for some concept, or “mathematical algorithm,” that this theory could be identified as referring to the “basic stuff,” we can find none except, conceivably, the element the state of which changes when a particle gets “created” or “annihilated”. … now, in the theory, there are not myriads and myriads of such elements. indeed there is just one! which means that, conceptually speaking, the theory is as far from atomism as it is conceivably possible for a theory to be. 30 it would seem that the most obvious conclusion is precisely that which is indicated by quantum field theory conjoined with the obvious conclusion that the ultimate quantum field must have mind-like qualitative features; otherwise none of us would have minds. in other words the fundamental ‘stuff’ of reality is a vast non-local quantum field of potentiality which has an internal qualitative aspect of non-individuated consciousness, awareness or cognizance. not only is this conclusion “as far from atomism as it is conceivably possible for a theory to be” it is also completely inconsistent with any kind of crude metaphysical materialism adopted by coyne with his “yeah those are solid things” approach. the above outline is an unbiased and correct account of the current evidence according to quantum theory, which is the most fundamental and precise account of the ultimate nature of the ‘physical’ world currently available to us. however, the comments made by coyne supporters on tsakiris’ website 31 would seem to indicate that they, like coyne himself, do not bother to familiarize themselves with the evidence before dashing to defend crude materialist views. the following are a selection of comments (which i comment on): one of the worst interviews i ever wasted my time listening to. it’s clear the host has an agenda and is only interested in forcing everything to fit it. you had as your guest one of the most renowned evolutionary biologists in the world, and all you can do is push your own wacky pet theories about consciousness? the ideas that tsakiris is trying to make coyne consider as significant for his own field of investigation are not tsakiris’ “wacky pet theories about consciousness”, they are notions suggested by the quantum evidence and considered as very real implications by many physicists. in fact some of the early founding fathers of quantum mechanics came to such conclusions. according to schrödinger, for instance: mind has erected the objective outside world … out of its own stuff. 32 and max planck came to a similar conclusion: all matter originates and exists only by virtue of a force... we must assume behind this force the existence of a conscious and intelligent mind. this mind is the matrix of all matter. 33 more recently quantum cosmologist andre linde has suggested: is it possible that consciousness, like spacetime, has its own intrinsic degrees of freedom, and that neglecting these will lead to a description of the universe that is dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 385-408 smetham, g. p., quantum genes[?]: bell’s theorem, quantum entanglement, consciousness & evolution issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 402 fundamentally incomplete? what if our perception is as real as (or maybe in a certain sense, are even more real than) material objects? 34 but committed muds simply dismiss such views by calling it “wacky” or full of “woo”: the idea that quantum effects change any previous observation of non quantum processes is just nonsense. it is the stuff of woo and charlatanism, not science. such assertions, however, are just not true. it is becoming clear now that quantum processes are found in situations where previously it was, dogmatically, asserted they were impossible. research on the internet will uncover articles in scientific journals announcing such discoveries as the possibility that “quantum entanglement that holds our dna together” 35 and “nobel prize for medicine in 2008, luc montagnier, is claiming that dna can send ‘electromagnetic imprints’ of itself into distant cells and fluids which can then be used by enzymes to create copies of the original dna” 36 , and “dna can discern between two quantum states, research shows” 37 , and: who said only plants are capable of photosynthesis? a study shows that an insect is also able to convert energy from sunlight, carbon dioxide and water into food. the study, entitled “light-induced electron transfer and atp synthesis in a carotene synthesizing insect“, published on august 16, shows that the pea aphid (acyrthosiphon pisum) can absorb energy from the sun and transfer it to a type of “cellular machinery” involved in energy production. 38 figure 5 pea aphid 39 the extent to which quantum effects operate in biological mechanisms is a matter (or nonmatter) for scientific investigation, not dogmatic abuse. in mud forums, however, dogmatic abuse to a large extent rules the day: this was very frustrating. the host has a profound misunderstanding of evolution, neurobiology and physics. then he tries to mush them all together to create an alternative reality with absolutely no evidence to back it up (and no, quoting papers you don’t understand doesn’t count as evidence). i don't know his background, but he surely appears completely deluded by his desire and perception that the “materialistic worldview is about to be overturned”, whatever that means. he should never interview a scientist again. just bring people like deepak chopra and have some fun in woo woo land. dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 385-408 smetham, g. p., quantum genes[?]: bell’s theorem, quantum entanglement, consciousness & evolution issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 403 although, as we have seen, there is serious and compelling scientific evidence that crude materialism cannot be true, those stuck in the mud worldview, without looking into the details of the evidence, assert that the notion that materialism has been undermined is nothing more than a ‘belief system’: after listening to a number of episodes of skeptico it is obvious to me that far from being an objective and dispassionate examination of the subjects examined, it is in fact a vehicle for propaganda in the service of your belief system. but you have stooped to new depths in claiming that quantum non-locality defeats materialism how does this claim match up with the facts described above, and the further fact that the most fundamental level of reality, the quantum field, is “insubstantial?” 40 here is another attempted mud defense: the quoted extract from the abstract appears to me to give the wrong impression out of its context. but don’t take my word for it read the complete abstract is here… scopus lists 90 articles citing this article and there are probably many others. no doubt alex, using his extensive knowledge of the literature of quantum theory, will be able to inform us precisely which ones cite it as “the final nail in the coffin of materialism.” again we find what seems to be either an inability to appreciate, or a wilful avoidance of, the obvious implications of assertions clearly made in the cited paper. here is a relevant passage from the abstract of the cited paper: most working scientists hold fast to the concept of ‘realism’ according to which an external reality exists independent of observation. but quantum physics has shattered some of our cornerstone beliefs. according to bell’s theorem, any theory that is based on the joint assumption of realism and locality (meaning that local events cannot be affected by actions in space-like separated regions) is at variance with certain quantum predictions. 41 to make the point more pointedly one might rewrite this for coyne and his infatuated mud fans: working scientists such as evolutionary biologists, jerry coyne being a case in point, hold fast to the concept of ‘realism’ according to which an external reality exists independent of observation … and, it should be apparent to anyone with moderate intelligence that the kind of materialism embraced by coyne does not include a type of ‘matter’ which is dependent upon observation! the fact is that the demonstration of the violation of bell’s inequality does undermine crude materialism. but the contributors to mud blogs never look into the evidence and arguments in the detail required to appreciate the facts. one might make a case that perhaps tsakiris was not as acute and incisive in his approach as he might have been, but this is a different issue. however, tsakiris’ suggestion that quantum discoveries must have implications for our understanding of the process of evolution is entirely reasonable. dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 385-408 smetham, g. p., quantum genes[?]: bell’s theorem, quantum entanglement, consciousness & evolution issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 404 in his introductory essay, a quantum origin of life?, for the collection of exploratory essays, quantum aspects of life, physicist paul davies suggests there are three possible configurations of the relationship between the classical level and the quantum level in the evolutionary process: 1) quantum mechanics played a key role in the emergence of life but then became subsidiary to classical processes. 2) life began classically and then somehow evolved a few quantum mechanisms to enhance efficiency. 3) life started out as a classically complex system, but later evolved towards “the quantum edge.” 42 but the notion that life started out classically and then discovered some quantum tricks is absurd. according to hawking and mlodinow “we are the result of quantum fluctuations in the early universe” so the entire process of the evolution of the universe and life had its origin in the quantum realm. in the light of this, and the fact that one of the most significant processes for life – photosynthesis – uses a fundamental quantum process, the notion that life had to hang around for the classical world to solidify and then later rediscovered the greater efficiency of quantum processes is ridiculous. furthermore, given the fact that quantum theory does undermine crude materialism, as the violation of bell’s theorem indicates, there is every reason to suppose that quantum effects might be important in life processes, including evolution. according to the geneticist steve jones: dna speaks a digital rather than analogue language and inheritance is based … on particles – genes – that can be recovered unchanged at any time. 43 however, as tsakiris pointed out to coyne, particles can also be quantum waves and quantum effects have now been found to be significant in ‘particles’ at the molecular level of genes. overall, then, there is good reason to suppose that quantum effects may be significant in the process of evolution. but such issues are brushed aside as a matter of dogmatic belief by coyne and his supporters as irrelevant. here is another defender of coyne’s materialist mud worldview: alex tsakiris: it’s the observer effect, jerry. it’s the double-slit experiment. it’s our… dr. jerry coyne: yeah, okay, what does that have to do with… alex tsakiris: are photons waves or particles, right? so it’s like… dr. jerry coyne: what does that have to do with evolution? alex tsakiris: it has to do with evolution because what we find is that it’s consciousness. if we put our consciousness one way or another it measures this way or that way. what a lousy interviewer. … making up references about quantum effects on evolution … here our doughty mud, starting out with an advance barrage of attempted satire and then taking his or her (almost certainly a ‘he’) lead from coyne’s performance, deploys a ridiculous avoidance tactic. because the paper cited by tsakiris does not explicitly state that quantum discoveries have implications for evolution theory, coyne and his followers claim that tsakiris is “making it up.” but this claim is absurd. the discovery that reality is not as ‘real’ as classical physics treated it as being, clearly has undermining implications for the materialist worldview. and classical physics was the kind of physics extant in darwin’s time, darwin lived in a mistaken ‘classical’ scientific worldview and darwinism is a ‘classical’ theory. as we have dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 385-408 smetham, g. p., quantum genes[?]: bell’s theorem, quantum entanglement, consciousness & evolution issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 405 seen, there is good reason to think that the violation of bell’s theorem means that entirely isolated self–enclosed information cannot be carried by independent gene units. it also implies, because of being dependent upon observation, that all matter is entangled with consciousness. this is why quantum decoherence theorist wojciech zurek has clearly said with regard to the ‘choice’ of quantum alternatives that: …the ultimate evidence for the choice of one alternative resides in our illusive “consciousness” 44 and roger penrose tells us that with regard to the quantum ‘collapse of the wavefunction’: …at the large end of things, the place where ‘the buck stops’ is provided by our conscious perceptions. … 45 none of this subtlety, however, has any interest for the defenders and proponents of mud: if anybody wonders who has the agenda here, this should make it obvious. care to show us that quote in the nature paper, alex? nonlocality is deep and profound, but it has nothing to do with evolution. and almost surely has nothing to do with consciousness either. such assertions would seem to indicate a deep and impressive commitment to the cause of ignorance. here is another misguided mud comment: so how have you managed to persuade yourself that consciousness might quite feasibly pre date life? surely consciousness is not a ‘thing’ that can (say) move around, but a property of (conscious) things such as brains. so just as a lamp (when switched off) does not become a lamp plus `brightness` which then floats away, so too does a brain, when unconscious, become an (unconscious) brain, not a brain and some free floating consciousness! if you do not believe that consciousness is a property of the brain but is somehow separate from it and irreducible (a la descartes), then how do you account for periods of unconsciousness, such as when in non-dream sleep or under anaesthesia? why on your woo model are you not still fully conscious, though temporarily unable to control your brain? if you think that consciousness might pre date life, then what exactly was conscious back then? but it is not the case that the new perspective required by the quantum evidence requires that we think, “a la descartes” that consciousness and matter are separate aspects of the process of reality, with consciousness being some kind of immaterial “free floating” field of awareness. it is vital to be aware that descartes and the other pre-quantum western philosophers did not have access to full knowledge of the nature of the ‘physical’ world. for them the quantum level was entirely hidden and therefore they essentially considered that the apparently ‘material’ world actually is as it appears solidly extended immutable ‘stuff’ with no subtle internal structure. even max planck, the instigator of quantum theory, at the beginning of his career thought that matter was internally continuous with no atomic structure 46 . from this perspective the apparent ontological aspects of ‘matter’ and ‘mind’ seem absolutely irreconcilable. the quantum revolution changes this situation dramatically for, as stapp points out, we now know that: dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 385-408 smetham, g. p., quantum genes[?]: bell’s theorem, quantum entanglement, consciousness & evolution issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 406 we live in an idealike world, not a matterlike world.’ the material aspects are exhausted in certain mathematical properties, and these mathematical features can be understood just as well (and in fact better) as characteristics of an evolving idealike structure. there is, in fact, in the quantum universe no natural place for matter. this conclusion, curiously, is the exact reverse of the circumstances that in the classical physical universe there was no natural place for mind. 47 in the new paradigm of the ‘quantum universe’ the apparent independent solidity of matter, which is an illusion (matter is 99.9999999999999% empty space!), is a solidification of quantum ‘dream-stuff’ which is a kind of infinite energetic potentiality. furthermore stapp indicates that this energy field is “idealike” and immaterial, a view which is shared by many significant physicists. certainly we know that the quantum fields which underlie the manifestation of the material world are insubstantial and immaterial. the evidence also suggests that they must also have a potentiality to produce consciousness and cognition within organic organisms. this further means that at the quantum field level there has to be vast potentiality and potential awareness. this is why planck, at the end of his career, said: i regard consciousness as fundamental. i regard matter as derivative from consciousness. 48 this does not mean, however, that planck thought that the quantum field is conscious in the same qualitative way that human beings are conscious, plotting and designing sentient beings in order to get a foothold in the material world so to speak. the immaterial ground quantum field of the process of reality is most appropriately conceived of as a vast ‘ocean’ of energetic potentiality that has an internal quality of the potential awareness of consciousness. the physicist david bohm described this as the holomovement within an ‘implicate order’: i propose something like this: imagine an infinite sea of energy filling empty space, with waves moving around in there, occasionally coming together and producing an intense pulse. let’s say one particular pulse comes together and expands, creating our universe of space-time and matter. but there could well be other such pulses. to us, that pulse looks like a big bang; in a greater context, it’s a little ripple. everything emerges by unfoldment from the holomovement, then enfolds back into the implicate order. i call the enfolding process “implicating,” and the unfolding “explicating.” the implicate and explicate together are a flowing, undivided wholeness. every part of the universe is related to every other part but in different degrees. 49 and for bohm, as for planck, schrödinger, heisenberg and other physicists, consciousness, or potential consciousness, is an innate and inseparable aspect of this immaterial realm which underlies the apparently material realm. furthermore, as bohm states, “every part of the universe is related to every other part but in different degrees;” this interconnection accounts for a deep level of the evolutionary interrelationships between creatures and environments. because of the deeply connected nature of the quantum field there must be a quantum informational interconnection between environments and the creatures within them. dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 385-408 smetham, g. p., quantum genes[?]: bell’s theorem, quantum entanglement, consciousness & evolution issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 407 1 http://whyevolutionistrue.wordpress.com/2012/02/15/alex-tsakiris-woomeister-and-coward/ 2 http://www.skeptiko.com/161-outspoken-atheist-jerry-coyne/ 3 http://en.wikipedia.org/wiki/anton_zeilinger 4 http://commons.wikimedia.org/wiki/file:anton-zeilinger-godany-portr%c3%a4t.jpg 5 barrow, john d., davies, paul c. w., harper, charles l. (eds.) (2004) 201 – anton zeilinger: ‘why the quantum? “it” from bit”? a participatory universe? three far-reaching challenges from john archibald wheeler and their relation to experiment.’ 6 d'espagnat, bernard, ‘the quantum theory and reality’ scientific american, nov. 197 7 http://whyevolutionistrue.wordpress.com/2012/02/15/alex-tsakiris-woomeister-and-coward/ 8 http://plato.stanford.edu/entries/qt-entangle/ 9 lockwood, michael (2005), 304 10 bell, j.s. [1964], “on the einstein-podolsky-rosen paradox,” physics, 1: 195–200. 11 http://plato.stanford.edu/entries/bell-theorem/ 12 zeilinger, anton (2010), 273 13 zeilinger, anton (2010) 14 ghirardi, g. (2005), 237 15 ghirardi, g. (2005), 236 16 ghirardi, g. (2005), 246 17 zeilinger, anton (2010), 285 18 rosenblum, b. and kuttner, f. (2006), 177-178 19 interview with tsakiris 20 turok, n. (2013), 206 21 zeilinger, anton (2010), 286 22 zeilinger, anton (2010), 264 23 zurek wojciech h. (2002). ‘ decoherence and the transition from quantum to classical – revisited’ in los alamos science number 27 2002 24 john d., davies, paul c. w., harper, charles l. (eds) (2004) p577 – wheeler, j a (1999) ‘information, physics, quantum: the search for links.’ in feynman and computation: exploring the limits of computers, ed. a. j. g. hey, p309 (314). cambridge, ma: perseus books. 25 ‘the evolution of reality’ – www.fqxi.org/community/articles/display/122 (the foundational questions institute) november 10, 2009. 26 decoherence and the transition from quantum to classical – revisited p22 27 mcfadden, johnjoe (2002) 28 hawking, stephen & mlodinow, leonard (2010), 136-140 29 hawking, stephen & mlodinow, leonard (2010), 286 30 d’ espagnat, b (2003), p317 31 http://www.skeptiko.com/161-outspoken-atheist-jerry-coyne/ 32 schrödinger, e. (1944) p121. 33 das wesen der materie” (the nature of matter), speech at florence, italy, 1944 (from archiv zur geschichte der max-planck-gesellschaft, abt. va, rep. 11 planck, nr. 1797) 34 barrow, john d., davies, paul c. w., harper, charles l. (eds) (2004) p451 – andrei linde: ‘inflation, quantum cosmology and the anthropic principle.’ 35 http://www.popsci.com/science/article/2010-06/quantum-entanglement-may-hold-dna-together-new-study-says 36 http://science.slashdot.org/story/11/01/13/0017256/nobel-prize-winner-says-dna-performs-quantum-teleportation 37 http://www.sciencedaily.com/releases/2011/03/110331104014.htm 38 http://infolikes.com/news/insect-capable-of-photosynthesis/# 39 http://myrmecos.net/insects/aphid4.html 40 allday, jonathan (2009) 41 http://www.nature.com/nature/journal/v446/n7138/abs/nature05677.html 42 abbott d., davies, p. c. w. & pati, a. k. (eds.) (2008), 6 43 jones, s. (2000), xxxi http://www.amazon.co.uk/s/ref=ntt_athr_dp_sr_1?_encoding=utf8&field-author=abbott%20derek%20et%20al&search-alias=books-uk&sort=relevancerank dna decipher journal | july 2013 | volume 3 | issue 4 | pp. 385-408 smetham, g. p., quantum genes[?]: bell’s theorem, quantum entanglement, consciousness & evolution issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 408 44 zurek wojciech h.(2002). ‘ decoherence and the transition from quantum to classical – revisited’ in los alamos science number 27 2002 45 penrose, roger (1995), 309 46 al-khalili, jim (2003) 47 stapp, henry (2004), 223 48 the observer (january 25th, 1931) 49 interview with david bohm, conducted by f. david peat and john briggs, was originally published in omni, january 1987. login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x microsoft word robertcampbell4_v2n3 dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 221-228 campbell, r., part i: a critique of river out of eden: the digital adam and eve issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 221 article part i: a critique of river out of eden: the digital adam and eve robert campbell * abstract the incredibly complex interdependent structural processes of the cell as it relates to organs and the host creature are not understood and yet darwinists of dawkins’ persuasion insist that it works and evolves by accident. the only purpose is the survival of dna sequences in a digital river out of eden that reduces us all to mindless robots driven by greed. recent evidence confirms each protein coding gene can code for many proteins through a complex variety of processes and epigenetic factors that can also employ the non coding sequences that constitute more than 95% of the human genome. new behavioral patterns are accommodated and can be heritable over generations without altering base-pair sequences of dna. the emergence of the relatively fixed vertebrate body plan with cerebral hemispheres anchored to an autonomic nervous system anticipated developments 400 million in the future together with hierarchical developments in the plants and invertebrates in tandem with geological evolution. key words: charles darwin, theory of evolution, cosmic order, intellegent direction, spirituality, atheist, richard dawkins. river out of eden ch. 1-the digital river: the double speak proceeds in dawkins’ first chapter [3] by suggesting that religions are grounded in ancestor worship and that it is real ancestors not supernatural gods that hold the key to understanding life. is religion really grounded in ancestor worship? according to the founders they are based upon direct experiential insights into a transcendent and intelligent creative order involving divinity, the dharma, and the tao in various traditions. the point here is not to justify traditional religions, nor the cultural biases that have become associated with them. the point is that darwinism is an unsubstantiated belief that cannot claim to be based upon direct experiential insight into the creative process. it is pure conjecture, yet dawkins insists that life is just digitized information in a river of genes out of eden. dawkins points out that ancestors were survivors and are rare compared to descendants, but this is not a very “astonishing” fact as he claims. it is hardly a profound or meaningful basis for a new belief system to explain the whole creative order. * correspondence: rober campbell, independent researcher. website: http://www.cosmic-mindreach.com e-mail: bob@cosmic-mindreach.com note: the articles presented in this issue are based on my book “downsizing darwin: an intelligent face for evolution” self-published in 1996 [1]. more information is available at my website [2]. dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 221-228 campbell, r., part i: a critique of river out of eden: the digital adam and eve issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 222 if a successful life is measured solely by prolific numbers of offspring, thus determining successful genes, and if this is the sole reason why birds fly well, fish swim well, and why we love life, sex and children, then the selfish gene is ultimately the only reality and greed is the only moral. by this standard we may be able to understand why we “love” our own children or close kin, but why should we love or even respect the children of others, except as potential mates to propagate our own greedy genes? social relationships all become reduced to strategic alliances of mutual greed. better to kill off others outside our alliances to make more room for own greedy genes to succeed, at least to the extent that we can do it successfully. mother theresa was obviously severely deranged, to say nothing of jesus christ or the buddha, or the countless selfless contributors to enhancing the human condition. and childless souls like isaac newton, copernicus, michelangelo, and leonardo were likewise all losers, unless we are to think of them as worker ants foregoing offspring so that others, who might happen to share some of their genes, may better survive. the most intelligent and compassionate among us must be blind slaves of genes, along with the most mindless of the propagating majority. this view of darwinism denigrates us all. it would leave us bereft of any sense of meaning to our being except the blind gratification of animal drives. insight into the creative order begins and ends with our own greedy flesh. darwin himself did not endorse such an extreme view. he took issue with the dogmatic genesis view held by the church, however he was not an atheist in the same extreme sense that a modern darwinist is. nothing was known of molecular biology during his time. genes, it is claimed, are not upgraded or otherwise altered in the using. they are passed on unchanged except for very rare random errors, a few of which may bestow certain advantages. now how does any biologist know with such supreme certainty that this is so? how does one know that a so-called “error” is really an error, not just sometimes, or most of the time, but always. since there is no decisive “proof” available, this must be accepted as an article of faith, along with the rest of the package. evidence to the contrary has been mounting over the past decade or more. the number of protein coding genes in the human genome, originally thought to be over 100,000, is now estimated at just over 20,000 and yet it is known that one gene can code for many proteins through a variety of processes. non-coding dna sequences called introns account for more than 95% of the base pairs in the human genome and used to be called junk dna. it is now known that non-coding sequences, together with epigenetic factors can drastically alter the pattern of gene expression. although epigenetic factors 1 such as dna methylation patterns and histone tail modifications, do not alter the base pair sequences of dna they are known to adjust gene expression to reflect specific behavior and circumstances 2 . acquired traits have been shown in various remarkable cases to be heritable from generation to generation. 3 1 campbell r. gene expression, 2011: http://www.cosmic-mindreach.com/gene_expression.html 2 morgan do. the cell cycle, principles of control. ch. 4.12. oxford univ. press, 2007. 3 carey, nessa. the epigenetics revolution. london: icon books, 2012 dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 221-228 campbell, r., part i: a critique of river out of eden: the digital adam and eve issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 223 there are related processes such as gene splicing that alter transcription. some dna sequences can change relative position (self-transpose) within the genome of a single cell by "copy and paste" or "cut and paste". transposition can create phenotypically significant mutations and alter the cell's genome size. and a host of small rnas transcribed from non-coding dna sequences are also known to regulate gene expression in various ways. there is also compelling evidence that evolution cannot proceed exclusively by rare random mutations since many processes in the cell are mutually interdependent as a set. professor michael j. behe in his book darwin’s black box, uses the example of a mouse trap to show that if any one part of even such a simple apparatus is missing the mouse trap will not work. a single cell is a far more complex interdependent apparatus. 4 genes, in this strange language of double speak, are then invested with values such as companionship. genes must be good at working cooperatively with other genes of the species, it is maintained, while at the same time maintaining that they compete with other genes. “good genes” know when and how to be altruistic to good collective advantage. these clusters of inanimate molecules that we call genes are invested with complex intentions and value judgments. this is quite apart from any sense of social propriety that we may entertain as individuals, and yet dawkins implies that our genetic inheritance predetermines our judgments as well. if our judgments are in fact predetermined why does richard dawkins feel a need to sway the world to his view? now genes of different species are said to be in different rivers that don’t have to cooperate, at least not in the same way, according to dawkins. it is an inverted river that keeps branching downstream, all the rivers diverging from common ancestors, all the way back to invertebrates, plants and bacteria and presumably to the first living cell, however it came to get started. it is maintained that major divergences of rivers, such as the mammals from the reptiles, did not in fact represent major events at the time, that they were no different in kind to any other divergence in species brought about by geographical separation. this is a little like saying that because a work of art begins with a single meaningless pencil stroke, the end result is only a meaningless scribble. accidental geographical separation is also considered necessary in order for diverging species to evolve in parallel. both the fossil record and the living record provide powerful evidence to the contrary. the first mammals diverged from the mammal-like reptiles in the triassic period early in the mesozoic era, about 225 million years ago 5 , when the reptiles were beginning to bloom into a great divergence of species. yet during the reptilian period the mammals experienced very little evolution apart from refinements associated with warm blooded activity, all being confined to small rodent-like creatures until nearly the end of the reptilian reign. 6 the reptiles completely dominated the scene, then abruptly became almost totally extinct about 65 million years ago. 4 behe, m.j. darwin’s black box. new york: touchstone books, 1998 5 purves b, orians g, heller c, sadava d. life, the science of biology, p 680. sunderland ma: sinauer. 1997. 6 pough fh, janis cm, heiser jb. vertebrate life, ch 19. prentice hall, 1999 dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 221-228 campbell, r., part i: a critique of river out of eden: the digital adam and eve issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 224 despite all the reptilian “success,” it wasn’t mammalian divergence from the end of the reptilian period that survived and blossomed in its turn. it was those tiny shrew-like rodents that had emerged near the beginning of the reptilian period, and that had undergone little change for 160 million years, that suddenly and rapidly exploded into a great divergence of mammalian species ancestral to those that we know today. the mammalian expansion had even started just before the dinosaurs met their demise, along with a global explosion of the flowering plants, and a diversification among the insects, which happened to provide a more efficient pollinating vector. a few flowering plants and insects had typically diverged much earlier, but not in abundance. after many millions of relatively stagnant years why should they choose that precise period to diversify? at the same time india had begun slamming into asia, pushing up the tibetan plateau. continents around the globe were under compression, rising and eventually creating vast areas of savanna where successive waves of mammalian herbivores could thrive and explore new mammalian forms. so it wasn’t just an accidental series of mutations among a few primitive mammalian rodents that heralded the beginning of the mammalian age. concordant developments among the plants and invertebrates provided an enriched food supply to support the higher metabolic rate of the mammals and birds. and global tectonics cooperated by providing appropriate terrain. a genetically unrelated diversity of factors converged in a relatively short space of time to make the event possible. the reptiles had had their day in the sun and it was time for them to make room for new developments not associated with the survival of dna sequences in their genes. should we now believe that the genetic sorting out of 160 million years of highly successful reptilian evolution, after the early rodent-like mammals had branched off, turned out to be a waste of time and a nearly complete failure? if they were so successful for so long, why didn’t they evolve again from the remaining reptilian stock? and are we to believe that all of the information genetically assimilated for successful survival strategies was suddenly forever lost to surviving reptiles, as well as to future generations of mammals? why then had mammalian evolution been so lethargic for so long, only to burst forth so quickly in such great diversity with the reptilian extinction? was it really just that they couldn’t compete with dinosaurs? it took the reptiles over 200 million years to explore the limits to size, while the mammals did it much faster in more refined body plans, once they got started. is this just another advantageous series of accidents that didn’t happen to come along until late and then came in a flurry? was there no integrating intelligence in the works that could reinvest the lessons learned by the dinosaurs to the advantage of the mammals? dawkins goes on to chastise his zoologist colleagues, some of whom are tempted to assign deep structural significance to the great divisions in the animal kingdom, since they represent the emergence of new blueprints or bauplans as they are sometimes called. he apparently believes that humans and cockroaches are equal players in the evolutionary theater, with any competitive edge going to the roaches, since they have been here relatively unchanged for a couple hundred million years and so have a highly successful survival record. is that beautiful and inspirational? dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 221-228 campbell, r., part i: a critique of river out of eden: the digital adam and eve issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 225 the fact remains that however modestly and gradually the vertebrates diverged from the invertebrates, there was a vastly different body plan associated with their emergence, linked to a completely new way in which to integrate their experience. with the primitive fish came the emergence of an autonomic nervous system coupled to cerebral hemispheres. worms, crabs, insects and the like, don’t have this complex apparatus. with the vertebrate animals emotive experience, associated with the autonomic nervous system, could be mirrored in cerebral awareness to some extent. the cerebral hemispheres are like a screen on which emotional experience is projected as if onto a tv screen where it can be observed. 7 this is the basis of self consciousness and it evolved into the remarkable ability to intentionally modulate emotive or emotional behavior in the higher vertebrates. higher vertebrates can select from a variety of emotional responses and tailor them to suit their circumstance. no one but dawkins is insisting that this unique new ability must have come into being perfectly formed. this is a smoke screen that he injects to refute the evidence. for some three hundred million years prior to the first vertebrates, the invertebrates were busy developing many different body plans with different sensory modalities and diverse means of locomotion, exploring them all to the full, from sponge and jelly fish to millipede, mollusk, ant, bee and octopus. then suddenly a whole new plan emerges that becomes anchored to a relatively fixed internal skeletal arrangement and limb structure, even similar sense and visceral organs from the reptiles to man. integrating the sensitive mobility of the vertebrates is an autonomic nervous system coupled to cerebral hemispheres. however it got started this is a profoundly different new body plan capable of higher levels of sentient awareness. this evolutionary development reflects an intelligence inherent in the creative process capable of anticipating future developments in broad outline, hundreds of millions of years in advance. there has been no significant vertebrate divergence from this common plan for three hundred million years, no millipede lizards or eight legged spidermen, no compound eyed aardvarks or hummingbird cocoons. the fact is that with the vertebrates the whole focus of evolution changed to a higher level of integrating experience, a more conscious and sentient level harnessed to a common skeletal and nervous system format. this did not occur within the infinitely more diverse format of invertebrate evolution. neither did invertebrate evolution have to explore the same limits to size that the vertebrates have. the invertebrates were focusing on methods of sensing and responding to a huge variety of circumstance, not on the limits to behavior associated with four limbs. there’s never been a forty ton spider, ant, or crab. even the giant mollusks and cephalopods are no match for dinosaurs and whales. these obvious facts have been conveniently ignored. the climb up the ladder of sentient awareness has integrated the whole of vertebrate evolution into a common scheme that has obviously drawn on the several hundred millions of years of prior 7 maclean pd. the triune brain in evolution: role in paleocerebral functions. ny: plenum press, 1990. dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 221-228 campbell, r., part i: a critique of river out of eden: the digital adam and eve issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 226 invertebrate experience. all the diverse modes of sensitive motility did not have to be re-explored again in order to settle on a single quadruped format with a common mode of nervous system integration. this is a powerful indication that the whole creative process is in communication with itself, just as the various parts of the human body are. why is no scientist trying to determine how? the current constraints of the darwinian paradigm preclude the question. it isn’t an easy thing to formulate an alternate paradigm. it is commonly believed that it all has to do with chemical messages. of course there is chemical signaling, but that isn’t all. it’s like saying because we send letters that we can’t sense another’s mood or meaning, or the feeling of spring. how is the sense in the message to be read and understood if there is no more to the creative order than inanimate messages going from place to place like billiard balls. there is nevertheless a rather obvious hierarchical order to the evolutionary process in which each higher level is dependent upon the capabilities achieved by the lower levels in the long hard climb toward higher levels of sentient awareness. we are indebted to plants for oxygen and food, to invertebrates for the basics of sensory response, and our autonomic nervous system is anchored firmly to the primitive parts of our cerebral hemispheres associated with the reptile and lower mammal. these are well established biological facts. although we are emotionally anchored to our early vertebrate ancestors, the neocortex (or new brain) has exploded in size with the higher mammals and man. this enhanced intellectual capacity is not directly colored by emotional input and thus has brought with it an increasing ability to modulate and tailor more primitive emotional urges to better consciously suit the needs of circumstance. we will return to this later. dawkins keeps shifting back and forth in double speak. his rivers of genes are now digital rivers, physical bits of genetic know-how that offer no place for values and purpose. but somehow there is only one genetic code for the whole of earthly life, from bacteria to humans (and perhaps only one in the universe if life originated from space). the chances of this happening twice by accident, he says, are about a million million million million million to one, so life on earth must have evolved from a single cell, he insists. there are other scientific options possible, which we will come to later, but he doesn’t acknowledge them since it would erode his argument. in fact the odds against life emerging on earth, or anywhere else, by accident are infinitely greater than those that he quotes but this fact is also ignored. genes are digital information and this, dawkins claims, has dealt the final killing blow to vitalism. by implication he means to also sweep aside any other possible belief about the nature of life. by some unexplained leap of logic he makes the remarkable statement that it is no longer possible to believe that there is anything fundamentally mysterious in living protoplasm. i am not contending here that genes do not encode discrete bits of information but how does one conclude from that bit of knowledge that there is nothing else whatever involved in the creative process? and if less than one percent of the diverging branches of the evolutionary tree have survived, are we then not forced to conclude that over ninety-nine percent of the information accumulated through the evolutionary process is forever lost to future generations and a waste of time? according to the same logic we may expect the percentage of retained information to get dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 221-228 campbell, r., part i: a critique of river out of eden: the digital adam and eve issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 227 smaller and smaller as the process proceeds. the genetic river must be drying up, despite all its branching and diversification. the dna struggle for survival is destined to lose. the contradictions to the exclusive darwinian argument keep multiplying with the diverging branches of the evolutionary tree. jumping from genes being encoded information to genes being capable of exclusively directing living processes is like saying that because a set of engineering drawings and specifications contain all the information necessary to erect a building that they can do it themselves. there is no team of architects or engineers producing the most incredibly complex of plans. they happen by accident, even though countless useless mistakes can apparently perpetuate themselves in reptiles for 160 million years before their demise. there is no construction company reading the plans, organizing and assimilating the skills, the equipment and the materials and then erecting the structures. all this happens by itself without supervision or management. and there is no budgeting, or financing, or sales involved. the chemical resources are assumed to be gratis and if there’s a surplus of cement more buildings can go up, whether there’s plumbing or electricity available for them or not, and without regard for whether the buildings are of the slightest use to anyone. buildings are infinitely simpler things than cells, not to mention multi-cellular creatures. there is no intelligent direction integrating and balancing the diverse requirements of biological structures, nor are there intelligent occupants in the biological buildings of dawkins’ world. that would include dawkins himself. “life is just bytes and bytes and bytes of digital information,” he says. let’s all go out and propogate as much as we can, for it is only the survival of our genes that matters, and for that who needs to study genetics, or anything else. not quite. there’s a bit more to it than that, says dawkins. bodies are important too. genes inhabit bodies he observes. a polar bear has about 900,000,000 cells grouped into a couple of hundred types for different body parts, he says, all with the same genes. how do the body parts differentiate? only certain genes are programmed to turn on in certain cells. how are they programmed? by the computer method known as bootstrapping, says dawkins, who confesses that there is an element of the chicken and egg paradox here, then hurries on to say it is not insuperable. how does bootstrapping work? by chemical differences caused by “polarities” within the fertilized egg as it divides again and again. how does the polarity come into being and function? he doesn’t pursue this process of regress further, for there surely seems to be some kind of incredible communication system at work, which intelligently organizes the orderly development of polar bears. that discovery would refute his whole argument. then there is the physical shaping of the embryo as it develops. how does a glob of replicating cells assume a complex functional form. he marvels at the process but he doesn’t touch on how this works. nor does he comment on how all the cells in the mature body somehow communicate with one another to maintain a balanced commitment of available resources to meet an immensely complex priority of mutual needs. the truth is that no scientist knows how it all works together. science doesn’t know how experience is organized and integrated. when it gets down to this fundamental level of abstraction the inquiry stops. dead in its tracks! it stops even though science implicitly acknowledges that genes are hierarchically ordered, that some genes control other genes that in turn control others. but if there is hierarchical order at work this contradicts random order as the driving mechanism. we can hardly believe that one of those billiard balls could suddenly dna decipher journal | november 2012 | volume 2 | issue 3 | pp. 221-228 campbell, r., part i: a critique of river out of eden: the digital adam and eve issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 228 become a cue ball and cue with the ability to shoot other billiard balls around at will with unerring accuracy. then come the blind assertions, the leaps of faith. dawkins invents a “...throbbing, heaving, pullulating, protoplasmic, mystic jelly,” new descriptions of life’s animating reality coined to ridicule all opposition to atomic billiards. “nineteen fifty-three, the year of the double helix, will come to be seen ... as the end of mystical and obscurantist views of life...” he says. really! what can it be but another obscurantist view of life! references 1. robert campbell, downsizing darwin: an intelligent face for evolution. mindreach library (1996). 2. http://www.cosmic-mindreach.com 3. richard dawkins, river out of eden: a darwinian view of life. basic books (1996). 4. richard dawkins, the blind watchmaker: why the evidence of evolution reveals a universe without design. w. w. norton & company (1996). 5. richard dawkins, the selfish gene. oxford university press (1990). 6. pough fh, janis cm, heiser bh. vertebrate life 5 th ed. nj: prentice hall, 1999 7. purves wk, orians gh, heller hc, sadava d, eds. life: the science of biology 5 th ed. sunderland ma: sinauer assoc, 1998. 8. morgan do. the cell cycle, principles of control. ch. 4.12. oxford univ. press, 2007. 9. gilbert sf. developmental biology 5 th ed. sunderland ma: sinauer assoc, 1997 10. voet d, voet jg, pratt cw. principles of biochemistry 4 th ed. john wiley & sons, 2012. dna decipher journal | october 2019 | volume 9 | issue 2 | pp. 86-90 86 pitkänen, m., could mars have intra-planetary life? essay could mars have intra-planetary life? matti pitkänen 1 abstract a popular article in national geographic tells about unexpected findings made by the first robotic geophysicist, the insight lander revealed in the european planetary science congress and in the american astronomical society. there are odd magnetic pulsations with frequency around 10 mhz occurring at martian night-time: for earth these pulsations occur in frequency range 1 mhz to 1 hz. mars has much stronger magnetic field as expected. the magnetic field was detected at heights 96-400 km. besides this there is evidence for the existence for a global electrically conductive layer about 6 km below the surface, which suggest an underground reservoir of water. this has enormous implications for potential existence of life in mars. there is also earlier evidence for the existence of salty, liquid water measuring about 19 km across. in this article i discuss the findings from tgd point of view. 1 introduction a popular article in national geographic (see http://tinyurl.com/y5unt6y7) tells about unexpected findings made by the first robotic geophysicist, the insight lander revealed in the european planetary science congress and in the american astronomical society. there are odd magnetic pulsations with frequency around 10 mhz [1] (see http://tinyurl.com/y3ll8kcg) occurring at martian night-time: for earth these pulsations occur in frequency range 1 mhz to 1 hz. mars has much stronger magnetic field as expected: the strength is rather near to that of earth at earth radius if it extends so far. the magnetic field was detected at heights 96-400 km. besides this there is evidence for the existence for a global electrically conductive layer about 6 km below the surface, which suggest an underground reservoir of water. this has enormous implications for potential existence of life in mars. there is also earlier evidence for the existence of salty, liquid water measuring about 19 km across (see http://tinyurl.com/ycjaky5g). in the sequel i will discuss the findings from tgd point of view. for years ago i developed what i called expanding earth model [8, 7] with motivation coming from the finding that if the radius of earth is 1/2 of its recent value, continents fit nicely together. this strengthens wegener’s finding. in tgd smooth cosmic expansion is replaced with a sequence of rapid steps, and the proposal was that the rapid expansion increasing the radius by factor 2 could explain the sudden emergence of highly developed life forms in cambrian explosion. they would have bursted from underground ocean as the crust of earth broke to continents and led to the formation of oceans. the model solves several problems related to the evolution and allows also new view about the evolution of climate replacing the snowball earth model. the new findings allow to develop the model further. 1. also mars would have magnetic field but it would contain only the part for which flux tubes carry monopole flux so that no currents would be required to maintain it. also earth would have monopole part of field besides ordinary part requiring currents to maintain it. the monopole part would correspond to what i have called endogenous magnetic field with strength 2/5 of the magnetic field of earth [5]. 1correspondence: matti pitkänen http://tgdtheory.com/. address: rinnekatu 2-4 a8, 03620, karkkila, finland. email: matpitka6@gamail.com. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/y5unt6y7 http://tinyurl.com/y3ll8kcg http://tinyurl.com/ycjaky5g http://tgdtheory.com/ mailto:matpitka6@gmail.com dna decipher journal | october 2019 | volume 9 | issue 2 | pp. 86-90 87 pitkänen, m., could mars have intra-planetary life? van allen belts would be present but carry dark matter in tgd sense and would bring ions of the solar wind to the interior of earth in particular to the ocean below martial surface. the ionosphere in the oceans below crust would not be lost to the outer space so that the oceans would serve as a womb for the prebiotic evolution. the model explains why the magnetic field has not been detected but explains the mysterious finding that auroras requiring the presence of magnetic field appear also in mars. 2. the standard model assumes that the outer core of mars somehow disappeared and that this led to the collapse of the magnetic field. tgd model suggests the opposite. mars has never had separate inner and outer cores. in the case of earth the expansion doubled the radius of the core and it split to inner and outer core and outer core gave rise to the ordinary magnetic field. 3. the prebiotic evolution in the interiors of earth and mars has been discussed already earlier [6, 2, 3]. the recent findings lead to a more detailed picture. solar radiation propagating as dark photon along monopole flux tubes to the underground oceans and transforming to ordinary photons (bio-photons) would make possible photosynthesis in the underground ocean producing also oxygen. this would allow oxygen based metabolism. the underground water containing the life forms would burst to the surface in the expansion. the emergence of the convective inner core would create ordinary magnetic field preventing the leakage of the atmosphere and life would continue to evolve in the oceans. 2 tgd based model for the findings and for intra-martial life the strange findings about mars [1] can be understood in the framework provided by tgd based model for expanding earth providing also explanation for the mysterious cambrian explosion assuming that the life developed in earth’s interior, tgd based notion of magnetic field, and dark matter identified as phases with nonstandard value heff = nh0 of planck constant. 2.1 connection with the model of expanding earth these findings bring in mind tgd based model for expanding earth [8, 7, ?] (see http://tinyurl.com/ yc4rgkco, http://tinyurl.com/yb68uo3y, and http://tinyurl.com/ya68nggs). 1. the observation is that if earth has radius one half of itse recent radius the continents fit nicely together to cover entire surface of earth. this lead to the proposal that during cambrian explosion in which highly developed life formed mysteriously emerged, the earth radius grew by factor 2 in a relatively short time. the life would have evolved in mother gaia’s womb, underground oceans perhaps between crust and astenosphere at depth not larger than 80 km, shielded from cosmic rays and meteoric bombardment. 2. the sudden expansion can be modelled in tgd inspired new physics as a phase transition increasing the p-adic length scale of earth and reducing the scale dependent cosmological constant assignable to earth by factor 1/4: these kind of phase transitions replace smooth cosmological expansion in tgd inspired cosmology. this led to the splitting of the continuous crust to continents and oceans emerged as the water from underground oceans containing the highly developed life forms bursted to the surface. 3. the intriguing coincidence is that mars has radius which is 1/2 of earth’s recent radius. could also mars have underground ocean with rather developed life forms waiting for the moment of birth? magnetic field is necessary in tgd based model of life and the article tells that mars has unexpectedly strong magnetic field. it also tells about underground ocean at death about 100 km! the boundary between earth’s core and astenosphere, where the ancient oceans might have been is at dept of about 80 km. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/yc4rgkco http://tinyurl.com/yc4rgkco http://tinyurl.com/yb68uo3y http://tinyurl.com/ya68nggs dna decipher journal | october 2019 | volume 9 | issue 2 | pp. 86-90 88 pitkänen, m., could mars have intra-planetary life? 2.2 there is something weird in the magnetic field of mars the assumption that magnetic field of mars can be approximated as a dipole field leads to a paradoxical situation in maxwellian framework. 1. wikipedia article about earth’s magnetosphere (see http://tinyurl.com/y3t78oka) gives a criterion for the height below which magnetic field can survive under the pressure caused by solar wind. the criterion reads rcf rp = ( b2 ρswv2sw )1/6 . here rp is planet radius, b is the strength of the magnetic field at its surface, and ρsw and vsw are the mass density and velocity of solar wind. the ratio rcf /rp is essentially the ratio of the density of magnetic energy and density of kinetic energy. this implies that the strength of b is about 10 times higher than the strength of the earth’s magnetic field at surface about .5 gauss. the recent findings should increase the earlier estimate rcf /rp ∼ 1 given in wikipedia. for earth the thickness of magnetosphere is about 10 times earth radius giving rcf /rp ∼ 11. 2. the strength of magnetic field behaves like 1/r3 in dipole approximation and scaling rp by factor 2 would reduce magnetic field strength at surface down by factor 1/8, which is near to value of the earth’s magnetic field strength be . could one think that also earth had similar magnetic field before the expansion an that the expansion of earth radius by factor 2 gave rise to the recent magnetic field? bmars ∼ 10be however suggests that the magnetic field of mars in dipole approximation should actually extend equally far as the earth’s magnetic field! this does not seem to make sense. could one think that the matter at the flux tubes of martian magnetic field is dark matter as heff = nh0 phases and is not visible in the ordinary sense. for instance, cyclotron energies proportional to heffeb/m would be much higher than expected. another option is that the magnetic field corresponds carries monopole fluxes at its flux tubes carrying dark particles. what looks mysterious is that if martian magnetic field is dipole field in reasonable approximation, it should be more or less like earth’s magnetic field! one would expect cyclotron radiation and van allen belts. why they are not seen? the answer could be simple. 1. also earth’s magnetic field would decompose to stable part for which flux tubes carry quantized monopole flux and ordinary part. monopole part does not need current to sustain it and this has been used to explain why earth’s magnetic field has not disappeared long time ago. the varying part of the earth’s magnetic field would be created by convection currents in the solar. since mars does not have outer core, it would not have this part of magnetic field. i have proposed this model for the maintenance of earth’s magnetic field at [5] (see http://tinyurl.com/y5anawyk). 2. i have assumed that dark matter as heff = nh0 phases of ordinary matter essential for life resides at the flux tubes of this field having strength which is 2/5 of the earth’s ordinary magnetic field. i have called this field endogenous magnetic field and its existence and existence of heff hierarchy was deduced from the explanation of quantal effects of elf em fields on vertebrate brain. if mars has only dark magnetic field, the magnetic field of mars could be invisible! the ordinary part of this magnetic field should appear in the analog of cambrian explosion as the radius of mars increases to that of earth and core radius increase by factor 2 and the core becomes unstable against division to two layers. 3. it has been thought that martian magnetic field is so weak because the outer core of mars has been seized up in distant past leading to a collapse of the magnetic field. could one think that the reverse of this process took place for earth in the expansion and created the outer core, perhaps by issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/y3t78oka http://tinyurl.com/y5anawyk dna decipher journal | october 2019 | volume 9 | issue 2 | pp. 86-90 89 pitkänen, m., could mars have intra-planetary life? splitting of the core to outer and inner core? this picture would fit nicely with the p-adic length scale hypothesis suggesting layered structures with thickness of layer coming as some power of 2: the thickness of core would have double and core would have divided to two layers. if the strength of the earth’s magnetic field has been stronger by factor 8 before cambrian explosion, this should be seen in magnetic records. the rotation of the outer core would create ordinary magnetic field after the expansion. before that various ions from solar wind would have entered to the dark flux tubes and entered to the interior of mars. same would have happened also in earth and would explain how oxygen atmosphere emerged in cambrian explosion and life could burst safely to the surface of mars. 4. intriguingly, mars has its own version of northern lights (see http://tinyurl.com/y5z7jlkb). without magnetic field auroras should not exist! could it be that they are dark auroras associated with dark magnetic field of mars. in reconnections of the magnetic field o martian magnetic field and those associated with solar wind dark ions would transform to ordinary ones and create norther and souther lights. van allen belts are in the height range .6-58 mm (earth radius is 6,4 mm). mars should have dark van allen belts along which ions of solar wind would end down to the interior of mars. 5. what about the pulsed oscillations of martian magnetic field at frequency around 10 ms, which corresponds to a period of 3.33... minutes detected at the night-side of mars? the pulsations could correspond to a biorhythm. also earth’s magnetic field has pulsations with frequencies varying between 1 mhz and 1 hz. 1 mhz corresponds to 3/3.6 minutes and 1 hz to average dna cyclotron frequency in endogenous magnetic field bend = .2 gauss identifiable as dark magnetic field. could these pulsations correspond to a heartbeat or breathing of martian magnetic mother gaia rather concrete pulsation of its magnetic body made from flux tubes and/or sheets? why the pulsations appear only at the dark side? could the pressure of the solar wind prevent the pulsations at the day-side? one can wonder what the measured magnetic field is. is it the sum of dark and ordinary part or only ordinary part. if test particles touch all space-time sheets involved, they experience the sum of the magnetic fields so that the usual measurements should give the sum. if it is only the ordinary part, one would still have the problem why the field having strength near to earth’s magnetic field is not visible as van allen belts for instance. the qft limit of tgd indeed corresponds to the replacement of space-times sheets with single region of minkowski space and the identification of fields as the sums of the induced fields from various space-time sheets. 2.3 intraplanetary life the new observations allow to make the existing model for intra-planetary life much more details. the following applies to both earth and mars. 1. at earth the multicellular life forms would have emerged in cambrian explosion suddenly from the earth interior as its size increased by factor 2. the expansion would be one stepwise cosmic expansion and associated with the decrease of length scale dependent cosmological constant associated with earth. same should happen in mars sooner or later. so that there is no reason to worry. if we destroy our species and many other at the same time, intelligent life forms will develop in mars. 2. if the multicellular life forms represented intra-terrestrial life, photosynthesis and even oxygen based life should have evolved in underground ocean. the breathing animals would be like fishes using the oxygen in water. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/y5z7jlkb dna decipher journal | october 2019 | volume 9 | issue 2 | pp. 86-90 90 pitkänen, m., could mars have intra-planetary life? 3. the dark magnetic flux tubes of planet would served as channels for solar photons propagating as dark photons to the ocean in the interior of the planet. dark photons would have transformed to ordinary photons (that is bio-photons) and used in photosynthesis making possible chemical energy storage. photosynthesis would have produced oxygen o2, which would not have been lost to outer space now: a good reason for intra-planetary life when oxygen atmosphere is missing. thus breathing animals would have become possible besides plants like organisms performing the photosynthesis. also animal-plants doing photosynthesis themselves can be considered. even we could use the metabolic energy stored chemically in manner analogous to photosynthesis. the machinery is very similar and there is evidence that even humans can use sunlight as metabolic energy. pollack effect [4] would be key element here. pollack effect generates charge separation and thus voltage and this gives rise to a battery. references [1] chi pj et al. insight observations of magnetic pulsations on martian surface: initial findings and implications. [2] pitkänen m. evolution in many-sheeted space-time. in genes and memes. online book. available at: http://www.tgdtheory.fi/tgdhtml/genememe.html#prebio, 2006. [3] pitkänen m. quantum gravity, dark matter, and prebiotic evolution. in genes and memes. online book. available at: http://www.tgdtheory.fi/tgdhtml/genememe.html#hgrprebio, 2014. [4] pitkänen m. pollack’s findings about fourth phase of water : tgd view. available at: http: //tgdtheory.fi/public_html/articles/pollackyoutube.pdf, 2014. [5] pitkänen m. maintenance problem for earth’s magnetic field. available at: http://tgdtheory.fi/ public_html/articles/bmaintenance.pdf, 2015. [6] pitkänen m. more precise tgd based view about quantum biology and prebiotic evolution. available at: http://tgdtheory.fi/public_html/articles/geesink.pdf, 2015. [7] pitkänen m. expanding earth hypothesis, platonic solids, and plate tectonics as a symplectic flow. available at: http://tgdtheory.fi/public_html/articles/platoplate.pdf, 2018. [8] pitkänen m. expanding earth model and pre-cambrian evolution of continents, climate, and life. available at: http://tgdtheory.fi/public_html/articles/expearth.pdf, 2018. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://www.tgdtheory.fi/tgdhtml/genememe.html#prebio http://www.tgdtheory.fi/tgdhtml/genememe.html#hgrprebio http://tgdtheory.fi/public_html/articles/pollackyoutube.pdf http://tgdtheory.fi/public_html/articles/pollackyoutube.pdf http://tgdtheory.fi/public_html/articles/bmaintenance.pdf http://tgdtheory.fi/public_html/articles/bmaintenance.pdf http://tgdtheory.fi/public_html/articles/geesink.pdf http://tgdtheory.fi/public_html/articles/platoplate.pdf http://tgdtheory.fi/public_html/articles/expearth.pdf introduction tgd based model for the findings and for intra-martial life connection with the model of expanding earth there is something weird in the magnetic field of mars intraplanetary life dna decipher journal | december 2015 | volume 5 | issue 3 | pp. 174-180 174 pitkänen, m., why information molecules containing aromatic rings should be so important? article why information molecules containing aromatic rings should be so important? matti pitkänen 1 abstract the basic message in the book, ”inner paths to outer space: journeys to alien worlds through psychedelics and other spiritual technics”, written by rick strassman et al, is that psychedelics might make possible instantaneous remote communications with distant parts of the universe. the objection would be that light velocity sets stringent limits on classical communications. in tgd framework this argument does not apply. in this article a model for remote mental interactions is constructed using basic notions of tgd inspired quantum biology such as magnetic body, dark photons and zero energy ontology. further, both psychedelics and dna contain aromatic rings. each base-pair would contain 1+2+1+1=5 (two rings from sugars) aromatic rings and longer dna sequences would define larger conscious entities. of course, all proteins contain these aromatic rings possibly integrating by flux tube connections to larger conscious entities. in this picture it would not be surprising of the basic information molecules would also involve aromatic rings. 1 introduction there is a book about psychedelics titled as ”inner paths to outer space: journies to alien worlds through psychedelics and other spiritual technics” written by rick strassman, slawek wojtowicz, luis eduardo luna and ede frecska [1].the basic message of the book is that psychedelics might make possible instantaneous remote communications with distant parts of the universe. the basic objection is that light velocity sets stringent limits on classical communications. in tgd framework this argument does not apply. second objection is that the communications require huge amount of energy unless they are precisely targeted. the third objection is that quantum coherence in very long, even astrophysical scales is required. in tgd framework these objections do not apply. in zero energy ontology (zeo) communications in both directions of geometric time are possible and kind of time-like zig-zag curves make possible apparent superluminal velocities. negentropic quantum entanglement provides second manner to share mental images, say sensory information remotely. the proposed model leads to a general idea that the attachment of information molecules such as neurotransmitters and psychedelics to a receptor as a manner to induce a remote connection involving transfer of dark potons signals in both directions of geometric time to arbitrarily long distances. the formation of magnetic flux tube contact is a prerequisite for the connection having interpretation as direct attention or sense of presence. one can see living organisms as systems continually trying to build this kind of connections created by a reconnection of u-shaped flux tubes serving as magnetic tentacles. the natural tgd inspired hypothesis about what happens at the level of brain to be discussed in sequel in detail goes as follows. 1. psychedelics bind to the same receptors as the neurotransmitters with similar aromatic rings (weaker assumption is that neurotransmitters in question possess aromatic rings). this is presumably consistent with the standard explanation of the effect of classical psychedelics as a modification of serotonin uptake. this binding replaces the flux tube connection via neurotransmitter to some part of the personal magnetic body with a connection via psychedelic to some other system, which might 1correspondence: matti pitkänen http://tgdtheory.com/. address: karkinkatu 3 i 3, 03600, karkkila, finland. email: matpitka6@gmail.com. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.com/ mailto:matpitka6@gmail.com dna decipher journal | december 2015 | volume 5 | issue 3 | pp. 174-180 175 pitkänen, m., why information molecules containing aromatic rings should be so important? be even in outer space. a communication line is created making among other things possible remote sensory experiences. magnetic fields extending to arbitrary large distances in maxwell’s theory are replaced with flux tubes in tgd framework. the magnetic bodies of psychedelics would carry very weak magnetic fields and would have very large heff maybe serving as a kind of intelligence quotient. 2. this would be like replacing the connection to the nearby computer server with a connection to a server at the other side of the globe. this would affect the usual function of transmitter and possibly induce negative side effects. clearly, tgd inspired hypothesis gives for the psychedelics much more active role than standard hypothesis. this mechanism could be a universal mechanism of remote mental interactions. 3. phychedelics can be classified into two groups depending on whether they contain derivative of amino-acid trp with two aromatic rings or phe with one aromatic ring. also dna nucleotide resp. its conjugate have 2 resp. 1 similar aromatic rings. this suggests that the coupling between information molecule and receptor is universal and same as the coupling between the two bases in dna double strand and consists of hydrogen bonds. this hypothesis is testable since it requires that the trp:s/phe:s of the information molecule can be brought to same positions as phe:s/trp:s in the receptor. if also protein folding relies on this coupling, one might be able to predict the folding to a high degree. 4. a highly suggestive idea is that molecules with aromatic rings are fundamental conscious entities at the level of molecular biology, and that more complex conscious entities are created from them by reconnection of flux tubes. dna/rna sequences and microtubules would be basic examples about this architecture of consciousness. if so, protein folding would be dictated by the formation trp-phe contacts giving rise to larger conscious entities. i have published the material of the article for about two years ago at my homepage in the chapter [2] of ”tgd based view about consciousness, living matter, and remote mental interactions” and this article written for about one year ago is revised. 2 some background about psychedelics phychoactive drugs can be classified into three basic types. some raise the activity level (excitation), some calm down (inhibition), and some change the character of consciousness profoundly. psychedelics/hallucinogens [1] belong to the third group. psychedelics (such as psilocin, psicylobin, dmt, lsd) containing aromatic rings and many of them (such as psilocin, psicylobin, dmt) attach to serotonin receptors. as the official term “hallucinogens” implies, psychedelic induced experiences are regarded as hallucinations in the materialistic world view although the denial of the reality of subjective experiences themselves requires a really hard-nosed skeptic. the title of the book reveals that the question posed in the book is whether these experiences could be about real world, kind of sensory input from distant parts of the universe. the indigenous people using ayahuasca and similar psychedelics have regarded these experiences involving meeting of representatives of other civilizations as perceptions about real worlds. also terence and dennis mckenna, who are pioneers of systematic study of the effects of various psychedelics, shared this view. in the materialistic ontology of standard physics this kind of interpretation is of course excluded. that hallucinations are in question is “obvious”, too obvious actually! the classical psychedelics are psilocin and psilocybin contained by mushrooms, dmt found in ayahuasca, and mescaline found in peyote cactus. dmt is an endogenous psychedelic and there is pumping of dmt through blood-brain barrier so that dmt could have important brain function. the aromatic ring structures of psychedelics and neurotransmitters involved provide a more concrete view about the situation. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2015 | volume 5 | issue 3 | pp. 174-180 176 pitkänen, m., why information molecules containing aromatic rings should be so important? 1. classical psychedelics are derivatives of two basic chemical groups: tryptamine and phenetylamine which in turn derive from the amino-acids trp and and phe. 2. trp is characterized by pair of aromatic rings (6-cycle and 5-cycle). psychedelic psilocin, psylocybin, dmt have 2 aromatic rings. neurotransmitter serotonin has also two aromatic rings. 3. phe has single aromatic ring (6-cycle). psychedelic mescaline has single aromatic ring. neurotransmitters dopamine and norepinephrine have one aromatic ring. note that both serotonin, dopamine, and norepinephrine are associated with mood disorders: clearly control in long time scales is in question, which in tgd framework suggests very large size scales for the parts of magnetic body involved. 4. remarkably, dna and rna nucleotides can be classified to those with two aromatic rings (pyrimidines a and g) and there conjugates with one aromatic ring (purines c, t and u). note that also his and tyr are amino-acids with single aromatic ring. information molecules involve often aromatic rings. for instance, hormones involve often complex rings structures. also hydrophobic second messengers (such as camp) involve aromatic rings. 5. lsd, which is synthetic psychedelic, has 3 6-rings and one 5-ring. 6. the classification of the neurotransmitter receptors provides further insights. they are classified into two groups. ligand gated receptors can be excited and inhibited by certain neural transmitters. g-protein coupled receptors modulate the actions of excitatory (glutamate,aspartate) and inhibitory neural transmitters (gaba, glycine). most neural transmitters bind to g-protein coupled receptors and this is true for classical psychedelics and for serotonin, dopamine, and norepinephrine. the first guess is that the presence of aromatic rings determines the character of the transmitter receptor pair and that g-protein coupled receptors having aromatic rings are above ligand gated receptors in the hierarchy and control them. they would correspond to two different levels in the hierarchy of magnetic bodies. note that also lsd binds to g-protein receptors. according to the book [1], pineal gland might be in a special role concerning psychedelics. 1. pineal gland is the only nucleus of brain, which does not appear as left-right pair: this suggests that is functions relates to a control of the entire brain in long time scales. descartes regarded pinearl gland as the seat of soul. pineal gland is also known as “third eye” and in lower species it indeed serves the function of eye. 2. pineal gland is responsible for the production of melatonin: the production rate varies with a circadian rhythm. melatonin is a serotonin derived hormone and therefore has 2 aromatic rings: this suggests that the amount of serotonin is higher in pineal gland than elsewhere in brain. melatonin helps in sleep disorders and affects also other parts of brain. one can ask whether melatonin is involved with establishing of distant flux tube connections during sleep not only in pineal gland but also in other parts of brain and whether these connections are built up during sleep. 3. there is some evidence that pineal gland can produce dmt from tryptamine believed to be released during dreaming, during spiritual and mystical experiences, and during the time of death. taking the title of the book seriously, one can ask whether this eye is able to see also to cosmic distances possibly using large heff photons and whether dmt is involved. 3 could instantaneous communications in cosmic scales be possible in tgd universe? in tgd inspired ontology the notion of magnetic body with astrophysical, galactic or even super-galactic size changes the situation completely. the basic communication tool would be touch of magnetic bodies isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2015 | volume 5 | issue 3 | pp. 174-180 177 pitkänen, m., why information molecules containing aromatic rings should be so important? generating reconnections and making possible signalling from the biological body ti the member of distant civilization. the perception of the biological body of alien would differ in no manner from that of my neighbor since the mechanisms would be the same as involved with the transfer of sensory data to my personal magnetic body and control commands from there to biological body (at least through genome). the basic objection against the possibility suggested by the title of the book is that finite light velocity poses absolute upper bound for the distance of objects with it is possible to be in contact during “trip”. one must be however very cautious here: the assumption that signals propagate only to singlet direction of time is essential also and derives from classical thermodynamics. in tgd framework second law continues to hold true but the arrow of geometric time for zero energy states changes in each state function reduction occurring to the either boundary of cd. hence instantaneous communications (“remote seeing” !) using reflection in time direction become possible even over cosmological distances and define among other things the mechanism of memory in tgd universe. time consuming and expensive space travel would become un-necessary: our magnetic body giving us cosmic size together with zero energy ontology making possible instantaneous “seeing” of both future and past by reflection of photons in time direction would be enough. memory and anticipation would be basic examples about seeing in time direction. this view would also resolve fermi paradox. we could be actually in a continual contact with the distant civilizations but without realizing it. one can ask whether similar contacts could take place in psychedelic induced experiences. memories and future plans would be examples of “seeing” in time direction. the continual re-creation of the universe by quantum jumps would of course mean that the actual future/past need not be same as those which are “seen”. shamans identify various plants as conscious entities teaching them in tgd framework this would translate to magnetic bodies of representatives of distant civilizations remotely teaching the representatives of more primitive civilizations. what is the precise meaning of the catchy phrases “communications with geometric past/future”, “time reflection”, and “seeing in time direction”. 1. the recent view about state function reduction in zero energy ontology leads to a precise identification of self as conscious entity. self corresponds to a sequence of state function reductions leaving the passive boundary of causal diamond (cd) invariant and also zero energy states correspond to superpositions of state pairs at opposite boundaries of cd. state function reduction leaves the member of the state pair at either boundary of cd (call it passive boundary) invariant this is the counterpart of zeno effect. in the analog of unitary evolution following each reduction the position of active boundary is shifted to geometric future and the state at it is changed. this is the counterpart of unitary time evolution at active boundary. the increase of the temporal distance between the tips of cd gives rise to the experienced flow of time. negentropy maximization principle (nmp) eventually forces the first reduction to the opposite boundary of cd: self dies and re-incarnates at the opposite boundary and growth of the cd continues at opposite direction. the new self has arrow of time opposite that for the old one. the first state function reduction generates negentropic entanglement and can increase the value of heff so that evolution becomes possible. 2. in this framework geometric memories correspond naturally to time reversed sub-selves defining mental images. the space-time region (active boundary of cd) wherefrom they receive sensory information is indeed in geometric past of the self so that the interpretation as episodal memory makes sense. also classical communications are naturally associated with sub-self and its time reversal. note that precognition is memory from the point of time-reversed self. during sleep we precognize our geometric future. consider now communications with distant objects in this framework. 1. negative energy signal would mean death of sub-self representing mental images and its re-incarnation in the geometric past accompanied by negative energy signa received by the new sub-self. the death isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2015 | volume 5 | issue 3 | pp. 174-180 178 pitkänen, m., why information molecules containing aromatic rings should be so important? of the time-reversed sub-self generates a sub-self with original arrow of time receiving the accompanying positive energy signal. the dying sub-self sends a signal received by its re-incarnation! 2. communications with distant parts of the cosmos would be experiencing the time reversals of one’s own mental images! we would be quite literally cosmic entities. study of cosmos would be study of our own minds. in this situation mind is only conscious about itself. if mind is conscious about other mind it must fuse with it to single mind by generating negentropic entangelment, otherwise it has no experience about other mind. as far conscious experience is involved, there is only one mind. this is the tgd analog for one mind theory and is able to avoid the paradox. if the sub-self representing self model dies as one falls in sleep and re-incarnates as its own time reversal at the opposite boundary of cd, sleep could involve communications with distant parts of the universe. pineal gland generating dmt could play a key role in this process. 4 the role of magnetic body in communications the first key idea is that molecules with aromatic rings are basic conscious entities at the level of biomolecules. second key idea is that psychedelic-receptor compex serves as a plug-in to cosmic internet. 4.1 why information molecules containing aromatic rings should be so important? i have considered the question of the title in [3]. the basis idea is that aromatic ring can carry the analog of supra-current as electron pair and this current generates a dipole magnetic field represented as flux tubes around the ring. this makes molecules with aromatic rings basic conscious entities in living matter. the flux tubes can carry dark matter and if there are several molecules with aromatic rings near each other, reconnections can take place and give rise to larger structures with building bricks connected by pairs of flux tubes carrying supra currents and dark cyclotron photon signals. dna would be the fundamental structure of this kind. each base-pair would contain 1+2+1+1=5 (two rings from sugars) aromatic rings and longer dna sequences would define larger conscious entities. microtubules contain also aromatic rings assignable to 2 amino-acids phe and trp appearing in the tubulin molecules. of course, all proteins contain these aromatic rings possibly integrating by flux tube connections to larger conscious entities. in this picture it would not be surprising of the basic information molecules would also involve aromatic rings. dna letters a,g and their conjugates t,c have the ring structures of trp and phe respectively and base pairs in the double dna strand correspond to trp and phe ring structures connected by hydrogen bonds. could the information molecule-receptor protein coupling rely on similar couplings with trp and phe playing the role of fundamental plugs. this hypothesis predicts that more complex information molecule-receptor pairs should have geometries in which trp:s and phe:s can meet each other naturally. also protein folding could involve similar trp-phe self-couplings by hydrogen bonds determining the folding to a considerable degree. protein folding would be determined basically by the generation of negentropic entanglement dictated by nmp and its understanding would require quantum theory of consciousness. 4.2 neurotransmitter receptor complex as plug-in to cosmic internet and a new perspective on remote seeing if one just for fun takes seriously the claims of shamans, one must ask whether our brain has well developed tools available for building contacts with distant civilizations and what these tools might be. the receptors of neural transmitters are obviously the natural candidates for the pathways to cosmos. in the case of neural transmitters these would serve as pathways to the personal magnetic body (with onion-like structure). neutral transmitters could be however replaced with psychedelics if they have a isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2015 | volume 5 | issue 3 | pp. 174-180 179 pitkänen, m., why information molecules containing aromatic rings should be so important? geometric structure allowing a binding to the corresponding receptors. if psychedelics have flux tube connections to very distant parts of the universe, a connection is generated. 1. one can argue that evolutionary pressures have forced living matter to develop highly standardized connections to various parts of the personal magnetic body and possibly also other magnetic bodies. personal magnetic body has astrophysical size and eeg frequencies would correspond to communications in earth size scale. receptors serving as josephson junctions emitting josephson radiation with frequency characterised by heff are natural candidates for plug-ins. 2. the model for cell membrane as josephson junction leads at the microscopic level to the view that the proteins associated with various ion pumps, channels, and receptors (of also neurotransmitters in postsynaptic junction) define josephson junctions to which magnetic flux tubes are associated and characterized by local value of josephson frequency, that is membrane potential and planck constant heff . as the information molecule is attached to a receptor, a connection to some part of the some magnetic body would be generated and split as the molecule is not present. these connections are possible in the scale cell, organelle, organ, organism, population and maybe even in the scale of cosmos. psychedelics affect serotonin receptors so that serotonin spends longer time in receptor. 3. the simplest picture is that the connection corresponds to a pair of flux tubes. as the connection is broken, the pair has suffered reconnection cutting it to two u-shaped closed flux tubes. when molecule is attached to the receptor, these u-shape closed flux tubes reconnect. the actual situation is of course expected to be more complex but the basic principle would be this. 4. neurotransmitters and also other information molecules can be seen as molecules at the ends of flux tubes having ends in some fixed subsystem x. the attachment of neurotransmitter to the receptor would builds a flux tube connection between postsynaptic neutron and x. the magnetic bodies in question characterised by passwords defined by collections of cyclotron frequencies corresponding to a hierarchy of space-time sheets. the josephson frequency associated with the receptor is inversely proportional to heff . the natural guess is that it corresponds to the cyclotron frequency of the magnetic body part for electron, proton, or some ion associated with it. josephson frequencies should serve as kind of passwords and receptors would be in one-one correspondence with these passwords defining gateways even to the outer space if the value of planck constant is large enough. the basic difference to ordinary view is that information molecules build only connections: after the establishment of a connection dark supracurrents and dark photons take care of the communication. attaching the information molecule to receptor is like clicking a link in web. 5. psychedelics would replace the ordinary neural transmitters building up this kind of flux tube connections in the normal situation so that the the connections could be to quite different places. one might be able to test this crazy hypothesis. 1. pineal gland could still serve as the “third eye” but utilizing large heff photons. fishes and birds are able to navigate to their birth places. this mechanism could involve dark electron cooper pairs at the magnetic flux tubes of earth’s magnetic field generated by visible photons with energies above energy of red light making possible to move along magnetic flux tube: as the direction of flight ceases to be along it and spin direction of cyclotron bose-einstein condensate changes, cyclotron transitions induce dark photon emission at energy of visible photons in turn generating visual sensation. this would explain why radiation at mev frequency leads to disorientation (cyclotron transitions are induced resonantly). this need not be enough. could also “remote seeing” by pineal gland using the dark light coming along flux tubes (or maybe even active variant of this process by sending light which is reflected back in time direction). what about remote seeing in the “usual” sense of the word: could psychedelics help also in this process? isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2015 | volume 5 | issue 3 | pp. 174-180 180 pitkänen, m., why information molecules containing aromatic rings should be so important? 2. the role of dmt is especially interesting. body synthesizes it and pumps it through blood-brain barrier. i learned in private discussion that the experiences induced by dmt are relatively predictable (terence mac kenna has described it as a sudden “dropping” to another world somewhere “below” through some kind of wall) whereas other psychedelic substances induce rather unpredictable experiences. could it be that dmt corresponds to a permanent connection to some fixed external magnetic body or to a higher layer of level of personal magnetic body with permanent reconnection to some part other magnetic body? dmt as also other psychedelic substances would only help to induce the signal as josephson radiation. this would be analog to the higher probability of remote mental interaction due to pre-bonding. what happens during sleep: is this connection generated during sleep: what about concentration of dmt during sleep in various brain regions. 3. the information molecule-receptor complex would be associated with the communications to a part of magnetic body determined by the flux tube assignable to the information molecule and possible communications from magnetic body as sensory experiences such as psychedelic experiences and mediated by radiation in opposite time direction. also control commands from magnetic body assumed to be realized as signals in opposite time direction as compared to sensory signals are important and a natural assumption is that the commands initiating gene expression enter through genome via flux sheets traversing through dna: the time scale for gene expression is slow and also other mechanisms are very probably involved. if both genome and cell membrane can (on general grounds it seems that they must do so) send signals in both time directions, the general vision about motor action as time reversal of sensory perception implies that cell membrane receives also control commands. more generally, the complex formed by reacting biomolecules and catalyst could form a complex receiving control commands from the magnetic body. a temporary fusion of a catalyst molecule and of reacting molecules could serve as the analog of the information molecule-receptor complex. the protein josephson junction associated with this complex would receive in a resonant manner cyclotron radiation from the magnetic body inducing a transition to a state in which the potential barrier preventing the reaction would be lower. 4. an interesting but ethically questionable test for the hypothesis would be following. transfer neurotransmitters associated with the of subject b to the brain of person a, and see what effect they have on conscious experience of a. if the proposal is correct, person a would have flux tube connection to the magnetic body of b, and might receive some memories of b for instance. could transplants induce similar effects? heart transplants are reported to have strange effects suggesting that heart (having a lot of neurons) has emotional memories. irrespective of whether one takes seriously the thought game leading to this proposal, one must admit that it would provide deep for the notion of “information molecule”. references [1] r. strassman et al. inner paths to outer space. http: // www. amazon. com/ inner-paths-outer-space-psychedelics/ dp/ 159477224x . park street press, rochester vermont, 2008. [2] m. pitkänen. meditation, mind-body medicine and placebo: tgd point of view. in tgd based view about living matter and remote mental interactions. onlinebook. http://tgdtheory.fi/public_ html/pdfpool/panel.pdf, 2012. [3] m. pitkänen. tgd based model for anesthetic action. http://tgdtheory.fi/public_html/ articles/anesthetes.pdf, 2015. isbn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. http://www.amazon.com/inner-paths-outer-space-psychedelics/dp/159477224x http://www.amazon.com/inner-paths-outer-space-psychedelics/dp/159477224x http://tgdtheory.fi/public_html/pdfpool/panel.pdf http://tgdtheory.fi/public_html/pdfpool/panel.pdf http://tgdtheory.fi/public_html/articles/anesthetes.pdf http://tgdtheory.fi/public_html/articles/anesthetes.pdf introduction some background about psychedelics could instantaneous communications in cosmic scales be possible in tgd universe? the role of magnetic body in communications why information molecules containing aromatic rings should be so important? neurotransmitter receptor complex as plug-in to cosmic internet and a new perspective on remote seeing login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 248-259 king, c., resurrection & resplendence issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 248 op-ed resurrection & resplendence chris king * abstract this article is about who i am, what i have discovered to date in this conscious, living universe, what i stand for, and how this can help you and your offspring and all life and the planet's verdant and abundant future. keywords: resurrection, resplendence, conscious, living universe, life, planet. physical incarnation and world view i am one chris king, born on the epiphany, as the plutonium began to roll out of hanford. i live in new zealand where i share a wilderness conservation reserve with a group of fellow stakeholders. i have also travelled widely in many parts of the world, spanning the north and south americas, europe, north africa, the near and middle east and central and south east asia. i have worked for many years of my life as a university academic, teaching mathematics, with a research interest in chaos theory, but my central scientific interests ad discoveries have been in the cosmological foundations for the origin of life and consciousness in the universe. i'm going to explain to you a view of conscious existence in the natural universe, which transcends religious world views and expands the scientific world view into a completely fulfilling resplendent journey that reflowers the living planet in abundance for the future generations of life, while enabling conscious existence over our lifetimes to become ever more * correspondence: chris king http://resplendence.org e-mail: dhushara@gmail.com dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 248-259 king, c., resurrection & resplendence issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 249 deeply aware of its calling and for the conscious universe to enter into a state of full realization of its existential being. my view of the cosmological universe is that it is founded on complementarities akin to the receptive yin and creative yang of taoism, underpinned by a root complementarity of the objective physical universe and subjective consciousness. all my scientific and visionary explorations are dedicated to understanding this root question, which lies at the centre of the cyclone revolving around scientific knowledge, the religious impulse, and the visionary quest. the root complementarity between consciousness and the universe is reflected in a chain of complementarities permeating the physical and biological realms, from the continuous and discrete wave and particle aspects of the quantum, through the bosons and fermions defining forces and radiation on the one hand and matter on the other, to order and chaos in dynamics and the sexual complementarity of ovum and sperm and female and male in complex organisms. a key idea in this chain is that there is a single verifiable cosmological description, based on complementary principles, which successfully describes all phenomena, from the physical universe, through the living organisms of the biota, to the subjective phenomena of conscious experience. this resolves the ultimate paradox of existence that all our experience of the world around us comes exclusively from our subjective conscious experiences, but we also know from these conscious experiences that if we are hit over the head or the blood supply to the brain is cut, we may lose consciousness, or even die and thus that our physical brains and bodies are necessary and integral to our existence in a way which is at least as fundamental as our ephemeral conscious experience. biocosmology in this cosmological scenario, we would expect life as the physical receptacle of consciousness to be a cosmological property as well, so we explore this first. in 1978 i proposed a biocosmological theory that the molecular form and emergence of life on earth was a cosmological consequence of the symmetry-breaking of the fundamental forces of nature in the cosmic origin, and that the living biota constitute the full and complete interactive consummation of these forces. there are four known fundamental forces: electromagnetism, the weak radioactive force exchanging neutrons and protons, the colour force binding the three quarks in each proton and neutron and inducing the strong nuclear force binding the nucleus together and driving the energy of the sun and stars, and finally universal gravitation. we exist in the universe as interactive structures of all four forces. in particular, molecules and molecular complexes constitute the most complex interactive structures generated by the first three forces in a hierarchy. the colour force gluons bind quarks to form hadrons including protons and neutrons which also exchange mesons, inducing the strong nuclear force which binds each atomic nucleus together. at the same time, the weak nuclear force, which is now known to be a symmetrybroken form of electromagnetism, balances the populations of protons and neutrons in the nuclei to minimize their energy due to electromagnetic repulsion of the protons positive charges thus http://dhushara.com/book/bchtm/biocos.htm dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 248-259 king, c., resurrection & resplendence issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 250 retaining their stability. finally the electromagnetic force binds electrons around the hundred or so stable atomic nuclei, forming atoms which then interact to form molecules. although electromagnetism is the most clearly understood of the forces, it still has exotic properties, which are key to the cosmological ability of the universe to sustain life. the electromagnetic charge interactions of interacting atoms and molecules are highly non-linear and result in a cascade of stronger and weaker bonding types which together make possible the formation of the complex fractal architectures we know of as tissues, composed of complex molecules forming larger molecular complexes, cell organelles, cells, tissues and finally organisms. these complex structures now coded in our genes are made possible because of this fractal force interaction on a cosmological footing. gravity then binds matter to form galaxies, stars and planetary systems, resulting in the garden of eden scenario of a net free energy input from each star onto the planetary surfaces of its solar system, resulting ultimately in biogenesis, the evolution of complex life and consciousness within the biota ultimately driven by photosynthetic energy. since then there have been major scientific strides confirming that energetic precursors of amino acids and the nucleotide components of our genetic apparatus, such as hcn and hcho and even some simpler amino acids such as glycine, can be found widely in the great gas clouds of the galactic nebulae such as orion. even more complex organic molecules have been found on comets and carbonaceous meteorites, including amino acids and nucleic acid bases. finally chemical gardens have been discovered on the sea floor which have been extant since the origin of earth's oceans that maintain a continuous nursery for chemical biogenesis. finally, many of the critical synthesis pathways have been elucidated from such organic molecules to the first rna-based life on earth, with evidence of living cells appearing in the fossil record very shortly after the earth's oceans condensed. once life began on earth, we have a much more complete account of genetic and organismic evolution, from the first archaea, bacteria and viruses through to the first higher eukaryote cells as a bacterial-archaeal endo-symbiosis, leading to multicelled organisms and ultimately to the conscious brains of animals and humans. the evidence for evolution is confirmed from three sources. the first discovered evidence was obvious phenotypic variations among organisms, such as those among darwin's finches of the galapagos, as they radiatively adapted across the archipelago's islands. the second is fossil evidence that shows extinct organisms with clear precursor relationships to living organisms alive today. the third source, that has recently become an informational explosion, is the comparisons of genetic sequences in the dna of diverse living species, which show an undeniable tree of evolutionary relationships with one another that now has made possible the construction of a comprehensive evolutionary tree of life from the first cells to all the organisms alive today. this epoch, from any rational point of view would now seem to be the clearest and most beautiful expression of the cosmological process we could ever conceivably discover, but has been relentlessly attacked by religious people in frank denial, because of a literal belief that god created the universe and all life within it, stemming from bibliolatry the false belief that the dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 248-259 king, c., resurrection & resplendence issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 251 bible and the allegorical passages of genesis are the literal world of god. this problem of denial of the cosmological sanctity of nature applies not only to christian and muslim thinking but also to eastern traditions, where reincarnation portrays a false view of nature as a degenerate conscious realm. it is complemented in monotheism by a false view of nature as flawed and bestial, to be controlled by human dominion, only to be discarded in the new heaven and earth of the "rapture" revealed in the end of days by god. vision quests both the eastern and western religious traditions suffer from a moral cosmology of pain and punishment which we know to be false, as the lessons of evolution show that adaption to fill all the diverse niches of life is the rule of flowering climax diversity and that morality is simply an adaptive response of some animal and human societies to inhibit intra-social strife to in turn promote inter-social competition and survival on growth of the social group. this division between the religious and scientific world views has led to a state of frank schizophrenia in a contemporary society starkly divided between religious affirmative beliefs and the scientific traditions of verifiable confirmation of nature and the physical world. it is a matter of dire concern that this is happening in a technologically advanced age, in which we have also assumed ultimate powers of nuclear mass annihilation, and human impacts are irreversibly destroying natural habitats on a global scale and precipitating potentially irreversible climate change, through exploiting earth's non-renewable resources, leading to a mass extinction of life's diversity and serious threats to the future viability of the human species. this brings us back to the nub of the question the ultimate meaning of life and conscious existence. the world's religions are founded on notions of the cosmos in which our conscious experience of the world plays a primary role in a greater conscious reality, consisting of deities and a conscious afterlife in other realms. science has had a great deal of trouble dealing with the central arena of consciousness, because subjective experience, although our central and only access to the physical world, is not an objective phenomenon that we can investigate, verify and replicate. for this reason, as soon as i gained a science degree and began graduate studies, i set out on a voyage of visionary discovery. i read deeply in mysticism and accounts of transcendent experiences of other peoples and cultures, took lsd just as the beatles were composing lucy in the sky with diamonds and proceeded to enter the psychedelic realm some 500 times, practicing deep meditation and retreats into wilderness settings. at the same time i explored eastern meditative traditions. on my first sabbatical after entering academic life, i wandered india as a sadhu, took buddhist initiations with the previous karmapa and yeshe dorje. complementing this, i travelled to the sources of the world's psychotropic and entheogenic power plants, from peyote with tellus goodmorning in the native american church, through sacred mushrooms in mexico to partaking ayahuasca in the peruvian amazon with senor trinico. since then i have continued to use and revere the living sacraments of sacred mushrooms, cacti and amazonian entheogenic http://dhushara.com/book/twelve/tw2.htm dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 248-259 king, c., resurrection & resplendence issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 252 species and consider these to be allies and teachers in the first person about the underlying depths of the conscious condition and the visionary and mystical paths. shamanic messianism in 1980 i had a mushroom vision that i would make a vision quest to jerusalem in the millennium if the world failed during the next twenty years to come to any real terms of protection for the future diversity of life on earth. this preconfigured my last academic sabbatical in 1999-2000, to address the mass extinction of life at the hands of humankind and to perform a key rite of passage from the age of apocalypse to the sustainable age of the tree of life in the religious tradition. i conceived this not as a religious undertaking as such, but as a shamanic vision quest to the source of the judeo-christian religious imperative. in this i assumed the role of a spiritual innovator, a life-unfolding successor to the life-terminating mission of yeshua's demise, consummating the violence of the apocalyptic tradition in the millennial transition to reparadise the earth. i thus set out with a small group of two friends and my eldest son, to travel to the us and on to south america to make a transit of the amazonian basin, filming the destruction of biodiversity and natural habitats. we circumnavigated bolivia during the burning season and then proceeded to cusco and down the urubamba, and through the pongo de manique and the ucayali, to pucallpa, where we again partook of ayahuasca, then traversing through iquitos to manaus and back up the madiera to the pantanal and on to rio. after this, we made a journey to jerusalem for the millennium, where we held a twelve day workshop on the sacred union of woman and man, consummating the apocalyptic epoch of triage and armageddon, in reflowering the earth as a living paradise, in the paradigm of the tree of life. the intention was not to change the world overnight, but to plant a seed for change in the form of performing rites of passage transforming the judeo-christian religious tradition, to conceptually bring this phase to a close in the closing circle of life of the planet, upon which we all depend in the advent of a global world culture. in the event, we held an overnight celebration of some hundred people on millennium eve on mount scopus, in which my vigil partner and namesake, jane king and i, pronounced the culmination of the apocalyptic paradigm in a revisioning of the jubilee passage of isaiah 61, which jesus read to begin his mission in his home synagogue at nazareth, in our case anointed in the sacred reunion of god and gaia, as both a bridegroom and bride together. on the epiphany, thirteen of us made a march from the ascension site on the mount of olives, down past the garden of gethsemane to the vale of kidron and to the eastern wall's gates of mercy, mentioned in ezekiel 44, currently filled with rubble by the muslims in an attempt to physically prevent the return of the messiah, declaring the gates wide open, as in isaiah 60, finally pronouncing the sacred marriage of the song of songs at the western 'wailing', wall. while there, the violin duet of the hymn to the epoch and the voices of participants in the celebration was included in the audio production. the entire vigil from jerusalem to the amazon is documented in the movie apocalypsia on youtube. i had adopted the cognomen dhushara. drawing attention to the paradox in christian origins, in reflowering the tree of life for the future epoch of goodness the true nature of the mashiach https://www.youtube.com/watch?v=9biwes8jnka http://www.dhushara.com/nino/index.htm#anchor859909 https://www.youtube.com/watch?v=i6wvm5gltw8 dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 248-259 king, c., resurrection & resplendence issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 253 actually is, even as solomon is to the shulamite in the song of songs. dhushara is the dionysian apotheosis of the old god of nabatea, manifesting yeshua's alter-persona, in his mission to transcend both the hebrew and fertility traditions. this mixed metaphor is central to the spread of christianity throughout the pagan world, to become a global religion, in effect bridging the hebrew apocalyptic tradition with the backdrop of fertility worship that was dominant across the border in nabatea's heyday in the same generation as jesus, by extolling jesus as a supernatural hero in the wider traditions of the near east. the complementation of israelite monotheism and the fertility worship of nabatea is an important episode, which everyone needs to fully understand in interpreting yeshua's mission as a transformative visionary, if dealing into a paradigm of religious and social violence, in the conflict between the perceived light and dark forces of good and evil. john the baptist was beheaded at herodias' request after her daughter salome danced the dance of the seven veils in front of herod's generals. in respect of their pleasure he offered her even half his kingdom a ritual invocation also seen in the book of esther's allegorical retelling of the same ritual sacrifice. this dance is the descent of inanna-ishtar to the underworld, stripped naked to the bone and is followed by the male sacrifice of dumuzi also named tammuz in the bible. herod and his generals were at machaerus on the nabatean border because herod, tetrarch of galilee had rejected his previous wife, the princess of nabatea, who had to escape in fear of her life, when herod took his cousin herodias, the wife of his brother philip tetrarch of the northern kingdom. herod was cursed by the baptist for so doing, leading to his imprisonment and eventual death, with his head served up on a plate to salome as her sacrificial reward. herod was at macherus because nabatea which was ruled by a king and queen consort, aretas and shalquat, was preparing to go to war with herod for threatening the life of their daughter. the mission of jesus is likewise set as a sacrificial context leading to his crucifixion. the baptist baptises jesus, who then embarks on a mission beginning with nearly being thrown off the cliffs of nazareth for citing namaan the syrian and the widow of sidon as more faithful, in reading the isaiah 61 passage in his home synagogue. this was a mission in which in which the jews accused him of blasphemy, likening him to beelzebub or ba'al zebul, the lord of flies, for practicing sorcery, including the dionysian water into wine, provoking storms, walking on water, terrifying a herd of pigs and eventually claiming to bring lazarus back from the dead. the mishnah, the first written record of jewish oral tradition notes "on the eve of the passover they hanged yeshu ... because he practiced sorcery and enticed and led israel astray." all these features of yeshua's mission, including his epiphany date, hark back to dionysus, the dark god of altered states, who in the nabatean heyday had taken over the older persona of dhushara the lord of seir, the ancient land noted in genesis. dhushara, like dionysus had a tragic mask that was supposed to confer immortal life on the believer. dhushara was accompanied in nabatea by three goddesses manat, al-lat and al-uzza also mentioned later in the quran. jesus continued to make a confluence between the fertility worship of nabatea and the israelite rural backdrop, on every high hill and under every green tree. he is supported in his mission by the women out of their very substance. he is anointed, not by a high priest as was solomon, but to his doom by a woman mary, who is also conflated with "a sinner", and he also dearly loved martha, but told her that mary had to play that good (ritual) part in the process. in the gnostic gospel of thomas, which predates many of the synoptic gospel sayings, he is said likewise to dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 248-259 king, c., resurrection & resplendence issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 254 have come up on salome's couch. his crucifixion becomes a multi-themed dionysian passion play, with the lazarus episode, turning the tables, performing the parade of the palm king, passing the sop in a ritual role to judas, then becoming a sacrifice overlooked by the women of galilee but cursing the women of jerusalem, set at nought by the roman saturnalia and condemned to the cross. the risen jesus is first seen by magdalen after harrowing hell for the three days of the dark moon. the crucifixion thus becomes a triple tragedy, insurrection to the romans, blasphemy to the jews, and the male sacrifice of the anointed king in the fertility tradition of the descent. his genealogy in matthew likewise cites four 'fallen' women, tamar, ruth, rachab and bathsheba, with mary likewise adopted by joseph as she was with child. this vigil was conceived as a rite of passage that could be recalled later in the cultural record as a key transformative celebration coming ahead of its time and as an affirmation of the idea of an archetypal throwing the covers off reality in the human collective consciousness that the word apocalypse or unveiling actually means a culmination of the endless future shock of the fall from eden, which is more fundamentally a fall from gatherer-hunter paradise into the apocalyptic wars and rumours of war, in the vying of cultures and religions through the ages, up to the scientific revolution, and the messianic principle as a manifestation of the heroic quest spanning jungian views of the collective consciousness also expressed in joseph campbell's work. the time for this is now with the closing circle of the biosphere subject to human impact and weapons of nuclear mass destruction being even more apocalyptically a turning point in earth's history than the time of jesus and the ensuing siege and fall of jerusalem, which killed an estimated 1.1 million people, precipitating the jewish diaspora. on my return journey, i visited the kali temples of kathmandu and varanasi to pay my respects to the tantric tradition of the sacred union of shakti and shiva. sexual paradox: reproductive conflict and human emergence following this episode i departed the religious tradition, and became a severe critic of religious fallacies, especially religious violence and the repression of women throughout the patriarchal epoch. i had come to realize that female reproductive choice, which had been repressed by the patriarchs for the last four to ten thousand years, was key to the emergence of human superintelligence and also epitomised the best features in human virtue, from astute mate choice, classification of plants and superior social intelligence and articulacy in women to skilled hunting, good story telling and resourceful parental husbanding in men. i coauthored with my life partner christine "sexual paradox: complementarity, reproductive conflict and human emergence" delineating these ideas. only three percent of mammals are socially monogamous because females give birth to life young, so their parenting investment is much greater and males tend to focus instead on fertilization. humans are at a biological extreme of mammals because human pregnancy is a particularly huge and risky investment for a woman making her social vulnerable, carrying accentuated risk of death in childbirth, years of breast feeding and infant care and long years of child rearing, the slow development of human children involves. this is complemented by mammalian xy chromosome inheritance providing a testing ground for male unique x http://dhushara.com/fallacies/fallacies.htm http://dhushara.com/fallacies/fallacies.htm http://dhushara.com/paradoxhtm/contents.htm dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 248-259 king, c., resurrection & resplendence issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 255 chromosome inheritance, while the female xx becomes a somatic chimera except in the germ line leading to the ova. sexual paradox is the prisoners dilemma of each human sex running, while "standing still" in a red queen evolutionary race with the other sex, in which neither sex's reproductive strategy has had the complete upper hand during our evolutionary emergence, with mutual mate choice, necessarily biased on the one hand by the evolutionary necessity for astute female reproductive choice negated in the last ten thousand years by attempts at patriarchal dominance to repress it. the book and subsequent research in the electronic version thus details both human evolution and the emergence of culture and the fallout, from the birth of agriculture and animal husbandry, leading to urbanization and the reproductive domination by patriarchal imperatives in culture and religion. the full impact of this became borne out, when comparative research of changes in mitochondrial and y-chromosome dna diversity showed up a crash in y-chromosome diversity consistent with the reproductive sex ratio declining from a natural two females to each reproducing male, due to higher variance in male reproductive success since all females can in principle become pregnant, to seventeen females to one reproducing male under the agricultural overlords, thus simultaneously preventing female reproductive choice and eliminating most males from the reproductive gene pool. consciousness, chaos and quantum reality complementing this i continued to author the dhushara research site dhushara.com, focused on bringing these themes together with a real time research description of reality of the universe in terms of biocosmology, the evolutionary tree of life, quantum reality and the neuroscience of consciousness, whose activities continue to be ongoing, updated daily as new research is published. i made a return exploration of the new generation of synthetic psychotropic agents, including the benzylphenylethylamine psychedelics, mdma or ecstasy, the dissociative anesthetic ketamine and a variety of synthetic cannabinoids and compiled a research review of the current state of the science of entheogens from all sources. at the same time i researched all the developments in neuroscience pertaining to how the brain might be able to respond to quantum phenomena, especially through the sensitivity of chaotic systems to arbitrarily small perturbations due to the notorious butterfly effect that a butterfly's eddy could become the kernel of a hurricane if the surrounding weather is in a state of chaotic sensitivity. i have also maintained an ongoing genetic description of the evolutionary tree of life using source research of all the genetic trees so far discovered to provide a comprehensive overview for other researchers bringing the whole picture together, complementing this with real time reviews of research progress in biochemical origins of life in the universe. http://dhushara.com/ http://dhushara.com/book/bchtm/biocos.htm http://dhushara.com/book/unraveltree/unravel.htm http://dhushara.com/paradoxhtm/quant.htm http://dhushara.com/stc/ct.htm http://dhushara.com/stc/ct.htm http://dhushara.com/psyconcs/psychconsc8.htm http://dhushara.com/psyconcs/psychconsc8.htm http://dhushara.com/book/unraveltree/unravel.htm http://dhushara.com/book/bchtm/biocos.htm dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 248-259 king, c., resurrection & resplendence issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 256 occasional circumstances also briefly drew me back into the apocalyptic tradition. about a month before the 9-11 attack on the world trade center i wrote the lyrics and later produced the song of the biosphere, and watched in uncanny horror live as the events unfolded on the bbc news. several of the lines were prescient enough to appear prophetic. this complements other prescient experiences. my life has been interspersed with sporadic instances of precognition, particularly in dreams. in the first, back when i was a student in england, having skeptically read j w dunne's "experiment with time", i had a double nightmare that i was being hideously stung. i told my wife about it when she woke to feed our infant daughter and then, about an hour later was stung wide awake after she later opened the bedroom window and a wasp flew in, so the dream was reported well before the actual event took place. this experience turned my awareness around full circle, from a classical science presumption of physical causality, with experiences such as prescience judged to be a contradictory illusion, to an appreciation that anticipation in real time may be the ultimate basis of consciousness and explain how it evolved. consciousness, even with a brain having some 10 10 neurons and 10 15 synapses, can only manage a digit span of about seven digits and, apart form a few savants, is a lousy calculator. but consciousness excels at the computationally intractable problems of the open environment, where it is the key to being able to survive under surprise attack by a predator and make complex assessments about survival in real time, where a computer might sit stranded with computational overload. this suggests that consciousness may be a form of real-time anticipation discovered by excitable cells. all living cells are ultimately powered by electrochemical energy transport of electrons and ions in respiration, photosynthesis and membrane excitability. chaotic excitation provides the cell with a direct sense of external environmental changes through sensitive dependence on external conditions, a version of the butterfly effect. multicelled animals have evolved excitable brains, still modulated by the same sappy neurochemical transmitters that single celled animals use for social signaling. this animals found a ready basis in chaotic neuro-excitability for forming an active real-time anticipatory internal model of the environment and this became the basis for the evolution of consciousness. we can see evidence for this in the broad spectrum edge-of-chaos dynamics of the brain's eeg, and in the way a transition from high energy chaos to explore all possibilities can be utilized in a phase transition to the solution. there is also evidence in the brain that very small instabilities at the synapse level can become amplified in a butterfly effect phenomenon called stochastic resonance into whole neurosystem excitations. thus it is possible for the brain when poised at a critical knife-edge to amplify effects of uncertainty down to the quantum level of individual molecules and ion channels. the brain also appears to use phase coherence in its global excitations to distinguish coherent phenomena which become the content of conscious attention from the ground swell of incoherent noise and out of phase local processing at the subconscious level. phase beats are likewise the foundation of the process defining quantum uncertainty, in which energy and http://www.dhushara.com/nino/index.htm#anchor250077 dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 248-259 king, c., resurrection & resplendence issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 257 frequency are equivalent and a certain amount of time is required at a certain frequency to count the wave beats of a quantum thus making it impossible to define the energy and time of a quantum within the limits of uncertainty. since the discovery of quantum reality, we know that the foundation units of the universe are quanta, which have both discrete particle and continuous wave properties at the same time. quantum uncertainty means the universe is not in principle predictable, except in statistical terms, when the same situation is repeated many times. we also know that, between particle creation and absorption, the wave function is a product of both its boundary conditions and so is sensitive to its own future in a kind of space-time handshaking. particles which become entangled by entering the same wave function also display instantaneous correlations which can be revealed when either particle is sampled, which likewise handshake between past and future. the idea that experiential consciousness is an anticipatory model of reality leads directly to a basis for the existence of free-will. the physical process is a chaotic one involving quantum uncertainty at the molecular level so the objective physical systems outcome is uncertain. a conscious experience or decision arises from a transition from chaos in which the outcome is uncertain to a resulting outcome. consciousness thus appears as a form of quantum computer drawing from the entanglements of uncertainty the history-making outcome. this ties in with a controversial aspect of quantum physics demonstrated in the cat paradox. quantum reality is always a superposition of possibilities the cat is both dead and alive with differing probabilities but the conscious observer finds it is actually alive or dead, in each case collapsing the quantum superposition to just one of the two. in a sense the entire process of history being formed around us is a huge chain of collapses of these parallel multiverses into the line of history we experience in the arrow of time. in this view, consciousness, as a complementary principle, plays a central formative role in the evolution of the physical universe. resurrection and resplendence a couple of years ago i had a form of a near death experience. i was riding my push bike at dusk. a thing i do to keep fit, rather than running after a serious accident in ecuador. i had been mugged in quito for my camera and thrown in front of a bus that hit me full on and then did a run, backing off and driving away leaving me lying on the road with a femur crushed at the hip, requiring an operation to insert a big pin in my hip leaving me on crutches for the rest of a 20 country journey through colombia, central america, mexico, the us, europe, jordan, israel and india. the next thing i knew was walking in the door of our house saying "what has happened to me?" to be greeted by christine's horrified face. i looked as if i looked like i had been hit by a train and thought i had been systematically beaten up all over again. my front teeth were knocked out and my left eye was swollen tight shut, with a large glancing wound across my forehead. on walking back out to the garage, i found the doors covered in blood and my bloodied bicycle and realized i had come off and hit the pavement without a helmet somewhere. christine rushed me dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 248-259 king, c., resurrection & resplendence issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 258 off to accident and emergency, where a couple of hours later i recalled the exact spot where i had fallen, subsequently pushing my mangled bike a mile or so across the city in the dark in a coma, of which i still have no recollection. fortunately i neither had a serious brain bleed or any subsequent signs of neurological damage. this threw me back into the consequences of my annihilation. what was it that i should have done before i was snuffed off the face of the earth? this was for me a timely reaffirmation of my life mission and i composed a resurrection song to make the fact clear. the answer to this existential crisis was to reveal the concept of resplendence the compassionate consciousness of the universe shining forth brightly. serendipitously i found the domain resplendence.org was still free, which i duly registered and set up the resplendence site as a web domain fertilizing the idea of resplendence as a biosphere regeneration principle based on, complementing scientific knowledge with a new subjective cosmological world view to transcend religion, replacing the imperative bondage of religio "to bind" with resplendere "to shine brightly" or "shine again". the introduction of consciousness back into the cosmic equation completely changes our view of the universe, from a cauldron of annihilating forces, doomed to wipe us all out in the sun becoming a red giant or later in the universal heat death, instead into an unveiling of reality through the agency of the conscious awareness of the biota. in this unveiling, nature is revealed as pivotal in our duty of care. we arise as incarnate conscious sentient beings in nature by evolution, through sexual recombination and fertility. we cannot live without natural food and the atmosphere provided by photosynthetic plants. complex organisms could not have evolved without sexuality and the endless evolutionary variety that sexual recombination provides. our viability as species and of all species depends on preserving the resilience of the biosphere, both from human impacts and natural causes such as asteroid impact and supernovas. alongside this no other human activity, belief, or hope has any real significance. the three key sacred principles are thus consciousness, sexuality and biodiversity. in turn this gives all of us as conscious beings a place in the unveiling of the cosmic process, through our consciousness and free-will as sentient beings, while we are alive. also we know in our heart of hearts that each of us is conscious in the same way. we are each the receptacle of the principle that enables the brain to support consciousness, so as we descend into the meditative reality, we are each one instance of an endlessly reincarnating resonance with collective consciousness. trapped in the mortal coil, we can easily become drawn into escaping into self-oriented egotism, but the realities of transient life in the biological realm mean we have to come to terms with the fact that the only things of any validity we can spend our time on are contributing to the unfolding of consciousness in the universe through the perennial immortality of the diversity of life. we thus need to respect nature and sexuality, for in sex, we as a species remain immortal, although mortal as individual organisms. sex enabled complex animals with conscious brains to evolve, so it must needs be respected as sacred to conscious existence, just as nature and its http://www.dhushara.com/nino/index.htm#anchor-resurrection-49575 http://resplendence.org/ http://resplendence.org/conscuniv/conscuniv3.htm http://dhushara.com/origsex/origsex.htm http://dhushara.com/biocrisis/biocrisis.htm dna decipher journal | december 2017 | volume 7 | issue 3 | pp. 248-259 king, c., resurrection & resplendence issn: 2159-046x dna decipher journal published by quantumdream, inc. www.dnadecipher.com 259 diversity is sacred as the manifestation of biological complexity and consciousness in the physical universe. in this process, we become as the gods. that is, the living biota are the receptacle of cosmic consciousness, which is the holy 'ghost in the machine' of the universe. and even when the universe comes to an end in the heat death, or big crunch, long after all life has ceased, spacetime remains eternal and the conscious flowering of the biota on the equator of the universe in cosmic space-time, is its consummation, its fulfillment and its raison d'etre. this is the only way the conscious universe can come about, as a integrative consummation of the forces of nature, mid-way through the universe's flight. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 58-88 58 pitkänen, m., a model for protein folding and biocatalysis article a model for protein folding and biocatalysis matti pitkänen 1 abstract the model for the evolution of genetic code leads to the idea that the folding of proteins obeys a folding code inherited from the genetic code. the flux connections between molecules containing dark matter in macroscopic quantum phase and characterized by two integers are the basic new physics element of the model. after some trials one ends up with a general conceptualization of the situation with the identification o magnetic flux tubes as correlates of attention at molecular level so that a direct connection with tgd inspired theory of consciousness emerges at quantitative level. this allows a far reaching generalization of the dna as topological quantum computer paradigm and makes it much more detailed. by their asymmetric character hydrogen bonds are excellent candidates for contracted magnetic flux tubes serving as correlates of attention at molecular level. one can consider two models. for the first model the flux tubes between amino-acids are assumed to determine the protein folding. 1. the constant part of free amino-acid containing o − h, o =, and nh2 would correspond to the codon xyz in the sense that the flux tubes would carry the ”color” representing the four nucleotides in terms of quark pairs. color inheritance by flux tube reconnection makes this possible. for the amino-adics inside protein o = and n − h would correspond to y z. also flux tubes connecting the acceptor atoms of hydrogen bonds are required by the model of dna as topological quantum computer. the long flux tubes between o = atoms and their length reduction in a phase transition reducing planck constant could be essential in protein-ligand interaction. 2. the model predicts a code for protein folding: depending on whether also = o − o = flux tubes are allowed or not, y = z or y = zc condition is satisfied by the amino-acids having n−h−−o = hydrogen bond. for = o−o = bonds y −yc pairing holds true. if one identifies hydrogen bond with flux tube (y (n) = z(n + k)) the model works badly for both options. if one assumes only that the presence of a flux tube connecting amino-acids in either direction (y (n) = z(n + k) or z(n) = y (n + k)) is a prerequisite for the formation of hydrogen bond, the model works. y = zc option predicts the average length of alpha bonds correctly. y = z rule is however favored by the study of alpha helices for four enzymes: the possible average length of alpha helix is considerably longer than the average length of alpha helix if gene is the unique gene allowing to satisfy y = z rule. the explicit study of alpha helices for four enzymes demonstrates that the failure to satisfy the condition for the existence of hydrogen bond fails rarely and at most for two amino-acids (for 2 amino-acids in single case only). for beta sheets there ar no failures for y = z option. 3. the information apparently lost in the many-to-one character of the codon-amino-acid correspondence would code for the folding of the protein and similar amino-acid sequences could give rise to different foldings. also catalyst action would reduce to effective base pairing and one can speak about catalyst code. the dna sequences associated with alpha helices and beta sheets are completely predictable unless one assumes a quantum counterpart of wobble base pairing meaning that n−h flux tubes are before hydrogen bonding in quantum superpositions of braid colors associated with the third nucleotides z of codons xy z coding for amino-acid. only the latter option works. the outcome is very simple quantitative model for folding and catalyst action based on minimization of energy and predicting as its solutions alpha helices and beta strands. 1correspondence: matti pitkänen http://tgdtheory.com/. address: köydenpunojankatu 2 d 11 10940, hanko, finland. email: matpitka@luukku.com. issn: 2159-0465 dna decipher journal june www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.com/ mailto:matpitka@luukku.com dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 58-88 59 pitkänen, m., a model for protein folding and biocatalysis second model represents a diametrical opposite of the first model in the sense in that it assumes flux tube connections only between amino-acids and water molecules. these flux tubes mediate an attractive (repulsive) interaction in the case of hydrophily (hydrophoby) due to the behavior of magnetic (presumably) interaction energy as a function of planck constant (or integers characterizing the level of dark matter) assignable to the flux tube. for hydrophoby (hydrophily) the interaction energy is minimized for long (short) flux tubes. the interaction between amino-acids is induced by this interaction in a manner analogous to how the interaction between electrons and ions induces secondary interaction between the members of a cooper pair. the model explains the basic qualitative aspects of protein folding and the quantitative model of folding based on amino-acid-amino-acid flux tubes allows a generalization which is however discussed at numerical level. 1 introduction the model for the evolution of the genetic code leads [16] to the idea that the folding of proteins obeys a code inherited from the genetic code. one can imagine several variants of this code. one of them is that amino-acid behaves like the conjugate yc of the middle nucleotide of the codon xy z coding for it. conjugation for amino-acids would correspond to the hydrophilic-hydrophobic dichotomy. also catalyst action could reduce to effective base pairing in this picture chemically and at the level of quarks associated with the flux tube to matter antimatter conjugation. the guess that amino-acid and its conjugate form pairs turned out to be wrong however and after various twists and turns i ended up with the hypothesis that the amino-acid in protein behaves like yczc where z corresponds to third nucleotide for some codon coding for the amino-acid. there exists a wonderful book ”proteins: structures and molecular properties” by thomas e. creighton published 1993 [13] and i am grateful for timo immonen for possibility to use the book. in the following i freely refer to the general facts discussed in this book rather than referring separately to every detail. 1.1 flux tubes as correlates of directed attention at molecular level after some trials one ends up with a general conceptualization of the situation with the identification of (”wormhole”) magnetic flux tubes as correlates for attention at molecular level so that a direct connection with tgd inspired theory of consciousness emerges at quantitative level. whether wormhole flux tubes or ordinary flux tubes are needed is not a completely settled question yet and the attribute ”wormhole” will not be used in the sequel. this suggests a generalization of the dna as topological quantum computer paradigm making it much more detailed. there are too many uncertainties involved to allow anything except playing with the options that one is able to imagine. there are two kinds of flux tubes. those between amino-acids and those between aminoacids and water molecules. the contractions of flux tubes in ~ changing phase transitions are expected to be important for protein folding and could also give rise to the interaction responsible for hydrophily and hydrophoby and be therefore highly relevant for protein folding. what is the relative importance of these two kinds of flux tubes? the first model assumed that only amino-acid-aminoacid flux tubes are relevant and assumed strong selection rules inspired by dna as tqc model. the second model which emerged year later represents an extreme in which only the flux tube connections between amino-acids and water molecules assumed to be responsible for hydrophily and hydrophoby induce the interactions between amino-acids as secondary interactions. this model works surprisingly well at qualitative level. 1.2 the model of folding code based on flux tube connections between aminoacids the first model assumes that only the flux tubes between amino-acids are relevant for protein folding. issn: 2159-0465 dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 58-88 60 pitkänen, m., a model for protein folding and biocatalysis 1.2.1 what kind of atoms can be connected by flux tubes? 1. hydrogen bonds play a key role in bio-catalysis but are not understood completely satisfactorily in the standard chemistry. hence the basic question is whether hydrogen bonds can be regarded as or are accompanied by short (wormhole) magnetic flux tubes: note that the subject-object asymmetry of directed attention would correspond to donor-acceptor asymmetry of they hydrogen bond. if this is the case, the identification of the magnetic flux tube connection as a prerequisite for a hydrogen bond or as hydrogen bond becomes natural. at least the atoms able to form hydrogen bonds could form flux tube contacts so that the model would be very predictive and would conform with the known important role of hydrogen bonds in bio-catalysis. 2. the fact that hydrogen bonds connect base pairs suggests a generalization of the notion of base pairing stating that under some conditions amino-acids coded by xy z and uycv can behave like base pairs. these amino-acic pairs correspond to pairs of amino-acid residues which are hydrophilic resp. hydrophobic and hydrophobic residue do not form hydrogen bonds in general. these flux tubes would thus be more general and in general long. the model for dna as topological quantum computer requires this kind of flux tubes and they would in general connect atoms or molecules which act as acceptors in hydrogen bonding: o = atom in amino-acid and aromatic ring are basic examples. 3. if one assumes that both n −h and o = associated with the constant part of the amino-acid can act as flux tube terminals and represent z and y nucleotides of the codon xy z coding for the amino-acid, one obtains y = z pairing of o = −o = flux tubes are allowed and y = zc pairing if only hydrogen bond like pairings are allowed. 1.2.2 color inheritance by a reconnection of flux tubes 1. there should exist some mechanism allowing amino-acids to inherit the base pairing property from the trnas associated with them so that one can identify amino-acid with the middle nucleotide of the codon coding it. if trna middle nucleotide is connected to o = of the amino-acid, this becomes possible since the reconnection of flux tubes preserves the ”color” of the flux tubes coded by (a,t,g,c) that is by the quark or anti-quark coding for the nucleotide. the temporary formation of a hydrogen bond between n −h and o = of two amino-acids as in the case of alpha helix would allow n −h to inherit the conjugate of the color associated with o =. alternative interpretation is that this hydrogen bond is possible only if the predetermined color of n −h is consistent with the inherited one. the inheritance of flux tube color would be a completely general mechanism and even the donor atoms in the residues of amino-acids could inherit the color of o = in this manner. 2. a possible interpretation for the fixing of the flux tube color is in terms of quantum measurement selecting one color from quantum superposition in the reconnection process. this would mean that the unitary process can bring superposition back and reconnection process can change the inherited color. the hydrogen bonds between water molecules could correspond to quantum superpositions of different colors. this superposition property might relate to the wobble base pairing phenomenon for the third nucleotide in trna. 1.2.3 folding code the identification of n −h as a representation for the conjugate of the third nucleotide z means that amino-acids would remember which codon coded them. if only hydrogen bond like flux tubes are allowed, flux tubes can connect only amino-acids satisfying y = zc. if = o − o = flux tubes are allowed y = z rule favored by the model of dna as topological quantum computer follows. the isospin symmetry of the third nucleotide implies that both rules are quite flexible. if one identifies hydrogen bond with flux tube (y (n) = z(n + k)) the model works badly for both options. if one assumes only that the presence issn: 2159-0465 dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 58-88 61 pitkänen, m., a model for protein folding and biocatalysis of a flux tube connecting amino-acids in either direction (y (n) = z(n + k) or z(n) = y (n + k)) is a prerequisite for the formation of hydrogen bond, the model works. y = z rule is favored by the study of five enzymes: the possible average length of alpha helix is considerably longer than the average length of alpha helix if gene is the unique gene allowing to satisfy y = z rule. the explicit study of alpha helices and beta sheets for these enzymes demonstrates that the failure to satisfy the condition for the existence of hydrogen bond fails rarely and at most for two amino-acids (for 2 amino-acids in single case only). y = z rule could mean a solution of the basic problem of proteonics: do genes determine the folding of proteins and how this would take place? the interpretation would be that the information loss suggested by the many-to-one character of the genetic code is only apparent. the apparently lost information which corresponds to the a−g and t −c symmetries of the third nucleotide codes for the hydrogen bonding and hence for the folding of the protein. the model in its most stringent form is easy to kill since in the case of alpha helices and beta sheets the hydrogen bonding fixes completely the dna sequence coding for the protein. a weaker variant of the model based on quantum variant of wobble base pairing: in this case there are no conditions on dna sequence. it turns out that only this variant works. hence hydrogen bonded amino-acid behave as if they were coded by the unique codon consistent with y = z rule. 1.2.4 quantitative model the quantitative model relies on the assumption that the contribution of a flux tube connecting two amino-acids to the potential energy depends only on the distance between the molecules in question. the extremals of the total interaction energy are same for any choice of the potential and only the absolute minimum of the interaction energy depends on the choice of the potential. the simplest potential corresponds to harmonic oscillator potential and would explain formation of alpha helices and beta sheets and with the fact that hydrophilic and hydrophobic residues tend to have a large distance and only few flux tube contacts. for large planck constant also long flux tubes could correspond to attractive harmonic oscillator potential. also the contribution of other interactions between neighboring amino-acids are expected to be present but are neglected in the simplest model. the model predicts alpha helices and beta sheets, and more generally, periodic structures, as solutions to energy minimization equations. 1.3 a model for protein folding based on flux tubes between amino-acids and water molecules this model represents a diametrical opposite of the first model in the sense in that it assumes flux tube connections only between amino-acids and water molecules. these flux tubes mediate an attractive (repulsive) interaction in the case of hydrophily (hydrophoby) due to the behavior of magnetic (presumably) interaction energy as a function of planck constant (or integers characterizing the level of dark matter) assignable to the flux tube. for hydrophoby (hydrophily) the interaction energy is minimized for long (short) flux tubes. the interaction between amino-acids is induced by this interaction in a manner analogous to how the interaction between electrons and ions induces secondary interaction between the members of a cooper pair. the model explains the basic qualitative aspects of protein folding and the quantitative model of folding based on amino-acid-amino-acid flux tubes allows a generalization which is however discussed at numerical level. several persons have helped me in writing the chapter behind this article. i want to express my gratitude to ulla mattfolk for informing about the idea of protein folding code and to dale trenary for interesting discussions, for suggesting proteins which could allow to test the model, and for providing concrete help in loading data help from protein data bank. also i want to thank timo immonen for discussions and for loaning the excellent book ”proteins: structures and molecular properties” of creighton. i am also grateful for pekka rapinoja for writing the program transforming protein data file to a form readable by matlab. issn: 2159-0465 dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 58-88 62 pitkänen, m., a model for protein folding and biocatalysis 2 a model for flux tubes biochemistry represents extremely complex and refined choreography. it is hard to believe that this reduces to a mere unconscious and actually apparent fight for chemical survival. in tgd universe consciousness would be involved even at the molecular level and magnetic body would be the choreographer whose dance would induce the molecular activities. this picture combined with the idea of standard plugs and terminals at which flux tubes end, leads to a to a picture allowing to formulate a model for protein folding. 2.1 flux tubes as a correlates for directed attention molecular survival is the standard candidate for the fundamental variational principle motivating the molecular intentional actions. there is entire hierarchy of selves and the survival at the higher level of hierarchy would force co-operation and altruistic behavior at the lower levels. one might hope that this hypothesis reduces to negentropy maximization principle [17] , which states that the information contents of conscious experience is maximized. if this picture is accepted, the evolution of molecular system becomes analogous to the evolution of a society. directed attention is the basic aspect of consciousness and the natural guess would be that directed attention corresponds to the formation of magnetic flux tubes between subject and target. the directedness property requires some manner to order the subject and target. 1. the ordering by the values of planck constant is what first comes in mind. the larger space-time sheet characterized by a larger value of planck constant and thus at a higher level of evolutionary hierarchy would direct its attention to the smaller one. 2. also the ordering by the value of p-adic prime characterizing the size scale of the space-time sheet could be considered but in this case directedness could be questioned. 3. attention can be directed also to thoughts. could this mean that attention is directed from real space-time sheets to p-adic space-time sheets for various values of primes but not vice versa? or could the direction be just the opposite at least in the intentional action transforming p-adic spacetime sheet to real space-time sheet? perhaps directions are opposite for cognition and intention. the generation of (wormhole) magnetic flux tubes could be the correlate for the directed attention, not only at molecular level, but quite generally. metaphorically, the strands of braid would be the light rays from the eyes of the perceiver to the target and their braiding would code the motions of the target to a topological quantum computation like activity and form a memory representation at least. the additional aspect of directed attention would be the coloring of the braid strands, kind of coloring for the virtual light rays emerging from the eyes of the molecular observer. in the case of dna this can induce a coloring of braid strands emerging from amino-acids and other molecules so that it would indeed become possible to assign to free amino-acid the conjugate of the codon xy z coding for it. attention can be also redirected. for this process there is a very nice topological description as a reconnection of flux tubes. what happens is that flux tubes a→ b and c → d fuse for a moment and become flux tubes a → d and c → b. this process is possible only if the strands have the same color so that the values of the quark charges associated with a and b are the same. 1. reconnection process can modify tqc programs. for instance, in the case of the flux tubes coming from nucleotides x and xc and ending to the lipid layer this process means that x and xc and corresponding lipids become connected and genome builds memory representation about this process via similar link. 2. reconnection process makes also possible what might be called color inheritance allowing aminoacids to inherit the conjugate colors of the nucleotides of the codon coding it. issn: 2159-0465 dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 58-88 63 pitkänen, m., a model for protein folding and biocatalysis 3. dna would have memory representation about molecular processes via these changing braiding topologies, and one could say that these molecular processes reflect the bodily motions of the magnetic body. entire molecular dynamics of the organism could represent an enormous tqc induced by the motor activities of the magnetic body. at the level of sensory experience similar idea has been discussed earlier [20] : out of body experiences (obes) and illusions such as train illusion could be understood in terms of motor action of magnetic body inducing virtual sensory percepts. attention can be also switched on and off. here the structure of the lipid ends containing two nearby situated = o:s suggest the mechanism: the short flux tube connecting = o:s disappears by reconnection mechanism with a pair of hydrogen bonded water molecules leading to a shortcut of the connecting flux tubes to = o − −h2o hydrogen bonds. the minimization of coulomb interaction energy at each end implies that re-appearance of the flux tubes creates a short flux tube with the original strand color. 2.2 does directed attention generate memory representations and tqc like processes directed attention induces braiding if the target is moving and changing its shape. this gives rise to a memory representation of the behavior of the object of attention and also to a tqc like process. a considerable generalization of tqc paradigm suggests itself. tqc could be induced by the braiding between dna and lipids, dna and proteins via folding processes, dna rna braiding and braiding between dna and its conjugate, dna and protein braiding. the outcome of tqc would be represented as the temporal patterns of biochemical concentrations and rates and there would be hierarchy of p-adic time scales and those associated with the dark matter hierarchy. for instance, the protein content of lipid membranes is about 50 per cent and varies between 25-75 per cent so that protein folding and lipid flow could define tqc programs as self-organization patterns. the folding of protein is dynamical process: alpha helices are created and disappear in time scale of 10−7 seconds and the side chains of protein can rotate. the details of the tqc like process depend on what one assumes. the minimal scenario is deduced from the transcription and translation processes and from the condition that magnetic body keeps control or at least keeps book about what happens using genome as a tool. the picture would be essentially what one might obtain by applying a rough model for web in terms of nodes and links. the reader is encouraged to use paper and pencil to make the following description more illustrative. 1. assume that mrna and dna remain connected by flux tubes after transcription and that only reconnection process can cut this connection so that mrna inherits the conjugate colors of dna. assume same for mrna and trna. assume that amino-acid associated with trna has similar flux tube connections with the nucleotides of trna. under these assumptions amino-acid inherits the conjugate colors of dna nucleotides via the connection line dna-mrna-trna-amino-acid faithfully if all links are correspond to quark pairs rather than their superpositions. wobble pairing for z nucleotide could actually correspond to this kind of superposition. 2. one can consider several options for the amino-acid-acid dna correspondence but trial-and-error work showed that a realistic folding code is obtained only if x, y , and z correspond to o − h, o =, and nh2 in the constant part of free amino-acid. during translation the formation of the peptide bond between amino-acids dehydration leads to a loss of o−h and one h from nh2. the flux tube from trna to o −h becomes a flux tube to water molecule inheriting the color of x so that o = −nh2 of the amino-acid inside protein represents the conjugate of y z. 3. hydrogen bonding between o = and nh of n:th and n+ k:th amino-acids inside alpha helices and n:th and n + 1:th amino-acids inside beta strands reduces effectively to base pairing characterized by y = z rule. assuming that flux tube is only a prerequisite for the formation of hydrogen bond, y (n) = z(n + k) or z(n) = y (n + k) allows the existence of hydrogen bond. the identification of issn: 2159-0465 dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 58-88 64 pitkänen, m., a model for protein folding and biocatalysis hydrogen bond with flux tube gives a more stringent condition y (n) = z(n+k). the first option is favored. either condition is extremely restrictive condition on the gene coding the amino-acid unless one assumes quantum counterpart of wobble base pairing for mrna or trna-amino-acid pairing in the case of z nucleotide (as one indeed must do). note that the o = atom of the amino-acid is in a special role in that it can have hydrogen bond flux tubes to donors and flux tube connections with o =:s of other amino-acids, the residues of amino-acids containing acceptors (say o = or aromatic ring), and with the aromatic rings of say atp. 4. the recombination process for two conjugate dna-mrna-trna-amino-acid links can transform the flux tubes in such manner that one obtains link between the = o:s of amino-acids a1 and a2 characterized by y and yc. besides hydrogen bonding this mechanism could be central in the enzyme substrate interaction. the process would pair trnas corresponding to y and yc together to give dna-mrna-trna-trna-mrna-dna link providing a memory representation about aminoacid pairing a1 −a2. one could say that magnetic body creates with the mediation of the genome dynamical tqc programs to which much of the bio-molecular activity reduces. not all however, since two amino-acid pairs a1 − a2 and a3 − a4 can recombine to a1 − a4 and a3 − a2 without dna knowing anything about it. magnetic body would however know. 5. the constant part of non-hydrogen bonded amino-acid inside protein would behave like yczc if amino-acid is coded by xy z. the cooh end of protein would behave like xcyczc. also flux tubes connecting the residue groups become possible and protein does not behave like single nucleotide anymore. by color inheritance everything resulting in the reconnection process between o = and nh2 and residues reduces in a well-defined sense to the genetic code. 2.3 realization of flux tubes the basic questions about flux are following. where do they begin, where do they end, and do they have intermediate plugs which allow temporary cutting of the flux tube. 2.3.1 where do flux tubes begin from? the view about magnetic body as a controller of biological body using genome as a control tool suggests that dna is to a high degree responsible for directed attention and other molecules as targets so that flux tubes emanate from dna nucleotides. the reason would be that the aromatic cycles of dna correspond to larger value of planck constant. some chemical or geometric property of dna nucleotides or of dna nucleotides of dna strand could raise them to the role of subject. aromatic cycle property correlates with the symmetries associated with large value of planck constant and is the best candidate for this property. if this picture is accepted then also some amino-acid residues might act as subjects/objects depending on the option. phe, his, trp, tyr contain aromatic cycle. the derivatives of trp and tyr act as neurotransmitters and his is extremely effective nucleophilic catalyst. this would make possible more specific catalytic mechanisms through the pairing of phe, his, trp, and tyr with residues having flux tube terminals. this raises the question about the physical interaction determining the color of the strand emerging from the aromatic cycle. the interaction energy of quark at the end of flux tube with the classical electromagnetic fields of nuclei and electrons of the ring should determine this. the wormhole contact containing quark/antiquark at the throat at space-time sheet containing nuclei and electrons could also delocalize inside the ring. one of the earliest hypothesis of tgd inspired model for living matter was that wormhole bose-einstein condensates could be crucial for understanding of the behavior of biomolecules [21] . wormhole throats with quark and antiquark at their throats appear also in the model of high tc superconductivity [15] . as far as couplings are considered, these wormhole contacts are in many respects analogous to the so called axions predicted by some theories of elementary particle physics. the wormhole issn: 2159-0465 dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 58-88 65 pitkänen, m., a model for protein folding and biocatalysis contact like property is by no means exceptional: all gauge bosons correspond to wormhole contacts in tgd universe. the only manner for the electronic space-time sheet to feed its electromagnetic gauge flux to larger space-time sheets using exactly two wormhole contacts is to use wormhole contacts with u and d at their ”upper” throat (t,g). for proton one would have d and u at their ”upper” throat (a,c). the presence of electron or proton at nucleotide space-time sheet near the end of flux tube might allow to understand the correlation. the transfer of electrons and protons between space-time sheets with different p-adic length scale is basic element of tgd based model of metabolism so that there might be some relation. 2.3.2 acceptors as plugs and donors as terminals of flux tubes? standardization constraint suggests that flux tubes are attached to standard plugs and terminals. the explicit study of various biological molecules and the role of water in biology gives some hints. 1. an attractive idea is that = o serves as a plug to which flux arrives and from which it can also continue. for the minimal option suggested by hydrogen bonding o = could be connected to two donors and o = could not be connected to o =. the assumption that the flux tube can connect also two o =:s represents a hypothesis going outside the framework of standard physics. a stronger assumption is that all acceptors can act as plugs. for instance, the aromatic rings of dna nucleotides could act as acceptors and be connected to a sequence of o = plugs eventually terminating to a hydrogen bond. 2. donors such as o − h would in turn correspond to a terminal at which flux tube can end. one might be very naive and say that conscious bio-molecules have learned the fundamental role of oxygen and water in the metabolism and become very attentive to the presence of = o and o−h. = o appears in cooh part of each amino-acid so that this part defines the standard plug. = o appears also in the residues of asp, glu, asn, gln. o − h groups appear inside the residues of asp,glu and ser, thr. 3. hydrogen bonds x −h −−y have the basic defining property associated with directed attention, namely the asymmetry between donor x and acceptor y . hence there is a great temptation consider the possibility that hydrogen bonds correspond to short flux tubes, that flux tubes could be seen as generalized hydrogen bonds. quite generally, y could be seen as the object of directed attention of x characterized by larger value of planck constant. the assumption that two o =:s, or even two acceptors of a hydrogen bond, can be connected by a flux tube means more than a generalization of hydrogen bond the connection with a donor would correspond only to the final step in the sequence of flux tubes and plugs giving rise to a directed attention. 4. this hypothesis makes the model rather predictive. for instance, n−h, nh2, o−h and much less often c−h and s−h are the basic donors in the case of proteins whereas o =, −o−, −n = s−s, −s− and aromatic rings are the basic acceptors. reconnection process should be involved with the dynamics of ordinary hydrogen bonding. reconnection process implies inheritance of the flux tube color and means a realization of the symbol based dynamics. it turns out that this hypothesis leads to a model explaining basic qualitative facts about protein folding. 2.4 flux tubes and dna the model of dna as topological quantum computer gives useful guide lines in the attempt to form a vision about flux tubes. it was assumed that braid strands defined by ”wormhole magnetic” flux tubes join nucleotides to lipids and can continue through the nuclear or cell membrane but are split during tqc. the hydrophilic ends of lipids attach to water molecules and self-organization patterns for the water flow in gel phase induce a 2-d flow in the lipid layer which is liquid crystal defining tqc programs at issn: 2159-0465 dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 58-88 66 pitkänen, m., a model for protein folding and biocatalysis the classical level as braidings. the flow indeed induces braiding if one assumes that during topological computation the connection through the cell membrane is split and reconnected after the halting of tqc. the challenge is to understand microscopically how the flux tube joins dna nucleotide to the phospholipid [9] . certainly the points at which the flux tubes attach should be completely standard plugs and the formation of polypeptide bonds is an excellent guide line here. recall that phospholipid, the tqc dancer, has two hydrophobic legs and head. each leg has at the hydrophilic end o=c-o-c part joining it to glyceride connected to monophosphate group in turn connected to a hydrophilic residue r. the most often appearing residues are serine, inositol, ethanolamine, and choline. only three of these appear in large quantities and there is asymmetry between cell exterior and interior. let us denote by = o1 and = o2 the two oxygens (maybe analogs of right and left hemispheres!) in question. the proposal is that dna nucleotide and = o1 are connected by a flux tube: the asymmetry between right and left lipid legs should determine which of the legs is ”left leg” and which o = is the ”left brain hemisphere”. = o2, the ”holistic right brain hemisphere”, connects in turn to the flux tube coming from the other symmetrically situated = o2 at the outer surface of the second lipid layer. besides this = o1 and = o2 are connected by a flux tube serving as switch on both sides of the membrane. during tqc the short o = −o = flux tube would experience reconnection with a flux tube acting as hydrogen bond between water molecules so that the connection is split and o =:s form hydrogen bonds. the reversal of this reconnection creates the connection again and halts the computation. the lipid residue r couples with the flow of the liquid in gel phase. since = o is in question the quark or antiquark at the end can correspond to the dna nucleotide in question. the necessary complete correlation between quark and antiquark charges at the ends of flux tubes associated with = o1 and = o2 can be understood as being due to the minimization of coulomb interaction energy. if one is ready to accept magnetic flux tubes between all acceptors then the aromatic rings of nucleotides known to be acceptors could be connected by a flux tube to the o = atom of the lipid or to some intermediate o = atom. the phosphate groups associated with nucleotides of dna strand contain also = o, which could act as a plug to which the flux tube from the nucleotide is attached. the detailed charge structure of the aromatic ring(s) should determine the quark-nucleotide correspondence. the connection line to the lipid could involve several intermediate o = plugs and the first plug in the series would be the o = atom of the monophosphate of the nucleotide. there is a strong temptation to assume that subset of xyp molecules, x = a,g, t,c, y = m,d, t act as standard plugs with x and phosphates connected by flux tubes to a string. this would make possible to engineer braid strands from standard pieces connected by standard plugs. dna nucleotide xmp would have flux tube connection to the aromatic ring of x and the o = of last p would be connected to next plug of the communication line. if so, a close connection with metabolism and topological quantum computation would emerge. phosphorylation would be an absolutely essential for both metabolism and buildup of connection lines acting as braid strands. o = −o = flux tubes could also act as switches inducing a shortcut of the flux tube connection by reconnecting with a hydrogen bond connecting two water molecules. this is an essential step in the model for how dna acts as topological quantum computer. this picture would fit with the fact that xyp molecules, in particular amp, adp, and atp, appear in bio-molecules involved with varying functions such as signalling, control, and metabolism. = o might act as a universal plug to which flux tubes from electronegative atoms of information molecules can attach their flux tubes. this would also provide a concrete realization of the idea that information molecules (neurotransmitters, hormones) are analogous to links in internet [18] : they would not represent the information but establish a communication channel. the magnetic flux tube associated with the information molecule would connect it to another cell and by the join to = o plug having flux tube to another cell, say to its nucleus, would create a communication or control channel. issn: 2159-0465 dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 58-88 67 pitkänen, m., a model for protein folding and biocatalysis 2.5 introns and dna-protein attachment an example is the situation in which protein acts as an enzyme attaching on dna. suppose that this process effectively reduces to a base pairing between amino-acid and dna nucleotide. protein can attach to any portion of dna. the simplest interaction is the attachment to the gene coding for the amino-acid itself but much more general enzymatic interactions are possible. it must be however noticed that dna sequence coding for given amino-acid sequences is considerably longer than amino-acid sequence: the sequence coding for 10 amino-acids is about 10 nm long whereas the corresponding straight amino-acid strand is about 4.7 nm long. it is known that dna can change its conformation from strand during enzyme-dna action [13] , and the contraction of dna strand might make possible to have enzyme-dna interaction involving fusion along several subsequent amino-acids. this kind of mechanism might work also in the case that attachment region corresponds to several exons. there is however no need to assume that subsequent amino-acids are form a contact with dna. one can of course ask whether genes containing introns tend to code for proteins which are used for topological quantum computations. introns, perhaps the repeating sequences with no obvious function, would have at least this useful function but very probably much more useful ones too (they are now known to be transcribed to rna and tgd suggest that language corresponds to intronic gene expression). the emergence of introns might be somewhat like the emergence of information society. the folding of proteins tends to be conserved in the evolution whereas primary structure can change quite a lot apart from some amino-acids critical for enzymatic action. this confirms with the effective base pairing interaction between amino-acids and dna to be discussed later and would mean that dnaamino-acid tqc programs are rather robust against mutations. 3 model for the folding code based on interactions mediated by flux tubes between aminoacids the model for the protein folding to be discussed in this section relies on the hypothesis that dark flux tube connections between amino-acids and their contractions in ~ changing phase transitions determine the dynamics of the folding. a model in which flux tubes between amino-acids and water molecules alone induce the interactions between amino-acids will be discussed in separate section. a realistic model might involve both kind of flux tubes. 3.1 4-d spin glass energy landscape and code of catalytic action there is a proposal that protein folding corresponds to a motion in a fractal spin glass energy landscape in presence of external perturbations due to the presence of water and leading to the bottom of some deep valley [12, 12] . in tgd framework 3-d spin glass landscape is replaced by 4-d one [19] . the vacuum degeneracy of kähler action implies 4-d spin glass energy landscape in the sense that quantum jump sequences lead to space-time sheets representing asymptotic self organization patterns depending only weakly on the initial conditions (with respect to subjective time measured as quantum jumps). proteins would be like skilled musicians possessing a repertoire of motor activities represented by deep valleys in 4-d spin glass landscape. this picture generalizes to the functioning of living matter in various scales and the quantum dynamics of brain is a natural application giving also connection with p-adicity since ultametric topology is naturally associated with the space of valley bottoms. in the case of catalytic reactions a quantum jump changing planck constant for some magnetic flux tubes connecting some living biomolecules (dna, rna, aminoacids, water(?),..) and changing the lengths of these flux tubes could be the basic mechanism leading from a given valley to a new one and the reduction of the genetic code to single nucleotide or di-nucleotide code would code this quantum jumps. issn: 2159-0465 dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 58-88 68 pitkänen, m., a model for protein folding and biocatalysis to me this proposal for the folding code or rather, the code of entire biocatalysis looks so beautiful that it deserves to be killedthis should be easy for a professional biochemist. if the hypothesis survives, it would provide a royal road to the understanding of the catalytic bio-chemistry. 3.2 flux tubes and amino-acids 3.2.1 matter antimatter asymmetry at the level of interactions of amino-acids the first thing that i learned was that in the case of amino-acid belonging to protein interior second nucleotide y in the codon xy z coding for amino-acid is what matters. only y = a,g amino-acid residue can form hydrogen bonds and is hydrophilic and thus interacts strongly with water and dna and rna. in t,c case the formation of hydrogen bonds is impossible or rare (ser,thr). in their interactions with water these amino-acids are passive, or rather-avoid waterand tend to interact with each other. this division is fundamental for the understanding of the interactions of amino-acids. the division of amino-acids to hydrophobic resp. non-hydrophobic ones corresponds to the assignment of quarks to a and g and antiquarks to t and c so that strong matter antimatter asymmetry is in question. similar asymmetry appears in cosmology: in tgd universe antimatter resides inside cosmic strings in the interior of big voids containing matter as galaxies at their boundaries so that one can understand why antimatter is not visible. 3.2.2 flux tubes can connect with all electronegative atoms the model for dinucleotide precursor code [16] involves precursors for which 3 precursors contain only oxygen ions or double bonded oxygens. the only possible conclusion is that oxygen can connect to any dna letter (quark or antiquark) and that first letter-precursor correlation is a selection of the most probable alternative. also in water oxygen atoms should form flux tube contacts with each other and amino-acids and dna. also nitrogen atoms might form similar flux tube connections and this was assumed in the model. same would apply to sulphur appearing in met and tyr and to electronegative atoms in general. 3.2.3 what can one learn from the formation of alpha helices and beta sheets? assume that hydrogen bonds correspond to flux tubes. the formation of peptide bonds by the elimination of h2o-molecules and generation of hydrogen bonds between n − h and o = is an essential step in the formation of alpha helices and beta sheets. second observation is that free amino-acids decompose naturally into three parts corresponding to o = coh, r, and nh2. one can also count o = as a separate unit so that there would be four units in this case. this suggests that amino-acid could correspond to the entire dna codon xy z coding for it. in this case there would be 2 flux tubes per amino-acid and one can consider the following options. 1. y could correspond to either r or o =. if hydrogen bonds correspond to flux tubes, r − y correspondence is not realistic. the reason is that r should be either donor or accept and hydrophobic amino-acids do not possess neither property. hence only o = can corresponds to y . 2. o − h could correspond to z , o = to y , and nh2 to x. for this option the amino-acid in protein would correspond to xy . if one identifies hydrogen bonds as special case of flux tubes, the hydrogen bonds of alpha helix would obey x − yc rule which seems too restrictive. 3. o −h could correspond to x , r or o = to y , and nh2 to z. for this option the amino-acid in protein would correspond to y z. in this case the hydrogen bond of alpha helix would obey y = zc rule which by the isospin symmetry of the last nucleotide of the codon might be flexible enough. issn: 2159-0465 dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 58-88 69 pitkänen, m., a model for protein folding and biocatalysis 3.2.4 interactions of proteins with ions and electrons proteins interact also with electrons and ions. typical process are the addition or removal of proton, electron, ion such ca++, or molecule such as o2. these interactions are not well understood. for instance, the interactions involve the transfer of electrons between ligand protein and protein inducing oxidation (electron is given), reduction (electron is received) or redox reaction (both reduction and oxidation take place). in metabolism redox process is central. these reactions are reversible and it is difficult to understand how electrons are able make their long journey from the interior of the ligand so fast and avoiding dissipative effects. the formation of cyclotron bose-einstein condensates of bosonic ions and electronic cooper pair condensates at the magnetic flux tubes connecting ligand and protein might provide the solution of the mystery. note that the new nuclear physics predicted by tgd predicts nuclei which can have anomalous em charge associated with the color fluxtubes connecting nucleons to nuclear string so that fermionic ions na+, cl−,k+ could have exotic bosonic counterparts. 3.3 trying to identify the folding code the basic question is what kind of generalized pairings are realistic for amino-acids. the identification of hydrogen bonds as flux tubes leads to rather unique identification of the pairing and excludes the naively expected y − yc pairing. 3.3.1 a trial for the folding code protein folding code is something which is expected to exist but is not understood [14] . this inspired a work which led to several trials for the folding code. also a natural generalization to a code for catalysis emerged. in the most plausible candidate for the code flux tubes are identified as correlates of directed attention at molecular level. by their asymmetry hydrogen bonds are identified as a special case of flux tubes. free amino-acid behaves like xcyczc and the amino-acid inside protein like yczc. there are two flux tubes per amino-acid corresponding to n −h and o = representing zc and yc. this leaves two options for pairing. 1. if o = can act as a terminal for hydrogen bond and long flux tube then n −h and y can connect simultaneously to o = and one has y = z pairing. 2. if o = can act as a terminal for only single flux tube representing y then reconnection process for n −h and o = flux tubes creates the hydrogen bond and y = zc pairing for amino-acids results both pairings are highly flexible so that obvious inconsistencies with the data about alpha helices and beta sheets are avoided. a highly non-trivial and testable prediction of both pairings is that the two identical proteins coded by different dna sequences can have different foldings since the allowed pairings are not identical. thus amino-acids would remember at the level of the braidings which dna sequence coded them. this prediction can be avoided only z flux tube corresponds to a quantum superposition of the nucleotides coding for the amino-acid in question so that one has quantum superposition over quark pairs associated with the third nucleotide. the two-point mutations possibly carried out intentionally by the magnetic body controlling the genome conserving amino-acid pairings by hydrogen bonds and thus perhaps also folding and the catalytic properties should transform y = zc (y = z) pair to an allowed pair of this kind so that quite wide repertoire of allowed 2-point mutations is available for this option. 3.3.2 y = zc or y = z pairing might work the isospin symmetry of the third nucleotide implies that y = zc pairing is quite flexible. roughly, the rule would allow flux tube connections only between amino-acids for which y and z correspond to quark and antiquark. the amino-acid pairs can be classified to three types. the amino-acid pairs for which issn: 2159-0465 dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 58-88 70 pitkänen, m., a model for protein folding and biocatalysis both amino-acids can act as acceptors and donors, the pairs for which amino-acids can act only as an acceptor or donor, and the pairs for which no flux tubes are possible. there are two options to be considered. option 1: flux tube in either direction between amino-acids is prerequisite for the existence of the hydrogen bond. in this case the condition is y (n) = z(n + k) or z(n) = y (n + k). option 2:hydrogen bond is identified as a flux tube. the condition is y (n) = z(n + k) and thus stronger than for the first option. the following table summarizes the allowed and non-allowed pairings for y = zc and y = z pairings. to understand the tables some notation conventions must be introduced. 1. let xij denote the amino-acids in i:th and j:th column of the code table. i, j = 1, 2 corresponds to hydrophobic amino-acid residues and i, j=3,4 to hydrophilic amino-acid residues. 2. for y = zc option the sets t, t, u, v,w,x are defined as t = {phe}, t = x12−t, u = {tyr, his, asn, asp, cys, arg, ser, gly}, v = {trp, gln, lys, glu, gly}, w = {gln, lys, glu, trp, arg, gly}, and x = {tyr, his, asn, asp, cys}. 3. for y = z option the sets t, t, u, v,w,x are defined as t={met}, t = x12−t, u = {trp, gln, lys, glu, arg, gly}, v = {tyr, his, asn, asp, cys}, w = {tyr, his, asn, asp, cys, arg, ser, gly}, and x = {gln, lys, glu, trp}. ser has been excluded from v since it appears also in the second column of the code table. a and d a or d no flux tubes x12 ×x12 t × t t × t t× t x34 ×x34 u × u u × v v × v x12 ×x34 x12 ×w t ×x t×x table 1. general structure of pairings for y = zc and y = z options. a and d means that both amino-acids can act as acceptors and donors. a or d that only acceptor or donor property is possible. some clarifying comments about the table are in order. 1. pro is an exception since z nucleotide cannot be represented in this case and pro can act as donor. this has not been taken into account in the tables. 2. the codons coding for the paired amino-acid give additional strong limitations on the pairing unless z corresponds to quantum superposition of quark pairs associated with the third nucleotide for the codons coding for the amino-acid. 3. depending on option either phe-phe or met-met hydrogen bonding is forbidden so that for hydrophobic amino-acids almost all pairings are possible. this might allow to select between the two options or kill both. the special role of met suggest that y = z pairing might be the right option. also the model for dna as tqc assumes that o = associated with lipids can act as a plug to which two flux tubes terminate. on the other hand, phe is also exceptional in the sense that it is the only amino-acid in x12 which has aromatic ring and can act as an acceptor. 4. the amino-acids which can act simultaneously as donors and acceptors are of special interest as far interactions between catalyst sites of protein and ligand are considered. second flux tube could be involved with the structure of the catalyst site and second flux tube with the bonding of between catalyst sites. this kind of amino-acids correspond to t × t , u × u , x12 ×w . for both options hydrophobic amino-acid can be connected with any other hydrophobic amino-acid. in the case that the two amino-acids are connected by two flux tubes one has stronger conditions giving (y1, z1) = (z2, y2)c or (y1, z1) = (y2, z2). 5. t × t, u × v , and t ×x correspond to pairings for which amino-acids can act as donor or acceptor only. the triplets abc in which (a, b) belongs to one of these sets should not appear in alpha helices. for instance, for y = z pairing hydrogen bonded xmety triplets with x, y in x12 should not be possible. 6. the hydrogen bonds of alpha helices and beta sheets provide a test for the model. for instance, the appearance of gly in the hydrophobic portions of alpha helices is consistent with both y = zc and y = z pairing. the alpha helix appearing as an example in [13] is consistent with both options. issn: 2159-0465 dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 58-88 71 pitkänen, m., a model for protein folding and biocatalysis 2. flux tube is identified as hydrogen bond the following table summarizes the allowed and non-allowed pairings for y (n) = zc(n+k) and y (n) = z(n+k) pairings in this case. the notational conventions are following. 1. let xij denote the amino-acids in i:th and j:th column of the code table. i, j = 1, 2 corresponds to hydrophobic amino-acid residues and i, j=3,4 to hydrophilic amino-acid residues. only the sets x12 and x23 are of interest. 2. for y = zc option the sets t1, t2, v,w are defined as t1 = {phe, pro}, t2 = {met, pro}, v = {trp, gln, lys, glu}, and w = {tyr, his, asn, asp, cys}. 3. for y = z option the sets t1, t2, v,w are defined as t1 = {met, pro}, t2 = {phe, pro}, v = {tyr, his, asn, asp, cys}, and w = {trp, gln, lys, glu}. ser has been excluded from v since it appears also in the second column of the code table. a×d no flux tubes x12 ×x12 x12 × t1 x34 ×x34 x34 × v x12 ×x34 x12 ×w x34 ×x12 x34 × t2 table 2. general structure of pairings for y = zc and y = z options. a and d refer to acceptor (o =) and donor n −h respectively. only non-allowed hydrogen bonded pairs are listed. some clarifying comments about the table are in order. 1. the two options are related by the duality t1 ↔ t2, v ↔ w . pro appears in the list because it contains no n −h group and cannot therefore act as donor. the fact that pro often appears as first amino-acid in alpha helix conforms with this. 2. the codons coding for the paired amino-acid give additional strong limitations on the pairing unless z corresponds to quantum superposition of quark pairs associated with the third nucleotide for the codons coding for the amino-acid. this could be interpreted as counterpart of wobble base pairing. 3. met (contains s), pro, and phe (only amino-acid with aromatic ring in x12) are exceptional for both options. x12× t1 and x34× t2 = o−−(h −n) hydrogen bonding is forbidden. this poses strong conditions at the boundaries of hydrophilic and hydrophobic regions. one might hope that either of these models could give a solution to the basic problem of proteonics whether genes code for the protein folding and how: the apparently lost information in the mapping of codons to aminoacids codes for the folding determined hydrogen bonds and more general flux tubes. the hydrogen bonds of alpha helices and beta sheets provide a test for the model. in absence of quantum counterpart of wobble base pairing for z both models allows to deduce from the mere aminoacid sequence and hydrogen bonding the dna sequence coding for the protein in the case of alpha helices and presumably also beta sheets. this is of course a testable prediction. for non-hydrogen bonded portions of protein this might not be possible and an interesting question is whether they tend to consist of aminoacids in sets t, v and t∪x so that hydrogen bonds are not allowed. in any case this would mean a solution to the basic problem of proteomics whether genes code for the protein folding and how: the apparently lost information in the mapping of codons to amino-acids codes for the folding determined hydrogen bonds and more general flux tubes. 3.3.3 tests for y = z and y = zc pairings the test consists of deducing the number n of pairs which did not satisfy the condition (a(ii), a(ii+ 4)) not equal to (t, t), or does not belong to (v × v ) or to t× v ). from this the average length l of portions satisfying alpha helix conditions k = 4 can be deduced as l = n/ntot, where ntot is the number of amino-acids in the sequence. the test was carried out for one structural unit of asparagine synthetase [2] , xylose isomerase [11] , hydrolase [8] , glutathione s-transferase [7] , and restriction endonuclease bamhi [3] . 1. option 1: flux tube from in direction is prerequisite for the formation of hydrogen bond issn: 2159-0465 dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 58-88 72 pitkänen, m., a model for protein folding and biocatalysis the table below represents the results of the test when flux tube from y (n) to z(n + k) or from z(n) to y (n+ k) is prerequisite for hydrogen bond. protein l(3) l(4) l(5) l(6) asparagin synthethase y = zc 11.8 15.0 12.2 13.2 y = z 55.0 47.1 47.1 47.1 xylose isomerase y = zc 10.2 9.7 12.4 11.3 y = z 24.8 24.8 16.5 26.4 hydrolase y = zc 13.8 18.4 16.6 12.8 y = z 55.3 20.8 33.2 27.7 glutathione s-transferase y = zc 12.4 12.4 13.1 15.0 y = z 35.0 35.0 26.3 30.0 bamhi y = zc 9.7 8.5 10.7 10.7 y = z 30.4 23.7 30.4 35.5 table 3. the average number l(k) of aminoacids in the portion of amino-acid sequence satisfying the conditions making possible (n, n+ k) hydrogen bonding for k = 3, 4, 5, 6 for y = zc and y = z option in the case that flux tube can connect y (n) to z(n+ k) or z(n) to y (n+ k). from table 3 one finds that the test for values of k different from k = 4 for helix gave also surprisingly large values of l(k) for y = z option. the average length of alpha helix is 10 amino-acids so that both options could work. y = zc option gives results rather near to this value. one can apply test also to individual alpha helices. for asparagin synthethase alpha helices correspond to the intervals [7,28], [76,84], [130,155], [170,177], [76,84], [170,177], [182,194], [256,268], [277,284], [297,305], [309,314], and [320,326] in the standard numbering of amino-acids. the test was done for k = 3, 4, 5, 6 assuming that the upper end of tested interval is 6 units higher. n = (0, 0, 0, 0) results for both options for all intervals except for the interval [7, 28] for y = zc for which one obtains n = (4, 2, 3, 3). hence y = z option is favored. in the case of remaining enzymes only long enough alpha helices were tested and the following table gives the results issn: 2159-0465 dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 58-88 73 pitkänen, m., a model for protein folding and biocatalysis alpha helix n(y = z) n(y = zc) xylose isomerase [74,93] (2,1,0,1)(met-lys) (1,5,1,0) [111,129] (0,1,0,1)(asn-asp) (2,1,0,0) [159,179] (0,1,0,0)(asp-tyr) (5,4,1,3) [201,223] (1,1,1,2)(met-tyr) (4,3,4,3) [245,255] (2,0,0,0) (0,1,1,0) [278,287] (0,1,0,0)(his-tyr) (0,0,0,1) [314,327] (0,0,2,1) (2,0,1,1) [349,374] (0,0,4,0) (3,4,1,2) [376,386] (1,0,0,0) (2,1,1,1) [393,399] (0,0,0,0) (0,0,0,1) [404,414] (0,0,0,0) (1,1,1,1) [424,435] (0,0,1,0) (2,1,2,0) hydrolase [39,50] (0,0,0,1) (2,1,2,1) [60,79] (0,1,0,0)(asn-asp) (2,2,3,1) [93,113] (1,1,0,1)(val-gly) (3,0,2,1) [115,121] (1,0,0,0) (0,0,0,0) [126,134] (0,0,1,0) (1,0,0,0) [143,155] (0,0,0,0) (0,0,0,1) glutathione s-transferase [12,24] (0,0,1,0) (0,0,0,0) [65,76] (0,0,1,0) (0,1,0,0) [83,108] (3,2,3,1)(met-glu-asp) (0,0,1,0) [111,134] (0,0,1,2) (3,1,4,2) [150,166] (1,1,2,0)(asp-leu) (1,1,1,0) [174,184] (0,0,0,0) (0,0,0,1) [187,194] (0,0,0,0) (0,0,0,0) bamhi [10,18] (0,0,0,0) (0,0,0,0) [20,34] (0,0,0,0) (0,1,1,1) [58,72] (1,0,1,1) (0,0,0,0) [79,84] (0,0,0,0) (0,0,0,0) [117,132] (0,0,0,0) (0,0,0,0) [146,150] (1,1,0,0) (0,0,0,0) [159,169] (0,0,0,0) (0,0,0,0) [200,205] (0,0,0,0) (0,0,0,0) table 4. the test for alpha helices of four enzymes. the first column gives the range of amino-acids defining the alpha helix in question. the vectors in second and third column give the numbers of failures for k = 3, 4, 5, 6 for (n, n+ k) helix (k = 4 is the most interesting value). the amino-acid-pairs for which the hydrogen bond does not exist for y = z option are given. the conclusions are following. 1. from table 4 it seems clear that y = zc option does not work satisfactorily whereas y = z option has rather few failures. 2. in the case of xylose isomerase and (y = z) option with k = 4 there are four helices for which failure occurs for single aminoacid. the prediction is that the corresponding hydrogen bonds are actually absent. 3. the worst failure occurs for glutathione s-transferase and involves two aminoacids which are at positions n and n+ 4. the hydrogen bonds are predicted to not exist between met-glu and glu-asp in met-glu-asp. beta sheets consist of beta strands which can be regarded as (n, n + 1) helices so that stability conditions correspond to k = 1. as the table below shows, there are no failures for y=z option whereas y = zc option has issn: 2159-0465 dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 58-88 74 pitkänen, m., a model for protein folding and biocatalysis several failures and very bad failure for glutathione s-transferase (3 failures for 4 units long strand). beta sheet n(y = z) n(y = zc) asparagin synthethase [113,122] 0 2 [233,240] 0 0 [245,255] 0 0 [290,297] 0 3 xylose isomerase [43,47] 0 0 [96,100] 0 2 [134,140] 0 1 [262,267] 0 0 [291,295] 0 0 hydrolase [14,19] 0 0 [25,28] 0 0 glutathione s-transferase [3,7] 0 0 [28,32] 0 3 [54,58] 0 0 [60,63] 0 0 bamhi [2,8] 0 0 [46,48] 0 0 [70,72] 0 0 [95,100] 0 0 [105,112] 0 0 [138,144] 0 0 [174,180] 0 0 [183,185] 0 1 table 5. the test for beta sheets of four enzymes. the first column gives the range of amino-acids defining the beta sheet in question. the vectors in second and third column give the numbers of failures for k = 1 for (n, n+ 1) helix. one might think that loops could contain amino-acids for which the hydrogen bonds to neighbors are not possible. the test for bamhi showed that this is not the case. only single loop failed for y = z option for k = 1, 2..., 4 and this occurred for k = 1. the remaining test is for whether the y = z pairing indeed can fix the dna sequence completely. bamhi begins as met glu val glu lys glu phe ile..... for beta sheet beginning from second amino-acid requires that the y=z rules holds true for subsequent codons in dna sequence aag ctt cct taa ttc cgg aag ... [4] . by comparing the z of a given codon in beta sheet to the y of the next codon inside beta sheet one finds that the y (n) = z(n+ 1) or z(n) = y (n + 1) fails. similar conclusion follows from an analogous check for the first alpha helix. situation is saved if the quantum counterpart of wobble base pairing is at work so that the flux tube from trna to n −h would in superposition of colors (quark pairs) corresponding to superposition nucleotides z in codons xy z for given x and y coding for the amino-acid in question. hydrogen bonded amino-acid sequence would behave as if it were coded by the unique dna sequence. note that for a given amino-acid x is unique except for leu and arg and y is unique except for ser. the n − h:s and o =:s for which hydrogen bonds are lacking could form hydrogen bonds with water molecules and o =:s could have long flux tubes with other o =:s in the protein. 2. option 2: flux tube is identified as hydrogen bond the following tables summarize the results of the test for y = z and y = zc option when flux tube is issn: 2159-0465 dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 58-88 75 pitkänen, m., a model for protein folding and biocatalysis identified as hydrogen bond. for the first option the average length of hydrogen bonded interval would be around 5 amino-acids for k = 4 helix for y = z and somewhat shorter for y = zc. bamhi is exceptional since in this case the length is 16.8 (10.4) amino-acids. for y = z (y = zc). there is no clear difference between the two alternatives in the case of alpha helices and neither alternative looks promising in this case. protein l(3) l(4) l(5) l(6) asparagin synthethase y = z 4.5 4.9 4.6 4.9 y = zc 4.2 4.7 5.3 4.6 xylose isomerase y = z 3.7 4.3 3.5 3.9 y = zc 4.0 3.0 4.1 3.8 hydrolase y = z 5.7 5.1 4.2 4.3 y = zc 4.6 5.0 6.1 5.1 glutathione s-transferase y = z 5.1 5.8 4.6 4.0 y = zc 4.5 3.6 4.0 4.7 bamhi y = z 11.3 16.8 15.6 12.9 y = zc 16.8 10.4 12.1 12.9 table 6. the average number l(k) of aminoacids in the portion of amino-acid sequence satisfying the conditions making possible (n, n+ k) hydrogen bonding for k = 3, 4, 5, 6 for y = zc and y = z option in the case that flux tube can connect y (n) to z(n+ k). issn: 2159-0465 dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 58-88 76 pitkänen, m., a model for protein folding and biocatalysis alpha helix n(y = z) n(y = zc) asparagin synthethase [7,28] (4,4,4,2) (6,4,3,5) [76,84] (1,0,1,1) (2,2,1,1 [130,155] (5,5,4,5) (2,2,2,1) [170,177] (0,0,1,1) (1,1,1,1) [182,194] (1,1,1,1) (2,2,1,1) [256,268] (1,3,0,3) (3,0,3,0) [277,284] (0,0,0,0) (0,0,0,0) [297,305] (0,0,0,0) (1,0,0,0) [309,314] (0,1,0,0) (2,0,1,0) [320,326] (1,1,0,0) (0,0,0,0) xylose isomerase [74,93] (6,1,6,4) (2,5,4,3) [111,129] (3,3,4,2) (4,4,4,3) [159,179] (3,4,6,3) (4,3,1,3) [201,223] (3,6,5,4) (5,7,4,4) [245,255] (1,1,1,1) (0,1,0,0) [278,287] (2,1,1,0)(his-tyr) (0,0,0,1) [314,327] (1,2,3,3) (2,3,2,2) [349,374] (4,3,8,6) (5,8,1,3) [376,386] (4,0,2,3) (1,4,3,0) [393,399] (0,0,0,0) (1,0,0,0) [404,414] (1,1,2,1) (3,3,1,1) [424,435] (1,2,0,2) (3,2,3,1) hydrolase [39,50] (2,3,0,2) (2,1,3,1) [60,79] (4,2,2,4)(asn-asp) (4,4,5,2) [93,113] (2,1,4,4)(val-gly) (3,2,1,1) [115,121] (0,1,0,0) (0,1,0,0) [126,134] (0,1,1,1) (1,0,0,0) [143,155] (0,1,1,1) (1,0,1,1) glutathione s-transferase [12,24] (1,4,2,4) (5,2,3,1) [65,76] (3,1,1,0) (2,1,1,1) [83,108] (5,3,5,5) (5,3,3,2) [111,134] (4,5,5,4) (4,5,3,3) [150,166] (2,2,3,0)(asp-leu) (4,3,1,3) [174,184] (0,0,0,0) (1,1,1,1) [187,194] (1,1,0,1) (0,2,0,1) bamhi [10,18] (0,0,0,0) (0,0,0,0) [20,34] (4,1,1,2) (2,5,4,2) [58,72] (3,1,2,4) (3,5,4,1) [79,84] (0,0,0,0) (0,0,0,0) [117,132] (0,0,0,0) (0,0,0,0) [146,150] (1,1,0,0) (0,0,0,0) [159,169] (0,0,0,0) (0,0,0,0) [200,205] (0,0,0,0) (0,0,0,0) table 7. the test for alpha helices of four enzymes in the case of y (n) = z(n + k) option. the first column gives the range of amino-acids defining the alpha helix in question. the vectors in second and third column give issn: 2159-0465 dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 58-88 77 pitkänen, m., a model for protein folding and biocatalysis the numbers of failures for k = 3, 4, 5, 6 for (n, n+ k) helix (k = 4 is the most interesting value). beta sheet n(y = z) n(y = zc) asparagin synthethase [113,122] 1 5 [233,240] 3 0 [245,255] 1 0 [290,297] 0 1 xylose isomerase [43,47] 0 1 [96,100] 2 4 [134,140] 2 0 [262,267] 2 1 [291,295] 0 1 hydrolase [14,19] 1 2 [25,28] 0 0 glutathione s-transferase [3,7] 0 1 [28,32] 1 3 [54,58] 4 1 [60,63] 0 0 bamhi [2,8] 0 0 [46,48] 0 0 [70,72] 2 0 [95,100] 0 0 [105,112] 4 0 [138,144] 0 0 [174,180] 0 0 [183,185] 1 2 table 8. the test for beta strands of four enzymes for y (n) = z(n + 1) option. the first column gives the range of amino-acids defining the beta sheet in question. the vectors in second and third column give the numbers of failures for k = 1 for (n, n+ 1) helix. 3.3.4 are = o −o = flux tubes present? y = z option for the folding code assumes that flux tubes can connect acceptor atoms by flux tubes. the pairing would be y − yc pairing considered in the original model as the only possible pairing. in amino-acids only o =:s not acting as acceptors for ordinary hydrogen bonds could have flux tube connections of this kind with each other or other molecules. 1. in the case of amino-acids y − yc pairing would be between amino-acid in x12 and amino-acid in x34 part of the code table. these connections would be typically associated with the portions of the protein between alpha helices and beta sheets. the k : th amino-acid (k = 3, 4 or 5) following pro would be an exception to this rule and this kind of flux tubes could be involved with the long scale stabilization of proteins. 2. the o = atom would effectively behave like yc. depending on whether it corresponds to quark or antiquark, the corresponding amino-acid would be typically hydrophilic or hydrophobicor rather able to form hydrogen bonds or not. since hydrophilic and hydrophobic residues tend to avoid each other the flux tubes in question should be rather long. the phase transitions increasing planck constant might make issn: 2159-0465 dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 58-88 78 pitkänen, m., a model for protein folding and biocatalysis this possible. this would bring in a strong long range correlation between the dynamics of the amino-acid residues belonging to the first and third (second and fourth) column of the code table. 3. = o − o = flux tubes could be also between different proteins. in the case of protein-ligand complex the planck constant changing phase transition reducing the length of this kind of flux tube could bring proteins together after which a recombination process the hydrogen bond connecting two water molecules would transform the bond to hydrogen bonds of o =:s with water molecules. 4. the phase transition increasing ~ would allow hydrophobic amino-acids to increase their distance from water molecules in a controlled manner. this could be essential for folding and make possible the formation of pockets connected by flux tubes of large ~ to water. in quantum models for evolution of consciousness these pockets are believed to play a prominent role. molecular sex in this sense would mean a correlation tending to keep partners at large distance except when ~ reducing phase transition occurs. 3.3.5 evolution and amino-acid pairings the evolution at the molecular level corresponds to the emergence of increasingly complex molecules using as basic building blocks amino-acid chains and non-translated residues attached to them in the post-translational processing of the amino-acid chains. also increasingly complex reaction paths emerge. molecular survival and the competition for the metabolic resources at molecular level could be seen as the basic driving force of this evolution. typically, in the original situation the enzymes would have received the substrate molecules from the environment but sooner or later this would have become difficult. the solution would have been a synthesis of the substrate from simpler ingredients by starting from some precursor. if molecules (with magnetic bodies included) are conscious entities able to direct attention, one can imagine that magnetic body controlling them with the mediation of genome and able to actively modify it, could help through modifications of the genome to create to the catalyst a binding site able to bind the precursor. immune system is doing this very intensively. if the enzyme binding the precursor already exists, a combination of genes coding for the enzyme and the enzyme having the metabolites as ligands could allow to achieve this. all this would reduce to the motor activities of magnetic body, in particular reconnection of flux tubes, a kind of dance of shiva. genome would not be anymore a sequence of dna developing through random mutations under selection pressures. in this framework amino-acids would have appeared before their precursors and possessed some function in rna world, say the catalysis of join of rna2 dinucleotides to the increasing chain as proposed in [16] . competition might have led to a situation in which rna2 learned to catalyze selectively the generation of amino-acids from much simpler precursors (three of the proposed precursors contain only c, = o, and o−) giving rise to positive feedback implying an exponential amplification of rna and amino-acid populations. the reduced genetic code would have been present at two levels. the reader can decide whether this is a shortcoming of the model or a fundamental biochemical duality. can one make any clear cut predictions about preferred mutations? 1. in tgd framework mutations are not expected to be always random point mutations but could be even a result of a purposeful action of the magnetic body. chemical similarity is expected to be conserved in good mutations. this is known to be the case. for y = z or y = zc pairing the simplest mutations should leave both y and z invariant so that only the first nucleotide x can suffer a mutation. 2. also bi-local mutations of the second and third nucleotides of codons forming y = z (y = zc) pair and conserving this property might occur and could be crucial for the coherence of the organisms. as found, the formation of flux tube between amino-acids a1 and a2 induces a flux tube between nucleotides y and z at the corresponding genes. this flux tube could force the possibly intentional mutations to occur as simultaneous mutations of the two genes so that y = z (y = zc) condition remains true for amino-acids connected by flux tube. 3. a new element is that isospin rotation of z nucleotide (a← g, t ← c) which does not affect amino-acid, affects its folding so that same protein might have different folding patterns and different catalytic properties corresponding to different codons coding for it. this would mean a breaking of the central dogma a the level of magnetic body. some examples are in order. the mutations ala/ser, ser/thr, ile/val/leu, asp/glu do not change y . lys/arg (a/g)), tyr/phe (a/u), gly/ala (g/c),... are also prevalent and one might hope that they correspond to binary mutations in some important cases. issn: 2159-0465 dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 58-88 79 pitkänen, m., a model for protein folding and biocatalysis 4. folding is known to be more conserved than amino-acid sequence [13] . since folding is a collective property of gene, local chemistry might not be enough and the proposed non-local conservation laws might be needed. two-point mutations would also correlate the mutations of the binding sites of protein and ligand. for the model assuming two flux tubes per amino-acid, the prediction would be conserved y = z (y = zc) pairs in genes coding for protein and ligand and these pairs might allow to deduce the paired points. this is consistent with the fact that hydrophobic (-philic) regions tend to be paired in the protein-ligand complex. the paired nucleotides need not belong to the same strand since genes are evenly distributed between strand and its conjugate and characterized by a,g surplus. 5. if the flux tubes can connect also side chains, the situation becomes more complex. there is a temptation to think that these flux tubes would connect only the nearby amino-acids of the same peptide and do not therefore affect the large scale dynamics of folding. this would be the case if the value of planck constant associated with these flux tubes is smaller than for the flux tubes connecting amino-acids as basic units. if flux tubes can begin from the aromatic side chains, the replacement of an aromatic side chain with an aromatic side chain is favored (also chemical similarity explains this). the most basic facts about folding do not provide obvious support for the idea about flux tubes between residues. i) hydrophobic residues tend to cluster in dense packing in protein interior (antimatter at quark level) and val (t ), leu (t ), ile (t ), phe (t ), ala (c), and gly (g) make 63 percent of the interior of protein: the special role of gly (matter rather than antimatter at quark level) is due to the reduction of the side chain to hydrogen atom. ii) asp (a), glu (a), lys (a) and arg (g) with ionized residues are mostly at the surface of protein and make 23 per cent of protein surface and 4 per cent of interior. as noticed earlier, matter and antimatter at quark level tend to be far from each other. this is consistent with y = z pairing between nearby amino-acids and absence of flux tubes between matter and antimatter if there are two flux tubes per amino-acid. iii) polar groups tend to be paired by hydrogen bonds and oppositely charged groups tend to be near each other. acidic cys residues tend to be in positions where they can form s−s bonds. this can be explained as being induced by y − y pairing in the proposed scenario. aromatic residues tend to have favorable electrostatic interactions with each other and with s,o and amino groups. 4 a simple quantitative model for protein folding and catalyst action assuming flux tubes between amino-acids levinthal paradox states that if protein folding is a process in which protein checks for all possible conformations, folding would take astrophysical time. small single domain proteins with lengths below 100 residues however fold in single step in millisecond time scale and longest folding times are measured in days. this suggests that protein folding is in some sense guided dynamical process and flux tubes would be the natural guides. it is possible to construct a simple quantitative model for protein folding and catalyst action assuming a long range interaction mediated by flux tubes between amino-acids obeying base pairing rule in some sense. a further assumption is that hydrogen bonds correspond to flux tubes. there are two options to consider. 1. if there is only single flux tube per amino-acid the rule implies that conjugate amino-acids are connected by a flux tube: this is conflict with the empirical facts. 2. if there are two flux tubes per amino-acid base pairing predicts that amino-adic pairing obeys y = z or y = zc rule depending on whether o =:s can act as intermediate plugs for flux tubes or not. the model is consistent with quantum criticality, and the general vision about 4-d spin glass landscape. the extremals are not completely deterministic just as vacuum extremals of kähler action and only absolute minimization of energy selects minima. the cautious interpretation is that absolute minimization of energy stabilizes various unstable patterns generated spontaneously by ordinary chemical interactions such as alpha helices and beta sheets. the interpretation of hydrogen bond in terms of flux tube suggests more bold interpretation. the principle is flexible enough to carry out this purpose but also poses strong constraints on how these patterns integrate to higher level structures. the disappearance of a subset of flux tubes does not spoil the extremal property although it increases its non-determinism and makes folding less predictable and in the case of binding sites it reduces the selectivity of catalyst action. the interpretation would be in terms of molecular ageing. the density of flux tubes can be seen as an analog for the resolution of quantum measurement which is issn: 2159-0465 dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 58-88 80 pitkänen, m., a model for protein folding and biocatalysis in a fundamental role in quantum tgd, as well as a direct correlate for cognitive and sensory resolutions. the model extends to a model of catalyst dynamics if one the relative motion of reactant molecules is slow in the time scale of folding dynamics so that adiabaticity assumption makes sense. in the following i often use the basic data which can be found from [13] without explicit reference. 4.1 the model let us assign potential energy to the flux tube connecting i:th and k(i):th amino-acid and depending only on the distance ri,k(i). what comes in mind first is the potential energy of harmonic oscillator: v (r) = kr2 2 . (4.1) k > 0 corresponds to harmonic oscillator. also k < 0 is possible in which case the distance between amino-acid and its conjugate tends to be maximized in equilibrium: this option turns out to be the more plausible one and conforms also with the notion of quantum criticality. besides this there is the constraint that the distances between amino-acid and its follower are constant: ri+1,i = r . using lagrange multipliers this gives rise to the action l = −e = −k 2 ∑ i r2i,k(i) + ∑ i λir 2 i+1,i . (4.2) energy is the negative of this action for static solutions. one could consider also adding kinetic term to this action to describe the dynamics of folding. this action is hoped to give only a qualitative view about folding and the ordinary chemical interactions should fix the details of the folding and select between different folding patterns. several amino-acid chains could be present and have mutual long range interactions. if n − h and o = both can be connected by flux tubes, each amino-acid gives two terms to the energy corresponding to the flux tube beginning from n −h and flux tube ending at o =. the extremals of this action satisfy ∂l ∂rki = 0 , i = 1, ..., n . (4.3) 1. if there is only single flux tube per amino-acid, this gives the conditions λi+1ri+1,i − λi−1ri,i−1 = −kri,k(i) , rj+1,j = r . (4.4) the geometric content of these conditions is that the vectors ri,k(i), ri+1,i, and ri,i−1 are in the same plane. 2. if there are two flux tubes per amino-acid (= oi −−(n −h)k1(i) and (n −h)i −−(o =)k2(i)) λi+1ri+1,i − λi−1ri,i−1 = −k[ri,k1(i) + ri,k2(i)] , rj+1,j = r . (4.5) in this the resultant of the vectors ri,k1(i) + ri,k2(i) would be in the plane determined by ri+1,i and ri,i−1. note that due to the lack of n −h in pro it can happen that there is only single flux tube per amino-acid. long range interactions of amino-acids with their conjugates would dictate the local folding of the amino-acid chain but extremum property alone does not say much about the lengths of the flux tubes. suppose that ri, ri,k(i), ri,i−1, λi−1 are known. can one solve λi+1 and ri+1,i? since the vectors are in the same plane, the linear dependence does not fix the direction of ri+1 in this plane but only the value of λi in this plane once ri+1 is fixed or vice versa. therefore the direction in the plane remains un-determined and equations of motion are not fully deterministic as far as extremals are considered. absolute minimization however eliminates this non-determinism by maximizing the distances ri,i(k) for k > 0 option. the expressions for λi result from elementary linear algebra by introducing dual basis of non-orthogonal basis defined by ri,k(i) and ri,i−1. issn: 2159-0465 dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 58-88 81 pitkänen, m., a model for protein folding and biocatalysis 1. in the case that there is single flux tube per amino-acid, one has λi+1 = −kei+1 · ri,k(i) , λi−1 = −kei−1 · ri,k(i) , ei+1 · ri+1,i) = 1 , ei+1 · ri,i−1) = 0 , ei−1 · ri+1,i) = 0 , ei−1 · ri,i−1) = 1 . (4.6) the non-determinism does not make it easy to find absolute minimum since non-determinism corresponds to circle (s1)2n for amino-acid sequence with n flux tube pairings. these conditions do not make sense when ri+1,i) and ri,i−1) are parallel: in this case the force must be parallel to ri+1,i). 2. for two flux tubes per amino-acid one has a slightly more complex expression for these conditions: λi+1 = −kei+1 · [ri,k1(i) + ri,k2(i)] , λi−1 = −kei−1 · [ri,k1(i) + ri,k2(i)] , ei+1 · ri+1,i) = 1 , ei+1 · ri,i−1) = 0 , ei−1 · ri+1,i) = 0 , ei−1 · ri,i−1) = 1 . (4.7) the strong resemblance with the dynamics defined by kähler action predicting spin glass degeneracy associated with vacuum extremals of kähler action and removed by small deformations to non-vacuum extremals raises the hope that the model indeed catches something essential about the notions of 4-d spin glass degeneracy and quantum criticality. 4.2 basic mathematical consequences consider first the basic consequences of the variational equations. 1. absolute minimization of energy is very powerful selection principle and expected to choose highly symmetric configurations such as α helices, β sheets, and more complex structures. if combined with adiabaticity assumption it could also allow to understand the dynamics of binding between two proteins and protein and dna/rna. 2. the extremals of k > 0 action are mirror images of k < 0 action so that the energy minimum for k > 0 is energy maximum for k < 0. if energy minimization is applied also the choice of y − y flux tubes, the connected amino-acids should be as near as possible which favors alpha helices and beta sheets. in light of this k > 0 option looks the realistic one. it could however be that for large distances the sign of the potential energy changes. for k > 0 option long flux tubes are not favored by energy minimization. the simplest cure would be large value of planck constant changing the scale of the potential. if the potential energy changes sign at large distances the situation changes also and ri,k(i) would be as large as possible subject to the condition from fixed chain length. 3. if the amino-acid is not paired, it does not experience the long range force and one has λi+1ri+1,i − λi−1ri,i−1 = 0 . (4.8) situation becomes non-deterministic and the portions of the amino-acid chain for which the amino-acids do not have a pair behave like random coils. this is encouraging since this kind of portions are present in folded amino-acids. the absence of n −h from pro allows to understand the very special role of pro as being associated with turns of alpha helices and beta sheets. 4. the disappearance of some flux tubes does not destroy a given solution of the conditions but makes it increasingly non-deterministic. the interpretation as a degradation or ageing at molecular level conforms with the interpretation of braiding as a basic characteristic of life. an attractive interpretation of the density of flux tubes is as correlate for resolution for cognition and sensory perception and motor action as counterpart of measurement resolution which is fundamental notion of quantum tgd. issn: 2159-0465 dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 58-88 82 pitkänen, m., a model for protein folding and biocatalysis 4.3 model for the helical structures α helix [13, 1] , which is only one member of a rich family of helical structures possible for amino-acid chains, serves as the first test for the model. as a matter fact, the specific properties of α helix are not relevant for the model discussed. 1. α helix has nearly vertical nh−−−o = hydrogen bond between i:th and i−4:th amino-acid. also (i, i−3) and (i, i− 5) bondings are possible. there are 3.6 residues per turn so that the basic structural unit has 5 turns and consists of 18 amino-acids. one residue corresponds to a vertical translation of 1.5 angstrom. the chain contains single amino-acid per length of about 3.8 angstrom and the angular separation of subsequent amino-acids is 100 degrees in the planar projection. 2. isolated α helices are not stable but can be stabilized by secondary coiling: their lifetime is of order 10−5 − 10−7 seconds. if the flux tubes are associated with hydrogen bonds, the instability would be naturally due to a reconnection process involving water molecules. consider now the model. 1. assume that hydrogen bond is accompanied by a special case of a flux tube resulting in the reduction of the value of planck constant. short flux tubes (hydrogen bonds) would connect i − k:th, i:th and i + k:th amino-acids, k = 3, 4 or 5. the forces between i−k:th and i:th and i:th and i+k:th amino-acid compensate each other exactly for an ideal helix so that the conditions are satisfied identically. this kind of mechanism work also for more general helices. y = z (y = zc) pairing poses special conditions on the helical structures themselves and also on the genes coding for these structures. 2. gly helices are consistent with both y = z and y = zc pairings. the spontaneous generation of unstable helices in sequences consisting of mere gly could be understood as the instability of gly-gly flux tubes against reconnection with hydrogen bonds connecting surrounding water molecules. also the sequences consisting of mere pro can give rise to unstable helices. pro does not possess n −h and the residue cannot act as a donor in hydrogen bond. this suggests that the residue of pro can have flux tubes connecting it to o = but not identifiable as ordinary hydrogen bond. there are also more complex structures formed form helices [13] . for coiled coils of two or more alpha helices consisting of repeating heptad unit of 7 amino-acids first and fifth amino-acids tend to be conjugates so that horizontal flux tubes connecting first and fifth amino-acids of neighboring could be responsible for the stability and make also possible the hydrophobic bonding between first and fourth residues. collagen [6] is a triplet helix and appears as a basic constituent of bones, tendons, skin, ligaments, blood vessels, and supporting membraneous tissues. the units of collagen triple helix consists of very long repetitive sequences of type (gly −xy )n, with a preponderance of pro for x (also lys residues are possible). gly-pro-y and gly-x-hyp appear often: here x and y are arbitrary amino-acids (hyp denotes hydroxyprolin with o = replaced with oh: this transforms pro from acceptor to donor). heating of collagen triple helix unfolds it and converts it to gelatin, in which polypeptide chains are dissociated, unraveled and disordered. cooling regenerates these conformations for short stretches. consider as a example collagen triplet helix [6] having gly − pro− y as a repeating unit. assume y = z or y = zc pairing. y − y hydrogen bonds are possible if y belongs to the group t or u . only phe (y = zc) or met (y = z) is excluded from t . y = zc corresponds to u = {tyr, his, asn, asp, cys, arg, ser, gly} and y = z to u = {trp, gln, lys, glu, arg, gly}. this prediction might kill the model. glys can be connected for both options. 1. the first model goes like follows. alpha helix structure is guaranteed by hydrogen bonds between the y :s inside each collagen unit (k = 3). the amino-acids glyi, i = 1, 2, 3, are connected by almost horizontal flux tubes cyclically as gly1−gly2, gly2−gly3, gly3−gly1. this cyclic bonding would induce the coiling of alpha helices. the free o =:s of pros could act as acceptors in the hydrogen bonds with the surrounding water molecules (for instance). for gly-x-hyp one would have similar structure but hyp would act as donor in the hydrogen bonds with water molecules. the objection is that if long hydrogen bonds are possible they would have been observed. 2. second model is based on the philosophy that coiling is a long range effect and must be due to = o −o = flux tubes. gly (y = g) and pro (y = c) can be connected for both options but only by single flux tube by the special properties of pro: this bonding would give n, n+ 4 hydrogen bond of alpha helix. the simultaneous presence of n, n+3 y −y bonds and n, n+4 pro-gly bonds might be made possible by coiling. hence the free o = in gly could be connected with a similar o = in the neighboring strand. gly1 − gly2, issn: 2159-0465 dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 58-88 83 pitkänen, m., a model for protein folding and biocatalysis gly2− gly3, gly3− gly1 cannot form a closed cycle but the repeating helical pattern gly1− gly2, gly3− gly1, gly2 − gly3 is possible and could produce the coiling. 4.4 model for β sheets beta strands are typically 4-5 amino-acids long structures. hydrogen bonds are of type (n, n+ 1) and β strands have 2 amino-acids per turn so that ri−1,i and ri,i+1 span a vertical plane and the equations of the model are trivially satisfied. beta strands as such are not stable. beta sheets [5] consisting of β strands which can be either parallel or antiparallel and are glued together by the interactions between residues. beta sheets are also slightly twisted which relates to the chirality of amino-acids. in the antiparallel case strand returns back and forms at the ends of sheet a loop so that so called β hairpin is formed. in parallel case the strand returns as alpha helix to the lower end of the sheet. at the time of writing of [13] the mechanism of formation of β sheets was not understood. if horizontal flux tubes between neighboring strands assignable to hydrogen bonds or =o-o= flux tubes between the residues are responsible for the stabilization of the beta sheet structure, then given residue must have two hydrogen bonds with same length to the amino-acids at right and left so that the contributions from right and left side to the force compensate each other and the force is automatically vertical as implied by the twisting angle of π per amino-acid in beta sheet. for self connecting flux tubes inside loops the force would be in the plane of loop and if the force is repulsive loop like structure is expected. the slight twisting of beta sheet represents a challenge for the model. tgd predicts large parity breaking and thus the twisting and preferred helicity at the level of principle but it is not clear whether the simplest model can explain the twisting. 4.5 secondary protein structures protein structures are divided into four classes on basis of their secondary structures [13, 10] . all these structures are consistent with the general model. 1. (α) containing only α helices, which must stabilize each other by horizontal flux tubes. 2. (β) containing only β sheets both usually antiparallel, which appear always in pairs packing against each other. horizontal flux tubes connecting the β sheets must act as stabilizers. 3. (α + β) proteins can contain only single β sheet, usually antiparallel, with α helices clustering together at one or both ends of the β sheet. antiparallel β sheet stabilizes itself. 4. (α/β) in which sheets and helices interact and often alternate along the polypeptide chain. single parallel β sheet and so called β barrel, kind of sandwich like structure, are basic examples here. the most spectacular barrel consists of 4+4 parallel β strands with α helices outside the barrel. concerning the organization of alpha helices and beta sheets to higher level structures the simplest guess is that the large planck constant flux tubes connecting random coil portions of the amino-acid sequence with each other or with free o = accompanying pros. the mere assumption that a given portion of coil has only long flux tubes to distant parts of the protein could explain random coil character. the failure of y = z condition implies this too. the notion of long hydrogen bond is somewhat questionable and long flux tubes connecting = o:s look more favorable. also free o =:s inside alpha helices and beta strands could be connected in this manner. 4.6 model for protein-protein binding sites binding sites obey geometric complementarity and are known to resemble protein interior being closely packed. this is also taken to mean that amino-acid chains run parallel to the surface although this statement is not made explicitly in [13] : one could see binding sites as part of interior which is in a direct contact with exterior, somewhat like a sensory organ like eye. the interface between similar sized proteins is large and tends to be flat (not expected if proteins make sharp turns at the interface rather than running parallel to the surface). various bonds eliminate electromagnetic interactions at the interface. the basic mechanism of binding would be based on the reduction of planck constant for the flux tubes connecting amino-acids. the high flexibility of y = z and y −zc pairings -especially in the hydrophobic regions in the center of the binding site where it allows all but met-met and phe-phe flux tubesmakes it an excellent candidate for a folding code. issn: 2159-0465 dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 58-88 84 pitkänen, m., a model for protein folding and biocatalysis the question is whether complementary of bonded amino-acids should induce the geometric complementary of the binding sites in the proposed model. 1. the binding sites could be connected by only very few flux tubes or flux tubes could connect all amino-acids in a pairwise manner: the first extreme is highly flexible whereas second extreme would produce maximal selectivity. complementary can thus be partial and its degree is predicted to correlate with the selectivity. the interpretation of disappearance of flux tubes as molecular ageing conforms with the gradual loss of selectivity implying reduced performance of immune system. 2. from the example of [13] about the interface of identical proteins in the quaternary structure of dimer one learns that the geometrically and physically conjugate interfaces of identical monomers pair to form sandwich like structures via so called isologous and heterologous pairings such that valleys and hills fit. the interfaces are reported to resemble closely packed protein interiors and contain hydrophobic residues in the center and hydrophilic residues at periphery. in the case of identical monomers y − z and y − zc pairing is possible for a very wide class of amino-acids. the prediction in the case of identical monomers would be that catalyst sites contain only very few amino-acids in the sets v and t defined previously. 3. also the flux tubes between = o atoms could be in key role in the protein-ligand interaction. the interfaces can be thought of as cutting protein along its interior: in center there are hydrophobic amino-acids and in periphery hydrophilic ones. the = o−o = flux tubes would connect periphery of a (b) to the center of b (a). the reduction of planck constant for would reduce the length of these flux tubes and bring protein and ligand close to each other so that hydrogen bond formation between residues could being. in this process the flux tube connecting o =: s could by reconnection transform to two hydrogen bonds connecting o =:s to water molecules. after the catalysis the reverse of this process would occur. 4. for single flux tube between o =:s of amino-acid and ligand the force would be along the line ri,k(i) connecting them, in the improbable case that the amino-acids of protein and ligand are connected by two hydrogen bond like flux tubes the force is in the direction of ri,k1(i) + ri,k2(i). the force is predicted to be in the plane spanned by ri+1,i and ri,i−1 for protein and in the corresponding plane for ligand. this is true if the amino-acid sequence at the surface is slightly curved in the direction of the conjugate amino-acid or in opposite direction. this condition is guaranteed by the geometric complementarity. 5. the mechanism for the formation of ligand-protein pairs would be very simple: the binding sites of protein and ligand could be coded by same gene or its mutation respecting the y so that the formation of copies of gene in dna would be the simplest mechanism to guarantee the prerequisites for geometric conjugation. geometric conjugation would result automatically if the flux tubes between interior and periphery of binding site determine its shape. 6. slow enough relative motion of molecules induces an adiabatic variation of the shapes of the binding sites so that lock and key mechanism becomes dynamical. the simplest possibility is that binding site and its conjugate behave like two eyeballs gazing each other as proteins move with respect to each other. this is possible if binding sites are separated from the rest of the protein by random pieces of chain. the analogy with eye might be actually deeper: i have proposed long time ago that directed attention in vision has as a space-time correlate flux tubes of topological light rays or both of these. wormhole magnetic flux tubes might indeed connect perceiver and the object perceived and serve as correlates of attention in macroscopic length scales. 7. also the hydrogen bonds between residues are important for the protein folding. the donor atoms of the residues can inherit the conjugate of the color of o = and acceptor atoms can inherit the color of n −h by temporary reconnection. therefore also the hydrogen bonds between residues of hydrophilic residues containing both donor and acceptor atoms would be restricted by the colors of atoms and would reflect genetic code. 8. geometric and physical conjugation (acids and basics combine in the interface) means that a virtual protein a+b is cut to pieces along the surface in the interior defining the interfaces. could this chopping of bigger proteins to smaller ones able to bind allow a realization at the level of genome in the sense that glued portions of protein would originate from same gene or its reversed version and thus satisfy y = zc or y = z rule approximately? could also protein interior involve pairings analogous to catalyst and ligand pairings? this would partially explain why protein folding is more sensitive to the mutations in the interior of protein. issn: 2159-0465 dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 58-88 85 pitkänen, m., a model for protein folding and biocatalysis 5 a model for protein folding based on flux tubes connections between water molecules and amino-acids the overall feelings about the model just discussed are somewhat mixed. 1. the ideas about flux tube as a correlates for a directed attention and about the connection between hydrogen bond formation and flux tube contraction involving change of planck constant are attractive. it would be nice if flux tubes between amino-acids could force the portions of amino-acid sequences to form representation about each other in their own geometry. what would be also nice that the notions of finite measurement resolution and cognitive resolution which are fundamental notions of quantum tgd would have direct correlates at the level of flux tube dynamics. 2. the model for protein folding involving only flux tube connections between amino-acids satisfying the proposed selection rules has however failures. this could be due to simple fact that the proposed selection rules are quite too restrictive. also the flux tube connections between amino-acids and water are important and might even determine the folding patters to a high degree via the induced secondary interactions between amino-acids. second model for protein folding to be discussed represents an extreme in which the flux tube connections between amino-acids and water molecules determined the dynamics of the folding. it seems that this model leads to a realistic qualitative picture about folding. also quantitative model can be constructed as a straightforward generalization of the model involving only the flux tube connections between selected amino-acids. 5.1 could there be new physics behind hydrophily and hydrophoby? one could accept just as a fact that magnetic flux tubes to the magnetic body of water mediate an interaction which is attractive or repulsive between water molecules and amino-acids and attractive between dna molecules and water. accepting that this induces interaction between amino-acids one could proceed to model building without any mention about tgd. one could also try to dig deeper and ask what might be the origin of this interaction. 1. option i: could one understand the interaction in terms of phase transitions changing the planck constant of the magnetic flux tube. the interaction would be repulsive (attractive) would result if the interaction energy increases (decreases) when planck constant is reduced. magnetic interaction energy is certainly the best candidate and could also imply the equivalence of the divisor code and dark baryon code. 2. option ii: could hydrophily and hydrophoby be described in terms of em interactions of quarks representing nucleotides in the model of dna as tqc. for instance, could amino-acids and water molecules be characterized by charges which are of opposite sign for water molecules and hydrophilic molecules and of same sign for water molecules and hydrophobic molecules. for option i, which represents completely new physics (using the standards of tgd!), the situation looks promising. the magnetic interaction energy assignable to the flux tube is a function of the integers (na, nb) characterizing the corresponding page of the book like structure associated with generalized imbedding space in particular of the planck constant of the flux tube and the minimization is performed by keeping the charges of the quarks possibly at its ends fixed. this new physics fits also nicely with the idea that magnetic body controls the living matter by utilizing phase transitions changing planck constant. what comes in mind in the case of option ii is that the ends of the flux tube carry opposite charges correlating with the codon coding for the amino-acid and giving rise to ordinary gauge interactions. unfortunately this scenario does not seem to work. 1. it was already found that (denoting codons by xy z) only y = a,g type amino-acid residue can form hydrogen bonds and is hydrophilic and thus interacts strongly with water and dna and rna. if water end of flux tube corresponds to anti-quarks the attractive interaction between quark and anti-quark at the ends of flux tube could relate to hydrophily. for hydrophobic amino-acids one would have interaction between identical quarks and already fermi statistics would cause repulsion. in dna as tqc model based on the coding of a,g and t,c in terms of quarks u,d and their anti-quarks hydrophily-hydrophoby dichotomy corresponds to matter-antimatter dichotomy for quark assigned to the ends of the flux tube. quarks and anti-quark have opposite charges. hence the flux tube ends of hydrophilic amino-acids could correspond issn: 2159-0465 dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 58-88 86 pitkänen, m., a model for protein folding and biocatalysis to quarks and water and hydrophobic ends of flux tubes to anti-quarks. therefore the dna as tqc model would predict the needed behavior of the forces. in the case of gly containing only hydrogen as residue the flux tube might be simply absent. 2. dna codons a,t,c,g are bases and thus polar and hydrophilic. in the case of dna charge conjugation for quarks corresponds to the puridine-pyrimidine complementarity corresponding to conjugation of nucleotides. the rule applying in the case of amino-acids would predict t,c to be hydrophobic nucleotides which does not make sense. therefore it seems that hydrophily and hydrophoby cannot reduce to the interactions of dark quarks and that they only represent conjugation of nucleotides symbolically. 5.2 an improved model for protein folding to begin with let us summarize some basic facts about protein folding. 1. hydrophily and hydrophoby play a key role in protein folding and dictate to a high degree the resulting folding patterns. this suggests that one cannot neglect the role of water in the process. 2. protein folding proceeds from short to long length scales starting with the formation of secondary structures such as alpha helices, beta sheets, and random coil portions and is followed by the formation of tertiary and higher structures. 3. the formation of hydrogen bonds is in a decisive role in the formation of secondary structures. the mechanism leading to their formation might be contraction of magnetic flux tube by a phase transition changing planck constant. 4. the folding patterns do not depend strongly on the precise primary structure, that is precise amino-acid decomposition which suggests that instead of the detailed chemistry the forces between quarks and antiquarks mediated by flux tubes is what matter so that hydrophily and hydrophoby would become the basic characterizers of the interaction. the phase transitions changing planck constant would indeed represent this kind of universal interactions independent of the chemistry. 5. in the first approximation amino-acids could be labeled by a variable telling whether it is hydrophobic, hydrophilic, or neither or these (gly). this approximation would be broken by special amino-acids which appear in edges if beta sheets (pro) and cys which often appear as s-s boded pair in junctions. by bringing in forces depending on the angles between tangent vectors of successive amino-acids and on amino-adics themseles this tendency could be modeled. 5.3 a model for which the magnetic body of water is involved the alternative approach to protein folding starts from the general vision about magnetic body containing dark matter as a controller of visible matter in living system. the protein and its magnetic body would be regarded as a living system in itself. 1. magnetic body must have large number of flux tube contacts to the visible matter. an excellent candidate for the magnetic body is that assignable with water and having flux tube connections to dna and both hydrophilic and hydrophobic amino-acids. the magnetic body could control and at least fasten the selforganization process leading to the folding pattern which by applying standard argument would otherwise take astronomical time otherwise. the two-step attractive connections between all hydrophilic amino-acids would be possible via the magnetic body of water. the non-hydrophilic amino-acids not in direct contact with water are known to be more like passive structural stuff responsible for a fixed structure but not so relevant for the functioning of the bio-molecule. hydrophily and hydrophoby would reflect the dependence of interaction energy on the value of planck constant associated with the flux tube mediating the interaction. 2. this picture implies a straightforward modification of the earlier model. the simplest model would minimize a potential function v expressible as a sum v = v1 +v2 +v3 of three terms. v1 would be sum of the values of a universal two-particle potential function vphi,phi(r) for arguments rij = |ri − rj | varying over all hydrophilic amino-acid pairs and giving rise to an attractive force. v2 would be a sum of a universal twoparticle potential function vpho,pho(r) for arguments rij = |ri− rj | varying over all hydrophobic amino-acid pairs. v3 would be would be sum of the values of a universal potential function vphi,pho(r) for arguments rij = |ri − rj | varying over all pairs of hydrophilic and hydrophobic amino-acids. this potential function issn: 2159-0465 dna decipher journal june www.dnadecipher.com published by quantumdream, inc. dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 58-88 87 pitkänen, m., a model for protein folding and biocatalysis would induce a repulsive force. besides this a constraint force due to the fact that amino-acids form a sequence would be present. 3. the resultant of the forces along lines connecting amino-acids would be parallel to the amino-acid sequence in the mechanical equilibrium. hydrogen bonds and other bonds are indeed formed between neighboring hydrophilic amino-acids and the contraction of the flux tubes connecting the amino-acids in question to the magnetic body of water could be the mechanism. the model seems to be consistent with the basic qualitative facts about folding. the quantitative testing of the model would require determination of the conformations minimizing the potential function subject to the constraint provided by amino-acid sequence. here of course the freedom to choose the three functions provides a considerable flexibility and symmetry arguments might allow to pose conditions on the form of these functions. 4. one could also include to the potential function describing a direct interaction with water molecules depending on parameters like ph affecting the folding pattern. the resultant for a given amino-acid would be sum of forces directed from a hydrophilic amino-acids to neighboring water molecules. it is not clear whether the normal component of this force could be compensated by the induced forces between amino-acids in a typical equilibrium configuration and the formation of hydrogen bonds involving the contraction of the flux tube could be the manner to achieve this. the alternative model is more complicated numerically than the model discussed and it would require a considerable amount of work to test it. in particular, the three universal potential functions involve free parameters even if one makes simplifying assumptions about their functional form (say simple behavior under scaling). 5.4 could one regard amino-acids and dnas of given type as analog of species? an interesting idea raised by the work with the model for protein folding is that the magnetic bodies amino-acids or dna codon of a given type could behave like single phase on their respective page of the book so that the mutual interactions of their magnetic bodies could affect considerably the behavior of this phase to first order although amino-acids themselves are at different positions and one might expect only small correlations between their motions. whether the dynamics of amino-acids of given type in protein folding are strongly correlated could be tested. in certain sense one could speak of single species formed by amino-acids of given type and folding as long range interaction could be seen as an outcome of self-organizing interaction between members of various species and between species themselves plus short range constraints due to the fact that amino-acids form a sequence. the question applies to dna and rna codons and also to larger units such as genes formed to which one could assign their own page of the book. water would represent the page to which all dnas can send flux tubes. even the notion of biological species could involve common dark space-time sheet(s) where the magnetic bodies of the members of species are and interact making the members of species to behave like single coherent unit. references biology [1] alpha helix. http://en.wikipedia.org/wiki/alpha_helix. [2] asparagine synthetase. http://www.pdb.org/pdb/files/11as.pdb. [3] bamhi. http://www.rcsb.org/pdb/files/1bam.pdb. [4] bamhi. http://rebase.neb.com/cgi-bin/seqsget?x55285. [5] beta sheet. http://en.wikipedia.org/wiki/beta_sheet. [6] collagen. http://en.wikipedia.org/wiki/collagen. [7] glutathione s-transferase. http://www.pdb.org/pdb/files/14gs.pdb. [8] hydrolase(o-glycosyl). http://www.pdb.org/pdb/files/107l.pdb. [9] phospholipids. http://en.wikipedia.org/wiki/phospholipids. issn: 2159-0465 dna decipher journal june www.dnadecipher.com published by quantumdream, inc. http://en.wikipedia.org/wiki/alpha_helix http://www.pdb.org/pdb/files/11as.pdb http://www.rcsb.org/pdb/files/1bam.pdb http://rebase.neb.com/cgi-bin/seqsget?x55285 http://en.wikipedia.org/wiki/beta_sheet http://en.wikipedia.org/wiki/collagen http://www.pdb.org/pdb/files/14gs.pdb http://www.pdb.org/pdb/files/107l.pdb http://en.wikipedia.org/wiki/phospholipids dna decipher journal | may 2013 | volume 3 | issue 1 | pp. 58-88 88 pitkänen, m., a model for protein folding and biocatalysis [10] secondary structures. http://en.wikipedia.org/wiki/secondary_structure. [11] xylose isomerase. http://www.pdb.org/pdb/files/1a0c.pdb. [12] m. buchanan. shape is all. new scientist, 2157, 1998. [13] t. e. creighton. proteins: structures and molecular properties. freeman, new york, 1993. [14] s. rackovsky. on the nature of the protein folding code. proc. natl. acad. sci. usa. http: // www. pubmedcentral. nih. gov/ articlerender. fcgi? artid= 45720 , 90(2), january 1993. books related to tgd [15] m. pitkänen. bio-systems as super-conductors: part i. in quantum hardware of living matter. onlinebook. http://tgdtheory.com/public_html/bioware/bioware.html#superc1, 2006. [16] m. pitkänen. evolution in many-sheeted space-time. in genes and memes. onlinebook. http: //tgdtheory.com/public_html/genememe/genememe.html#prebio, 2006. [17] m. pitkänen. negentropy maximization principle. in tgd inspired theory of consciousness. onlinebook. http://tgdtheory.com/public_html/tgdconsc/tgdconsc.html#nmpc, 2006. [18] m. pitkänen. quantum model for nerve pulse. in tgd and eeg. onlinebook. http://tgdtheory.com/ public_html//tgdeeg/tgdeeg/tgdeeg.html#pulse, 2006. [19] m. pitkänen. quantum theory of self-organization. in bio-systems as self-organizing quantum systems. onlinebook. http://tgdtheory.com/public_html/bioselforg/bioselforg.html#selforgac, 2006. [20] m. pitkänen. tgd based model for obes. in tgd inspired theory of consciousness. onlinebook. http://tgdtheory.com/public_html/tgdconsc/tgdconsc.html#obe, 2006. [21] m. pitkänen. wormhole magnetic fields. in quantum hardware of living matter. onlinebook. http: //tgdtheory.com/public_html/bioware/bioware.html#wormc, 2006. issn: 2159-0465 dna decipher journal june www.dnadecipher.com published by quantumdream, inc. http://en.wikipedia.org/wiki/secondary_structure http://www.pdb.org/pdb/files/1a0c.pdb http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=45720 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=45720 http://tgdtheory.com/public_html/bioware/bioware.html#superc1 http://tgdtheory.com/public_html/genememe/genememe.html#prebio http://tgdtheory.com/public_html/genememe/genememe.html#prebio http://tgdtheory.com/public_html/tgdconsc/tgdconsc.html#nmpc http://tgdtheory.com/public_html//tgdeeg/tgdeeg/tgdeeg.html#pulse http://tgdtheory.com/public_html//tgdeeg/tgdeeg/tgdeeg.html#pulse http://tgdtheory.com/public_html/bioselforg/bioselforg.html#selforgac http://tgdtheory.com/public_html/tgdconsc/tgdconsc.html#obe http://tgdtheory.com/public_html/bioware/bioware.html#wormc http://tgdtheory.com/public_html/bioware/bioware.html#wormc introduction flux tubes as correlates of directed attention at molecular level the model of folding code based on flux tube connections between amino-acids what kind of atoms can be connected by flux tubes? color inheritance by a reconnection of flux tubes folding code quantitative model a model for protein folding based on flux tubes between amino-acids and water molecules a model for flux tubes flux tubes as a correlates for directed attention does directed attention generate memory representations and tqc like processes realization of flux tubes where do flux tubes begin from? acceptors as plugs and donors as terminals of flux tubes? flux tubes and dna introns and dna-protein attachment model for the folding code based on interactions mediated by flux tubes between aminoacids 4-d spin glass energy landscape and code of catalytic action flux tubes and amino-acids matter antimatter asymmetry at the level of interactions of amino-acids flux tubes can connect with all electronegative atoms what can one learn from the formation of alpha helices and beta sheets? interactions of proteins with ions and electrons trying to identify the folding code a trial for the folding code y=zc or y=z pairing might work tests for y=z and y=zc pairings are =o-o= flux tubes present? evolution and amino-acid pairings a simple quantitative model for protein folding and catalyst action assuming flux tubes between amino-acids the model basic mathematical consequences model for the helical structures model for sheets secondary protein structures model for protein-protein binding sites a model for protein folding based on flux tubes connections between water molecules and amino-acids could there be new physics behind hydrophily and hydrophoby? an improved model for protein folding a model for which the magnetic body of water is involved could one regard amino-acids and dnas of given type as analog of species? dna decipher journal | december 2016 | volume 6 | issue 3 | pp. 134-149 134 pitkänen, m., can quantum biology really do without new physics? article can quantum biology really do without new physics? matti pitkänen 1 abstract quantum biology is now taken rather seriously. photosynthesis and avian navigation are two key applications of quantum biology. the basic problem in both cases is posed by the fact that the magnetic interaction energy in earth’s magnetic field is roughly million times smaller than thermal energy. the so called radical-pair mechanism (rpm) was proposed already in the 60’s as a possible solution to the problem posed by anomalously large effect in epr and nmr experiments. according to rpm, a radical pair is accompanied by electron pair, which is in a superposition of spin triplet and singlet states and behaves as quantum coherent system for a time sufficiently long to induce chemical effects. the hyperfine interaction of the members of the electron pair with the nuclei of radicals would amplify the effect. the neutralization of radical pair puts an end to the coherence interaction period. the proposal is that rpm gives rise to chemical compass making possible avian navigation. there is however a problem. rpm has been observed in laboratory only for magnetic fields in the range 1 mt-10 t. earth’s magnetic field is only 2 per cent of the lower bound so that it is quite possible that rpm is not at work. this opens up the door for new quantum physics proposed by tgd based model of quantum biology. in this approach magnetic body acts as as intentional agent using biological body as a sensory receptor and motor instrument. macroscopic quantum coherence is made possible by dark matter realized as a hierarchy of heff = n × h phases. in this article rmp is summarized and compared with the tgd based vision. also the possible connection between avian navigation and circadian clock suggested by the fact that both involve photoreceptor known as cryptocrome and a possible connection with gravitaxis are considered in tgd framework. 1 introduction i was recently contacted by a friend with whom we have had several interesting discussions about consciousness and neuroscience. she sent several links related to certain aspects of quantum biology about which i had not been aware and these links inspired this article. 1.1 background one of the proposals of quantum biology is a quantum mechanism for the mysterious looking ability of birds and fishes to find back to the place, where they were born. it is believed that navigation involves detection of the inclination of the local magnetic field of earth but not its direction as in the ordinary ordinary compass. the alternative option states that birds have an analog of compass in their brain. the challenge is to understand what is the mechanism making possible to get the information about magnetic field and how this information is transformed to a chemical signal and eventually to a pattern of nerve pulses. in tgd framework one can challenge the assumption that the magnetic field of earth is what makes possible the navigation and even what the navigation means. quantum biologists try to solve the problem using standard quantum physics. the formidable looking problem is that the energy scale for magnetic energies is extremely small. in the magnetic field of earth the magnetic interaction cyclotron energy for electron is by factor of order one million below the thermal energy. if one believes of quantum physics in its standard form, one should understand how it is possible to generate a signal making possible non-trivial chemical effects. the proposal that has gained widest 1correspondence: matti pitkänen http://tgdtheory.com/. address: karkinkatu 3 i 3, 03600, karkkila, finland. email: matpitka6@gmail.com. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.com/ mailto:matpitka6@gmail.com dna decipher journal | december 2016 | volume 6 | issue 3 | pp. 134-149 135 pitkänen, m., can quantum biology really do without new physics? acceptance is known has as radical-pair mechanism (rpm) [2, 5, 6] and has raised hopes about circumvent this problem. the answer to the question whether rpm works is very important from the point of view of tgd based explanation for macroscopic quantum effects in living matter since tgd based model involves new quantum physics via the hypothesis that dark matter corresponds to heff = n× h phases located at flux tubes of “magnetic body” (mb). if rpm fails, tgd based quantum biology would be the next natural trial (if science proceeded by trying first all options that fail). i received links to several articles and list them here to help the interested reader. the following list is about phenomena involved. • cryptochrome mediates light-dependent magnetosensitivity of drosophila’s circadian clock by yoshii et al [4] (see http://tinyurl.com/zvlmxp6). cryptochrome (cry) (see http://tinyurl. com/create.php) has been proposed to be the photoreceptor being involved with both circadian rhythms and magnetosensitivity. in response to light cry slows down the circadian clock and eventually leads to an arhythmic behavior. the response to magnetic fields in the range around 3 gauss (6 times the strength of be = .5 gauss) was found to be slowing down of the circadian clock. clock response to magnetic field was present in the presence of blue light but absent in red-light illumination. this suggests that the blue light is necessary for any response at all and that magnetic field affects the response. this response could be understood as the effect as the activation of cry by the external field but one can consider also more complex mechanisms. this finding is taken as a support for rpm, which predicts that the response depends on wave-length and strength of magnetic field. • circadian and geotactic behaviors: genetic pleiotropy in drosophila melanogaster by clayton [3] (see http://tinyurl.com/j4vmr8c) tells about correlation between circadian rhythms and gravitaxis (geotaxis). the following excerpt from the abstract gives some idea about the findings. two of these genes, cryptochrome (cry) and pigment-dispersing-factor (pdf) are integral to the function of biological clocks. pdf plays a crucial role in maintaining freerunning circadian periods. the cry gene alters blue-light (< 420 nm) phototransduction which affects biological clocks, spatial orientation and taxis relative to gravity, magnetic fields, solar, lunar, and celestial radiation in several species. the cry gene is involved in phase resetting (entrainment) of the circadian clock by blue light (< 420 nm). the following articles are about radical-pair mechanism. • chemical magnetoreception in birds: the radical pair mechanism by rodgers and hore [2] (see http://tinyurl.com/zsg4b95). the abstract of the article is too long to be attached here but very informative and honestly tells the situation in the field. abstract describes the basic problem that rpm must solve: the magnetic interaction energy of electron with the earth’s magnetic field is by 6 orders of magnitude too low. the abstract also mentions that with few exceptions rpm has been observed only in magnetic field intensities 10 gauss10 tesla. the exception would be avian compass and photosynthesis! the strength of 10 gauss field is 50 times higher than the strength of earth’s magnetic field of be ∼ .5 gauss so that it is far from proven that rpm could be behind the avian chemical compass and unreasonable effectiveness of photosynthesis. quantum biology might require new physics! • the radical pair mechanism and the avian chemical compass: quantum coherence and entanglement by zhang et al [5] (see http://tinyurl.com/zvcguuz). the abstract gives brief summary of the radical pair mechanism. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/zvlmxp6 http://tinyurl.com/create.php http://tinyurl.com/create.php http://tinyurl.com/j4vmr8c http://tinyurl.com/zsg4b95 http://tinyurl.com/zvcguuz dna decipher journal | december 2016 | volume 6 | issue 3 | pp. 134-149 136 pitkänen, m., can quantum biology really do without new physics? we review the spin radical pair mechanism which is a promising explanation of avian navigation. this mechanism is based on the dependence of product yields on 1) the hyperfine interaction involving electron spins and neighboring nuclear spins and 2) the intensity and orientation of the geomagnetic field. this review describes the general scheme of chemical reactions involving radical pairs generated from singlet and triplet precursors; the spin dynamics of the radical pairs; and the magnetic field dependence of product yields caused by the radical pair mechanism. the main part of the review includes a description of the chemical compass in birds. we review: the general properties of the avian compass; the basic scheme of the radical pair mechanism; the reaction kinetics in cryptochrome; quantum coherence and entanglement in the avian compass; and the effects of noise. we believe that the quantum avian compass can play an important role in avian navigation and can also provide the foundation for a new generation of sensitive and selective magnetic-sensing nano-devices. the basic idea of rpm is that the creation of electron pairs in states, which are quantum coherent superpositions of spin singlet and triplet states of two electrons, have hyperfine magnetic interactions with nuclear spins giving rise to anomalously large epr and nmr signals. the small mass of electron is essential but still the problem in the case of avian compass and photosynthesis is to understand how quantum coherence time can be long enough for large enough effect to result before the neutralization of the radical pair. • the radical-pair mechanism as a paradigm for the emerging science of quantum biology by kominis [6] (see http://tinyurl.com/glegn3u). the radical-pair mechanism was introduced in the 1960’s to explain anomalously large epr and nmr signals in chemical reactions of organic molecules. it has evolved to the cornerstone of spin chemistry, the study of the effect electron and nuclear spins have on chemical reactions, with the avian magnetic compass mechanism and the photosynthetic reaction center dynamics being prominent biophysical manifestations of such effects. in recent years the rpm was shown to be an ideal biological system where the conceptual tools of quantum information science can be fruitfully applied. we will here review recent work making the case that the rpm is indeed a major driving force of the emerging field of quantum biology. the claim rpm as a new paradigm could be motivated by the observation that radical pairs are formed also in the photosynthesis. as already found, the problem is that the magnetic field of earth is only two percent of the minimal value of the magnetic field needed for rpm according to the laboratory experiments. it is worth of emphasizing that rpm was introduced as early as 1960’s to explain anomalously large epr and nmr signals in chemical reactions of organic molecules. in tgd i ended up to the hypothesis heff hypothesis [22] and stronger heff = hgr hypothesis [23] through the attempt to understand the observation of the pioneers of bio-electromagnetism (see for instance [8, 9, 10] that elf radiation in eeg frequency range has quantal looking effects on living matter at harmonics of cyclotron frequencies of biologically important ions in endogenous magnetic field bend = .2 gauss, which might correspond to the field strength at the flux tubes of earth’s magnetic field inside organism tuned to give rise to cyclotron frequencies ideal for biology. cyclotron energies for ions are ridiculously small as compared to thermal energy and large heff seemed to be the only possible explanation. could large heff effects been observed already around 1960’s without realizing that new quantum physics is in question? issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/glegn3u dna decipher journal | december 2016 | volume 6 | issue 3 | pp. 134-149 137 pitkänen, m., can quantum biology really do without new physics? 1.2 some hints it seems that several biological phenomena could use the same mechanism rpm would be this mechanism if standard quantum theory is enough to understand these phenomena. 1. magneto-sensitivity and circadian clock seem to be related: light-activated photoreceptors cryptochromes (crys) serve also as magnetic sensors and the external magnetic fields slow down circadian rhythm. 2. also gravitaxis that is the ability to move in direction parallel or opposite to the gradient of local gravitational field could relate to this mechanism. this requires that organism is able to perceive the gradient for the strength of the local gravitational field. blue light is necessary for the magnetoreception and the establishment of circadian rhythm with period of order 24 hours. this is an important hint but leaves much open. is just the presence of blue light enough for establishing to put the circadian clock ticking or does the periodic variant of the amount of blue light give rise to internal clock? blue light seems to have health effects. for instance, exposure to blue light at night time could be harmful to health (see http://tinyurl.com/mggpafe). in particular, too much blue light at night time could affect the circadian clock and too much blue light could lead to sleep disorders and various negative health effects such as several types of cancer (breast, prostate), diabetes, heart disease, and obesity. it is known that the amount of blue light correlates with melatonin secretion. this would suggest that the periodic variation of the intensity of blue light is what gives rise to internal clock. of course, there are very probably several cues used by internal clock (for instance, birds are not dead matter behaving as robots!) and the variation of the intensity of blue light could be only one of them. it has been also found (see http://tinyurl.com/zvlmxp6) that the presence of external magnetic fields in the range around 3 gauss (earth’s magnetic field has nominal value .5 gauss so that this field is 6 times stronger) tends to increase the period of the circadian clock. this would suggests that the clock in question does not use only the amount of blue light as a cue. before continuing it is good to list some abbreviations. electromagnetic (em), exclusion zone (ez), radical-pairing mechanism (rpm) are standard notions. at least for tgd inspired notions appear in the sequel: topological geometrodynamics (tgd), strong form of holography (sh), zero energy ontology (zeo), causal diamond (cd), magnetic body (mb), biological body (bb). 2 how to understand circadian clock, magneto-sensing and gravitaxis in tgd framework? that photoreceptors responsible for circadian rhythms are involved with magnetoreception and the presence of blue light is necessary for magnetoreception are the basic challenges for any model. in rpm model this would follow from the assumption that blue light generates radical-pairs interacting with magnetic field but why just rpm should be crucial for photoreception? why not some “easier” mechanism? could bio-rhythms be due to some deeper quantum mechanism involving magnetic fields in an essential manner? of course, rpm could still be involved but with non-standard value of planck constant if tgd view is correct. non-standard value of planck constant could be involved even with the original anomalies associated with epr and nmr. i have described briefly what tgd is in the appendix and recommend it for the reader before continuing. 2.1 basic problems and basic principles in appendix i summarize what tgd and tgd inspired theory of quantum biology and quantum consciousness are. here i just list the basic ideas relevant to the model considered. the basic elements of issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/mggpafe http://tinyurl.com/zvlmxp6 dna decipher journal | december 2016 | volume 6 | issue 3 | pp. 134-149 138 pitkänen, m., can quantum biology really do without new physics? this model are mb following from the many-sheeted view about space-time and distinguishing between tgd and maxwell’s theory and the hierarchy of planck constants heff = n × h possibly satisfying the additional constraint heff = hgr giving connection with quantum gravity which would allow macroscopic quantum phases in arbitrarily long length scales in tgd universe. the key principles and mechanism should be same as in tgd based model of quantum biology. 1. magnetic body (mb) of living organism has a fractal structure corresponding to body parts labelled by corresponding cyclotron frequency scales. mb serves as an intentional agent receiving sensory data from biological body (bb) and controlling it. bb and mb must communicate and dark photons would make this possible. eeg would be one example of this communication and mb would receive by sensory data from cell membrane as dark generalized josephson photons and control bb by dark cyclotron photons with the mediary of genome (at least) [12, 16, 15]. eeg would generalize to other frequency ranges and generalized eeg rhythms could emerge in this manner. dark phases of matter emerge at quantum criticality which is central element of the model. as a matter fact, tgd universe is in well-defined sense quantum critical. 2. one cannot avoid the following questions. is the avian navigation an automatic process. could mb control it? is conscious intelligence and volition involved so that the mechanism in question would be only a tool. is the mb in question that of species or does the bird decide whether to follow the flux tubes of the personal mb connecting the bird to where it was born or in the horizontal direction defined by the mb of earth? one must leave these questions open although the idea that the bird follows the horizontal flux tubes connecting it to the birth place (and assignable to the species?) is very attractive and would not favor the flux tubes of earth which are not horizontal. 3. quantum criticality allows several values of planck constant are possible. the interpretation is in terms of long range as quantum fluctuations and quantum coherence in various length scales would have a universal explanation. quantum criticality would be a general property of living matter and crucial also now. 4. the most economic assumption is that the mechanism is same as in the case of cell membrane identified as generalized josephson junction coding nerve pulse sequences and membrane oscillations to eeg and in this manner sending sensory information to mb of the brain. i have indeed proposed long time ago that also biomolecules act as josephson junctions. in fact, the cell membrane identified as generalize josephson junction reduces microscopically to an array of generalized josephson junctions defined by membrane proteins. for generalized josephson junction josephson energy 2ev for cooper pair is replaced with its sum with the difference of cyclotron energies at different sides of the cell membrane. electronic cooper pairs would be naturally involved but also bosonic ions and cooper pairs of fermionic ions can be considered for large values of heff and are indeed in crucial role in tgd based model of cell membrane. one of the first applications of tgd inspired biology was the explanation of so called comorosan effect [7, 1] in terms of bio-molecular josephson junctions [18]. the model assuming generalized josephson junctions applies in the case of general biomolecules and suggests that there is universal 5 second josephson time involved. this would require rather large value of heff (josephson frequency is inversely proportional to 1/heff ) since the voltage involved is expected to be rather high in molecular length scales. 5. the basic assumption would be that blue light kicks the photoreceptor cry to an excited state, which is quantum critical and generates large heff phases possibly satisfying also the heff = hgr condition with several values of heff at the flux tubes. note that each flux tube carries only one kind of charged particle if it corresponds to a unique value of planck constant. dark charged particles are like books on shelves and the situation is just the opposite for the random dense soup of bio-molecules assumed in standard biochemistry. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2016 | volume 6 | issue 3 | pp. 134-149 139 pitkänen, m., can quantum biology really do without new physics? the basic prediction would be the dependence of the effect on strength of magnetic field as in case of rpm. the slowing down of the rhythm in presence of external be could be understood if the cyclotron energy difference in be between ground state and excited state changes so that the energy difference becomes smaller and flux tube in question has smaller value of bgal: this could be due to the change of the net charge of the molecule. one should explain several phenomena using the same model. 1. navigation involving perception of earth’s magnetic field, which possibly weakens to endogenous magnetic field which is 2/5 of it inside brain. a constraint to heff emerges from the condition that cyclotron frequency is in visible-uv range. if one demands heff = hgr = gmdm/v0 one finds that dark mass md is of order 10−4me and that it would correspond to a spherical layer of dark mass at distance of moon. skeptic of course begins to talk about occam’s razor. this layer is however natural in the model of dark matter. one could of course just speak about heff and forget hgr = heff . the important point is that the notions introduced are not ad hoc notions but follow naturally from the very general assumptions of tgd as unification of fundamental interactions (see appendix). 2. the challenge is to understand circadian rhythm with period about 24 hours. there is some evidence for the importance of the galactic magnetic fields for living matter. one such piece of evidence is the observation that the occurrence of tinnitus seems to appear rhythmically but with respect to galactic time. galactic magnetic field of strength of about 1 nt could provide explanation. there is also earlier rather mysterious observation that precognition events seem to occur near galactic midday [11]: this observation is of course not taken seriously by skeptics but deserves to be noticed. a possible test for the tgd based model is that the bio-clock actually measures sidereal rather than circadian time. the galactic cyclotron time for hgr associated with earth mass me is very natural if flux tubes carry earth’s gravitational field is very near to 12 hours for galactic magnetic field a fraction of nt. cyclotron frequency would generate the biorhythm in manner analogous to that happening in the case of eeg. only frequency scale would be much longer. more precisely, according to the estimate of [22] the cyclotron time of dna in bend equal to 1 s is scaled up to 11.7 hours in bgal=.63 nt. this estimate is obtained by accepting the heff = hgr = gmm/v0 hypothesis by identifying m as earth’s mass, and by assuming that the parameter r = v0/vrot,m for earth has the same value as for sun. one has v0 ' 2−11 for sun from the bohr orbit model for the orbits of inner planets originally proposed by nottale and vrot is the rotational velocity of sun. it is needless to emphasize that this estimate involves uncertainties and that the value of bgal assignable to the flux tubes has a distribution, which could be as wide as that for the energies of bio-photons. there are however good hopes of obtaining the circadian (or possibly sidereal) rhythm with natural choice of parameters. 3. the tgd description of gravitaxis should involve the flux tubes carrying gravitational flux of earth. the same mechanism might be behind ordinary sensing of the gravitational acceleration. a good guess is that this magnetic field has same strength as galactic magnetic field bgal to which earth’s mass would be associated via hgr. the heff should be correspondingly higher to guarantee that dark cyclotron energy is in visible-uv range. the energy of blue light is good candidate now for exciting the quantum critical state in which this value of heff is realized. gravitaxis would require the detection of the strength of earth’s gravitational field coded into the density of flux tubes parallel to it. the system should be able to detect the density of the flux tubes and this would occur naturally at quantum criticality via reconnections with these flux tubes and involving dark photons with energies in visible-uv range. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2016 | volume 6 | issue 3 | pp. 134-149 140 pitkänen, m., can quantum biology really do without new physics? 4. two magnetic fields bend and bgal would be involved as also two values of planck constant but cyclotron energies would be same and in bio-photon energy range. the two mbs should be be able to communicate and one can consider the possibility that the spectrum of ionic cyclotron frequencies for bend = .2 gauss in eeg range corresponds to electronic cyclotron frequencies for a spectrum of values of ggal. this assumption would fix the parameters of the model to very high degree. interestingly, according to tgd based quantum model for hearing [14], the audible frequencies would be coded by the thickness of flux tubes (or equivalently by the value of the magnetic field) and galactic flux tubes would give rise to a similar coding. could hearing actually use the flux tubes of bgal? if so, the ranges for audible frequencies and for bio-photon energies measured as number of octaves would be same. the range of frequencies audible for humans is about 10 octaves beginning from 20 hz. hence the spectrum of bio-photons should extend from say 1 ev to 10 kev. dark ir photons are also predicted as a josephson radiation from cell membrane with energies of photons of order 2ev ∼ .1 ev (coulomb energy of cooper pair assignable to cell membrane josephson junction and roughly twice the thermal energy eth = 3t/2 ' .5 ev at physiological temperature 330 k). i do not know whether ir energies are excluded as bio-photon energies and therefore whether the range of bio-photon frequencies could actually begin from .1 ev. if so, bio-photon energies would extend up to 1 kev. it is important to notice that the mb involved with navigation could be earth’s mb or galactic mb if its flux tubes correspond to personal mb of the organism connecting it to its birth place. it is quite possible that both mbs are be involved. one can imagine endless variety of models and the proposed model can be defended by the fact that it is based on the same mechanism as the quantum model for communications between bb and mb giving as special case the model of cell membrane. 2.2 could circadian rhytms be analogous to eeg rhythms in tgd universe? in tgd universe it is natural to think that the circadian rhythms and in fact all biorhythms are basically analogous to eeg rhythms. 1. in tgd eeg frequencies would correspond basically to cyclotron frequencies in and endogenous magnetic field of .2 gauss which is 2/5:th of earth’s magnetic field carrying dark particles (in tgd sense) having non-standard value heff = n×. 2. the energies of cyclotron photons, which would be extremely small and much below thermal energy for the ordinary value of planck constant, are scaled up by factor n by e = heff × f formula and can have non-trivial biological effects. 3. a further proposal is that the formulate heff = hgr = gmm/v0 holds true at least for large values of heff . here hgr is gravitational planck constant assignable to magnetic flux tubes mediating gravitational interaction, v0 is a parameter with dimensions of velocity, m is the mass of the dark charged particle at the flux tubes, and m is some large mass. this formula guarantees that cyclotron energies proportional to hgreb/m do not depend on the mass m of the charged particle for given charge. this in turn implies that dark cyclotron energy spectrum is universal. the hypothesis is that the transformation of dark photons to ordinary photons produces ordinary photons identifiable as bio-photons. if so the energies would be in visible-uv range and would dark photons could induce transitions of biomolecules and could serve as a biochemical control tool of the mb. if one accepts hgr = heff hypothesis for eeg, the value of the mass m should be around m = md ∼ 10−4me for eeg. using some additional cues given by tgd based view about how planets were condensed around dark matter blobs forming spherical cells or tubes around sun or actually any astrophysical object, i have proposed a possible identification of md as a mass of issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2016 | volume 6 | issue 3 | pp. 134-149 141 pitkänen, m., can quantum biology really do without new physics? spherical shell of dark matter assignable to earth at the distance of moon [22, 23]. here skeptic of course has an excellent opportunity to introduce occam’s razor and i am of course ready to consider also the option that heff = hgr does not hold true at the flux tubes of bend. what about the identification of circadian rhythms as cyclotron frequencies? 1. the general idea is that the flux tubes of both earth’s magnetic field and of galactic magnetic field can locally self-organize into complex braided structures serving defining the mbs of organisms, which would therefore be parts of much biffer organism. the flux tubes could connect living systems to each other and for instance, birds and fishes to their birth places. 2. the cyclotron time is much longer than for eeg rhythms and the natural guess is that the flux tubes of interstellar (galactic) magnetic field with field strength varying around the mean value bgal ∼ 1 nt are involved. the spectrum of cyclotron times would be of correct order of magnitude. hgr = heff hypothesis essential for the coupling of mb to biochemistry would be satisfied for m = me in hgr = gmm/v0 so that one cannot assume that only dark mass contributes to the large mass in hgr. 2.3 trying to figure out the general mechanism the details of the mechanism could be fixed by empirical input and using second assumption above as a guideline. 1. to my best understanding the role of rpm for avian chemical compass is speculative. rpm has been indeed observed only for magnetic fields stronger than 10 gauss. therefore it can be challenged. even the notion of chemical compass is speculative. 2. the large cyclotron energies of dark charged particles would solve the problem caused by the extreme smallness of the electronic cyclotron energies this could be the case even for ions. radical pairs and electron pairs assigned with them could of course be present also in tgd inspired model. even pairs of ions and bosonic ions. 3. in tgd context one could assume only spin singlet or triplet cooper pairs with large value of heff = hgr in bend = 0.2 gauss. the existence of superconducting phase would require that cooper pairs assignable to several cry molecules reside at same flux tube pairs. this would make the process quantum coherent in longer scale. 4. quantum criticality is needed and could be associated with the emergence of high tc superconductivity and would correspond to the transversal oscillations of magnetic flux tubes analogous to phonons assumed in ordinary superconductivity and also in rpm. they would lead to a transitions between flux tube pair with shape of flattened square and pair of pairs flux tubes of similar shaped induced by reconnection somewhere along flux tube pair. in transition to superconductivity long flattened square would stabilize. above transition temperature shorter flattened square shapes would be stable and one would have super-conductivity but in short scale only. 5. electron pairs would be analogous to cooper pairs and if there is many of them in the system one would speak of super-conductivity. in tgd inspired quantum biology the electron pairs might be cooper pairs with members at flux tubes, which are either parallel or antiparallel. spin singlet and triplet cooper pairs would correspond to flux tubes with opposite and parallel fluxes. the quantum coherent fluctuation between them assumed in the model does not look possible in tgd framework and is not needed. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2016 | volume 6 | issue 3 | pp. 134-149 142 pitkänen, m., can quantum biology really do without new physics? 6. spin singlet cooper pairs would result for closed flux tubes with the shape of flattened square. if one has pairs of this kind of flux tubes in parallel and close enough to each other, the second member of the cooper pair could hop to second flux tube of the other flux tube pair so that members of the pair would be at flux tubes with parallel magnetic fields and form triplet. this kind of hopping could gives rise to the coherent quantum transitions between spin singlet and triplets and the ratio of singlets and triplets would be different from one in the final state and depend on the value of magnetic field and cause a chemical effect. this assumption need not be necessary for the model to work. the control by mb could be much more direct and take place at bio-photon energies. 7. dark photons are somehow emitted and go to the flux tubes of bgal in the case of circadian rhythm and gravitaxis. in the case of avian navigation the flux tubes could be those of bend (be could be equal to bend inside brain) or those of bgal. the model of cell membrane as generalized josephson junction with membrane proteins (channels and pumps) suggests a model in which the emission of dark photons could be generalized josephson radiation with energy determined as difference of cyclotron energies plus ordinary josephson energy. dark josephson photons going to the flux tubes of earth equal to bend = 2be/5 inside organism. from blackman’s experiments. this would give rise to magneto-detection of be . the mechanism would be exactly like the mechanism communicating sensory data to mb from cell membrane and allowing mb to control cell via genome using dark cyclotron photons. one can however consider also the replacement of bend with bgal. one can imagine also the analog of rpm mechanism. in this case the dark electron pairs would fluctuate quantum coherently between spin singlet and triplet state and also interact with nuclear spins of the radical pair. the fusion of radical pair to a neutral state would destroy the quantum coherence. by a generalization of uncertainty principle cyclotron time would define the natural time scale and would be much longer than the time scale of coherence for rpm model. maybe this could allow to test heff hypothesis. 2.4 more concrete model for the mechanism of magnetoreception and circadian rhythms it is could to list some basic facts first. 1. photopigment cry must be excited by blue light needed to perceive magnetic field. 2. cry interacts with magnetic field to establish the biorhythm. 3. external magnetic fields around 3 gauss in presence of blue light slowed down the speed of the circadian clock. what is the mechanism giving rise to the circadian clock? the naive guess is that circadian rhythm corresponds to the periodic variation of the sensitivity to the external magnetic field determined by the amount of solar light. this certainly serves as a cue for the behavior and affects directly neuronal level but need not give rise to the fundamental biorhythm. the simplest model does not explain why the circadian clock slows down (leading eventually to the loss of circadian rhythm) in external magnetic fields bext not too far from 3 gaussabout 6 times the value of earth’s magnetic field? hence it seems that the amount of blue light alone is not behind the clock mechanism but something more delicate is involved. the cyclotron frequencies assignable to weak external magnetic field (say bgal whose flux tubes mediate gravitational interaction) as primary sources of circadian rhythms and controlled by bext somehow are suggested by the tgd inspired model of eeg. the following picture suggests itself in tgd framework, where mb containing dark matter as large heff = hgr phases of ordinary matter controls biochemistry in quantum coherent manner in scales of even entire organism. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2016 | volume 6 | issue 3 | pp. 134-149 143 pitkänen, m., can quantum biology really do without new physics? 1. basic entities are cry molecule and its mb carrying some internal magnetic field bend (to be not confused with bend ' .2 gauss) and having large heff . mb of galactic magnetic field bgal: this in order to obtain cyclotron frequencies of order 24 hours for protons and ions. magnetic flux tubes of galactic mb carrying cyclotron bose-einstein condensates for electrons, protons, ions each of them with heff = hgr proportional to the mass of charged particle in question. different charged particles at their own flux tubes like books in the shelves of library. 2. photons of blue light excite cry. excited cry gradually returns to the ground state. this should lead to emission of dark cyclotron photons with cyclotron frequency of magnetic field involved for some charged particles at flux tubes? transformation to dark cyclotron photons increasing hbar to ~eff = n× ~ takes place only at quantum criticality for the emitted photons. this might select the transitions corresponding to blue light. 3. the two mbs should interact by dark radiation at cyclotron frequencies. the excitations of cry molecule by blue light would decay to ground state and emit dark photons with energy of blue light but with the cyclotron frequency for protons/ions of or order 24 hours. magnetic field with the strength not too far from 1 nt, the strength of galactic magnetic field seems to be the most natural possibility. 4. cry’s mb must reconnect with that of galactic mb. reconnection makes possible resonant interaction at multiples of cyclotron frequency. large heff and biophoton hypothesis require that the energies involved are in visible-uv range. blue light is in this range. 5. the resonant interaction would give rise to the perception of earth’s mb and make possible navigation: bird would fly to in the direction, where it perceives the flux tubes of earth’s mb. 6. circadian rhythm would correspond to the galactic cyclotron frequency which would be same for all charged particles with the same charge by hgr = heff hypothesis implying that dark cyclotron photons have universal energy spectrum in the range of biophoton energies. why the external magnetic field with strength of order 3 gauss has the slowing down effect? cry should be able to couple to magnetic fields of this order of magnitude. the coupling should reduce the frequency of the emitted dark photons. it would seem that the frequency of dark photons emitted by cry is reduced. this requires that the energy difference for its excited and ground states is reduced. if the ground state and excited state have different the difference of total energies contains the difference of cyclotron frequencies proportional to charge difference and magnetic field. if this difference is negative, its magnitude increases with bext so that the frequency of emitted photons reduced. hence the cry couples to flux tubes with weaker galactic magnetic field. this slows down the clock. one can of course adopt a conservative attitude and consider a minimal modification of rpm by assuming quantum criticality and by replacing the planck constant with heff = n × h eit n ≥ 50. the excitation of cry molecule responsible for the phenomena described could indeed involve generation of radical pair in presence of blue light. the decay of rpm to neutral pair could produce photons transforming to dark photons at flux tubes? if so, the decoherence produced by the decay of rp would be compensated by coherence at the level of dark matter: negentropy maximization principle (nmp) [13] would suggest this. 2.5 gravitaxis and heff = hgr hypothesis gravitaxis might relate to the basic hypothesis about dark matter in tgd universe as large heff phases: one would have heff = hgr = gmm/v0, v0 is velocity parameter, m is some large mass, now presumably earth’s mass. this hypothesis is originally due to nottale and plays key role in tgd inspired quantum biology. what sensing a gradient in gravitational field could mean from the point of view of this hypothesis? issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2016 | volume 6 | issue 3 | pp. 134-149 144 pitkänen, m., can quantum biology really do without new physics? 1. the simplest model assumes that the flux tubes along with gravitational interaction is mediated, are magnetic flux tubes with vanishing kähler magnetic field but non-vanishing electromagnetic and z0 magnetic fields. these flux tubes would be vacuum extremals in absence of volume term in action. the volume term is proportional to cosmological constant and induced by the twistor lift of tgd [24]. the flux tubes carrying magnetic monopole flux would be assigned to non-gravitational interactions: this distinction looks natural but does not seem to be necessary. 2. the density of the gravitational magnetic flux tubes must correlate with the average intensity of gravitational field at grt limit of tgd. at fundamental level of many-sheeted space-time the detection of gravitational field strength would reduce to the detection of the density of these flux tubes. this detection would reduce to the same mechanism which makes possible magneto-sensitivity making possible avian navigation, biological clocks, and basic step of photosynthesis. the overall conclusion is that tgd based quantum biology neatly unifies the description of several phenomena suggesting quantum biology in terms of magnetic body and dark matter as large heff phases. tgd based model is also needed since rpm proposal predicts effect which is at most 2 per cent of that needed to explain the observations. 3 appendix: what tgd is? since the purpose is to see the representations through tgd lense it is polite to first to tell to the reader what tgd is. the reader interested in details can find them for instance in [21]. 3.1 why tgd? the first question is “why tgd?”. the attempt to answer this question requires overall view about the recent state of theoretical physics. obviously standard physics plagued by some problems. these problems are deeply rooted in basic philosophical one might even say ideological assumptions which boil down to -isms like reductionism, materialism, determinism, and locality. thermodynamics, special relativity, and general relativity involve also postulates, which can be questioned. in thermodynamics second law in its recent form and the assumption about fixed arrow of thermodynamical time can be questions since it is hard to understand biological evolution in this framework. clearly, the relationship between the geometric time of physics and experienced time is poorly understood. in general relativity the beautiful symmetries of special relativity are in principle lost and by noether’s theorem this means also the loss of classical conservation laws, even the definitions of energy and momentum are in principle lost. in quantum physics the basic problem is that the non-determinism of quantum measurement theory is in conflict with the determinism of schrödinger equation. standard model is believed to summarize the recent understanding of physics. the attempts to extrapolate physics beyond standard model are based on naive length scale reductionism and have products grand unified theories (guts), supersymmetric gauge theories (susys). the attempts to include gravitation under same theoretical umbrella with electroweak and strong interactions has led to super-string models and m-theory. these programs have not been successful, and the recent dead end culminating in the landscape problem of super string theories and m-theory could have its origins in the basic ontological assumptions about the nature of space-time and quantum. 3.2 tgd and grt the new view about space-time as 4-d surface in certain fixed 8-d space-time is the starting point motivated by the above mentioned energy problem of general relativity and means in certain sense fusion of the basic ideas of special and general relativities. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2016 | volume 6 | issue 3 | pp. 134-149 145 pitkänen, m., can quantum biology really do without new physics? the higher-dimensional space-time is 8-d h = m4×cp2: empty minkowski space m4 of special relativity with points replaced by 4-d cp2 (complex projective space of 4 real dimensions). the symmetries of special relativity are preserved but lifted to the level of h so that classical conserved quantities like energy exist. cp2 in turns codes in its geometry the standard model symmetries and quantum numbers and its spinor connection codes for classical electroweak gauge fields. their projections to space-time surface are dynamical. also classical color fields can be understood. these geometrized fields are expressible only in terms of four cp2 coordinates and cannot as such directly correspond to those of standard model. how standard model emerges as a limit of tgd will discussed below. rather recently [24] i have discussed twistor lift of tgd replacing space-times with the twistor spaces and h with the product of twistor spaces of m4 and cp2, which are unique as 4-d spaces in the sense that they have twistor spaces with kähler structure making possible to lift the kähler action to 6-d one. the theory dimensionally reduced to a 4-d theory containing cosmological constant and gravitational constant as additional constants besides cp2 radius and kähler coupling strength. 3.3 tgd and string models tgd can be also seen as a generaralization of hadronic string model or of superstring models by replacing strings with 3-d surfaces and 10-d space-time with 8-d m4×cp2. 3-space as we experience it corresponds to a large 3-surface to which smaller 3-surfaces are glued by wormhole contacts. these smaller 3-surfaces we would interpret as physical objects with shape and size and when they are really small, we call them elementary particles. we would directly see this extremely complex space-time geometry. this geometry has fractal hierarchical structure: 3-surfaces glued to larger 3-surfaces glued to.... as a matter fact, string world sheets and what i call partonic 2-surfaces in 4-d space-time regarded as space-time surface turn out to be fundamental objects of also tgd forced by very general principles such as well-definedness of em charge and strong form of holography (sh) implied by strong form of general coordinate invariance [17]. sh states that information given at these 2-surfaces allows to deduce information about quantum states and classical dynamics: effective 2-dimensionality in the sense of information theory would be in question. 3.4 tgd based ontology tgd forces to dramatically generalize the ontology of standard model and grt. 1. the new view about space-time differs radically from that of grt. space-time surfaces are topologically non-trivial in all scales. they have typically finite size and obey size scale hierarchy. one can glue space-time sheets to larger space-time sheets to get a fractal scale hierarchy with sheets glued to larger sheets by wormhole contacts and having interpretation as correates for physical objects. second key difference is that space-time surfaces can have also regions with euclidian signature of the induced metric time and space are geometrically in the same role. wormhole contacts are this kind of regions and serve as building bricks of elementary particles and are identifiable as lines of generalized scattering diagrams. 2. a new view about classical fields emerges distinguishing tgd from maxwell’s theory. one can say that each physical object has field identity field body consisting of space-time sheets. the notion of magnetic body (mb) turns out to be central in tgd inspired biology and adds mb to the pair organism-environment as a third member. the communications from bb involve classical radiation fields: eeg is one example of this communication from the brain to the mb of brain. the size scale of mb is typically considerably larger than that of bb: even of order earth size scale or even larger. mb makes possible remote mental interactions and could be behind the morphic fields of sheldrake. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2016 | volume 6 | issue 3 | pp. 134-149 146 pitkänen, m., can quantum biology really do without new physics? 3. how tgd relates to grt and standard model? the basic idea is that the sheets of many-sheeted space-time obeying extremely simple physics (only 4 analogs of field variables plus sh realized by preferred extremal property implying effective 2-dimensionality of dynamics) are lumped together and identified as grt space-time differing slightly from flat m4. the deviation comes in the following manner. the deviations of the induced metric for space-time sheets from m4 metric (empty space metric) are summed up to give grt gravitational field as deviation from m4 metric. induced gauge potentials known once space-time surface is known are summed up in the same manner to give the gauge potentials of standard model. this because test particle experiences the sums of various induced fields associated with space-time sheets. ordinary linear superposition is replaced at fundamental level with the set theoretic union for space-time sheets. 4. the hierarchy of planck constants heff = n×h was originally motivated by certain strange findings in neuroscience about effects of elf em fields on vertebrate brain [20, 19]. first it was postulated that dark matter corresponds to phases of ordinary matter with heff = n×h having certain special kind of space-time surfaces (singular n-sheeted covering spaces) as correlates. later it turned that these phases are actually predicted by basic tgd: in tgd framework planck constants is for single space-time sheet h and only effectively heff = n×h but at qft limit one can say that heff = n×h is strictly true. later the view about dark matter as evolved and according to the recent view dark matter would emerge at quantum criticality (perhaps even at ordinary criticality) and would be a correlate for long range quantum fluctuations and long range quantum coherence. various quantal length scales are indeed typically scaled up by n. this suggests that biosystems are quantum coherent and quantum critical because mb contains dark matter. mb containing dark matter would serve as intentional agent receiving sensory data from bb and controlling bb. eeg and its generalizations to various frequency ranges based on dark photons would be the tool for this. the dark cyclotron photons assignable to given charged particle would have very specific value of heff guaranteeing that cyclotron energy scale does not depend on particle mass and would be in the range of biophoton energies (visible and uv). biophotons would result in the phase transition heff → h. also dark photons in ir range (josephson photons assignable to cell membranes) are predicted. biochemistry would not be enough to understand the biology. mb and its “motor actions” would be crucial for understandind bio-catalysis, in particular the miraculous property of biomolecules to find each other in the molecular crowd. 5. zero energy ontology (zeo) is a further new piece of tgd ontology. in standard ontology the state of system at fixed value of time characterize the time evolution of the system. classically the state is typically characterized by particle positions and velocities and by values of say maxwellian fields and their time derivatives. field equations in principle allow to deduce the time evolution from these. in zeo one introduces causal diamond (cd). cd is intersection of future and past directed lightcones (penrose diagram) with points replaced by cp2. cds are assumed to form a fractal scale hierarchy. cd has two light-like boundaries: “future” and “past” boundary. light-likeness means that 3-d m4 projection of given boundary correspond to a sphere expanding with light-velocity. physical states are replaced with zero energy states analogous to physical events consisting of initial and final states. initial/final state can be assigned to 3-d intersections of space-time surfaces with the “future”/“past” boundary of cd. zeo is consistent with the crossing symmetry of quantum field theories and with the conservation laws. it is however extremely flexible since any zero energy state is in principle achievable by a sequence of quantum jumps. the analog of ordinary positive energy can be assigned with either “future” or “past” boundary and the arrow of time is different issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2016 | volume 6 | issue 3 | pp. 134-149 147 pitkänen, m., can quantum biology really do without new physics? for these states. zeo leads to a quantum measurement theory allowing to circuvemtn the basic problem of standard quantum measurement theory due to the non-determinism of state function reduction contra determinism of unitary time evolution. 6. p-adic and adelic physics are further new ontological elements of tgd. p-adic numbers are generalizations of real numbers, and there are infinite number of p-adic number fields for each prime p = 2, 3, 5, .... i ended up with p-adic physics almost accidently by playing with p-adic generalization of thermodynamics and finding that p-adic thermodynamics can reproduce elementary particle masses with minimal assumptions and thus replaced higgs mechanism with more fundamental theory. the properties of p-adic number led soon to the proposal that p-adic number fields are correlates for cognition and imagination. much later this led to the unification of real physics and various p-adic physics in terms of adelic physics fusing all these number fields to a bigger structure. why p-adic physics is so nice that one can talk about p-adic imbedding space and space-time surfaces as kind of cognitive representations of real space-time surfaces. in particular, sh allows to assign p-adic space-time surface to given set of string world sheets and partonic 2-surfaces as preferred extremal but no necessary to real one. all imaginations cannot be realized! also p-adic generalization of shannon entropy makes sense but it can be negative. one can say that entanglement carries negative p-adic entropy positive negentropy although real entropy is non-negative. the interpretation is in terms of conscious information naturally assignable to cognition. 3.5 tgd, quantum measurement theory, and consciousness tgd inspired theory of consciousness can be seen as quantum measurement theory in zeo. observer as an outsider becomes a part of physical system. observer does not cause state function reductions but as a concious entity is a sequence of state functions on same boundary of cd generalized zeno effect. 1. the maximization of negentropy gain in state function reduction becomes the basic variational principle of consciousness theory consistent with second law which applies at the level of ensembles and is closely related to the growth of real entanglement entropy. i refer to this principle as negentropy maximization principle (nmp). 2. in zeo state function reduction can take place to either boundary of cd. in a sequence of reductions to a fixed boundary the boundary itself remains fixed as also the states at it possibly entangled with those at the opposite boundary. this boundary is referred to as “passive”. the second “active” boundary drifts farther away from the passive boundary and the states at it change. each step can be regarded as time localization localizing the active boundary of cd. self corresponds to this sequence of state function reductions. the permanent part of self “soul” corresponds to the unchanging part of self and changing part corresponds to consciousness determined byt sensory input. in particular, the experience about flow of time corresponds to the drift of the active boundary of cd farther away. self is a generalized zeno effect. 3. eventually nmp forces the first reduction to the opposite boundary to occur. this is the counterpart of the usual large and non-deterministic quantum jump assignable to quantum measurement. self dies and re-incarnates as time reversed self since the cd starts to increase in size in opposite time direction. this prediction has rather radical implications. some of the implications deserve to be noticed. 1. one ends up with a new view about time. geometric time as fourth space-time coordinate (or time coordinate as distance between the tips of cd) is not same as subjective time defined by a sequence of state function reductions. the consciousness experience associated with each reduction has the issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | december 2016 | volume 6 | issue 3 | pp. 134-149 148 pitkänen, m., can quantum biology really do without new physics? changing components with contents coming from the active boundary so that subjective time is mapped to discrete clock time. 2. selves having hierarchy of cds as imbedding space correlate form a hierarchy. subself is assumed to be experienced as mental image and subsubselves as kind of average sub-subself so that self is not drowned to microscopic information. subconscious corresponds to conscious sub-sub-... -selves. we are ourselves mental images of some higher level self and the hierarchy continues ad infinitum with entire universe at the top. references [1] murogoki p comorosan s, hristea m. on a new symmetry in biological systems. bull math biol, page 107, 1980. [2] rodgers ct and hore pj. chemical magnetoreception in birds: the radical pair mechanism. pnas. http: // tinyurl. com/ zsg4b95 , 106:353–360, 2016. [3] clayton dl. circadian and geotactic behaviors: genetic pleiotropy in drosophila melanogaster. journal of circadian rhytms. http: // dx. doi. org/ 10. 5334/ jcr. 140 , 12(1):1–5, 2016. [4] yoshii t et al. cryptochrome mediates light-dependent magnetosensitivity of drosophila’s circadian clock. plos biol. available at: http://tinyurl.com/zvlmxp6, 7(4), 2009. [5] zhang y et al. the radical pair mechanism and the avian chemical compass: quantum coherence and entanglement. arxiv.org. available at: http://tinyurl.com/zvcguuz, 2015. [6] kominis ik. the radical-pair mechanism as a paradigm for the emerging science of quantum biology. arxiv.org. available at: https://arxiv.org/abs/1512.00450, 2015. [7] comorosan s. on a possible biological spectroscopy. bull math biol, page 419, 1975. [8] blackman cf. effect of electrical and magnetic fields on the nervous system, pages 331–355. plenum, new york, 1994. [9] blackman cf et al. effects of elf fields on calcium-ion efflux from brain tissue, in vitro. radiat res, 92:510–520, 1982. [10] blackman cf et al. a role for the magnetic field in the radiation-induced efflux of calcium ions from brain tissue, in vitro. bioelectromagn, 6:327–337, 1985. [11] spottiswoode j. geomagnetic fluctuations and free response anomalous cognition: a new understanding. j parapsychol. available at: http://www.jsasoc.com/docs/jp-gmf.pdf, 2002. [12] pitkänen m. dark matter hierarchy and hierarchy of eegs. in tgd and eeg. onlinebook. available at: http://tgdtheory.fi/public_html/tgdeeg/tgdeeg.html#eegdark, 2006. [13] pitkänen m. negentropy maximization principle. in tgd inspired theory of consciousness. onlinebook. available at: http://tgdtheory.fi/public_html/tgdconsc/tgdconsc.html#nmpc, 2006. [14] pitkänen m. quantum model for hearing. in tgd and eeg. onlinebook. available at: http: //tgdtheory.fi/public_html/tgdeeg/tgdeeg.html#hearing, 2006. [15] pitkänen m. quantum model for nerve pulse. in tgd and eeg. onlinebook. available at: http://tgdtheory.fi/public_html/tgdeeg/tgdeeg.html#pulse, 2006. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/zsg4b95 http://dx.doi.org/10.5334/jcr.140 http://tinyurl.com/zvlmxp6 http://tinyurl.com/zvcguuz https://arxiv.org/abs/1512.00450 http://www.jsasoc.com/docs/jp-gmf.pdf http://tgdtheory.fi/public_html/tgdeeg/tgdeeg.html#eegdark http://tgdtheory.fi/public_html/tgdconsc/tgdconsc.html#nmpc http://tgdtheory.fi/public_html/tgdeeg/tgdeeg.html#hearing http://tgdtheory.fi/public_html/tgdeeg/tgdeeg.html#hearing http://tgdtheory.fi/public_html/tgdeeg/tgdeeg.html#pulse dna decipher journal | december 2016 | volume 6 | issue 3 | pp. 134-149 149 pitkänen, m., can quantum biology really do without new physics? [16] pitkänen m. quantum model of eeg. in tgd and eeg. onlinebook. available at: http: //tgdtheory.fi/public_html/tgdeeg/tgdeeg.html#eegii, 2006. [17] pitkänen m. wcw spinor structure. in quantum physics as infinite-dimensional geometry. onlinebook. available at: http://tgdtheory.fi/public_html/tgdgeom/tgdgeom.html#cspin, 2006. [18] pitkänen m. wormhole magnetic fields. in quantum hardware of living matter. onlinebook. available at: http://tgdtheory.fi/public_html/bioware/bioware.html#wormc, 2006. [19] pitkänen m. quantum mind and neuroscience. in tgd based view about living matter and remote mental interactions. onlinebook. available at: http://tgdtheory.fi/public_html/tgdlian/ tgdlian.html#lianpn, 2012. [20] pitkänen m. quantum mind, magnetic body, and biological body. in tgd based view about living matter and remote mental interactions. onlinebook. available at: http://tgdtheory.fi/public_ html/tgdlian/tgdlian.html#lianpb, 2012. [21] pitkänen m. why tgd and what tgd is? in topological geometrodynamics: an overview. onlinebook. available at: http://tgdtheory.fi/public_html/tgdview/tgdview.html#whytgd, 2013. [22] pitkänen m. criticality and dark matter. in hyper-finite factors and dark matter hierarchy. onlinebook. available at: http://tgdtheory.fi/public_html/neuplanck/neuplanck.html#qcritdark, 2014. [23] pitkänen m. quantum gravity, dark matter, and prebiotic evolution. in genes and memes. onlinebook. available at: http://tgdtheory.fi/public_html/genememe/genememe.html#hgrprebio, 2014. [24] pitkänen m. from principles to diagrams. onlinebook.available at: http://tgdtheory.fi/ public_html/tgdquantum/tgdquantum.html#diagrams, 2016. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.fi/public_html/tgdeeg/tgdeeg.html#eegii http://tgdtheory.fi/public_html/tgdeeg/tgdeeg.html#eegii http://tgdtheory.fi/public_html/tgdgeom/tgdgeom.html#cspin http://tgdtheory.fi/public_html/bioware/bioware.html#wormc http://tgdtheory.fi/public_html/tgdlian/tgdlian.html#lianpn http://tgdtheory.fi/public_html/tgdlian/tgdlian.html#lianpn http://tgdtheory.fi/public_html/tgdlian/tgdlian.html#lianpb http://tgdtheory.fi/public_html/tgdlian/tgdlian.html#lianpb http://tgdtheory.fi/public_html/tgdview/tgdview.html#whytgd http://tgdtheory.fi/public_html/neuplanck/neuplanck.html#qcritdark http://tgdtheory.fi/public_html/genememe/genememe.html#hgrprebio http://tgdtheory.fi/public_html/tgdquantum/tgdquantum.html#diagrams http://tgdtheory.fi/public_html/tgdquantum/tgdquantum.html#diagrams introduction background some hints how to understand circadian clock, magneto-sensing and gravitaxis in tgd framework? basic problems and basic principles could circadian rhytms be analogous to eeg rhythms in tgd universe? trying to figure out the general mechanism more concrete model for the mechanism of magnetoreception and circadian rhythms gravitaxis and heff=hgr hypothesis appendix: what tgd is? why tgd? tgd and grt tgd and string models tgd based ontology tgd, quantum measurement theory, and consciousness dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 172-203 172 pitkänen, m., quantum gravitation & topological quantum computation exploration quantum gravitation & topological quantum computation matti pitkänen 1 abstract in this article the connection of quantum gravitation, as it is understood in the tgd framework, with topological quantum computation (tqc) is considered. i sketched the first tgd based vision about dna as a tqcer for about 13 years ago. in particular, a model of the system consisting of dna and nuclear/cell membrane system acting as a tqcer was discussed. tgd has evolved a lot after this and there are several motivations for seeing what comes out from combining the recent view about quantum tgd and tgd inspired quantum biology with this model. 1. there is a rather detailed view about the role of dark matter as phases of ordinary matter with the effective planck constant heff = nh0. large values of heff allow to overcome the problems due to the loss of quantum coherence. this leads to the notion of the dark dna (ddna), whose codons are realized as dark proton triplets and proposed to accompany the ordinary dna. also dark photon triplets are predicted and one ends up to a model of communications and control based on dark cyclotron resonance in which codons serve as addresses and modulation of the signal frequency scale codes the signal to a sequence of pulses. nerve pulses could be one application. 2. quite recently, also the understanding of the possible role of quantum gravitation in biochemistry, metabolism, bio-catalysis, and in the function of dna has considerably increased. the gravitational variants of hydrogen bonds and valence bonds between metal ions having very large value of heff = hgr, where hgr = gmm/v0 is the gravitational planck constant originally introduced by nottale, are in a key role in the model and explain metabolic energy quantum as gravitational energy liberated when dark protons ”drops” from a very long gravitational flux tube in the transition hgr → h. also electronic metabolic energy quantum is predicted and there is empirical support for this. 3. a further motivation comes from the number theoretic vision of quantum tgd. galois groups as symmetry groups represent new physics and the natural questions are whether galois groups could give rise to number theoretic variants of anyons and what could the tgd counterparts of the condensed matter (effective) majorana electrons proposed by kitaev as anyon like states? the answer is that quantum superpositions of symmetric hydrogen bonded structures of form x..h-h+x-h...x are excellent candidates for the seats of dark (heff > nh0 > h) bi-localized electrons defining tgd analogs of condensed matter majorana electrons. the galois groups permute the roots of a polynomial, which determines a space-time region by m8 − h duality. the roots correspond to mass squared values, in general algebraic numbers, and thus to mass hyperboloids in m4 c ⊂m8 c . the h images correspond to 3-hyperboloids with a constant value a = an of light-cone proper time. therefore the galois group can permute points with time-like separation. note however that the real or rational parts of two values of a can be same. this looks very strange at first but actually confirms with the fact that time-like braidings defining tqc correspond in tgd time-like braidings (involving also reconnections) of string like objects defining string world sheets, which are not now time evolutions of space-like entities as physical state but correspond to time-like entities defining boundary data necessary for fixing holography completely. their presence is forced by the small failure of the determinism of the action principle involved and is completely analogous to the non-determinism for soap films with frames serving as seats for the failure of determinism. 1correspondence: matti pitkänen http://tgdtheory.com/. address: rinnekatu 2-4 a8, 03620, karkkila, finland. email: matpitka6@gamail.com. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.com/ mailto:matpitka6@gmail.com dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 172-203 173 pitkänen, m., quantum gravitation & topological quantum computation 4. braidings appear therefore at the level of fundamental tgd and correspond to string world sheets. they are possible only in 4-d space-time but not in string models. also tqc-like processes appear automatically at the level of fundamental physics. in particular, the number theoretical state function reduction cascade for the galois group following the time evolution induced by braiding can be regarded as a generalization of a decomposition of integers to primes: now primes are replaced by simple groups defining primes for finite groups. nature is doing number theory! 5. also zero energy ontology (zeo) brings in new elements. the change of the arrow of time in ”big” state function reductions (bsfrs) implies that dissipation with a reversed arrow of time provides an automatic error correction procedure. also tqc in which the arrow of time varies for sub-modules, can be considered. 1 introduction in this article the connection of quantum gravitation, as it is understood in the tgd framework, with topological quantum computation (tqc) is considered. i sketched the first tgd based vision about dna as a tqcer for about 13 years ago. in particular, a model of the system consisting of dna and nuclear/cell membrane system acting as a tqcer was discussed [19, 18, 31]. tgd has evolved a lot after this and there are several motivations for seeing what comes out from combining the recent view about quantum tgd and tgd inspired quantum biology with this model. 1. there is a rather detailed view about the role of dark matter as phases of ordinary matter with the effective planck constant heff = nh0. large values of heff allow to overcome the problems due to the loss of quantum coherence. this leads to the notion of the dark dna (ddna), whose codons are realized as dark proton triplets and proposed to accompany the ordinary dna [35, 61]. also dark photon triplets are predicted [20] [45, 52] and one ends up to a model of communications and control based on dark cyclotron resonance in which codons serve as addresses and modulation of the signal frequency scale codes the signal to a sequence of pulses. nerve pulses could be one application. 2. quite recently, also the understanding of the possible role of quantum gravitation in biochemistry, metabolism, bio-catalysis, and in the function of dna [60] has considerably increased. the gravitational variants of hydrogen bonds and valence bonds between metal ions having very large value of heff = hgr, where hgr = gmm/v0 is the gravitational planck constant [39] [28, 25, 26] originally introduced by nottale [7], are in a key role in the model and explain metabolic energy quantum as gravitational energy liberated when dark protons ”drops” from a very long gravitational flux tube in the transition hgr → h. also electronic metabolic energy quantum is predicted and there is empirical support for this. 3. a further motivation comes from the number theoretic vision of quantum tgd. galois groups as symmetry groups represent new physics [51, 49, 50] and the natural questions are whether galois groups could give rise to number theoretic variants of anyons and what could the tgd counterparts of the condensed matter (effective) majorana electrons proposed by kitaev [6] as anyon like states? the answer is that quantum superpositions of symmetric hydrogen bonded structures of form x..hh+x-h...x are excellent candidates for the seats of dark (heff > nh0 > h) bi-localized electrons defining tgd analogs of condensed matter majorana electrons. the galois groups permute the roots of a polynomial, which determines a space-time region by m8 −h duality. the roots correspond to mass squared values, in general algebraic numbers, and thus to mass hyperboloids in m4 c ⊂ m8 c . the h images correspond to 3-hyperboloids with a constant value of light-cone proper time. therefore the galois group permutes points with time-like separation. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 172-203 174 pitkänen, m., quantum gravitation & topological quantum computation this looks very strange at first but actually confirms with the fact that time-like braidings defining tqc correspond in tgd time-like braidings (involving also reconnections) of string like objects defining string world sheets, which are not now time evolutions of space-like entities as physical state but correspond to time-like entities defining boundary data necessary for fixing holography completely. their presence is forced by the small failure of the determinism of the action principle involved and is completely analogous to the non-determinism for soap films with frames serving as seats for the failure of determinism. 4. braidings appear therefore at the level of fundamental tgd and correspond to string world sheets. they are possible only in 4-d space-time but not in string models. also tqc-like processes appear automatically at the level of fundamental physics. in particular, the number theoretical state function reduction cascade for the galois group [47] following the time evolution induced by braiding can be regarded as a generalization of a decomposition of integers to primes: now primes are replaced by simple groups defining primes for finite groups. nature is doing number theory! 5. also zero energy ontology (zeo) [41, 55] brings in new elements. the change of the arrow of time in ”big” state function reductions (bsfrs) implies that dissipation with a reversed arrow of time provides an automatic error correction procedure. also tqc in which the arrow of time varies for sub-modules, can be considered. 1.1 two visions about physics in tgd framework tgd leads to two visions about physics discussed in [46, 56]. in the first vision [14, 13, 17] physics is seen as geometry of space-time identified as 4-surface in h = m4 × cp2, and at a more abstract level, geometry of the ”world of classical worlds” (wcw) consisting of space of preferred extremals (pes) of the basic action principle defining analogs of bohr orbits as minimal surfaces with singularities. in the second vision [29] physics is reduced to number theoretic concepts and 4-surfaces in m8 analogous to momentum space define the basic objects. m8 −h duality [42, 43], analogous to momentumposition duality, relates the two visions. the 4-surfaces in m8 c (complexified m8), which has interpretation as complexified octonions, are required to be associative in the sense that their normal space is quaternionic. for given space-time region, they are determined by the roots of polynomial p of real argument continued to polynomials in m8 c . the roots define a collection of mass shells of m4 c ⊂ m8 c and by holography they define a 4-d surface of h. the action principle at the level of h is determined by the twistor lift of tgd and is the sum of 4-d kähler action and volume term (cosmological constant). it is not fully deterministic and space-time surfaces in h as pes analogous to bohr orbits can be regarded as analogs of soap films with frames, which correspond to singularities at which determinism fails. the frames provide additional holographic data besides the hyperbolic 3-surfaces corresponding to light-bone proper times a = an which are determined by the roots of p . frames include light-like orbits of partonic 2-surfaces and string world sheets connecting them. what is new, and consistent with zero energy ontology (zeo) [33], is that space-like data are not enough for holography, also time-like data is required and the string world sheets turn out to be absolutely essential for braiding and tqc. 1.1.1 physics as geometry the basic elements of physics as geometry are following. 1. space-time is identified as minimal 4-surface [57] in h = m4 × cp2. holography follows from general coordinate invariance and implies what might be called bohr orbitology. it turns out that holography is not quite strict. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 172-203 175 pitkänen, m., quantum gravitation & topological quantum computation 2. twistor lift of tgd [27] [58, 59] replaces space-time surface with what can be regarded as a counterpart of its twistor space having x4 as a base space and sphere cp1 as a fiber. the twistor structure is induced from the product of t (m4) × t (cp2) of twistor spaces t (m4) tc(p2), which are the only twistor spaces allowing kähler structure. the induced twistor structure and determined by an action principle with is 6-d kähler action existing only for m4 and cp2. twistor structure requires dimensional reduction so that one bundle structure and the action reduces to a sum of a volume term having interpretation in terms of cosmological constant and of 4-d kähler action as analog of maxwell action. pes realizing the holography are identified as minimal surfaces [57], which, apart for lower-dimensional singularities, are also locally extremals of the 4-d kähler action and possess a holomorphic structure reducing the field equations to algebraic conditions analogous to cauchy-riemann conditions. one can regard the space-time surface as an analog of soap film spanned by frames assignable to the singularities at which minimal surface property fails but extremal property for the entire action remains true so that conservation laws are not lost. as in the case of ordinary soap films, frames are seats of finite non-determinism interpreted as space-time correlates of quantum non-determinism. 3. the concrete study of the extremals of the action principle leads to the identification of the basic candidates for the basic pes. from the point of view of tqc, magnetic flux tubes are the most interesting objects and define counterparts of the braid strands. the notion of magnetic body (mb) is central. its detailed identification is still far from complete: for the latest view about gravitational mb see [60]. 1.1.2 physics as a generalized number theory and m8 −h duality physics as (a generalized) number theory is the dual vision of tgd. 1. p-adic physics emerged originally from a model for the particle massivation based on p-adic thermodynamics for the mass squared of the particle [15, 12]. from the beginning it was clear that various p-adic physics had to be fused with the real number based physics to a larger framework, which could be called adelic physics. for mathematical reasons, the natural interpretation of various p-adic physics would be in terms of physical and mathematical correlates of cognition. number theoretical universality stating that the basic equations of tgd are number-theoretically universal and make sense in all number fields is a natural constraint on the theory. 2. m8−h duality [42, 43] realizes the number theoretical vision about tgd and also holography. m8 c identified as complexified m8 and interpreted as complexified octonions, is analogous to momentum space and 4-surfaces define the basic objects at the level of m8. the 4-surfaces in m8 c (complexified m8), which have an interpretation as complexified octonions, are required to be associative in the sense that their normal space is quaternionic. these 4-surfaces are determined by the roots of polynomials of real argument continued to polynomials in m8 c . the roots define a collection of 3-d mass shells of m4 c ⊂m8 c and by holography they define a 4-d surface of m8 c . physical states correspond to 4-momenta at these mass shells analogous to fermi balls. m8 − h duality, analogous to momentum-position duality, relates the two visions by mapping the 4-surfaces in m8 to those in h. m8 − h duality generalizes to the level of twistor space [42, 43, 56, 58, 59]. 3. one can assign to a given polynomial an algebraic extension of rationals. the collection of points of the 4-surface of m8 c defines a cognitive representation. the mass shells as sources of holographic data are however number theoretically exceptional in that the number of points with algebraic m8 c coordinates is infinite: cognitive explosion takes place both at the level of m8 and h: these values of the light-one proper time a correspond to very special moments in the life of self, kind of moments of enlightenment. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 172-203 176 pitkänen, m., quantum gravitation & topological quantum computation in m8 the points of mass shells are identifiable as quark momenta assumed to be algebraic integers just as ordinary momenta for particles in a box are integers with suitable choice of momentum unit. these momenta can also be interpreted as points in extension of p-adic numbers so that number theoretical universality follows. the p-adic prime in question is identified as the largest ramified prime of the extension considered. this gives rise to a hierarchy of algebraic extensions and cognitive representations as unique discretizations of the 4-surface in m8 and space-time surface and suggests a generalization of computationalism replacing integers with the hierarchy of algebraic integers for extensions of rationals. 4. the dimension n of algebraic extension is identified as an effective planck constant heff = nh0 where h0 < h is true. the identification of the value of n0 in h = n0h0 has been proposed [54]. the phases of ordinary matter labelled by the value of n behave in many respects as dark matter and the identification as dark matter has been proposed. a particularly important class of phases corresponds to heff = nh0. these phases would play a central role in living matter. the relationship with galactic dark matter is however somewhat unclear. what makes these phases so important is the scale of quantum coherence is expected to scale like heff . dark phases are also expected to have very weak interaction with ordinary matter and the proposal is that living matter is controlled by this kind of phases located at mb and approaching only slowly thermal equilibrium with it: this would have interpretation as aging [62]. the small value of h and thermal fluctuations spoiling quantum coherence and entanglement belong to the key problems of qc and dark matter could solve these problems. 5. galois confinement [49] states that physical states have total momenta, whose components are ordinary integers. galois confinement provides a universal mechanism for the formation of bound states. galois confinement also applies in spin degrees of freedom and provides spin representations for the covering of the galois group. the number theoretic degrees of freedom are of special interest in qc and suggest that number theoretic quantum computation (nqc) as a counterpart of tqc, which would involve what might be called galois anyons. the galois group could allow identification as a subgroup of the braid group. this would mean strong restrictions on tqc. 6. m8 −h duality leads to a view about the construction of the counterpart of s-matrix in the tgd framework [58, 59]. s-matrix would be replaced by the analog of kähler metric in fermionic degrees of freedom [48], which by the infinite dimension of fock space is expected to be highly unique as also the kähler metric of wcw [14, 13, 17]. incoming and outgoing states of particle scattering would be galois singlets constructed from lower level states which need not be galois singlets. quarks, whose momenta at mass shells are algebraic integers are free and the scattering would be mere reorganization of galois singlets to new ones. scattering could be also seen as analog of qc and computation in an extension of rationals: both the input and output would consist of a set of rational integer valued momenta and scattering would map them to each other. this applies in the twistor picture also to spins having a representation as points of the twistor sphere s2 known as bloch sphere. in this case number theoretic constraints suggest that the set of quantization axes corresponds to a finite discrete subgroup of so3) assignable to regular polygons and platonic solids. the quark momenta belonging to the extensions of rationals are invisible, which implies invisible algebraic complexity of cognition and brings in mind unconscious information processing. quantum physics and psychoanalysis would meet! issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 172-203 177 pitkänen, m., quantum gravitation & topological quantum computation 1.2 zero energy ontology (zeo) and qc the first basic motivation for the introduction of zeo was that by the general coordinate invariance space-time surface as a preferred extremal is a more natural notion than 3-surface. for exact holography, these notions are equivalent but the identification of space-time surface as minimal surface predicts a small violation of the strict holography identifiable as a correlate for quantum non-determinism associated with the physics of cognition or possibly quite generally. this non-determinism would be essential for the possibility of tqc in tgd. second motivation was the basic problem of quantum measurement theory to which zeo provides an elegant solution if one assumes that the arrow of time changes in ”big” state functions reductions (bsfrs) as analogs of ordinary sfrs. in ”small” sfrs, which are analogs of ”weak” measurements introduced in quantum optics, the arrow is not changed [33] [41, 55]. in the tgd framework, quantum measurement theory generalizes to a quantum theory of conscious experience in which ssfr defines the basic element of conscious experience. bsfr has an interpretation as a counterpart of death/sleep. the change of the arrow of time in bsfrs has profound implications in quantum biology. since the dissipation with a reversed arrow of time for a subsystem looks like selforganization from the point of view of a system with an opposite arrow of time [40]. the arrow of time can change for macroscopic time periods at the mbs with large heff and since mb controls the ordinary matter, it induces not only effective quantum coherence but also an effective reversal of time also at this level. the basic ideas of zeo [41, 55] are following. 1. in zero energy ontology (zeo) [41, 55], the pair of incoming and outgoing states of particle scattering are replaced with zero energy state and zero energy states define scattering amplitudes as entanglement coefficients. 2. at the level of h, positive and negative energy parts of zero energy states are located at boundaries of causal diamonds (cd), which form a fractal hierarchy. at the level of m8, they reside at the boundaries of mass shells, which corresponds to the roots of the polynomial defining the spacetime region. m8 −h duality maps these points to the boundary of cd. one can also consider an alternative for which mass shells as hyperbolic spaces h3 ⊂ m8 are mapped to their counterparts in h by a map which is essentially inversion (uncertainty principle). 3. scattering events [58, 59] are qc like events. input (output) data correspond to incoming (outgoing) quark momenta identified as algebraic integers in an extension of rationals and to spins. since fermionic fock state basis defines a boolean algebra, the fermionic states define quantum analog of boolean algebra, and the scattering amplitudes could be also seen as a quantum generalization of boolean maps and realizing statements which are true that is consistent with laws of physics. these transitions could be interpreted in terms of boolean cognition. the replacement of the s-matrix with kähler metric in fermionic hilbert space degrees of freedom represents a new element. the analog of unitary transformation is assigned with cd and from the point of view of qc, cd could be interpreted as an embedding space analog of gate. since gates allow control bits not affected by the unitary transformation, also the boolean functions, which are not 1-1, can be realized as unitaries. same is expected to be true also now. 4. the scattering amplitudes correspond a tensor net-like structure. physical states are galois singlets consisting basically of free quarks. at the number theoretical level, scattering can be seen as a recombination of galois singlets to new ones. zeo could have a profound impact on qc. 1. negentropy maximization principle (nmp) [16] [53] is the variational principle of tgd inspired theory of consciousness. negentropy can correspond to the sum of p-adic negentropies or to the sum issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 172-203 178 pitkänen, m., quantum gravitation & topological quantum computation or p-adic and real negentropies, which can be possible and tends to be so by nmp. for both options, nmp guarantees that the p-adic entanglement negentropy increases and is positive. it however also forces the real entanglement entropy to grow. nmp therefore implies cognitive evolution but also second law. from the point of view of qc, this picture is very promising since the laws of physics would take care that the entanglement negentropy grows and also that negentropic entanglement tends to be stable. this is quite contrary to what standard physics predicts. this leads to evolution [37, 38] in the sense that the dimension n = heff/h0 of the extension of rationals as a measure of algebraic complexity tends to increase since this provides larger negentropic resources. this evolution takes place at mb in human length and time scales and the challenge is to learn to manipulate dark matter. 2. bsfr could take care of error correction automatically since for the reversed arrow of time dissipation looks like error correction by self-organization. this error correction is a key feature of living matter but has remained poorly understood. one can also ask whether bsfrs could make possible qcs involving sub-qcs in both time directions. could the use of sub-programs with opposite time direction allow a faster qc. 1.3 finite field approximation and qc number theoretic vision about qc leads to new ideas about qc itself. 1. the momenta in the extension of rationals as algebraic integers can be interpreted as p-adic integers in the induced extension of p-adic numbers. the p-adic number field corresponds to prime p, which is the maximal ramified prime for the polynomial in quesetion. in the approximation o(p) = 0 they define a finite field f (p, n) having dimension is is not larger than the dimension of extension but can be smaller. the number of elements is pn and the situation corresponds to n pinary digits, qupits, instead of qubits. tqc using elements of f (p, n) is an attractive possibility. besides this one has also spin degrees of freedom. 2. the elements of f (p, n) can be regarded as roots of some, in general non-unique, polynomial with degree pn. this polynomial is in general not the polynomial inducing the extension of p-adic numbers. 3. the galois group for the finite field should transform to each other the roots of the originalpolynomial interpreted as a polynomial in f (p, n) and is a subgroup of the galois group for the polynomial having all points of f (p, n) as its roots. the automorphism group of quaternions is analogous to galois group and in the tgd framework with discretization it looks like a natural notion. 1. in the continuous case, the automorphism group of quaternions is the rotation group so(3) having su(2) as covering group. in the discrete situation, one expects it to be a finite group and would correspond to symmetries of platonic solid in non-abelian case and to the symmetries of a regular polygon in abelian ase. icosahedron, tetrahedron, and octahedron have triangles as faces and the proposal is that genetic code realized in terms of bioharmony [20] [45] corresponds to so called icosa-tetrahedral tessellation of h3 [52]. 2. therefore genetic code and bioharmony could closely relate to the quaternionic aspects of number theoretic physics and perhaps also to tqc for quantum variant su(2)q of quaternionic automorphisms acting in the normal space of the space-time surface. a natural proposal is that the points of the icosahedron and tetrahedron correspond to points for the discretized unit sphere known as bloch sphere defining possible directions of the quantization axis of spin in tqc. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 172-203 179 pitkänen, m., quantum gravitation & topological quantum computation 3. the finite subgroups of su(2) are associated with the hierarchy of inclusions of hyper-finite factors of type ii1 and the proposal is that the inclusion of these factors define finite measurement resolution such that the included factor defines the resolution [32, 23]. 1.4 tqc and the new view about space-time the new view about space-time is highly relevant for the tgd view of tqc. 1.4.1 galois anyons the basic problem of the tgd inspired model of tqc is the identification of the topological qubit identified as an anyon-like state in standard tqc. one could say that topological qubit or its analog does not correspond to quantum state but representation of braid group or quantum group assignable to chern-simons action. topological qubits also satisfy a nice algebra defined by the decomposition rules of the representations of the braid group. the motivation for this identification is that topological qubits are expected to be highly stable since the change of the representation is not expected to be probable unlike the change of spin direction. the non-local character is also an important aspect. the braids defining tqc program as unitary representation of the braid group allows to identify the gates, which are universal in the sense that they have finite computational accuracy. the increase of the order of the covering group as a finite covering of the permutation group sn for n braid strands allows to improve the accuracy. kitaev [5, 4] has proposed [6] that anyon-like bi-localized states of condensed matter majorana fermions could define stable qubits. majorana electrons would be superpositions of electron states localized at the ends of a superconducting wire and would have parity +/− 1 under permutations of ends of the wire. in tgd framework the electrons defining analogs could be bi-localized states with localization to the ends of a monopole flux tube or pair of them. galois degrees of freedom are a new element and anyons could correspond to multi-localized states defining representations of galois group at its orbits consisting of points of the cognitive representation at mass shell h3. also spin degrees of freedom would define galois representation. if the braidings correspond to lifts of number theoretic symmetries, galois group corresponds to a subgroup of the braid group. in the standard picture of tqc, a computationally interesting situations corresponds to non-abelian anyons to guarantee that the states defining topological qubits form a higher-d space. this means that the swap ab ↔ ba is not a commutative operation inducing a mere phase anymore. since the status of majoran fermions is unclear, it is still unclear whether any anyonic system satisfies this constraint. galois groups are in general non-commutative so that this problem disappears. physical states would be galois singlets and anyon-like states would be their building bricks just as quarks would define building bricks of general galois singlets including also leptons and various bosons. since galois non-singlet cannot appear as a free particle, one could also understand topological entropy associated with anyons as relating to the entanglement with environment forced by galois singletness in spin degrees of freedom. 1.4.2 braidings and reconnections as basic elements of tqc tqc in the tgd universe involves also other new elements besides galois groups. 1. the flux tubes connecting the nodes of a tensor net-like structure define natural candidates for braid strands. both space-like and time-like braiding are possible. time-like braiding defining tqc of the moving nodes connected by flux tubes induces a space-like braiding so that the tqc is recorded to memory as a kind of log file. dance metaphor expresses this neatly: dancers at the parquette are connected by threads, which get braided and form a memory issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 172-203 180 pitkänen, m., quantum gravitation & topological quantum computation representation about the dance. this mechanism could define quite a general representation of memories based on space-time topology. 2. the fusion defined by the tensor product for the representation of the braid group or associated quantum groups is a key operation in standard quantum computation. the decomposition of the tensor products gives a superposition of topological qubits or more general qubit-like entities an interesting question is whether the fusion could have a more concrete topological meaning. could the fusion of flux tubes correspond to a formation of a bound state of flux tubes inside a flux tube? 3. tqc as a braid generalizes to tensor-net (for tensor nets in tgd sense see [24] [36]). the nodes can have m incoming qubits and n outgoing qubits. the node corresponds to a quantum computation defined as a map between the incoming and outgoing qubits. in the framework, the nodes would correspond to cds for m 6= n is not a unitary transformation 1-1 transformation but can be an injection so that it is still an isometry at the level of the state space. 4. besides swap as the basic braiding operation, also reconnection, having the same effect as far as initial and final states are considered, appears as a basic operation. when the incoming and outgoing qubits cannot move, reconnection could take the same role as swap and make tqc possible. 5. one can wonder whether this more general view about tqc could be realized in quantum biology. could biochemical reactions correspond to fusions of braids of a tensor net, could reconnections and braidings make it possible to have a larger repertoire of tqcs. could zeo-based error correction requiring only time reversal play a key role in tqc. 1.4.3 different tgd based views of tqc tgd suggests several different perspectives of tqc. 1. in the flux tube picture, the basic elements are braiding, reconnections and fusions in which flux tubes could even form a bound state inside a larger flux tube so that the fusion could have a geometric meaning. at the level of h, fusion could correspond to a process in which the incoming particles arriving into the cd form a tensor product. inside cd fusion occurs and gives rise to a decomposition of irreps. measurement selects one irrep first and outgoing states are obtained by an sfr cascade reducing the total galois group to the factors defined by relative galois groups by a cascade of ssfrs defining cognitive measurements. dance metaphor implies a mechanism of memory with spatial braidings representing spatial braidings. this mechanism would be realized in all scales and define kinds of topological akashic records. if reconnection is equivalent with swap operation, then tqc is also possible without braiding induced by the motions of braid ends. 2. cds are counterparts of gates at the level of h and define a fractal hierarchy of gates with sub-cds defining sub-modules. space-time surface in h can be also seen as a 4-d soap film with frames as seats of non-determinism and one could assign mental images with this non-determinism. this suggests that the gates at space-time level correspond to the frames whereas cds would correspond to entire tqcs at the level of h. this also suggests that tqc in the tgd sense must allow intermediate ssfrs at the frames. the situation is far from obvious since fractality is also present and involves a hierarchy of cds. the m8 − h-duality provides a further view about tqc. a highly attractive idea is that tqc programs can be constructed as functional composites of polynomials giving rise to extensions of extensions of .... and inclusion hierarchies of corresponding galois groups, each defining a normal subgroup of its sup-group. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 172-203 181 pitkänen, m., quantum gravitation & topological quantum computation the normal subgroup hierarchy makes it possible to understand cognitive measurements as ssfr cascades reducing the representation of the galois group to a product of representations for the subgroup and normal subgroup associated with it. this decomposition could generalize the decomposition of the anyonic representations. this would also suggest a deep connection with the paradigm in which computations are functions. 2 what could the replacement of the braid group with the galois group mean? the replacement of the braid group acting on anyons with the galois group looks a rather innocent proposal first but has profound implications. the reason is that the galois group permutes the roots of the polynomial p , which correspond to different mass shells in m8 and therefore different values of light-cone proper time in h. 2.1 functional composition of the polynomials and many-particle states functional composition of the polynomials is proposed to give rise to many-particle states. 1. the roots of p correspond to mass shells. quarks have momenta at these complex mass shells. roots and corresponding momenta are in general complex algebraic numbers and total momenta and mass squared values are real by galois confinement. 2. functional composite p = pn ◦ ... ◦ p1 of polynomials defines the interactions of particles in the number-theoretical picture. functional composites are proposed to define particles as many-quark states and further functional compositions make it possible to engineer many particle states formed from these. 3. one can also consider iterates of a polynomial as analogs of many particle states involving only a single kind of particle. functional decomposition gives as roots inverse iterates of the roots of the polynomial q in p = q◦q...◦q [44, 58, 59]. asymptotically they give rise to an analog of the true julia set (https://mathworld.wolfram.com/juliaset.html) as a boundary of the filled julia set. the inverse iterates near the boundary of the julia set would correspond to very nearly the same mass squared values and thus proper time constant hyperboloids. 4. one can regard the roots of pi as roots with respect to the variable y = pi−1 ◦ ...p1(x) if y = pi−1 ◦ ...p1(x) defines the ground state coordinate. heff = n0h0 would define a natural ground state for which heff = nh would hold true. 5. if the polynomials appearing in the composite satisfy pi(0) = 0, one has ”inheritance of roots”. the roots yi of pi are mapped to their inverse images (pi−1 ◦ ...p1)−1(yi) = p−1 1 ◦p−1 2 ... ◦p−1 i−1(x). this inheritance brings in mind conserved genes. a weaker form of ”inheritance” would be that some polynomials, say p1, p2, ..., pk at the lowest level have pk(0) 6= 0. for p = q ◦ pf , where pf = x2 − x− 1 is ”fibonacci polynomial”, the roots would be of form (−1± √ 5 + 4yn)/2, where yn is a root of q. note that one has p1(0) 6= 0. if one has pk(0) 6= 0 for k > 1, the roots of p1 are roots of any p and therefore universal. this suggests the possibility that the ground state polynomial corresponding to heff = h = n0h0 is non-vanishing at origin. 2.1.1 ground state polynomial the ground state polynomial pg corresponding to heff = h = nh0 is of special interest physically. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://mathworld.wolfram.com/juliaset.html dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 172-203 182 pitkänen, m., quantum gravitation & topological quantum computation 1. the arguments allowing to deduce the value of n0 in h = nh0 lead to a conclusion that the ground state polynomial pg [54] corresponding to heff = h = n0h0 corresponds to a galois group with 7!2 elements. 2. this allows several options. for instance, the semidirect product s7 o s7 could act as a galois group. s7 decomposes to a semidirect product of the simple alternating group a7 and z2 acting as a normal group. s7 can appear as a maximal galois group for a polynomial of order 7. in this case s7 could correspond to qa = p7 ◦p2 or qb = p2 ◦p7 and one would have four options p = qi ◦qj . also p7 ◦ p7 ◦ p2,a ◦ p2,b p2,a ◦ p2,b ◦ p7 ◦ p7 are possible. 3. second roots appear in all basic formulas of quantum mechanics. therefore one can argue that p2 should appear at the bottom of the composite polynomial defining the ground state. fibonacci quantum computation involves golden mean and the roots x± = (−1 ± √ 5)/2 of fibonacci polynomial pf (x) = x2 − x − 1. all roots would appear as pairs with members related by the galois group of pf . for p1 = pf and pk(0) = 0 for k > 1 (inheritance), the roots of pf are roots of any p and golden mean would play a key role in fundamental physics. 2.1.2 mass squared formula and inheritance hypothesis for galois singlets, the total momentum has components, which are ordinary integers. also mass squared is integer. 1. if the stringy mass formula m2 = n holds true for the quark mass squared values as roots of a polynomial, one must have m2 = ∑ m2 i = n. this requires that the sum of the inner products of quark momenta vanishes. the interpretation would be as an additivity of conformal weights. if every root is realized as quark momentum, m2 = ∑ m2 i equals the constant coefficient of the total polynomial p giving m2 = p (0). 2. if the strong form of inheritance holds true, one has ∑ m2 i = 0 so that the total conformal weight vanishes. could the interpretation be in terms of conformal invariance? could one say that the tachyonic total mass squared assignable to the space-like states defined by braid strands compensates for the non-tachyonic total mass squared? total momentum would be light-like and the m8 −h duality should be defined as the map pk → mk = ~effpk/(p0)2 wheremk belongs to the light-like boundary of cd containing the cds assignable to the mass squared values as sub-cds. 3. in p-adic mass calculations the total conformal weights are however non-vanishing and real. what could this mean? (a) the thermal excitations should be excitations of the m2 = 0 state due to interaction with the environment, which extends the system. the thermal excitations would be described by polynomials qex = pex ◦ p . the roots of qex would include, besides roots of p (inheritance), also the roots yn of pex and these correspond to non-vanishing values of p (yn). yn 6= 0 would give non-vanishing mass for the thermalized subsystem defined by p . (b) if one gives up the ”inheritance” hypothesis and allows pi 6= 0, one has m2 = ∑ m2 i = pn(0). monic polynomials p (x) = xn + an−1x n−1 + ... + a0 are good candidates for the allowed polynomials. the coefficients ak are integers so that the mass squared as a conformal weight∑ m2 i = a0 is an integer. 2.1.3 decomposition of galois group to a product of relative galois groups the galois group gal for an extension of extension.... decomposes to a product of the relative galois groups galk/galk−1. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 172-203 183 pitkänen, m., quantum gravitation & topological quantum computation 1. one can speak of the ground state characterized by some galois group gal0. ordinary planck constant h would correspond to gal0 and in [54] it was proposed to be a product of permutation groups s7 giving n0 = (7!)2. this allows to interpret cp2 length scale squared as n0lp 2, lp planck length. galois group can be identified as a relative galois group: as galois group for extension of the extension defining the ground state. 2. the structure of the galois group reflects the functional composition involving a large number of identical polynomials with the same mass spectrum as free particles. in the functional composite p ◦q the mass spectrum s of p is mapped to q−1(s). large number of iterations of p produces julia set as a fractal. one can speak of an asymptotic mass spectrum. 3. the orbit of galois group consists of mass shells and its cognitive representation can contain momenta at these mass shells. galois symmetry would be a discrete symmetry connecting quarks with different mass values (which are counterparts of virtual masses rather than real masses). galois symmetry would be analogous to a dynamical symmetry and would not commute with poincare and lorentz symmetries. physical states are galois singlets and have well defined real mass squared. galois singlet property of physical states would imply that these symmetries would be respected. physical states correspond to a cd containing sub-cds... and at the lowest level there would be quarks. essentially 4-d objects would be in question. 2.2 m8 −h duality at the level of m4 m8 − h duality maps the algebraic physics at the level of m8 formulated using polynomials to the geometric physics at the level of h = m4 × cp2 formulated using variational principle and partial differential equations. the preferred extremal property required by general coordinate invariance reduces the number of solutions of field equations so that they can correspond to a much smaller set of solutions of algebraic equations. the holographic aspects of m8 −h duality have been already considered and in the following only the map m8 ⊃m4 → h ⊃m4 is discussed. 1. m8−h duality maps the surfaces of m8 to minimal surfaces in h having singularities at which only the field equations for the full action containing also kähler action besides the volume term hold true. m8 −h realizes holography: the mass shells determined by the roots of p can be continued to 4-surfaces containing them. 2. the precise form of m8−h duality is not quite clear. the first question is whether one should allow complexification of m4 as at the h side. one could define the h image as mk = ~effre[pk/m2], where pk is the quark momentum and at mass shell m2. mk would define some geometric objects in h. for physical states m2 is integer and corresponds to a finite value of a = ~eff/m. if the stringy mass formula m2 = ∑ m2 i = 0 is true, the image belongs to the light-cone boundary. the image could be a geodesic line of h parallel to mk, which could start from the origin from the common center of cds forming a fractal russian doll hierarchy or from the tip of a given sub-cd. the image could also be identified as a point or a set of points. the point could be identified as the intersection of these lines with the boundary of the sub-cd defined by the mass value or its real part. also the intersections with boundaries of all sub-cds involved can be considered. also the map of mass shells to m8 to hyperboloids a = an, where a is light-cone proper time and an is inversely proportional to mass to realize uncertainty principle, makes sense. 3. the image of the orbit of the galois group would correspond to a geodesic line starting at the centers or tips of various cds defined by the mass shells. if the cds are inside each other like a russian doll, the geodesics intersect the a = an hyperboloids and the boundaries of corresponding issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 172-203 184 pitkänen, m., quantum gravitation & topological quantum computation sub-cds corresponding to different values of the light-cone proper time a and are time ordered. what is highly non-trivial is that the points at the orbit have timelike distances. 2.3 the orbits of the galois group in h transform hyperboloids to each other mass squared values correspond to the roots an of a polynomial and are in general complex algebraic numbers. their real projections can be negative and therefore tachyonic. the big surprise during writing of this article was the trivial observation that the galois group permutes the mass shells defined by the roots of p . if the real projections of mass shells to m4 are mapped to h, galois group can connect points with different values of complex ”cosmic time” a = an. this does not conform with the idea that the particles of the physical state always have space-like distance but could conform with zeo and non-determinism inspiring the view that time-like braiding is a physical state rather than its time evolution. note however that the spatial distance (m1 −m2)2 in h is space-like for (e1 ≥ m2 1 +m2 2)/m2 in the coordinate system in which m2 and p2 have a vanishing spatial part. this holds true also for the m4 images. 2.3.1 orbits of the galois group as braidings? could the orbits of the galois group for off-mass shell states be identified as braidings? 1. if the braiding is time-like, the value of the real part of the proper time parameter corresponding to the mass shells or cd sizes increases along the orbit. this would conform with the idea that the orbit of the galois group consists of images of mass shells at the quark level. it also conforms with the breaking of lorentz and poincare symmetries at the level of the galois group. this finding also justifies the galois confinement: physical states correspond to a single value of a. 2. what about number theoretic anyons? these anyons must have non-trivial galois quantum numbers and algebraic momenta. here the relative galois group is a convenient concept. galois non-singlet property is with respect to the relative galois group and one can forget the huge complexity of the galois singlet ground state altogether. 2.3.2 do galois anyons require tachyonic states? the momenta of quarks define the basic representation of the galois group. one can also imagine representations in spin degrees of freedom. if only the spin degrees of freedom carry galois quantum numbers, the space-time action of the galois group is trivial. this does not look attractive and does not conform with time-like braiding. anyon property therefore suggests the presence of tachyonic momenta. 1. i have played with the idea that quarks and also weak bosons appear in the scale of cells in living matter as dark quarks or even scaled variants with very small mass. how could the dark quarks manifest themselves? i have proposed that the protons of dark nucleon triplets representing codons are connected by meson-like bonds, which could be colored and confine codons to genes. this could the case also for the bonds connecting nucleons in the ordinary nuclei. strong interaction would also make it possible to have dark neutrons. i have assigned the z3 galois group with the dark nucleon triplets defining dark codons: this is required by the correct statistics in the model of the genetic code. could galois group z3 correspond to the center z3 of the color group su(3)? issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 172-203 185 pitkänen, m., quantum gravitation & topological quantum computation 2. in the original proposal for dna tqc [18], quark triplets were indeed considered instead of dark nucleon triplets. dark tachyonic electrons assignable to symmetric hydrogen bonded structures looks like a more realistic option. one can also consider mesons with quark and antiquark ends associated with the ends of the space-like braid strands. dark tachyonic electrons could be associated with the ends of string world sheets for which the time dimension corresponds to a space-like normal dimension. could one assign a colored quark pair to anyon-like electron? leptohadrons [30] are a basic prediction of tgd and there is empirical evidence for them. the predicted mass of the lepto-electron is very nearly the same as electron mass and evidence for its existence was found already in the seventies. lepto-electron would be a color octet: this is allowed in the tgd framework. lepto-hadron is associated with the breaking of parity symmetry in nuclear collisions involving strong electric and magnetic fields not orthogonal to each other. its description involves chernsimons kähler action associated also with anyons. the notion of induced gauge field allows its interpretation as su(3) chern-simons action. a possible identification of lepto-electron would be as an anyon for which electron would be accompanied by a color octet quark pair formed by the quarks at the ends of the flux tube. 3. polynomials can also have roots corresponding to space-like mass squared values. could dark quarks be tachyonic in the sense that they have a negative real part of mass squared so that time direction as a normal direction for this object would be naturally space-like? 4. could one see time-like braids structures as genuinely 4-d objects predicted by zeo and the failure of the strict determinism of the action principle? singularities as frames span 4-d soap films serve as a source of non-determinism. 2.3.3 how could dark dna correspond to time-like braids strands for dark dna? the following represents a long list of cautious proposals represented as questions. 1. can one galois symmetries acting in time direction have projections acting effectively as 3-d symmetries of ordinary matter at time=constant surface. the galois group at the level of (presumably gravitational) mb does not act at the level of ordinary matter. could the time-like braids at the level of the dark dna correspond to the ordinary dna strands in the sense that the temporal sequences would be mapped to spatial sequences by some simple rules? 2. could genes have a representation as time-like braids? could one imagine a pile of or ordinary dna strands and their dark counterparts at different values of a = an such that time like braid strands would have the same dna content as the dna in a = constant or t = constant plane. for instance, could the intersections of the points of cognitive representation at a = an hyperboloids with t = constant hyperplane define the dna strand. the codons of dark dna as a temporal sequence would correspond to codons of the ordinary dna unless one assumes that only identical codons correspond to the orbits of the galois group. this looks like a more reasonable option. codons themselves would correspond to orbits of the discrete and finite subgroups of automorphisms of quaternions acting as symmetries of platonic solids and regular polygons. therefore two kinds of galois groups would be involved. 3. could the physical dna correspond to the space-like braidings assignable to the time-like braidings of dark dna? could one realize the representations of the galois group by using these projections at the level of ordinary dna. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 172-203 186 pitkänen, m., quantum gravitation & topological quantum computation 4. could identical codons of a gene correspond to projections of points related by the galois group? if so, the collections of identical codons (64 of them) would correspond to 64 orbits and the anyons would be realized at these collections as wave functions. different representations would correspond to different anyons serving as number theoretical qupits. 2.3.4 string world sheet interpretation of time-like braidings at the level of h m8 − h duality implies time-like braids correspond to physical states rather than time evolutions of an ordinary physical state localizable to time= constant hyperplane. the time-like character of states conforms with zeo and is implied by the predicted non-determinism in which the singularities of the minimal surface correspond to loci for the failure of strict determinism. these singularities define analogs of frames for the space-time surface as an analog of a 4-d soap film. they are a necessary part of the data allowing to realize holography. m8−h duality [42, 43] predicts candidates for the singularities as loci of non-determinism. the following argument suggests that the 2-d orbits of braid strands defined by string world sheets as fundamental objects of the tgd universe giving rise to braidings could characterize the non-determinism. 1. 3-d light-like surfaces defining orbits of partonic 2-surfaces starting at the boundaries of cd and 2d string world sheets connecting two light-like 3-surfaces. strong form of holography, whose status is uncertain, states that only the partonic 2-surfaces at the boundaries of cd are needed. 2. string world sheets would provide additional data to fix the preferred extremal and the failure of 4-d determinism manifested as the failure of the minimal surface property would be localizable to the string world sheets. according to the dance metaphor, the ends of the strings would represent dancers and strings would represent the threads connecting their feet. string world sheets would be necessary for fixing the space-time surface. this is a profound deviation from string models, where data at time=constant section would fix the time evolution. in fully deterministic physics, the direction of time coordinate is normal to t = constant slice. the normal directions of the string world sheet are analogous to time direction: that they are space-like conforms with tachyonicity. string world sheet would represent a tachyonic virtual particle exchange between particles with time-like momenta. 3. also strings are minimal surfaces apart from singularities. reconnection is a singularity at which the string world sheets intersect at a single point and involves failure of determinism. the effect of reconnection is the same as that of braiding (swap). reconnection therefore corresponds to the swap gate in tqc. 4. the 4-d character of the space-time surface implies that the strings develop spatial braiding during the dance and can also reconnect. this does not happen in super string models with 10-d embedding space for strings. the braiding and reconnection patterns would represent the time evolution of string-like entries in 4-d space-time so that tqc would reduce to a string model-like theory with one important exception: braiding and reconnections are not possible in string models. gravitational flux tubes would be one particular case of flux tubes. they seem to be key players in biology and provide a quantum gravitational view about metabolism, biocatalysis, and dna [60]. tqc involves braiding and flux tubes with strings attached with them: tqc would have a direct connection with string model type description of quantum gravitation and other interactions. tachyonicity of the time-like braids as physical states could be therefore understood. one can look at the situation also from the point of m8 −h duality to gain additional perspective. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 172-203 187 pitkänen, m., quantum gravitation & topological quantum computation 1. virtual particles of qft picture would in tgd framework have a discrete mass squared spectrum give by the roots of a polynomial and thus algebraic, in general complex, numbers [58, 59]. their finite number in zero energy state would resolve the divergence problem of qfts. only quarks appear as fundamental fermions. mass squared values and momenta of many quark states constructed are in an extension of rationals without the condition of galois confinement implying stringy mass squared spectrum and integer valued momentum components using the scale of cd as unit. 2. quarks at mass shells of m4 ⊂ m8 are mapped to geodesic lines of h by m8 −h duality. they can be also space-like unless one assumes that the real parts of the roots of p are non-negative. for negative real parts, the momenta would be space-like and define points outside the sub-cd but a larger cd could contain them. could the total momentum of say 3-quark state possibly associated with codon (3n quark state associated with a gene) be tachyonic? could the tachyonic quark triplets be located along the time-like braid strand associated with the codon and define a tachyonic many-quark states? 3. for anyons as tachyons galois confinement must fail and they should correspond to virtual states made from quarks. could the strands of a space-like braid as a string with quark and antiquark at its ends define an entity analogous to a virtual meson? could this meson-like entity have non-trivial color quantum numbers? how do galois confinement and color confinement relate? at the level of ”world of classical worlds” (wcw) quark color corresponds to partial waves in cp2 for cm degrees of freedom for the partonic 2surfaces associated with quark. at the level of the space-time surface there are no color partial waves since fermions do not have color as a spin-like quantum number. i have proposed a z3 subgroup of the galois group as a counterpart for z3 ⊂ su(3). correct statistics requires antisymmetry with respect to galois z3. one must take this with caution: maybe the braid statistics of anyons could solve the statistics problem. note however that braid statistics is analogous to fermi statistics in that two particles are not possible in the same state. the original proposal for dna as a tqcer, was that dna and nuclear membrane are connected by flux tubes having quark and antiquark at their ends. also dna strands would be connected by this kind of strands. the proposal was motivated by the observations and the classical counterpart of color gauge field is proportional to the induced kähler form, and can define a coherent field in arbitrarily long scales. i gave up this proposal a long time ago but it seems that this proposal had some seed of truth in it. anyonic electrons replace quarks and antiquarks. 1. what comes in mind first is that the dna strand and its conjugate involve, besides dark nucleon triplets, also dark quark/antiquark triplets forced by the time-likeness of the braiding regarded as a physical state in zeo. this however leads to problems since dark nucleons are strongly favored. doubling of the genetic code without need for it looks ugly. the mere quantum gravitational modification of the standard chemistry should be enough. most importantly, tachyonicity does not require single quark states. also the dark anyonic electrons could be virtual particles carrying tachyonic momenta. the 3+3 dark electrons assignable to the asymmetric hbs of form o..h-n would provide electronic realization of the genetic code. the dark codons would serve as names, addresses in the symbolic dynamics of tqc involving the resonance mechanism of communications requiring addresses. the dark anyonic electrons assignable with g-c bonds would carry tachyonic momenta and make the braiding possible. the tachyonic electronic momenta assignable to bonds symmetric o...h-o type bonds connecting water molecules and phosphates would be realized in the same way. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 172-203 188 pitkänen, m., quantum gravitation & topological quantum computation 2. it is good to bring in mind the possible weak points of the scenario once again. dark protons are strongly suggested by the pollack effect and the proposed picture about dark gravitational hbs with delocalized dark protons [60]. in the original view, dark protons screened the negative charge of phosphates. in the new picture the negative charge of phosphate is assignable with bi-localized (anyonic/dark/virtual) electrons of o...h-o +o-h...h: at the level of ordinary matter, dna is not negatively charged. in qft language, one might perhaps say that a dark electron is exchanged between the ends of the flux tube associated with the dark hb. 2.3.5 connection with time-like character of music experience and cognition a connection with the model of dna based on bioharmony is suggestive. 1. dna and rna codons are identified as points at the orbits of icosahedral and tetrahedral subgroups of quaternion automorphisms. amino acids (aas) have been identified as orbits of the icosahedral and tetrahedral groups, which are discrete subgroups of quaternionic automorphisms, which is completely analogous to galois groups. 2. harmony is the basic element of music and music involves time in an essential way. same is true of cognition. perhaps the time-like braid strands could give a concrete content to the proposal. codons would correspond to 3-chords and gene would correspond to a piece of music in a much more concrete way than originally proposed. genes would also represent primitive cognitions. 2.4 cognitive measurement cascades as counterparts of measurements of anyon charges the measurements of topological charges reduce the tensor products for the representations of the braid group to irreducible representations. what would the counterpart for this process be at the level of the nqc? 1. i have discussed cognitive measurements [34, 47] as a cascade of ”small” state function reductions (ssfrs) for the irreducible representations of the galois group of extensions of extensions of.... . the full galois group has a representation as a product of relative galois groups rn = galn/galn−1. the ssfr cascade means a reduction of the representation to a product of representations of the relative galois groups rn. 2. this measurement cascade would be the opposite for the measurement of anyonic topological charges involving an analogous decomposition of the tensor product of representations to irreducible representations of the full braid group. in zeo, the counterpart for the measurement of topological charges would correspond to the time reversal of this process starting with bsfr, which creates a completely entangled state as the representation of the full galois group, and is followed by ssfr cascade proceeding in an opposite time direction. the formation and decomposition of tensor products would occur in different time directions. 2.5 comparison of standard view about tqc with the tgd view it is useful to compare the standard view about tqc with its tgd counterpart. 1. qubits as states are replaced by representations of the braid group characterized by the value of the topological charge and of the quantum group g assignable to the chern-simons action. quantum groups [3, 1, 2] are discussed from the tgd point of view in [21] and in chapters about possible role of von neumann algebras known as hyperfinite factors of type ii1 in tgd [32, 23]. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 172-203 189 pitkänen, m., quantum gravitation & topological quantum computation quantum group su(2)q quantum group characterized by quantum phase q = exp(iπ/k), k = 5, is the simplest option. one can say that anyons correspond to electrons assignable to the orbits of 2-d systems, whose time evolution could be described by chern-simons action. in tgd, these 3-surfaces would correspond to the light-like orbits of partonic 2-surfaces which for larger values of heff can have rather large size. for hgr = gmm/v0 the gravitational compton length for a particle with mass m is gm/v0 = rs/2v0 independent of the mass of the particle and for earth this gives .45 cm for v0 = c, one half of the schwartschild radius. 2. topological qubits correspond to topological charges such as the already mentioned parity for condensed matter majorana electrons, which would have degenerate energies because they correspond to momentum vectors k and −k differing by lattice momentum. 3. quite generally, quantum measurements are hilbert space projections. measurement of qubit corresponds to a measurement of a topological charge. the qubit can be measured by a fusion process for the representations of the gauge group g. fusion means a formation of a tensor product of representations and could result as a final state of tqc. measurement means a projection to a particular representation characterized by a topological charge. one can also consider the opposite operation in which one decomposes a given representation to a direct sum of product representations and projects out one particular product representation by measuring topological charges for the composites. 4. fibonacci tqc with quantum group su(2)q for quantum phase q = exp(iπ/5), serves as the simplest candidate for an interesting tqc. condensed matter majorana fermions could correspond to fibonacci anyons with q = exp(iπ/5) (https://phys.org/news/2014-12-fibonacci-quasiparticle-basis-future-quantum.html). the fusion for fibonacci anyons is non-commutative and non-associative. these properties are coded by a non-commutative r matrix and non-trivial f matrix (see appendix). for a fusion of n representations the number of degenerate ground states is n :th fibonacci number. this has a counterpart in tgd. 1. in the tgd framework, galois group elements in general change the value of cosmic time as a real part of the root of the polynomial defining the mass shell in m8 and its image in h. therefore the associated virtual quark states are not energy degenerate. that mass squared values for anyons are different conforms with the idea of time-like braiding as a genuine quantum state rather than time evolution of quantum state, which is natural in zeo. one can of course challenge this assumption. for states containing n particles with the same polynomial p and represented as an iterate p ◦ .... ◦ p mass squared values as roots approach to julia set for p , and this could give rise to approximate degeneracy of mass squared values and corresponding values of light-cone proper time a. one can also consider a situation in which one has several roots with the same real part (say roots of a second order polynomial). one can ask whether the analogs of condensed matter majorana fermions correspond to these kinds of states. 2. the topological structure in question would be realized in terms of the space-time topology as a monopole flux tube not possible in maxwellian electrodynamics. also the strings assignable to the flux tubes and corresponding string world sheets as representation of time-like braiding inducing space-like braiding would play a key role. chern-simons action would be assigned to the light-like 3-surfaces defining the orbits of partonic 2-surfaces and string world sheets would connect these orbits. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://phys.org/news/2014-12-fibonacci-quasiparticle-basis-future-quantum.html dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 172-203 190 pitkänen, m., quantum gravitation & topological quantum computation 3. the quaternionic automorphism group, defining the analog of the galois group and having su(2) or its quantum variant as a covering group, serves as the analog of the gauge group g and acts in the normal space of the space-time surface. discrete and finite subgroups assignable to the platonic solids and regular polygons define the natural finite discretizations of this group. the braid group could be replaced with a subgroup identifiable as the galois group for an extension of rationals or for extension of extension of rationals. also this group can be non-abelian and would be naturally represented as a subgroup of the braid group. 4. time reversed fusion corresponds to a cognitive measurement cascade consisting of unitary evolutions followed by ssfrs as counterparts of ”weak” measurements. cognitive measurement cascade and its reversal are initiated by a bsfr changing the arrow of time. two subsequent bsfrs would correspond to fusion and its reversal and the time evolution between them would correspond to the braiding as a unitary evolution. in tgd inspired theory of conscious experience, the sequence of ssfrs gives rise to the flow of consciousness. 5. quantum group su(2)q for fibonacci tqc has an interpretation as quantum automorphism. what makes this biologically highly interesting is that the twist exp(iπ/5) is realized geometrically in the structure of the dna. this suggests that dna and dark dna could involve tqc. one can wonder whether genes with n codons correspond to a fusion of n fibonacci representations. 2.6 could the mb of dna perform intentional tqc? in tqc and also in ai as human endeavours, human intention plays a key role. this fact has been often forgotten by ai extremists. the braiding defining the tqc would be constructed using technological tools developed by humans. what about the situation at the level of dna based tqc? could the mb of dna play the role of humans to some degree? what kind of quantum computations could the mb of dna perform? 1. when the braid ends can participate in the flow defined by cellular water or by 2-d liquid defined by the lipids of the cell membrane in liquid crystal phase, one can consider the possibility that the mb induces this flow and in this way builds time-like tqc program, which is also stored as spatial braiding to memory. as will be found in the next section, this situation would be true for braids possibly defined by the gravitational flux tubes connecting the oxygens of phosphates of dna with the lipid ends of nuclear or cell membrane containing also phosphates. also the gtps and gdps of microtubules contain phosphates and their oxygens could be connected with those of lipid phosphates. the braiding would serve a memory storage purpose. if mb can induce the flow of water or of lipids, one can say that it can build tqc programs. for instance, a representation of function involving two registers could be constructed by starting from entangled register and using the flow of water or lipids to induce the needed braiding for the second register implying the entangled state ∑ |n〉〈f(n)| . the tqc ending with cognitive state function reduction cascade would define a conscious cognitive representation of the flow. 2. it will also be found that a-g base pairs by the n...h-n ↔ n-h...n symmetry of gravitational flux tubes define candidates for hbs assignable to tqc. in this case the braid ends cannot move but the reconnections of braid strands could produce braiding and tqc. similar situation is true for the sequence of identical dna codons of, say, genes. they could define an orbit of the galois group and give rise to its representation. there would be 63 types of orbits which could decompose to separate representations corresponding to various codons. besides single electron states also many electron states would be possible. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 172-203 191 pitkänen, m., quantum gravitation & topological quantum computation in this kind of situation, the cognitive measurement cascade would give rise to a conscious cognition at dna level. in zeo, reconnections would be forced by the preferred extremal property and unavoidable by the 4-d character of the space-time surface. therefore they would reflect the underlying physics. the failure of the strict determinism could be interpreted as a selection between a finite number of alternatives at the frames defining the space-time surface as a 4-d analog of soap film. the analog of tqc would give rise to a sensory perception accompanied by cognition. factorization of integers into primes is one of the most interesting applications of qc. at first, it looks unlikely that the mb of dna could be able to do something like this. however, finite groups have a prime decomposition to a product of finite groups and in the same way galois groups have a decomposition to a product of relative galois groups, which do not have a similar decomposition. group theoretical prime decomposition is analogous but more general than the prime decomposition of integers and more general composition of algebraic numbers to algebraic primes. since groups with a prime number of elements are certainly prime groups, prime factorization would follow as a consequence and would be a side product of any cognitive ssfr cascade. this conforms with the paradoxical finding that idiot savants, who do not have any idea about the notion of prime, can factorize large integers [22]. could quantum fourier transform (qft) have any analog at the level of dna? the states in the irreps of the galois group serve as candidates for the plane waves defining fourier components. could cognitive measurements naturally involve a measurement of these quantum numbers as eigen values for maximal set of commuting galois group elements acting as a minimal galois transformation. for instance, a rotation by exp(i2π/n) would be analogous to this kind of transformation in zn. these measurements would induce a localization to a single fourier component and repeated measurements of the same state would give the probabilities of various fourier components. these states are superpositions of states at mass shells with varying mass squared and involve time delocalization making sense by the finite nondeterminism. a repeated measurement of galois momenta would make it possible to find the factors of an integer as in the ordinary qc. 3 dna as quantum gravitational tqcer? in this section a detailed model for dna as a tqcer will be developed. the attribute ”quantum gravitational” is not necessary since also smaller values of heff than hgr can be considered. 3.1 concrete questions concerning dna tqc before representing a concrete model for tqc using galois anyons as qubits, the basic questions are discussed. 3.1.1 how could dna qubits be realized physically? for tqc temperature topological charge identifiable replaces spin as qubit. in the tgd framework galois charges replace topological charges and one can talk about galois anyons. the basic question is how dna makes it possible to realize anyonic qubits. 1. dark nucleons associated with dark dna codons, that is with o...h-o type hbs cannot realize dynamical qubits in terms of spin because the codons must be fixed if they are to represent genetic code. only in the communications based on resonant cyclotron transitions their states can temporarily change but should return back to the original state as a state of minimum (free) energy. one can assign to a-t, g-c pairs 1+1 asymmetric hbs, which do not allow electronic anyons. this gives rise to 3 +3 dark electrons, which could give rise to dark representation of the genetic code. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 172-203 192 pitkänen, m., quantum gravitation & topological quantum computation the tentative interpretation is that the dark codons define the analog of computer hardware with a fixed rom. the dark codons would serve as addresses in the resonance mechanism: the analogy with lisp is obvious. 2. the dynamical working memory should correspond to an anyonic realization of qubits. a dark electron associated with the quantum hb of type x...h-x +x-h...x can give rise to two bi-localized states with odd and even z2 parity where z2 exchanges the ends of hb. these two dark electron states could serve as anyons. this could work for electrons of o...h-o bonds between the oxygens of phosphate and water molecules. this could be also the case for the n...h-n bond of c-g base pair, which is symmetric. the hb can be assigned with c codon. in this case, the notion of z2 anyon makes sense and could make possible tqc using gravitational variants of symmetric hbs of c-g base pairs (hhttps://cutt.ly/wgnddj3). 3.1.2 how could the unitary time evolution be realized? superpositions of hbs of type x...h-x + x-h...x could give rise to electronic anyons with bi-localized dark electrons. depending on the situation, braiding or reconnections having, at least apparently, the same effect would define the unitary gates. 1. if the molecules containing x can move, braiding is possible. this is the case if the hbs are associated with the phosphates of lipids of the cell membrane forming a liquid crystal and connect them to the molecules of the cellular water. in the sol phase for intracellular water, the flow of water molecules could define braiding. the original proposal [18, 31] was that the flux tubes connecting the oxygens of the phosphates associated with the dna strand with the phosphates of the lipid ends would define tqcer. the flow of the lipids of the lipid layer forming a 2-d liquid could define a braiding and thus tqc program. for gravitational flux tubes this option could make sense. the oxygens of the phosphates of dna could be also connected with the molecules of the water surrounding the dna if they can move. in this case, the dance metaphor makes sense: the tqc as time-like braiding produces a log file as a spatial braiding. 2. for n..-h-h + n-h...n hbs of c-g base pairs the nitrogen atoms cannot move. the reconnections of dark braid strands could produce the same effect as braiding and induce flux tube connections between c:s and g:s belonging to distinct c-g pairs. for gravitational flux tubes these connections could be very long. string word sheets are fundamental objects in tgd and by the 4-dimensionality of the space-time surface, 2-d string world sheets at flux tubes representing the orbits of space-like braids intersect at a discrete set of points and for preferred extremals the reconnections are forced by topology. the non-determinism is associated with the choice whether the time-like strand pair ac+ bd transforms to ac+bd or ad+bc. 3.1.3 what about ordinary qc or tqc using electron spin of hb as qubit? i do not understand tqc enough to say whether electron spin could also appear as a qubit when braidings and reconnections define the gates. in any case, this option meets the same objections as the qc option since a very low temperature would be needed in the standard physics framework. 1. the hyperfine splitting (https://cutt.ly/ogndea3), causing the 21-cm line of hydrogen, corresponds to the magnetic interaction energy of nuclear dipole moment with electron’s magnetic field issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. hhttps://cutt.ly/wgnddj3 https://cutt.ly/ogndea3 dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 172-203 193 pitkänen, m., quantum gravitation & topological quantum computation and is proportional to heff . the energy of hydrogen hyperfine splitting is ∆e = 5.89 × 10−6 ev. this corresponds to a temperature of 5.89× 10−2 k. if the electrons are dark, the energy of hyperfine splitting is proportional to heff . the energy is above thermal energy at room temperature for heff/h > 5× 103. note that the temperature t at the mb of dna is assumed to be very low but during aging identified as an approach to thermal equilibrium with the biological body t is assumed to increase and approaches the hagedorn temperature assignable to the flux tubes of mb [62]. 2. if spin serves as a qubit, the manipulation of electronic qubits by changing their spin direction using photons or braiding or reconnection, which at least apparently seems to have the same effect as braiding, would be needed. both braiding and reconnection involve the replacement a → c + b → d with a → d + b → c but reconnection involves temporary touch of the braid strands which might have some effect. 3.2 number theoretical generalization of kitaev’s proposal kitaev [5, 4] has proposed an elegant model for tqc using as qubits the two states of condensed matter majorana fermion [6] with two bi-localized states, which have parities +1 and -1 under z2 symmetry. 3.2.1 galois group as subgroup of braid group and galois anyons in the tgd framework, the representations of the galois group would naturally replace these representations and one could speak of tqc which is also number theoretic as far as anyon-like states are considered. topological robustness would be replaced by number theoretical robustness due to the fact that the extension of rationals depends only weakly on the polynomial: this is obvious from the fact, the number of extensions is finite for a polynomial of given degree. m8 − h duality [42, 43] indeed implies that a given space-time region is determined by a polynomial. in qft approximation one is forced to replace many-sheeted space-time with ordinary space-time and the nice picture is lost. one might however hope that in tqc this loss is fatal. 1. galois group replaces z2. instead of topological charges, one can speak of number theoretical charges. representations of the galois group would correspond to number theoretical qubits. number theoretical anyon would be identified as a superposition of states localized at points of orbit of galois group z2 associated with dna double strand. as already found, the galois ground state corresponding to heff = h = n0h0 is not completely unique but would naturally correspond to a polynomial pg = qg ◦ p2 where p2 is second order polynomial, all roots of p = p1 ◦ pg appear in pairs x ± y and z2 permutes the members of the pairs. fibonacci polynomial pf = x2 − x− 1 is highly attractive candidate for p2 and would give the roots (1 ± √ 5)/2 as roots of all polynomials p . also the twisting geometry of dna favors fibonacci tqc, which is also the minimal option. 2. hydrogen bonds x...h-x and x-h...x are symmetric and their possibly gravitationally dark variants, could give rise to states with opposite parity. the electron of the hydrogen could define the number theoretic anyon. 3. the gravitational flux tubes as counterparts of h-bonds could define the braid strands but alsos smaller values heff ≥ h assignable to electromagnetic flux tubes could work. braiding would take place for these strands. 4. what about the protonic option for x...h-x type hbs based on the identification of anyons as delocalized states of the dark proton with opposite parity? also now one can consider a superposition issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 172-203 194 pitkänen, m., quantum gravitation & topological quantum computation of n-h...n and n...h-n gravitational bonds and two different parity states with respect to z2. the quantum gravitational model for the metabolic energy quanta however suggests that the dark proton is localized mostly in the interior of the gravitational flux tube so that the dark proton should not have a large amplitude at the ends of the flux tube. hydrogen bonded structures of type x...h-x populate living matter. water and dna and the first examples that come into mind. 1. the hydrogen bonds between water molecules are of type o..h-o. hydrogen bonded water molecule clusters could give rise to multiply localized anyonic states of electrons and serve as tqcers. 2. the hbs of the oxygens of phosphate atoms with oxygens of water molecules allow poly-localized electrons if the hb is superposition of o-...h-= and o-h...h. this would allow to associate electronic anyons and tqc also with the dark nucleon triplet codons, which cannot have dynamical spin. 3. g-c base pair has one n..h-n type hbs (hhttps://cutt.ly/wgnddj3). n-h...n ↔ n...h-n are could be possible for h−eff > h hbs, and could lead to the delocalization so that one could assign anyonic state with galois z2 symmetry with it. the g-c base pairs of the dna double strand could define a sequence of topological qubits. note that the splitting of the n-h...n bond in the g-c base pair leading to n + h-n is known to occur during dna transcription and replication and also in the temporary splitting of the hb [60]. 4. benzene allows delocalized states of electron pairs, which could be poly-localized and be analogous to z6 anyons. also z2 and z3 anyons can be considered. the atoms of the aromatic ring could be connected by flux tubes with heff > h and perhaps even heff = hgr. in dna , the sequences of the aromatic 5and 6-rings, possibly defining z5 and z6 anyons, could give rise to a delocalization of the anyonic states along dna strands possibly involving gravitational analogs of valence bonds. 5. in dna strand nucleotides a and g contain aromatic 5and 6rings glued together whereas t and c contain aromatic 6-ring (hhttps://cutt.ly/wgnddj3). the members of base pairs contain fused 5and 6-ring and 6-ring respectively. one can wonder whether the galois representations associated with these structures in the double dna strand structure could make possible tqc. also the side chains of amino acids phe, tyr, and trp contain aromatic rings and hbs between oxygens of water molecules might be relevant for information processing at, say, microtubular level. 3.2.2 the non-symmetric hbs of base pairs and possible new dark realizations of the genetic code the symmetric hbs of c-g base pairs (hhttps://cutt.ly/wgnddj3) would be in a very special role. what about the remaining non-symmetric hbs associated with codons? 1. besides n..h-n hb there are 3+3 electrons per codon with asymmetric hb of form x..h-y, with x,y= o,n or n,o. the proposal that an electronic variant of metabolism is realized, leads to the question of whether the spins of these 6 electrons could realize genetic code as a 6-bit code. now only the analogs of dna codons would be realized. 2. for asymmetric hbs, anyonic dynamics for electrons is not possible but the electronic dark codons could serve as addresses in the resonance mechanism of communication based on the transformation of josephson radiation to pulse sequences by cyclotron resonance [61, 60]. this is possible if the electrons are dark so that the energy of the hyper-fine splitting is scaled so that it is higher than thermal energy. this would require heff ≥ 50. one can also imagine resonance-based communications between dark electron 6-plets and dark nucleon triplets using dark photons. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. hhttps://cutt.ly/wgnddj3 hhttps://cutt.ly/wgnddj3 hhttps://cutt.ly/wgnddj3 dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 172-203 195 pitkänen, m., quantum gravitation & topological quantum computation 3. the dark proton at flux tube and dark electron at the hydrogen end could define an analog of dark h atom. dark h would have 4=3+1 spin states with spins 1 and 0 and these states could define the analogs of nucleotides in 1-1 correspondence with a,t,c,g. c as a special codon would naturally correspond to the spin singlet. hyper-fine splitting for this dark atom would distinguish between triplet and singlet. for large heff the energy this splitting would be above thermal energy so that the spin configurations would be stable. these observations challenge the details of the earlier view [61] about the genetic code. 1. the dark nucleon realization of the genetic code [61] predicts both dnda, drna, dtrna, and daas. one can criticize the realization since also neutrons are required. the model of the code has several variants but the most recent model [60] requires dark variants of both neutron and proton residing at the gravitational flux tube defining gravitational hb connecting the oxygens of phosphate and water. the charge of the delocalized dark proton would not be visible in the scale of dna so that its replacement with dark neutron would not affect the situation in this scale. dark protons would be generated from ordinary protons in pollack effect [9, 8, 11, 10]. they could transform to dark neutrons by the dark variant of strong interactions or of weak interactions at the gravitational flux tubes. dark weak interactions could be realized in even cellular scales and imply that dark variants of weak bosons are massless in the scales below the dark compton length of weak bosons. this would explain chiral selection of biomolecules difficult to understand in the standard model. the conserved vector current hypothesis (cvc) and partially conserved axial current hypothesis (pcac) [30] relate the descriptions of hadrons in terms of strong and weak interactions, which suggests that these views might provide dual descriptions. the duality might in fact reduce to m8 −h duality. the interpretation of anyonic electron as a color octet electro-pion [30] involving color octet meson-like state associated with the gravitational flux tube was already discussed. if hb is associated with oxygen of phosphate (water molecule), the hydrogen of phosphate (water molecule) would look negatively charged. for anyonic states the electron of h would spend half of the time near the two oxygens involved implying that negative charge would be delocalized in a longer scale. 2. could the standard genetic code be associated with the electron triplets at hb associated with base pairs rather than with the phosphate water hbs? one can imagine two realizations. (a) for both dark dna strands, both dark proton triplet and dark electron triplet would have 23 dark entangled states and together they would combine to form 64 states. could they provide a dark realization of the genetic code consistent with the chemical genetic code? (b) could the dark protons at the hbs associated with base-pairs pair with dark electrons at their ends give rise to analogs of dark h atoms? this could give 64 states perhaps allowing an interpretation as a dark realization of genetic code. there are objections against both proposals. the counterparts of rna,trna, and aas are not predicted so that the correspondence with the chemical realization of the genetic code is not plausible. dark codons would have integer spin varying from 0 to 3 and the code table does not show any grouping of codons to these multiplets containing an odd number of states. to sum up, it would seem that several realizations of the genetic code are possible as indeed suggested by the proposed universality of the genetic code [52, 61]. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 172-203 196 pitkänen, m., quantum gravitation & topological quantum computation 3.2.3 could protonic and electronic anyons define a pair of registers? two registers are needed to represent a boolean function x → y = f(x) in terms of entanglement (see appendix). n qubits represent the values of x and y. the simplest representation of f is as a maximally entangled state ∑ |n〉〈f(n)| . in this representation quantum fourier transform (qft) is exponentially faster than the ordinary fast fourier transform. also the quantum counterparts of number theoretic algorithms such as finding prime factors and greatest common divisor are faster than their classical counterparts. how could one realize these registers in the recent case? there should be a natural interaction inducing the entanglement between qubits. the realization of the genetic code fixes the states of dark proton and electron triplets completely for a given codon so that these qubits are non-dynamical. in the case of hbs of type x...h-x, this however leaves the anyonic degrees of freedom assignable to the dark electron as z2 degeneracy and perhaps also with dark protons as a similar degeneracy. the entanglement between electronic and protonic anyons would commute with the spin degrees of freedom. could the two registers correspond to electronic and protonic anyons? could the braidings of the flux tube, possibly induced by reconnections, generate entanglement between these anyons? the objection is that the anyonic dark protons would not be delocalized in long scales as the model for metabolic energy quantum requires. the metabolic dark proton states would correspond to different states concentrated near the top of the gravitational flux tube. 4 appendix: basic concept and ideas of quantum computation i am not a specialist in quantum computation and since some readers might also have the same problem, i have added some remarks about qc, which i believe to be relevant for this article. i have discussed the tgd view about tqc for about 13 years ago [19, 18, 31]. these chapters reflect my views at that time and a lot has happened in the tgd based view of quantum biology after that. perhaps i also have a little bit deeper understanding of tqc now. 4.1 about key ideas of qc in the following the basic ideas qc and tqc are briefly described. 4.1.1 gates as unitary transformations quantum computation can be seen as circuits consisting of gates, which realize unitary transformations assigning to n incoming qubits n = m outgoing qubits: unitary forces m = n. for qubits, which reduce to ordinary bits one obtains as a special case boolean functions from n to n bits. unitarity forces m = n but by using control qubits for which nothing happens in the the gate but the outcome from the remaining qubits depends on the value of the control qubit, one can realize also gates which for bits reduce to boolean maps from n bits to a smaller number of bits so that ordinary logic circuits can be realized as a special case. n-gates with n = 1, 2, 3 are enough for obtaining a universal set of gates. the interested reader can learn details from the slides of viterbi: for instance the slides at https://cutt.ly/egnsmcr describe quantum fourier transform. 1. 1port represents a unitary transformation of a single qubit. (a) phase gate, hadamard gate and rotations by pauli spin matrices are basic gates of this kind. discrete rotation as su(2) transformation represents the general unitary transformation. rotation is specified by two orthogonal rotation axes and by 3 rotation angles. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://cutt.ly/egnsmcr dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 172-203 197 pitkänen, m., quantum gravitation & topological quantum computation (b) discrete subgroups of rotation group assignable to platonic solids and regular polygons define especially interesting selections for the set of possible quantization axes and for the possible directions of spin representable as a point of bloch sphere. for platonic solids the subgroup of su(2) is discrete. these subgroups can produce unitary transformation in a finite accuracy only but one can consider the possibility of transformations obtained as products of elements of these subgroups. (c) quantum variant of su(2) emerges in tqc and also the braid group defines a quantum variant of the permutation group as a finite covering of the braid group. the gates in topological computation correspond to the elements of the braid group. in the tgd framework, su(2) has a representation as the covering of the automorphism group of quaternions (analogous to galois group) acting in the normal space of the space-time surface. 2. arbitrary n ×n -d unitary transformation can be constructed as a product of 2-d unitary transformations. in the n = 2n case, the transformation can be represented at qubit level and using control gates one can represent unitary transformations by using qubit representation with n < 2n. the representation of a general unitary transformation in dimension n requires of order n2n gates. the subset needed as unitary transformations is however believed to be much smaller than all possible transformations. 3. swap, which permutes subsequent incoming qubits and cnot are examples of 2-gates. 4. the notion of controlled gate generalizes to n qubits. toffoli gate as ccnot defines a 3-gate and together with 1and 2-gates it defines a universal set of gates. 4.1.2 bloch sphere and platonic solids block sphere gives a parameterization for the directions of the spin quantization axis and spin has two directions for a given quantization axis. in the twistorialization of tgd at the level of m8 c this interpretation of the twistor sphere is natural [42, 43]. 1. in the number theoretic vision these directions correspond to sines and cosines and in the number theoretic vision these must belong to the extension of rationals considered assignable to a given space-time region. this discretization can be interpreted in terms of finite measurement resolution. 2. the allowed quantization directions are obtained from each other by the transformations of the rotation group su(2). if these rotations form a finite group, only the symmetry groups of platonic solids and regular polygons are possible. for platonic solids there are 4, 6, 8, 12, and 20 quantization axes corresponding to tetrahedron, octahedron, cube, icosahedron and cube. 4.1.3 some applications of qc examples of the applications of qc working faster than their classical counterparts are discussed in the wikipedia article (https://cutt.ly/8hs5qdg). for instance, the following examples are discussed. 1. a very simple application is the finding of the inverse image of function by measurement the of value of function f = f(n) for ∑ |n〉〈f(n)| giving the superposition ∑ |n〉〈f(n) = y|. in a more general case this localization gives the inverse image of a map f of m-d discrete space to n-d discrete space. the repeated application of this algorithm can be used to find the boundary of a region of the inverse image of f . 2. quantum fourier transformation calculates a discrete fourier transformation exponentially faster than ordinary fast fourier transform. other related applications find a prime factor of integer, issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://cutt.ly/8hs5qdg dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 172-203 198 pitkänen, m., quantum gravitation & topological quantum computation period of a periodic function represented as an entangled state ∑ |n〉〈f(n)| of two registers as, and number theoretic logarithm. quantum fourier transform (qft) is discussed (https://cutt.ly/egnsmcr) takes place exponentially faster than the classical fast fourier transform. for n = 2n qubits the number of computation steps is o(n) whereas classically it is o(n2n). the discrete fourier transform has a huge number of both physical and number-theoretical applications. qft can be represented in terms of n qubit registers as an un-entangled product of states of n qubits and this state can be constructed using only gates inducing phase rotations rk = ep(i2π/k) of qubits, hadamard gates producing the superposition of 0 and 1, and control gates. 3. there is an algorithm calculating the phase produced by a unitary transformation: this algorithm involves one additional qubit, whose phase is opposite. 4. there is a search algorithm, which increases the probability of the searched integer before localization in discrete space defined by integers. the number of trials is o( √ n) whereas classically it is o(n). 5. error correction algorithms localizing the logical qubits relevant for the computation to a subspace of logical qubits. these algorithms detect the error by using parity qubits and correct the error by action of a unitary gate in the case that the number of errors is below a given number. 4.1.4 finding a period of a periodic function one assumes that the function f(n) is periodic but the period is not known. the entangled state of the registers is ∑ |n〉〈f(n)|. 1. one assumes that one has measured y = f(x) and has obtained ∑ |n〉〈f(n) = y|. if f is periodic, one obtains a superposition of points n0 + nr, where n0 is the offset and r is the period, which should be measured. 2. a qft is performed for the input register. one obtains a superposition for states with momenta mn/r. 3. the measurement of momentum this state gives momentum state with momentum pm = mn/r for some m, which is however unknown. 4. the operation is repeated. this gives a series of outcomes m1,m2,m3, .... eventually the minimum value of momentum corresponds to m = 1. 4.2 about key ideas and notions of tqc it is appropriate to briefly recall the basic ideas and concepts of tqc [19]. 4.2.1 topological gates and qubits the topological stability of braiding guarantees that the tqc program coded by the braiding is robust against perturbations. if qubits were spins, there would still be the instability of qubits and entanglement caused by the interaction of spins with the environment, in particular thermal instability. 1. qubits as spins are replaced by representations of the braid group characterized by the value of the topological charge and the quantum group gq assignable to the chern-simons action. the quantum group su(2)q is the simplest option. topological charge replaces spin as qubit. one can say that anyons correspond to electrons assignable to 2-d topological structures, whose time evolution as 3-surfaces could be described by chern-simons action. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://cutt.ly/egnsmcr dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 172-203 199 pitkänen, m., quantum gravitation & topological quantum computation the mathematics of quantum groups [3, 1, 2] is discussed from the tgd point of view in [21] and in the chapters about the possible role of von neumann algebras known as hyperfinite factors of type ii1 (hffs) in tgd [32, 23]. quantum groups would be assigned to the inclusions of hffs characterizing the finite measurement resolution. cognitive representations are an alternative way to describe the finite measurement resolution. 2. topological qubits correspond to topological charges such as the already mentioned parity for the condensed matter majorana electrons, which would have degenerate energies because they correspond to momentum vectors k and −k differing by lattice momentum. the idea of kitaev [5, 4] [6] is to use anyons as topological qubits instead of spin. the condensed matter majorana electrons bi-localized at the ends of superconducting wire have two states with opposite parities associated with the exchange of the ends of the wire. these states with degenerate energies would serve as qubits, which would be much more stable than spins. 3. topological approach allows to realize gates in terms of braiding operation. braid group bn as a covering of the permutation group of n braid strands would define the allowed unitary transformations induced by braidings. this implies finite accuracy but the increase of the covering improves the accuracy. this allows to overcome the problem of the hamiltonian approach in which the gate hamiltonian defining the unitary transformation must be ”on” for a very precise time ∆t . it is not easy to arrange this by external interaction. a possible way to avoid this altogether is to assume a permanent hamiltonian but allow the qubit system to move with a fixed velocity past the hamiltonian system with a velocity, which gives the desired ∆t . 4. non-abelianity is required since the manifold of the energy degenerate states in which the braid group would act, is determined by states and must be a higher-dimensional representation of the braid group in order to give rise to a large enough number of logical qubits. there exist no wellestablished candidate for the needed non-abelian anyon yet. 4.2.2 r and f matrices rand f matrices are central notions in tqc (https://arxiv.org/pdf/2005.03236.pdf) and characterize what happens in the fusion of the representations of quantum groups. these matrices are believed to characterize quantum phases as topological orders and were discovered in 2-d fractional quantum hall systems. 1. fusion corresponds to a tensor product, which is commutative and associative for ordinary group representations. for quantum groups and braid groups, the discrete group elements are replaced by flows in plane so that the situation changes. the commutativity of the product ab of the representations is lost and associativity for the product a(bc) of three representations is only modulo unitary transformation: a(bc) is equal to (ab)c only modulo unitary transformation. 2. r matrix characterizes the braid operation, swap, in which the two braid strands are permuted by flow-like continuous transformation. braiding as an element of bn replaces the discrete permutation of adjacent braid strands as an element of sn . the r-matrix characterizes the effect of the braid operation and reduces to a phase in the abelian case but is a genuine matrix in the physically more interesting non-abelian situation. 3. f matrix characterizes the associativity modular unitary transformation for fusion operations. the f matrix is trivial for the ordinary tensor product . this means that the fusions a(bc) and (ab)c produce different states but do not change the state-space. f-matrix f (a, b, c) relates these two states as a unitary transformation in the tensor product of the 3 state spaces. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://arxiv.org/pdf/2005.03236.pdf dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 172-203 200 pitkänen, m., quantum gravitation & topological quantum computation 4. fibonacci quantum computation with quantum group su(2)q for quantum phase q = exp(iπ/5) represents the simplest example of a non-commutative situation (https://phys.org/news/2014-12-fibonacci-quasiparticle-basis-future-quantum.html). for a fusion of n representations the number of energy degenerate ground states is n :th fibonacci 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[27] pitkänen m. some questions related to the twistor lift of tgd. in towards m-matrix: part ii. available at: https:/tgdtheory.fi/pdfpool/twistquestions.pdf, 2019. [28] pitkänen m. tgd and astrophysics. in physics in many-sheeted space-time: part ii. available at: https:/tgdtheory.fi/pdfpool/astro.pdf, 2019. [29] pitkänen m. tgd as a generalized number theory: quaternions, octonions, and their hyper counterparts. in tgd as a generalized number theory: part i. available at: https:/tgdtheory. fi/pdfpool/visionb.pdf, 2019. [30] pitkänen m. the recent status of lepto-hadron hypothesis. in hyper-finite factors and dark matter hierarchy: part ii. available at: https:/tgdtheory.fi/pdfpool/leptc.pdf, 2019. [31] pitkänen m. three new physics realizations of the genetic code and the role of dark matter in bio-systems. in genes and memes: part ii. available at: https:/tgdtheory.fi/pdfpool/ dnatqccodes.pdf, 2019. [32] pitkänen m. was von neumann right after all? in hyper-finite factors and dark matter hierarchy: part i. available at: https:/tgdtheory.fi/pdfpool/vneumann.pdf, 2019. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https:/tgdtheory.fi/pdfpool/nmpc.pdf https:/tgdtheory.fi/pdfpool/wcwnew.pdf https:/tgdtheory.fi/pdfpool/wcwnew.pdf https:/tgdtheory.fi/pdfpool/dnatqc.pdf https:/tgdtheory.fi/pdfpool/tqc.pdf https:/tgdtheory.fi/pdfpool/harmonytheory.pdf https:/tgdtheory.fi/pdfpool/bialgebra.pdf https:/tgdtheory.fi/pdfpool/aitgd.pdf https:/tgdtheory.fi/pdfpool/aitgd.pdf https:/tgdtheory.fi/pdfpool/vneumannnew.pdf https:/tgdtheory.fi/pdfpool/tensornet.pdf https:/tgdtheory.fi/pdfpool/qastro.pdf https:/tgdtheory.fi/pdfpool/hgrprebio.pdf https:/tgdtheory.fi/pdfpool/twistquestions.pdf https:/tgdtheory.fi/pdfpool/astro.pdf https:/tgdtheory.fi/pdfpool/visionb.pdf https:/tgdtheory.fi/pdfpool/visionb.pdf https:/tgdtheory.fi/pdfpool/leptc.pdf https:/tgdtheory.fi/pdfpool/dnatqccodes.pdf https:/tgdtheory.fi/pdfpool/dnatqccodes.pdf https:/tgdtheory.fi/pdfpool/vneumann.pdf dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 172-203 202 pitkänen, m., quantum gravitation & topological quantum computation [33] pitkänen m. zero energy ontology. in towards m-matrix: part i. available at: https:/tgdtheory. fi/pdfpool/zeo.pdf, 2021. [34] pitkänen m. quantum measurement and quantum computation in tgd. available at: https: /tgdtheory.fi/public_html/articles/qmeasuretgd.pdf., 2015. [35] pitkänen m. about physical representations of genetic code in terms of dark nuclear strings. available at: https:/tgdtheory.fi/public_html/articles/genecodemodels.pdf., 2016. [36] pitkänen m. could categories, tensor networks, and yangians provide the tools for handling the complexity of tgd? available at: https:/tgdtheory.fi/public_html/articles/yangianagain. pdf., 2017. [37] pitkänen m. philosophy of adelic physics. in trends and mathematical methods in interdisciplinary mathematical sciences, pages 241–319. springer.available at: https://link.springer. com/chapter/10.1007/978-3-319-55612-3_11, 2017. [38] pitkänen m. philosophy of adelic physics. available at: https:/tgdtheory.fi/public_html/ articles/adelephysics.pdf., 2017. [39] pitkänen m. about the physical interpretation of the velocity parameter in the formula for the gravitational planck constant . available at: https:/tgdtheory.fi/public_html/articles/vzero. pdf., 2018. [40] pitkänen m. quantum self-organization by heff changing phase transitions. available at: https: /tgdtheory.fi/public_html/articles/heffselforg.pdf., 2019. [41] pitkänen m. some comments related to zero energy ontology (zeo). available at: https: /tgdtheory.fi/public_html/articles/zeoquestions.pdf., 2019. [42] pitkänen m. a critical re-examination of m8 −h duality hypothesis: part i. available at: https: /tgdtheory.fi/public_html/articles/m8h1.pdf., 2020. [43] pitkänen m. a critical re-examination of m8 −h duality hypothesis: part ii. available at: https: /tgdtheory.fi/public_html/articles/m8h2.pdf., 2020. [44] pitkänen m. could quantum randomness have something to do with classical chaos? available at: https:/tgdtheory.fi/public_html/articles/chaostgd.pdf., 2020. [45] pitkänen m. how to compose beautiful music of light in bio-harmony? https://tgdtheory.fi/ public_html/articles/bioharmony2020.pdf., 2020. [46] pitkänen m. summary of topological geometrodynamics. https://tgdtheory.fi/public_html/ articles/tgdarticle.pdf., 2020. [47] pitkänen m. the dynamics of ssfrs as quantum measurement cascades in the group algebra of galois group. available at: https:/tgdtheory.fi/public_html/articles/ssfrgalois.pdf., 2020. [48] pitkänen m. zero energy ontology, hierarchy of planck constants, and kähler metric replacing unitary s-matrix: three pillars of new quantum theory (short version). available at: https:/tgdtheory. fi/public_html/articles/kahlersm.pdf., 2020. [49] pitkänen m. about the role of galois groups in tgd framework. https://tgdtheory.fi/public_ html/articles/galoistgd.pdf., 2021. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https:/tgdtheory.fi/pdfpool/zeo.pdf https:/tgdtheory.fi/pdfpool/zeo.pdf https:/tgdtheory.fi/public_html/articles/qmeasuretgd.pdf https:/tgdtheory.fi/public_html/articles/qmeasuretgd.pdf https:/tgdtheory.fi/public_html/articles/genecodemodels.pdf https:/tgdtheory.fi/public_html/articles/yangianagain.pdf https:/tgdtheory.fi/public_html/articles/yangianagain.pdf https://link.springer.com/chapter/10.1007/978-3-319-55612-3_11 https://link.springer.com/chapter/10.1007/978-3-319-55612-3_11 https:/tgdtheory.fi/public_html/articles/adelephysics.pdf https:/tgdtheory.fi/public_html/articles/adelephysics.pdf https:/tgdtheory.fi/public_html/articles/vzero.pdf https:/tgdtheory.fi/public_html/articles/vzero.pdf https:/tgdtheory.fi/public_html/articles/heffselforg.pdf https:/tgdtheory.fi/public_html/articles/heffselforg.pdf https:/tgdtheory.fi/public_html/articles/zeoquestions.pdf https:/tgdtheory.fi/public_html/articles/zeoquestions.pdf https:/tgdtheory.fi/public_html/articles/m8h1.pdf https:/tgdtheory.fi/public_html/articles/m8h1.pdf https:/tgdtheory.fi/public_html/articles/m8h2. pdf https:/tgdtheory.fi/public_html/articles/m8h2. pdf https:/tgdtheory.fi/public_html/articles/chaostgd.pdf https://tgdtheory.fi/public_html/articles/bioharmony2020.pdf https://tgdtheory.fi/public_html/articles/bioharmony2020.pdf https://tgdtheory.fi/public_html/articles/tgdarticle.pdf https://tgdtheory.fi/public_html/articles/tgdarticle.pdf https:/tgdtheory.fi/public_html/articles/ssfrgalois.pdf https:/tgdtheory.fi/public_html/articles/kahlersm.pdf https:/tgdtheory.fi/public_html/articles/kahlersm.pdf https://tgdtheory.fi/public_html/articles/galoistgd.pdf https://tgdtheory.fi/public_html/articles/galoistgd.pdf dna decipher journal | july 2022 | volume 12 | issue 2 | pp. 172-203 203 pitkänen, m., quantum gravitation & topological quantum computation [50] pitkänen m. does the notion of polynomial of infinite order make sense? https://tgdtheory.fi/ public_html/articles/transcendgalois.pdf., 2021. [51] pitkänen m. galois code and genes. https://tgdtheory.fi/public_html/articles/galoiscode. pdf., 2021. [52] pitkänen m. is genetic code part of fundamental physics in tgd framework? available at: https: //tgdtheory.fi/public_html/articles/tih.pdf., 2021. [53] pitkänen m. negentropy maximization principle and second law. available at: https:// tgdtheory.fi/public_html/articles/nmpsecondlaw.pdf., 2021. [54] pitkänen m. questions about coupling constant evolution. https://tgdtheory.fi/public_html/ articles/ccheff.pdf., 2021. [55] pitkänen m. some questions concerning zero energy ontology. https://tgdtheory.fi/public_ html/articles/zeonew.pdf., 2021. [56] pitkänen m. tgd as it is towards the end of 2021. https://tgdtheory.fi/public_html/ articles/tgd2021.pdf., 2021. [57] pitkänen m. what could 2-d minimal surfaces teach about tgd? https://tgdtheory.fi/public_ html/articles/minimal.pdf., 2021. [58] pitkänen m. about tgd counterparts of twistor amplitudes. https://tgdtheory.fi/public_ html/articles/twisttgd1.pdf., 2022. [59] pitkänen m. about tgd counterparts of twistor amplitudes. https://tgdtheory.fi/public_ html/articles/twisttgd2.pdf., 2022. [60] pitkänen m. how animals without brain can behave as if they had brain. https://tgdtheory.fi/ public_html/articles/precns.pdf., 2022. [61] pitkänen m. the realization of genetic code in terms of dark nucleon and dark photon triplets. https://tgdtheory.fi/public_html/articles/darkcode.pdf., 2022. [62] pitkänen m and rastmanesh r. aging from tgd point of view. https://tgdtheory.fi/public_ html/articles/aging.pdf., 2021. issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://tgdtheory.fi/public_html/articles/transcendgalois.pdf https://tgdtheory.fi/public_html/articles/transcendgalois.pdf https://tgdtheory.fi/public_html/articles/galoiscode.pdf https://tgdtheory.fi/public_html/articles/galoiscode.pdf https://tgdtheory.fi/public_html/articles/tih.pdf https://tgdtheory.fi/public_html/articles/tih.pdf https://tgdtheory.fi/public_html/articles/nmpsecondlaw.pdf https://tgdtheory.fi/public_html/articles/nmpsecondlaw.pdf https://tgdtheory.fi/public_html/articles/ccheff.pdf https://tgdtheory.fi/public_html/articles/ccheff.pdf https://tgdtheory.fi/public_html/articles/zeonew.pdf https://tgdtheory.fi/public_html/articles/zeonew.pdf https://tgdtheory.fi/public_html/articles/tgd2021.pdf https://tgdtheory.fi/public_html/articles/tgd2021.pdf https://tgdtheory.fi/public_html/articles/minimal.pdf https://tgdtheory.fi/public_html/articles/minimal.pdf https://tgdtheory.fi/public_html/articles/twisttgd1.pdf https://tgdtheory.fi/public_html/articles/twisttgd1.pdf https://tgdtheory.fi/public_html/articles/twisttgd2. pdf https://tgdtheory.fi/public_html/articles/twisttgd2. pdf https://tgdtheory.fi/public_html/articles/precns.pdf https://tgdtheory.fi/public_html/articles/precns.pdf https://tgdtheory.fi/public_html/articles/darkcode.pdf https://tgdtheory.fi/public_html/articles/aging.pdf https://tgdtheory.fi/public_html/articles/aging.pdf introduction two visions about physics in tgd framework physics as geometry physics as a generalized number theory and m8-h duality zero energy ontology (zeo) and qc finite field approximation and qc tqc and the new view about space-time galois anyons braidings and reconnections as basic elements of tqc different tgd based views of tqc what could the replacement of the braid group with the galois group mean? functional composition of the polynomials and many-particle states ground state polynomial mass squared formula and inheritance hypothesis decomposition of galois group to a product of relative galois groups m8-h duality at the level of m4 the orbits of the galois group in h transform hyperboloids to each other orbits of the galois group as braidings? do galois anyons require tachyonic states? how could dark dna correspond to time-like braids strands for dark dna? string world sheet interpretation of time-like braidings at the level of h connection with time-like character of music experience and cognition cognitive measurement cascades as counterparts of measurements of anyon charges comparison of standard view about tqc with the tgd view could the mb of dna perform intentional tqc? dna as quantum gravitational tqcer? concrete questions concerning dna tqc how could dna qubits be realized physically? how could the unitary time evolution be realized? what about ordinary qc or tqc using electron spin of hb as qubit? number theoretical generalization of kitaev's proposal galois group as subgroup of braid group and galois anyons the non-symmetric hbs of base pairs and possible new dark realizations of the genetic code could protonic and electronic anyons define a pair of registers? appendix: basic concept and ideas of quantum computation about key ideas of qc gates as unitary transformations bloch sphere and platonic solids some applications of qc finding a period of a periodic function about key ideas and notions of tqc topological gates and qubits r and f matrices login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x dna decipher journal | june 2016 | volume 6 | issue 2 | pp. 81-98 81 pitkänen, m., on the representations of genetic code by dark nuclear strings in tgd framework article on the representations of genetic code by dark nuclear strings in tgd framework matti pitkänen 1 abstract the mainstream view of evolution as a random process suggests that genetic code is pure accident. the author is of the view that something so fundamental as life cannot be based on pure randomness. tgd has led to several proposals for genetic code, its emergence and various realizations based on purely mathematical considerations or inspired by physical ideas. one can argue that genetic code is realized in several manners just like bits can be represented in very many manners. two especially interesting proposals have recently emerged. the first proposal is based on geometric model of music harmony involving icosahedral and tetrahedral geometries. the second proposal has two variants based on the concept of dark nuclear strings: the original version maps codons to dark nucleons and the latest version maps codons to dark 3-nucleon states. both models predict correctly the numbers of dna codons coding for a given amino-acid but the latter model is favoured by some recent findings which suggest pairing between dna nucleotides and dark nucleons. further, the counterparts of rna,trna, and amino-acids are predicted. keywords: dna, genetic code, dark, nuclear string, tgd framework. 1 introduction the view about evolution as a random process suggests that genetic code is pure accident. my own view is that something so fundamental as life cannot be based on pure randomness. tgd has led to several proposals for genetic code, its emergence, and various realizations based on purely mathematical considerations or inspired by physical ideas (see chapters of [10] and [14, 13]). one can argue that genetic code is realized in several manners just like bits can be represented in very many manners. two especially interesting proposals have emerged. the first one is based on geometric model of music harmony [19] involving icosahedral and tetrahedral geometries. second one having two variants is based on dark nuclear strings. both models predict correctly the numbers of dna codons coding for a given amino-acid. in the sequel the nuclear string variant and also its connection with the model of harmony is discussed in detail. it is good to start with an overall view about physical realization of genetic code that i have discussed during last twenty years. 1.1 genetic code and combinatorial hierarchy the first proposal [11] was purely mathematics inspired and in terms of so called combinatorial hierarchy consisting of certain mersenne primes mk = 2k − 1 via the formula m(n + 1) = mm(n) having interpretation in terms of abstraction. the list beginning from m(1) = 2 is 2,m2 = 3,m3 = 7,m7 = 127,m127 = 2127− 1: it is not known whether subsequent integers are mersenne primes. the idea is that the 2k − 1 points define almost full boolean algebra spanned by k bitsone visualization is as a polygon. the algebra defined k − 1 bits is maximal full boolean sub-algebra having interpretation as maximal number of mutually independent statements, which can hold true simultaneously. for m7 (k = 3) one 1correspondence: matti pitkänen http://tgdtheory.com/. address: karkinkatu 3 i 3, 10360, karkkila, finland. email: matpitka6@gmail.com. isbn: issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.com/ mailto:matpitka6@gmail.com dna decipher journal | june 2016 | volume 6 | issue 2 | pp. 81-98 82 pitkänen, m., on the representations of genetic code by dark nuclear strings in tgd framework would have 2 bits and 4 codons. for m7 one would have k = 7 and 6 bits and genetic code. for m127 one would have 126 bits and one would have ”memetic” code realizable in terms of sequences of 21 dna codons. 1.2 geometric theory of harmony and genetic code the idea that the 12-note scale could allow mapping to a closed path going through all vertices of icosahedron having 12 vertices and not intersecting itself is attractive. also the idea that the triangles defining the faces of the icosahedron could have interpretation as 3-chords defining the notion of harmony for a given chord deserves study. the paths in question are known as hamiltonian cycles and there are 1024 of them [1]. there paths can be classified topologically by the numbers of triangles containing 0, 1, or 2 edges belonging to the cycle representing the scale. each topology corresponds to particular notion of harmony and there are several topological equivalence classes. in the article [20] i introduced the notion of hamiltonian cycle as a mathematical model for musical harmony and also proposed a connection with biology: motivations came from two observations. the number of icosahedral vertices is 12 and corresponds to the number of notes in 12-note system and the number of triangular faces of icosahedron is 20, the number of amino-acids. this led to a group theoretical model of genetic code and replacement of icosahedron with tetra-icosahedron to explain also the 21st and 22nd amino-acid and solve the problem of simplest model due to the fact that the required hamilton’s cycle does not exist. the outcome was the notion of bioharmony. all icosahedral hamilton cycles with symmetries(z6,z4, zrot 2 and z2refl turned out to define harmonies consistent with the genetic code. in particular, it turned out that the symmetries of the hamiltonian cycles allow to to predict the basic numbers of the genetic code and its extension to include also 21st and 22nd amino-acids pyl and sec: there are actually two alternative codes maybe dna and its conjugate are talking different dialects! one also ends up with a proposal for what harmony is leading to non-trivial predictions both at dna and amino-acid level. the conjecture is that dna codons correspond to 3-chords perhaps realized in terms of dark photons or even ordinary sound. there are 256 different bio-harmonies and these harmonies would give additional degrees of freedom not reducing to biochemistry. music expresses and creates emotions and a natural conjecture is that these bio-harmonies are correlates of emotions/moods at bio-molecular level serving as building bricks of more complex moods. representations of codons as chords with frequencies realized as those of dark photons and also sound is what suggests itself naturally. this together with adelic physics involving hierarchy of algebraic extensions of rationals would explain the mysterious lookin connection between rational numbers defined by ratios of frequencies with emotions. 1.3 letter-wise representations of genetic code in terms of single particle states the model for dna-cell membrane system as topological quantum computer with lipids and dna nucleotide or codons connected by flux tubes led to a proposal for the correspondence of letters of genetic code with particle states. 1. the original proposal was that the 4 letters a,t,c,g correspond to dark u and d quark and their antiparticles u and d . quarks and their antiparticles would reside at the ends of the flux tube. spin would not matter in this model. the obvious criticism is that introducing dark antiquarks is too far fetched. 2. one can also consider a variant for which one has u and d quarks and spin matters. 3. tgd based model of bio-superconductivity assumes that flux tubes appear as pairs with members of cooper pair at parallell flux tubes [15, 16]. this suggests that electron pairs at in spin 1 and isbn: issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | june 2016 | volume 6 | issue 2 | pp. 81-98 83 pitkänen, m., on the representations of genetic code by dark nuclear strings in tgd framework spin 0 states could realize the code. the spin of the electrons would matter and one would obtain 4 states two qubits in correspondence with a,t,c,g. also the model of dark nuclear strings allows to imagine letter-wise representations of the genetic code. the model for cold fusion based on the findings of prof. holmlid and his group [2, 4] leads to the idea that pollack’s ezs [21] are accompanied by dark nuclear strings consisting of dark protons connected by color flux tubes analogous to mesons [22, 25]. color bonds would have quark and antiquark at their ends [14]. this leads to non-trivial predictions and nuclear anomalies giving support for the notion of nuclear string have emerged, the latest anomaly is so called x boson with mass of 17 mev [5, 3] having identification as p-adically scaled analog of pion. dark protons could also decay to neutrons by dark weak decays rapidly since dark weak bosons are effectively massless below dark compton length. furthermore, proton plus negatively charged color bond could behave like neutron as far as chemistry is considered. the x boson anomaly of nuclear physics [5] suggests that the flux tubes in the ground state correspond to pion-like states which can be colored: this could bind the nucleons to form a nucleus. the evidence for the occurence of cold fusion in living matter gives support for the role of dark nuclear strings [18] [25]. one can consider several representations of the genetic code in this framework. consider first models for which letters are represented separately. 1. dark protons and neutrons have 4 spin states and could correspond to letter a,t,c,g. in this case dark color bonds would not matter. a rather convincing proposal for a pathway leading to a selection purines as dna nucleotides has been proposed [6]. tgd based model [23] suggests that acidic solutions contain dark protons and purine results when the precursor amine combines with dark proton such that the proton remains dark. could dna nucleotide pair with dark protons and neutrons (resulting in dark beta decay from dark proton strings yielded by pollack’s mechanism)? 2. also the 4 states of dark color bonds between dark nucleons (3 pion-like states and one eta meson like state: spin 1 bonds would be analogous to ρ and ω mesons and have higher mass) correspond to letters a,t,c,g. now the dark protons and neutrons would not matter. this option would require that the character of the nucleotide correlates with the color flux tube attached to the dark proton. they would have at their ends charge conjugate color bonds. the states would be of form uu, dd, ud, du with the ordering of q and q correlating with the direction in which transcription and replication take place being thus same or opposite). for conjugate strand the direction of strand would be opposite in the sense that one would have uu, du, du, uu. for this option one could consider the strands of dark dna double strand being connected by flux tube pairs resulting when u-shaped color flux tube have reconnected. if color flux tubes are colored, color confinement could bind the dark protons to dark nucleus. similar mechanism could be at work for the ordinary nuclei. the basic problem of all the proposals based on letter-wise correspondence is that they do not even try to explain the numbers of dna codons coding for a given amino-acid and are also silent about trna. 1.4 codon-wise representations of genetic code realized in terms of dark nuclear strings for this option entire codons rather than letters would be represented. the difference between two representations is analogous to that between spoken and written languages. in spoken languages words are not analyzed further to letters. these models are able to predict also the numbers of codons coding for a given amino-acid successfully. 1. the geometric theory of harmony represents codons as 3-chords without assigning fixed notes to a,t,c,g and explains also dna-amino-acid correspondence. isbn: issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | june 2016 | volume 6 | issue 2 | pp. 81-98 84 pitkänen, m., on the representations of genetic code by dark nuclear strings in tgd framework 2. the map of codons to the dark nucleon states of dark nucleon consisting of dark u and d type quarks does the same and also predicts the degeneracies successfully. 3. this model can be modified by replacing u and d by dark nucleon states p and n without any change in predictions related to genetic code. the evidence that dna codons indeed couple to dark nucleon states [23] supports this option. in the sequel i consider the models mapping dna codons to dark nucleons and then generalize the model so that it applies to triplets of dark nucleons. 2 models of genetic code based on dark nuclear strings water memory is one of the ugly words in the vocabulary of the main stream scientist. the work of pioneers is however now carrying fruit. the group led by jean-luc montagnier, who received nobel prize for discovering hiv virus, has found strong evidence for water memory and detailed information about the mechanism involved [13, 17], [7]. the work leading to the discovery was motivated by the following mysterious finding. when the water solution containing human cells infected by bacteria was filtered in purpose of sterilizing it, it indeed satisfied the criteria for the absence of infected cells immediately after the procedure. when one however adds human cells to the filtrate, infected cells appear within few weeks. if this is really the case and if the filter does what it is believed to do, this raises the question whether there might be a representation of genetic code based on nano-structures able to leak through the filter with pores size below 200 nm. the question is whether dark nuclear strings might provide a representation of the genetic code. in fact, i posed this question year before the results of the experiment came with motivation coming from the attempts to understand water memory. the outcome was a totally unexpected finding: the states of dark nucleons formed from three quarks can be grouped to multiplets in one-one correspondence with 64 dnas, 64 rnas, and 20 amino-acids and there is natural mapping of dna and rna type states to amino-acid type states such that the numbers of dnas/rnas mapped to given amino-acid are same as for the vertebrate genetic code. 2.1 mapping dna and amino-acids to dark nucleon states the dark model emerged from the attempts to understand water memory [13]. the outcome was a totally unexpected finding [14, 13]: the states of dark nucleons formed from three quarks connected by color bonds can be naturally grouped to multiplets in one-one correspondence with 64 dnas, 64 rnas, 20 amino-acids, and trna and there is natural mapping of dna and rna type states to amino-acid type states such that the numbers of dnas/rnas mapped to given amino-acid are same as for the vertebrate genetic code. the basic idea is simple. the basic difference from the model of free nucleon is that the nucleons in question maybe also nuclear nucleons consist of 3 linearly ordered quarks just as dna codons consist of three nucleotides. one might therefore ask whether codons could correspond to dark nucleons obtained as open strings with 3 quarks connected by two color flux tubes or as closed triangles connected by 3 color flux tubes. only the first option works without additional assumptions. the codons in turn would be connected by color flux tubes having quantum numbers of pion or η. this representation of the genetic would be based on entanglement rather than letter sequences. could dark nucleons constructed as string of 3 quarks using color flux tubes realize 64 dna codons? could 20 amino-acids be identified as equivalence classes of some equivalence relation between 64 fundamental codons in a natural manner? the codons would be not be anymore separable to letters but entangled states of 3 quarks. if this picture is correct, genetic code would be realized already at the level of dark nuclear physics and maybe even in ordinary nuclear physics if the nucleons of ordinary nuclear physics are linear nucleons. isbn: issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | june 2016 | volume 6 | issue 2 | pp. 81-98 85 pitkänen, m., on the representations of genetic code by dark nuclear strings in tgd framework chemical realization of genetic code would be induced from the fundamental realization in terms of dark nucleon sequences and vertebrate code would be the most perfect one. chemistry would be kind of shadow of the dynamics of positively charged dark nucleon strings accompanying the dna strands and this could explain the stability of dna double strand having 2 units of negative charge per nucleotide. biochemistry might be controlled by the dark matter at flux tubes. the ability of the model to explain genetic code in terms of spin pairing is an impressive achievement, which i still find difficult to take seriously. 1. the original model mapping codons to dark nucleon states assumed the overall charge neutrality of the dark proton strings: the idea was that the charges of color bonds cancel the total charge of dark nucleon so that all states uuu, uud, udd, ddd can be considered. the charge itself would not affect the representation of codons. neutrality assumption is however not necessary. the interpretation as dark nucleus resulting from dark proton string could quite well lead to the formation the analog of ordinary nucleus via dark beta decays [25] so that the dark nucleus could have charge. isospin symmetry breaking is assumed so that neither quarks nor flux tubes are assigned to representations of strong su(2). there is a possible objection. for ordinary baryon the mass of ∆ is much larger than that of proton. the mass splitting could be however much smaller for linear baryons if the mass scale of excitations scales as 1/heff as indeed assumed in the model of dark nuclear strings [22, 25]. 2. the model assumes that the states of dna can be described as tensor products of the four 3-quark states with spin content 2⊗ 2⊗ 2 = 4⊕ 21⊕ 22 with the states formed with the 3 spin triplet states 3⊗ 3 = 5⊕ 3⊕ 1 with singlet state dropped. the means that flux tubes are spin 1 objects and only spin 2 and spin 1 objects are accepted in the tensor product. one could consider interpretation in terms of ρ meson type bonding or gluon type bonding. with these assumptions the tensor product (2⊗ 2⊗ 2)⊗ (5⊕ 3) contains 8× 8 = 64 states identified as analags of dna codons. the rejection of spin 0 pionic bonds looks strange. these would however occur as bonds connecting dark codons and could correspond to different p-adic length scale as suggested by the successful model of x boson [26]. one can also ask why not identify dark nucleon as as closed triangle so that there would be 3 color bonds. in this case 3 ⊗ 3 ⊗ 3 would give 27 states instead of 8 (⊕1). this option does not look promising. 3. the model assumes that amino-acids correspond to the states 4 × 5 with 4 ∈ {4 ⊕ 2 ⊕ 2} and 5 ∈ {5 ⊕ 3}. one could tensor product of spin 3/2 quark states and spin 2 flux tube states giving 20 states, the number of amino-acids! 4. genetic code would be defined by projecting dna codons with the same total quark and color bond spin projections to the amino-acid with the same (or opposite) spin projections. the attractive force between parallel vortices rotating in opposite directions serves as a metaphor for the idea. this hypothesis allow immediately the calculation of the degeneracies of various spin states. the code projects the states in (4 ⊕ 2 ⊕ 2) ⊗ (5 ⊕ 3) to the states of 4 × 5 with same or opposite spin projection. this would give the degeneracies d(k) as products of numbers db ∈ {1, 2, 3, 2} and db ∈ {1, 2, 2, 2, 1}: d = db × db. only the observed degeneracies d = 1, 2, 3, 4, 6 are predicted. the numbers n(k) of amino-acids coded by d codons would be [n(1), n(2), n(3), n(4), n(6)] = [2, 7, 2, 6, 3] . the correct numbers for vertebrate nuclear code are (n(1), n(2), n(3), n(4), n(6)) = (2, 9, 1, 5, 3). some kind of symmetry breaking must take place and should relate to the emergence of stopping codons. if one codon in second 3-plet becomes stopping codon, the 3-plet becomes doublet. if 2 isbn: issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | june 2016 | volume 6 | issue 2 | pp. 81-98 86 pitkänen, m., on the representations of genetic code by dark nuclear strings in tgd framework codons in 4-plet become stopping codons it also becomes doublet and one obtains the correct result (2, 9, 1, 5, 3)! it is difficult to exaggerate the importance of this simple observation suggesting that genetic code is realized already at the level of dark or even ordinary nuclear physics and bio-chemistry is only a kind of shadow of dark matter physics. 2.2 objections based on group theory and statistics the model and its generalization replacing u, d with nucleon states p, n works amazingly nicely but is better to try to invent objections against the proposal and try to find inconsistencies. fermi and bose statisticsare the most obvious providers of killer arguments. 1. the basic objection is that if the quarks are organized in linear structures, one cannot talk about representation of 3-d rotation group since symmetry breaking to so(2) acting along common axis which could be either the local axis along dark dna helix of the axis of the entire helix. the linear ordering of the quarks is not consistent with the full harmonics. rather, harmonics restricted to half space 0 ≤ θ ≤ π/2 (π ≥ θ ≥ π/2) should characterize the ”upper” (”lower”) flux tube direction at the position of quark in the middle. if reflection along quantization axis and so(2) generate the symmetries one still has labelling of the states by angular momentum projection and states form doublets (m,−m). the representations of so(3) split into these representation and the numbers of states with given spin projection remain the same. therefore the predictions for the numbers of dna codons coding given aminoacid are not changed. it is quite possible that braid statistics made possible by 1-dimensionality is needed to realize the idea about ordering and this would allow to have full dna multiplets. 2. in quark model one forms tensor product of tensor products of 3 quark spin states and 3 quark isospin states and by color singletness requires that the state is completely antisymmetric in quark degrees of freedom. the state is completely symmetric in the non-colored degrees of freedom. one obtains only two representations ∆↔ (3/2, 3/2) and n = (1/2, 1/2) with positive parity. in quark model context the presence of other tensor products in (4⊕ 21 ⊕ 22)s ⊗ (4⊕ 21 ⊕ 22)i is forbidden. one reason is that spatial wave function is assumed to be symmetric in ground state. this forbids 22 in spin degrees of freedom. symmetrization leaves only the ∆ and n (note that the total number of these state is 20!). now strong isospin is broken and it is natural to not include it to the tensor product. 3. the presence of 22 would be forbidden in quark model since it would require antisymmetric spatial wave function to compensate for the antisymmetry of 22. in the recent case the situation is 1dimensional and the ordering along nuclear string forces localization of quarks and one cannot have identical wave functions for quarks. 1-d situation also suggests strongly braid statistics. perhaps the situation could be understood in terms of fermionic oscillator operators along nuclear string having anti-commutation relations corresponding to non-trivial braid statistics maybe making the statistics commutative. this could naturally allow anti-symmetrization along nuclear string for 22 states. 4. if one assumes ordinary statistics, one could one take care of the statistics of the 16 states in 22 ⊗ (5 ⊕ 3) by assuming that for 22 the color state is symmetric and thus 10-d representation of su(3). the state associated with color flux tubes cannot compensate this color (triality is 1) since it must correspond to triality zero representation. if the colors of dna strand and conjugate correspond to 10 and 10 and color entanglement cold guarantee color singletness for the codon pairs. this would however require anti-quarks for the conjugate strand. isbn: issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | june 2016 | volume 6 | issue 2 | pp. 81-98 87 pitkänen, m., on the representations of genetic code by dark nuclear strings in tgd framework 3 10:s associated with 3 codons contains in their tensor product a singlet (see http://tinyurl. com/zjxxqhj). minimal color singlet dark dna sequence would requite 3 color codons. one can of course wonder whether the presence of 3 decouplet codons 2 at the beginning and 2 at end and one in the middle could define genes as basic units. 5. the statistics problem is encountered also for the flux tubes. 5 (and 1) as symmetric representation is allowed by statistics but triplet is antisymmetric and thus not allowed. again braid statistics might help. if one assumes that the flux tubes are colored say color octets and color wave function for flux tube pairs is antisymmetric, one can achieve bose statistics for 3. flux tube pair would correspond to 8 ∈ {8 × 8} and minimum of two flux codons would be needed for color singletness in flux tube degrees of freedom. 6. for the counterparts of amino-acids one has only 4 ⊗ 5 allowed also by statistics considerations assuming color singlets. could distinction between dna/rna and amino-acids related to statistics, perhaps braid statistics. the suggested role of braid strands possibly connecting dna double strands and dna double strands and lipid layers of cell membrane encourages the question whether the dna strand and its conjugate entangle via via the reconnection of the color flux tubes defining u-shaped ”tentacles” to a flux tube pair connecting the strands. for amino-acids they would not be needed. same could happen in the transcription process of dna to mrna and in the translation process for mrna tentacles and those associated with trna. 2.3 also the mapping of dna and amino-acids to dark 3-nucleon states is possible the assumption that entire codon rather than letter corresponds to a state of dark proton does not conform with the model for the origin of purines as dna nucleotides [23] assuming that purines and in fact all nucleotides are combined with dark proton unless one assumes that 3 nucleotides combine with the same dark proton. this looks somewhat artificial but cannot be excluded. amazingly, the arguments of the model involve only the representations of rotation group and since p and n have same spin as u and d, the arguments generalize to 3nucleon states (ppp, ppn, pnn, nnn) connected by two color bounds and organized to linear structures. concerning genetic code, exactly the same predictions follow in the recent formulation of the model. in this case quark color is not present. one could however use the 1-dimensionality and the ordering of dark nucleons as already described. this variant has several nice features. the model is consistent with the model for dark nucleon strings consisting of nucleons and color bonds between them. there is no need to introduce ∆ type nucleon states and colored states are not needed in fermionic sector. color bonds must be colored if one wants ordinary bosonic statistics for flux tubes but here braid statistics might help. colored bonds could of course have some important function. 2.4 ordinary or braid statistics? there are four options to consider: ordinary/braid statistics (1/2) and dark nucleon/dark nucleon triplet as representation of dna codon (a/b). one has options 1a,1b,2a,2b. 1. option 1a. for the ordinary statistics amino-acid like dark nucleons are color singlets. part of dna codons represented as dark nucleons and would be colored and 10-d representation of su(3). dark amino-acids need not have color bonds with dark parts of other colored biomolecules like dna,rna, with exception possible formed by dark trna. dna double strand could realize color confinement via the reconnection of color flux tubes. 2. option 1b. option 1b requires in ordinary statitics for antisymmetric doublet an antisymmetric wave function for the 3 nucleons not allowing constant valued wave function also disfavored by the linear ordering. this condition might have the same implications as braid statistics. isbn: issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/zjxxqhj http://tinyurl.com/zjxxqhj dna decipher journal | june 2016 | volume 6 | issue 2 | pp. 81-98 88 pitkänen, m., on the representations of genetic code by dark nuclear strings in tgd framework 3. options 1a and 1b. dna is the only molecule that appears as double strands. a possible explanation is that codons and anticodons are paired by u-shaped flux tubes associated with the color bonds of dark dna to form color singlets. nucleonic colors would sum up to zero along the strand. 4. option 2a. for braid statistics it could be possible to avoid colored states of nucleon and flux tubes altogether. 5. option 2b. the codons would have no color and amino-acids could obey braid statistics reducing to ordinary statistics. this would not be the case for dna/rna. 2.5 objections against the identification of codons as dark nucleon states consider next some particle physicist’s objections against the option mapping codons to dark nucleon states. 1. the realization of the model requires the dark scaled variants of spin 3/2 baryons known as ∆ resonance and the analogs (and only the analogs) of spin 1 mesons known as ρ mesons. the lifetime of these states is very short in ordinary hadron physics. now one has a scaled up variant of hadron physics: possibly in both dark and p-adic senses with latter allowing arbitrarily small overall mass scales. hence the lifetimes of states could be scaled up. 2. both the absolute and relative mass differences between ∆ and n resp. ρ and π are large in ordinary hadron physics and this makes the decays of ∆ and ρ possible kinematically. this is due to color magnetic spin-spin splitting proportional to the color coupling strength αs ∼ .1, which is large. in the recent case αs could be considerably smaller say of the same order of magnitude as fine structure constant 1/137 so that the mass splittings could be so small as to make decays impossible. the color magnetic spin interaction energy give rise to hyperfine splitting of quark in perturbative qcd is of form ec ∝ ~gb/m, where m is mass parameter which is of the order of baryon mass. magnetic flux scales as ~ by flux quantization and if flux tube thickness scales as ~2, one has b ∝ 1/~. mass splittings would not depend on ~, which does not make sense. mass splitting becomes small for large ~ if the area of flux quantum scales as ~2+n, n > 0 so that color magnetic hyper-fine splitting scales as 1/~n from flux conservation. the magnetic energy for a flux tube of length l scaling as ~ and thickness s ∝ ~2+n has order of magnitude g2b2ls and does not depend on ~ for n = 1. maybe this could provide first principle explanation for the desired scaling. the size scale of dna would suggest that single dna triplet corresponds to 3 angstrom length scale. suppose this corresponds to the size of dark nucleon. if this size scales as √ ~ as p-adic mass calculations suggest, one obtains a rough estimate ~/hbar0 = 238. the proton-∆ mass difference due to hyper-fine splitting would be scaled down to about 2−38 × 300 mev ∼ 10−9 ev, which is completely negligible in the metabolic energy scale .5 ev. if the size of dark nucleon scales as ~ the mass difference is about 12 ev which corresponds to the energy scale for the ionization energy of hydrogen. even this might be acceptable. for these reasons the option mapping codons to dark nucleon triplets is clearly favored and will be discussed in the following. 3 more detailed view abot the model mapping codons to dark 3-nucleon states the model based on dark 3-nucleon states is discussed seems more realistic and will be discussed in more detail in the sequel. isbn: issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | june 2016 | volume 6 | issue 2 | pp. 81-98 89 pitkänen, m., on the representations of genetic code by dark nuclear strings in tgd framework 3.1 could dark dna, rna, trna and amino-acids correspond to different charge states of codons? if dark codons correspond to dark nucleon triplets as assumed in the following considerations there are 4 basic types of dark nucleon triplets: ppp, ppn, pnn, nnn. also dark nucleons could represent codons as uuu, uud, udd, ddd: the following discussion generalizes as such also to this case. if strong isospin/em charge decouples from spin the spin content is same independently of the nucleon content. one can consider the possibility of charge neuralization by the charges assignable to color flux tubes but this is not necessarily. in any case, one would have 4 types of nucleon triplets depending on the values of total charges. could different dark nucleon total charges correspond to dna,rna, trna and amino-acids? already the group representation content perhaps correlating with quark charges could allow to distinguish between dna, rna, trna, and amino-acids. for amino-acids one would have only 4× 5 and ordinary statistics and color singlets. for dna and rna one would have full multiplet also color non-singlets and for trna one could consider (4 ⊕ 21 ⊕ 22) × 5 containing 40 states. 31 is the minimum number of trnas for the realization of the genetic code. the number of trna molecules is known to be between 30-40 in bacterial cells. the number is larger in animal cells but this could be due to different chemical representations of dark trna codons. if the net charge of dark codon distinguishes between dna,rna, trna, and amino-acid sequences, the natural hypothesis to be tested is that dark ppp, ppn, pnn, and nnn sequences are accompanied by dna,rna, trna, and amino-acid sequences. the dark beta decays of dark protons proposed to play essential role in the model of cold fusion [22, 25] could transform dark protons to dark neurons. peptide backbones are neutral so that dark nnn sequence could be also absent but the dark nnn option is more natural if the general vision is accepted. there is also the chemically equivalent possibility that only dark protons are involved: dark proton + neutral color bond would represent proton and dark proton + negatively charged color bond would represent neutron. at this moment it is not possible to distinguish between these two options. is this picture consistent with what is known about charges of amino-acids dna,rna, trna, and amino-acids? consider first the charges of these molecules. 1. dna strand has one negative charge per nucleotide. also rna molecule has high negative charge. this conforms with the idea that dark nucleons accompany both dna and rna. dna codons could be accompanied by dark ppp implying charge neutralization in some scale and rna codons by dark ppn. the density of negative charge for rna would be 2/3 for that for dna. 2. arg, his, and lys have positively charged side chains and asp,glu negative side chains (see https: //en.wikipedia.org/wiki/amino_acid). the charge state of amino-acid is sensitive to the ph value of solution and its conformation is sensitive to the counter ions present. total charge for amino-acid in peptide however vanishes unless it is associated with the side chain: as in the case of dna and rna it is the backbone whose charge is expected to matter. 3. amino-acid has central c atom to which side chain, nh2, h and cooh are attached. for free amino-acids in solution water solution nh2→ nh+ 3 tends to occur ph=2.2 by receiving possibly dark proton whereas cooh tends to become negatively charged above ph= 9.4 by donating proton, which could become dark. in peptide oh attach to c and one h attached to n are replaced with peptide bond. in the ph range 2.2-9.4 amino-acid is zwitterion for which both cooh is negatively charged and nh2 is replaced with nh+ 3 so that the net charge vanishes. the simplest interpretation is that the ordinary proton from negatively ionized cooh attaches to nh2 maybe via intermediate dark proton state. 4. the backbones of peptide chains are neutral. this conforms with the idea that dark amino-acid sequence consists of dark neutron triplets. also free amino-acids would be accompanied by dark isbn: issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://en.wikipedia.org/wiki/amino_acid https://en.wikipedia.org/wiki/amino_acid dna decipher journal | june 2016 | volume 6 | issue 2 | pp. 81-98 90 pitkänen, m., on the representations of genetic code by dark nuclear strings in tgd framework neutron triplets. if the statistics is ordinary only 4 dark nnn states are possible as also 5 dark color flux tube states. 5. trna could involve dark pnn triplet associated with the codon. an attractive idea is secondary genetic code assigning rna codons to trna-amino-acid complex and projecting 8 ⊗ (5 ⊕ 3) containing 64 dark rna spin states to 8 ⊗ 5 containing 40 dark trna spin states with same total nucleon and flux tube spins. dark trna codons would in turn be attached to dark amino-acids by a tertiary genetic code projecting spin states 8⊗ 5 to 4⊗ 5 by spin projection. in the transcription dark trna would attach to dark mrna inducing attachment of dark amino-acid to the growing amino-acid sequence and trna having only dark trna codon would be left. the free amino-acids in the water solution would be mostly charged zwitterions in the ph range 2.2-9.4 and the negative charge of coo− would be help in the attachement of the free amino-acid to the dark proton of trna codon. therefore also the chemistry of free amino-acids would be important. an interesting question is why pnn triplets for trna would only 5 in flux tube degrees of freedom entire 8 in nucleon degrees of freedom. for rna consisting of ppn triplets also 3 would be possible. what distinguishes between ppn and pnn? the model should explain the widely different properties of dna,rna , trna, and amino-acids. there are two options. 1. dna/rna/amino-acid codons could correspond to ppp/ppn/nnn and trna would correspond to pnn (order is not necessarily this). different charge or dark codons explain why dna (rna) has h (oh) in 2′ position. the repulsive coulomb energy between dark codons would be stronger for dna and the compensation of this forces by the magnetic tension associated with the flux tube pair connecting codon and anticodon this might have something to do with the stability of dna double strand. (a) the instability of rna as compared to dna would result from the instability of the ribose in rna (deoxiribose in dna) as indeed believed. the absence of rna double strands could be due to the instability of the flux tube pair assignable to n-n. this trivially implies absence of replication and transcription if it is based on same mechanism as in the case of dna. (b) pnn structure could explain why trna does not form sequences and allow to understand wobble pairing, which states that the third mrna codon does not correspond to unique trna anticodon but one has c,a,u → i and u→ i. due to the symmetries of the third letter of the codon, this is consistent with the genetic code. the physical explanation for wobble base pairing could relate to pnn structure of trna. if the charge ordering is random one would have nnp,npn,pnn and c,a,u→ i could correspond to these 3 situations whereas for u→ i the correspondence would not depend on the ordering. also for rna one would have ppn,pnp, npp degeneracy but in this case one would have charge independence. a possible charge pairing between rna and trna would be p↔n. the charge pairing between dna and rna could be p→ n for the third least significant letter of dna. this would minimize the coding errors possibly induced this pairing. (c) one can criticize the charge assignment ppn (possibly allowing permutations) for rna codons. could dark weak beta decays give rise to 1-d lattice like structure? could the repetitive structure be due to energy minimization. 2. could the correspondence be letterwise? for dna a,t,c,g would correspond to p, and for rna a,c,g to p and u to n. codons not containing u wold be ppp type codons and one can wonder why the oxiribose for them is not replaced with de-oxiribose. the possible presence of n in dark codons could explain why rna sequences are highly unstable and why they do not replicate and transcribe. an interesting question is how the rna world vision relates to this general picture. isbn: issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. dna decipher journal | june 2016 | volume 6 | issue 2 | pp. 81-98 91 pitkänen, m., on the representations of genetic code by dark nuclear strings in tgd framework 3.2 replication, transcription, translation the formation of flux tube pairs between molecules would be central in replication and transcription and in all bio-catalysis. dark dna would replicate first to dark dna or mrna. this requires that the building bricks of dark dna and mrna emerge from environment perhaps by mechanism involving reconnection for the magnetic tentacles and reduction of heff bringing the molecules near each other. flux tube pairs between dark dna codons and and their conjugates (individual dark rna codons) would be formed during replication (transcription). the formation of flux tube pair between mrna and dark trna part of trna would bring trna to mrna, where amino-acid would associate with the growing amino-acid sequence. for options 1a and 1b based on ordinary statistics color singletness condition could play an important role in the replication and transcription. 1. if the value of heff before reconnection and contraction of flux tube dictating the scale of color confinement is large enough, colored dark nucleons could float as free possibly colored states in the environment for option 1a). for option 1b dark nucleons could be present in environment this could relate directly to the ionization in electrolyte. for options 1a and 1b dark codons representing dark trna molecules would accompany them. 2. for options 1a) and 1b) color confinement in flux tube degrees of freedom by forming dark color flux tube pairs between dark dna and its conjugate in codon-wise manner could give rise to dna double strands as chemical shadows of dark double strands. the coupling between codon and anticodon would be defined by the condition that the total color bond spins of paired codons are opposite. quark color could be compensated for option 1a along dna strand: 3 10:s give singlet. one can of course ask whether dark dna rna sequences exist rather than being built during replication and transcription. 3.3 are sound-like bubbles whizzing around in dna essential to life? i got a link to a very interesting article [i2] about sound waves in dna (see http://tinyurl.com/ z7hod9b). the article tells about thz de-localized modes claimed to propagate forth and back along dna double strand somewhat like bullets. these modes involve collective motion of many atoms. these modes are interpreted as a change in the stiffness of the dna double strand leading to the splitting of hydrogen bonds in turn leading to a splitting into single strands. the resulting gap is known as transcriptional bubble propagating along double strand is the outcome. i do not how sound the interpretation as sound wave is. it has been proposed that sound waves along dna give rise to the bubble. the local physical properties of dna double strand such as helical structure and elasticity affect the propagation of the waves. specific local sequences are proposed to favor a resonance with low frequency vibrational modes, promoting the temperary splitting of the dna double strand. inside the bubble the bases are exposed to the surrounding solvent, which has two effects. bubbles expose the nucleic acid to reactions of the bases with mutagens in the environment whereas so called molecular intercalators may insert themselves between the strands of dna. on the other hand, bubbles allow proteins known as helicases to attach to dna to stabilize the bubble, followed by the splitting the strands to start the transcription and replication process. the splitting would occur at certain portions of dna double strand. for this reason, it is believed that dna directs its own transcription. the problem is that the strong interactions with the surrounding water are expected to damp the sound wave very rapidly. authors study experimentally the situation and report that propagating bubbles indeed exist for frequencies in few thz region. therefore the damping deo not seem to be effective. how this is possible? as an innocent layman i also wonder how this kind of mechanism can be selective: it would seem that the bullet like sound wave initiates transcription at many positions along dna. the transcription should be localized to a region assignable to single gene. what could guarantee this? isbn: issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/z7hod9b http://tinyurl.com/z7hod9b dna decipher journal | june 2016 | volume 6 | issue 2 | pp. 81-98 92 pitkänen, m., on the representations of genetic code by dark nuclear strings in tgd framework can tgd say anything interesting about the mechanism behind transcription and replication? 1. in tgd magnetic body controls and coordinates the dynamics. the strongest hypothesis is that basic biochemical process are induced by those for dark variants of basic bio-molecules (dark variants of dna, enzymes,...). the belief that dna directs its own transcription translates to the statement that the dark dna consisting most plausibly from sequences of dark proton triplets ppp at dark magnetic flux tubes controls the transcription: the transcription/replication at the level of dark dna induces that at the level of ordinary dna. 2. if the dark dna codons represented as dark proton triplets (ppp) are connected by 3 flux tube pairs, the reverse of the reconnection should occur and transform flux tube pairs to two u-shaped flux tubes assignable to the two dark dna strands. dark proton sequences have positive charge +3e per dark codon giving rise to a repulsive coulomb force between them. there would be also an attractive force due to magnetic tension of the flux tubes. these two forces would compensate each other in equilibrium (there also the classical forces due to the negatively charged phosphates associated with nucleotides but these would not be so important). if the flux tube pairs are split, the stabilizing magnetic force however vanishes and the dark flux tubes repel each other and force the negatively charged dna strands to follow so that also ordinary dna strand splits and bubble is formed. the primary wave could therefore be the splitting of the flux tube pairs: whether one can call it as a sound wave is not clear to me. perhaps the induced propagating splitting of ordinary dna double strand could be regarded as an analog of sound wave. the splitting of flux tube pairs for a segment of dna would induces a further splitting of flux tubes since repulsive coulomb force tends to drive the flux tubes further away. the process could be restricted to dna if the ”upper” end of the split dna region has some dark dna codons which are not connected by flux tubes pairs. this model reason why for dark proton sequences. 3. this model does not yet explain how the propagating splitting wave is initiated. could a quantum phase transition increasing the value of heff associated with the flux tube pairs occur for some minimal portion of dark dna ”below” the region associated with gene and lead to the propagating wave induced by the above classical mechanism? that the wave propagates in one direction only could be due to chirality of dna double helix. an interesting question is how the rna world vision (see https://en.wikipedia.org/wiki/rna_ world) relates to this general picture. 1. there are strong conditions on the predecessor of dna and rna satisfies many of them: reverse transcription to dna making possible transition to dna dominated era is possible. double stranded rna exists https://en.wikipedia.org/wiki/rna#double-stranded_rna in cells and makes possible rna genome: this would however suggest that cell membrane came first. rna is a catalyst. rna has ability to conjugate an amino-acid to the 3′ end of rna and rna catalyzes peptide bond formation essential for translation. rna can self-replicate but only relatively short sequences are produced. 2. tgd picture allows to understand why only short sequences of rna are obtained in replication. if the replication occurs at the level of dark ppn sequences as it would occur for dna in tgd framework, long rna sequences might be difficult to produce because of the stopping of the propagation of the primary wave splitting the flux tube pairs. this could be due to the neuron pairs to which there is associated no coulomb repulsion essential for splitting. 3. in tgd framework rna need not be the predecessor of dna since the evolution would occur at the level of dark nucleon strings and dna as the dark proton string is the simpest dark nucleon string and might have emerged first. dark nuclear strings would have served as templates and biomolecules would have emerged naturally via the transcription of their dark counterparts to corresponding biopolymers. isbn: issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://en.wikipedia.org/wiki/rna_world https://en.wikipedia.org/wiki/rna_world https://en.wikipedia.org/wiki/rna#double-stranded_rna dna decipher journal | june 2016 | volume 6 | issue 2 | pp. 81-98 93 pitkänen, m., on the representations of genetic code by dark nuclear strings in tgd framework 3.4 is bio-catalysis a shadow of dark bio-catalysis based on generalization of genetic code? protein catalysis and reaction pathways look extremely complex (see http://tinyurl.com/kp3sdlm) as compared to replication, transcription, translation, and dna repair. could simplicity emerge if biomolecules are identified as chemical shadows of objects formed from dark nuclear strings consisting of dark nucleon triplets and their dynamics is shadow of dark stringy dynamics very much analogous to text processing? what if bio-catalysis is induced by dark catalysis based on reconnection as recognition mechanism? what if contractions and expansions of u-shaped flux tubes by heff increasing phase transitions take that reactants find each other and change conformations as in the case of opening of dna double strand? what if codes allowing only the dark nucleons with same dark nuclear spin and flux tubes spin to be connected by a pair of flux tubes? this speculation might make sense! the recognition of reactants is one part of catalytic action. it has been found in vitro rna selection experiments that rna sequences are produced having high frequency for the codons which code for the amino-acid that these rna molecules recognize (http: //tinyurl.com/kp3sdlm. this is just what the proposal predicts! genetic codes dna to rna as 64 → 64 map, rna to trna as 64 → 40, trna to amino-acids with 40 → 20 map are certainly not enough. one can however consider also additional codes allowed by projections of (4 ⊕ 21 ⊕ 22) ⊗ (5 ⊕ 3(⊕1)) to lower-dimensional sub-spaces defined by projections preserving spins. one could also visualize bio-molecules as collections of pieces of text attaching to each other along conjugate texts. the properties of catalysts and reactants would also depend by what texts are ”visible” to the catalysts. could the most important biomolecules participating biochemical reactions (proteins, nucleic acids, carbohydrates, lipids, primary and secondary metabolites, and natural products, see https://en.wikipedia.org/wiki/biomolecule) have dark counterparts in these sub-spaces. the selection of bio-active molecules is one of the big mysteries of biology. the model for the chemical pathway leading to the selection of purines as nucleotides [23] assumes that the predecessor of purine molecule can bind to dark proton without transforming it to ordinary proton. a possible explanation is that the binding energy of the resulting bound state is higher for dark proton than the ordinary one. minimization of the bound state energy could be a completely general criterion dictating which bio-active molecules can pair with dark protons. the selection of bio-active molecules would not be random after all although it looks so. the proposal for dna-nuclear/cell membrane as topological quantum computer with quantum computations coded by the braiding of magnetic flux tubes connecting nucleotides to the lipids wlead to the idea that flux tubes being at o=-bonds [9]. 3.5 comparing tgd view about quantum biology with mcfadden’s views mcfadden [8] has very original view about quantum biology: i have written about his work for the first time for years ago, much before the emergence of zeo, of the recent view about self as generalized zeno effect, and of the understanding the role of magnetic body containing dark matter [12]. the pleasant surprise was that i now understand mcfadden’s views much better from tgd viewpoint. 1. mcfadden sees decoherence as crucial in biological evolution: here tgd view is diametric opposite although decoherence is a basic phenomenon also in tgd. 2. mcfadden assumes quantum superpositions of different dnas. to me this looks an unrealistic assumption in the framework of peo. in zeo it is quite possible option. 3. mcfadden emphasizes the importance of zeno effect (in peo). in tgd the zeo variant of zeno effect is central for tgd inspired theory of consciousness and quantum biology. mc fadden suggests that quantum effects and zeno effect are central in bio-catalysis: the repeated measurement keeping reactants in the same position can lead to an increase of reaction rate by factors of order billion. isbn: issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/kp3sdlm http://tinyurl.com/kp3sdlm http://tinyurl.com/kp3sdlm https://en.wikipedia.org/wiki/biomolecule dna decipher journal | june 2016 | volume 6 | issue 2 | pp. 81-98 94 pitkänen, m., on the representations of genetic code by dark nuclear strings in tgd framework mcfadden describe enzymes as quantum mousetraps catching the reactants and forcing them to stay in same position. the above description for how catalysis catches the reactants using u-shaped flux tube conforms with mousetrap picture. mcfadden discusses the action of enzymes in a nice manner and his view conforms with tgd view. in zeo the system formed by catalyst plus reactants could be described as a negentropically entangled sub-self, and self indeed corresponds to a generalized zeno effect. the reactions can proceed in shorter scales although the situation is fixed in longer scales (hierarchy of cds): this would increase the length of the period of time during which reactions can proceed and lead to catalytic effect. zeno effect in zeo plus hierarchies of selves and cds would be essentially for the local aspects of enzyme action. 4. protons associated with hydrogen bonds and electronic cooper pairs play a universal role in mcfadden’s view and the localization of proton in quantum measurement of its position to hydrogen bond is the key step of enzyme catalysis. also tgd dark protons at magnetic flux tubes giving rise to dark nuclear strings play a key role. for instance, mcfadden models enzyme catalysis as injection of proton to a very special hydrogen bond of substrate. in tgd one has dark protons at magnetic flux tubes and their injection to a properly chosen hydrogen bond and transformation to ordinary proton is crucial for the catalysis. typical places for reactions to occur are c=o type bonds, where the transition to c-oh can occur and would involve transformation of dark proton to ordinary proton. the transformation of dark proton to ordinary one or vice versa in hydrogen bonds would serve as a biological quantum switch allowing magnetic body to control biochemistry very effectively. what about electronic cooper pairs assumed also by mcfadden. they would flow along the flux tube pairs. can cooper pairs of electrons and dark protons reside at same flux tubes? in principle this is possible although i have considered the possibility that particles with different masses (cyclotron frequencies) reside at different flux tubes. mcfadden [8] has proposed quantum superposition for ordinary codons: this does not seem to make sense in peo since the chemistries of codons are different) but could make sense in zeo. in tgd one could indeed imagine quantum entanglement (necessary negentropic in p-adic degrees of freedom) between dark codons. this ne could be either between additional degrees of freedom or between spin degrees of freedom determining the dark codons. in the latter case complete correlation between dark and ordinary dna codons would imply also the superposition of their tensor products with ordinary codons. the ne between dark codons could also have a useful function: it could determine physically gene as a union of disjoint mutually entangled portions of dna. genes are known to be highly dynamical units, and after pre-transcription splicing selects the portions of the transcript translated to protein. the codons in the complement of the real transcript are called introns and are spliced out from mrna after the pre-transcription (see https://en.wikipedia.org/wiki/rna_splicing). what could be the physical criterion telling whether a given codon belongs to exonic or intronic portion of dna? a possible criterion distinguish between exons and introns is that exons have ne between themselves and introns have no entanglement with exons (also exons could have ne between themselves). introns would not be useless trash since the division into exonic and exonic region would be dynamical. the interpretation in terms of tgd inspired theory of consciousness is that exons correspond to single self. 3.6 is there a connection between geometric model of harmony and nuclear string model of genetic code? there should exists a connection between the geometric model of harmony and genetic code and the model of genetic code discussed. isbn: issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://en.wikipedia.org/wiki/rna_splicing dna decipher journal | june 2016 | volume 6 | issue 2 | pp. 81-98 95 pitkänen, m., on the representations of genetic code by dark nuclear strings in tgd framework 1. dark dna strands could be connected by color flux tubes to form a double strand by reconnections of u-shaped color flux tubes. what would induce a codon-wise or letter-wise pairing of dna codons and their conjugates represented as dark quark triplets to form double dna strand? cyclotron resonance could accompany reconnection (magnetic field strength would be identical and reconnection could occur). 2. one has the correspondence codon↔ state of dark nucleon or codon↔ state of dark nucleon triplet. the geometric model of harmony and genetic code [19] represents the codons as 3-chords. the 3chord would be represented in terms of cyclotron frequencies of dark photons assignable to the 3 dark quarks (nucleons) in the state. each quark-color bond pair (including the pion-like bond) could be in 12 states with corresponding cyclotron frequency mappable to the basic octave. the cyclotron frequency triplets would be same for codons and conjugates. the only manner to understand the scale is in terms of spectrum of magnetic field strengths for u-shaped flux tube pairs. this would require 3 pairs of flux tubes between the dark codons of dna strands. if the quarks inside linear dark proton are connected by color flux tubes (like protons in the model of dark nucleus). reconnection for u-shaped flux tube connecting quarks would give rise to the double strand formed by dark proton strings. the magnetic field strength of the 3-flux tubes would be determined by the state of dark proton and would be same for dna and rna codons and also for rna codons and corresponding trna-amino-acid complexes. the cyclotron frequencies would define a scaled up variant of pythagorean scale projected to the basic octave [19]. this option does not favor the idea about separater 4-letter code. 3. the geometric model for harmony is formulated in terms of orbits of the subgroups of the isometry groups of tetrahedral and icosahedral geometries. the dnas coding particular amino-acid correspond correspond to the orbit of the triangle of icosahedron corresponding to the amino-acid. the decomposition 60 → 20 + 20 + 20 suggests strongly decomposition of i to 20 z3 cosets containing 3 elements each other and in correspondences with the triangular faces of icosahedron. 4. the model of the genetic code just discussed relies on the model of dark nucleon based on group theory. the symmetric groups of platonic solids are in turn associated with inclusion of hyper-finite factors and appear in mc kay correspondence, whose proof involves decompositions of su(2) representations to the representations of the discrete subgroups of platonic solids. a further observation is that the numbers of elements for isometries of icosahedron and tetrahedron are 60 and 4 respectively: the sum is 64. could the action of z3 leaving face invariant could be posed as an additional condition on amino-acids and reduce the amino-acid representation to 4⊗ 5. 5. in the geometric model of harmony genetic icosahedral 20+20+20 part of the code involves a combination of three different hamilton’s cycles mapping 60 dnas to 20 amino-acids: in terms of icosahedral group i and its coset space i/z3 these maps correspond to coset projections. could the decomposition (4⊕ 21 ⊕ 22)⊗ (5⊗ 3) be understood in terms of a reduction to icosahedral and tetrahedral subgroups of rotation group or of their spin coverings. in this process finite-dimensional representation of so(3) decomposes to a direct sum of representations of the discrete subgroup if its dimension is larger than any of the dimensions of representations of the finite sub-group (for basic facts about these see http://tinyurl.com/ho4onbs). one might hope that the decomposition of the representations of so(3) appearing in the above formula under icosahedral group and or tetrahedral group could allow to understand the emergence of dna, rna, trna, and amino-acids as kind of symmetry breaking. 6. in the geometric model of harmony 64-codon code [19] is obtained as a fusion 60-codon code assignable to icosahedron + 4 codon code assignable to tetrahedron. there are actually two codes corresponding to tetrahedron and icosahedron as disjoint entities and tetrahedron glued to icosahedron along one face. the model explains the two additional amino-acids pyl and sec coded for a variant of the genetic code. isbn: issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tinyurl.com/ho4onbs dna decipher journal | june 2016 | volume 6 | issue 2 | pp. 81-98 96 pitkänen, m., on the representations of genetic code by dark nuclear strings in tgd framework how could these two successful models relate to each other? in p-adic physics of cognition platonic solids and polygons can be seen as discrete approximation for sphere [24] and biomolecules could be understood as cognitive representation in the intersection of real and p-adic space-time surface consisting of algebraic points. could one assign icosahedron and tetrahedron to a codon in some concrete manner? could the attachment of tetrahedron to icosahedron along one face have concrete meaning? the answer seems to be negative. 1. one can about the interpretation of the 12 vertices of the icosahedron how number 12 could be assigned with the genetic code? the vertices correspond to notes perhaps represented as magnetic field strength at the flux tubes assignable to color bonds. this field strength should be determined by the spin state of dark 3-nucleon. no concrete nuclear string counterpart seems to exist for the closed hamiltonian cycle consisting of 12 notes and in case of tetrahedral extension of 13 notes. 12 vertices of icosahedron correspond to 12 notes and 20 faces to 3-chords so that there is not need for more concrete correspondence. 2. the attachment of tetrahedron to icosahedron would bring in further note very near to one of the notes of pythagorean scale and corresponding 3-chords. this has concrete interpretation and there is no need to make this more concrete at the level of geometry of dna. if icosahedron and tetrahedron are disjoint one obtains four additional codons. it seems that all these 4 3-chords be assigned with the 3 color bonds, one note for each of them. what distinguishes at the level of dark nucleon string the situations in which tetrahedron is attached and non-attached to the color bond? in presence of attachment there would be 1 shared 3-chord corresponding to stop codon assignable with the shared face. the 13:th note appearing in 4 3-chords differs very little from one of the notes of the icosahedral scale: this corresponds to the fact that 12 perfect quints do not quite give 7 octaves as already pythagoras realized. crazy question: could this small difference relate to the small relative mass difference (mp − mn)/mp ' .0014 making itself possible visible in cyclotron frequency scale? the idea does not seem plausible: [(3/2)12 − 27]/27 ' .014 is 10 times larger than (mp −mn)/mp ' .0014. the conclusion is that genetic code can be understand as a map of stringy nucleon states induced by the projection of all states with same spin projections to a representative state with the same spin projections (total quark spin and total flux tube spin). genetic code would be realized at the level of dark nuclear physics and biochemical representation would be only one particular higher level representation of the code. a hierarchy of dark baryon realizations corresponding to p-adic and dark matter hierarchies can be considered. translation and transcription machinery would be realized by flux tubes connecting only states with same quark spin and flux tube spin. references [1] icosahedral graph. wolfram mathworld. available at: http://mathworld.wolfram.com/ icosahedralgraph.html. [2] holmlid l badiei s, patrik pu. laser-driven nuclear fusion d+d in ultra-dense deuterium: mev particles formed without ignition. laser and particle beams. http://tinyurl.com/pm56kk3., 28(02):313–317, 2012. [3] feng jl et al. evidence for a protophobic fifth force from 8be nuclear transitions. available at: http://arxiv.org/abs/1604.07411, 2015. [4] holmlid l and kotzias b. phase transition temperatures of 405-725 k in superfluid ultra-dense hydrogen clusters on metal surfaces. aip advances. available at: http://tinyurl.com/hxbvfc7, 6(4), 2016. isbn: issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://mathworld.wolfram.com/icosahedralgraph.html http://mathworld.wolfram.com/icosahedralgraph.html http://tinyurl.com/pm56kk3 http://arxiv.org/abs/1604.07411 http://tinyurl.com/hxbvfc7 dna decipher journal | june 2016 | volume 6 | issue 2 | pp. 81-98 97 pitkänen, m., on the representations of genetic code by dark nuclear strings in tgd framework [5] krasznahorkay a et al. observation of anomalous internal pair creation in 8be: a possible indication of a light, neutral boson. available at: https://arxiv.org/abs/1504.0152, 2016. [6] carell t et al. a high-yielding, strictly regioselective prebiotic purine nucleoside formation pathway. science. available at:http://science.sciencemag.org/content/352/6287/833, 352(6287):833– 836, 2016. [i2] gonzalez-jimenez m et al. observation of coherent delocalized phonon-like modes in dna under physiological conditions. nature comm. available at:http://tinyurl.com/hhtwdym, 2016. [7] montagnier l et al. electromagnetic signals are produced by aqueous nanostructures derived from bacterial dna sequences. interdiscip sci comput life sci . available at: http: //www.springerlink.com/content/0557v31188m3766x/, 2009. [8] mcfadden j. quantum evolution. w. w. norton & company., 2000. [9] pitkänen m. dna as topological quantum computer. in genes and memes. onlinebook. available at: http://tgdtheory.fi/public_html/genememe/genememe.html#dnatqc, 2006. [10] pitkänen m. genes and memes. onlinebook. available at: http://tgdtheory.fi/public_html/ genememe/genememe.html, 2006. [11] pitkänen m. genes and memes. in genes and memes. onlinebook. available at: http: //tgdtheory.fi/public_html/genememe/genememe.html#genememec, 2006. [12] pitkänen m. evolution in many-sheeted space-time. in genes and memes. onlinebook. available at: http://tgdtheory.fi/public_html/genememe/genememe.html#prebio, 2006. [13] pitkänen m. homeopathy in many-sheeted space-time. in bio-systems as conscious holograms. onlinebook. available at: http://tgdtheory.fi/public_html/hologram/hologram.html# homeoc, 2006. [14] pitkänen m. nuclear string hypothesis. in hyper-finite factors and dark matter hierarchy. onlinebook. available at: http://tgdtheory.fi/public_html/neuplanck/neuplanck.html# nuclstring, 2006. [15] pitkänen m. quantum model for bio-superconductivity: i. in tgd and eeg. onlinebook. available at: http://tgdtheory.fi/public_html/tgdeeg/tgdeeg.html#biosupercondi, 2006. [16] pitkänen m. quantum model for bio-superconductivity: ii. in tgd and eeg. onlinebook. available at: http://tgdtheory.fi/public_html/tgdeeg/tgdeeg.html#biosupercondii, 2006. [17] pitkänen m. the notion of wave-genome and dna as topological quantum computer. in genes and memes. onlinebook. available at: http://tgdtheory.fi/public_html/genememe/genememe. html#gari, 2006. [18] pitkänen m. more precise tgd view about quantum biology and prebiotic evolution. in genes and memes. onlinebook. available at: http://tgdtheory.fi/public_html/genememe/genememe. html#geesink, 2015. [19] pitkänen m. geometric theory of harmony. available at: http://tgdtheory.fi/public_html/ articles/harmonytheory.pdf, 2014. [20] pitkänen m. pythagoras, music, sacred geometry, and genetic code. available at: http: //tgdtheory.fi/public_html/articles/pythagoras.pdf, 2014. isbn: issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. https://arxiv.org/abs/1504.0152 http://science.sciencemag.org/content/352/6287/833 http://tinyurl.com/hhtwdym http://www.springerlink.com/content/0557v31188m3766x/ http://www.springerlink.com/content/0557v31188m3766x/ http://tgdtheory.fi/public_html/genememe/genememe.html#dnatqc http://tgdtheory.fi/public_html/genememe/genememe.html http://tgdtheory.fi/public_html/genememe/genememe.html http://tgdtheory.fi/public_html/genememe/genememe.html#genememec http://tgdtheory.fi/public_html/genememe/genememe.html#genememec http://tgdtheory.fi/public_html/genememe/genememe.html#prebio http://tgdtheory.fi/public_html/hologram/hologram.html#homeoc http://tgdtheory.fi/public_html/hologram/hologram.html#homeoc http://tgdtheory.fi/public_html/neuplanck/neuplanck.html#nuclstring http://tgdtheory.fi/public_html/neuplanck/neuplanck.html#nuclstring http://tgdtheory.fi/public_html/tgdeeg/tgdeeg.html#biosupercondi http://tgdtheory.fi/public_html/tgdeeg/tgdeeg.html#biosupercondii http://tgdtheory.fi/public_html/genememe/genememe.html#gari http://tgdtheory.fi/public_html/genememe/genememe.html#gari http://tgdtheory.fi/public_html/genememe/genememe.html#geesink http://tgdtheory.fi/public_html/genememe/genememe.html#geesink http://tgdtheory.fi/public_html/articles/harmonytheory.pdf http://tgdtheory.fi/public_html/articles/harmonytheory.pdf http://tgdtheory.fi/public_html/articles/pythagoras.pdf http://tgdtheory.fi/public_html/articles/pythagoras.pdf dna decipher journal | june 2016 | volume 6 | issue 2 | pp. 81-98 98 pitkänen, m., on the representations of genetic code by dark nuclear strings in tgd framework [21] pitkänen m. pollack’s findings about fourth phase of water : tgd view. available at: http: //tgdtheory.fi/public_html/articles/pollackyoutube.pdf, 2014. [22] pitkänen m. cold fusion again . available at: http://tgdtheory.fi/public_html/articles/ cfagain.pdf, 2015. [23] pitkänen m. one step further in the understanding the origins of life. available at: http:// tgdtheory.fi/public_html/articles/purineorigin.pdf, 2016. [24] pitkänen m. p-adicizable discrete variants of classical lie groups and coset spaces in tgd framework. available at: http://tgdtheory.fi/public_html/articles/padicgeom.pdf, 2016. [25] pitkänen m. strong support for tgd based model of cold fusion from the recent article of holmlid and kotzias. available at: http://tgdtheory.fi/public_html/articles/holmilidnew.pdf, 2016. [26] pitkänen m. x boson as evidence for nuclear string model. available at: http://tgdtheory.fi/ public_html/articles/xboson.pdf, 2016. isbn: issn: 2159-046x dna decipher journal www.www.dnadecipher.com published by quantumdream, inc. http://tgdtheory.fi/public_html/articles/pollackyoutube.pdf http://tgdtheory.fi/public_html/articles/pollackyoutube.pdf http://tgdtheory.fi/public_html/articles/cfagain.pdf http://tgdtheory.fi/public_html/articles/cfagain.pdf http://tgdtheory.fi/public_html/articles/purineorigin.pdf http://tgdtheory.fi/public_html/articles/purineorigin.pdf http://tgdtheory.fi/public_html/articles/padicgeom.pdf http://tgdtheory.fi/public_html/articles/holmilidnew.pdf http://tgdtheory.fi/public_html/articles/xboson.pdf http://tgdtheory.fi/public_html/articles/xboson.pdf introduction genetic code and combinatorial hierarchy geometric theory of harmony and genetic code letter-wise representations of genetic code in terms of single particle states codon-wise representations of genetic code realized in terms of dark nuclear strings models of genetic code based on dark nuclear strings mapping dna and amino-acids to dark nucleon states objections based on group theory and statistics also the mapping of dna and amino-acids to dark 3-nucleon states is possible ordinary or braid statistics? objections against the identification of codons as dark nucleon states more detailed view abot the model mapping codons to dark 3-nucleon states could dark dna, rna, trna and amino-acids correspond to different charge states of codons? replication, transcription, translation are sound-like bubbles whizzing around in dna essential to life? is bio-catalysis a shadow of dark bio-catalysis based on generalization of genetic code? comparing tgd view about quantum biology with mcfadden's views is there a connection between geometric model of harmony and nuclear string model of genetic code? login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x dna decipher journal| january 2011 | vol. 1 | issue 1 | pp. 110-145 110 pitkänen m. dna as topological quantum computer: part i article inaugural issue dna as topological quantum computer: part i matti pitkänen1 abstract this is the first part of the article representing a vision about how dna might act as a topological quantum computer (tqc). tqc means that the braidings of braid strands define tqc programs and m-matrix (generalization of s-matrix in zero energy ontology) defining the entanglement between states assignable to the end points of strands define the tqc usually coded as unitary time evolution for schrödinger equation. before a representation of the model of tqc general vision about what happens in quantum jump, which at least in formal sense can be regarded as quantum computation, is represented. included is also a section about modification of thermodynamics required by the possibility of negentropic entanglement. the modification corresponds simply to the replacement s → s −n for the entropy in standard thermodynamics. the implications of this replacement are however highly non-trivial. the generalization of the second law allows to understand the thermodynamical aspect of topological quantum computation. one can understand why living matter is so effective entropy producer as compared to inanimate matter and also the characteristic decomposition of living systems to highly negentropic and entropic parts as a consequence of generalized second law. adp-atp process of metabolism provides a concrete application for the generalized thermodynamics and allows to see this process as a transfer of negentropic entanglement. also dna double strand for which sugar-phosphate backbone consists of xmps, x= a,t,c,g containing negentropy carrying phosphate bonds can be seen as analogous to conscious brain with dna strands representing right and left hemispheres. one can end up to the model of topological quantum computation in the following manner. 1. darwinian selection for which the standard theory of self-organization provides a model, should apply also to tqc programs. tqc programs should correspond to asymptotic self-organization patterns selected by dissipation in the presence of metabolic energy feed. the spatial and temporal pattern of the metabolic energy feed characterizes the tqc program or equivalently sub-program call. 2. since braiding characterizes the tqc program, the self-organization pattern should correspond to a hydrodynamical flow or a pattern of magnetic field inducing the braiding. braid strands must correspond to magnetic flux tubes of the magnetic body of dna. if each nucleotide is transversal magnetic dipole it gives rise to transversal flux tubes, which can also connect to the genome of another cell. as a matter fact, the flux tubes would correspond to what i call wormhole magnetic fields having pairs of space-time sheets carrying opposite magnetic fluxes. 3. the output of tqc sub-program is probability distribution for the outcomes of state function reduction so that the sub-program must be repeated very many times. it is represented as four-dimensional patterns for various rates (chemical rates, nerve pulse patterns, eeg power distributions,...) having also identification as temporal densities of zero energy states in various scales. by the fractality of tgd universe there is a hierarchy of tqcs corresponding to p-adic and dark matter hierarchies. programs (space-time sheets defining coherence regions) call programs in shorter scale. if the self-organizing system has a periodic behavior each tqc module defines a large number of almost copies of itself asymptotically. generalized eeg could naturally define this periodic pattern and each period of eeg would correspond to an initiation and halting of tqc. this brings in mind the periodically occurring sol-gel phase transition inside cell near the cell membrane. there is also a connection with hologram idea: eeg rhythm corresponds to reference wave and nerve pulse patters to the wave carrying the information and interfering with the reference wave. 4. fluid flow must induce the braiding which requires that the ends of braid strands must be anchored to the fluid flow. recalling that lipid mono-layers of the cell membrane are liquid 1matti pitkänen http://tgd.wippiespace-com/public_html. address: köydenpunojankatu 2 d 11 10940, hanko, finland. email: matpitka@luukku.com. issn: issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. http://tgd.wippiespace-com/public_html mailto:matpitka@luukku.com dna decipher journal| january 2011 | vol. 1 | issue 1 | pp. 110-145 111 pitkänen m. dna as topological quantum computer: part i crystals and lipids of interior mono-layer have hydrophilic ends pointing towards cell interior, it is easy to guess that dna nucleotides are connected to lipids by magnetic flux tubes and hydrophilic lipid ends are stuck to the flow. 5. the topology of the braid traversing cell membrane cannot be affected by the hydrodynamical flow. hence braid strands must be split during tqc. this also induces the desired magnetic isolation from the environment. halting of tqc reconnects them and make possible the communication of the outcome of tqc. there are several problems related to the details of the realization. 1. how nucleotides a,t,c,g are coded to the strand color and what this color corresponds to physically? there are two options which could be characterized as fermionic and bosonic. i) magnetic flux tubes having quark and anti-quark at their ends with u,d and uc, dc coding for a,g and t,c. cp conjugation would correspond to conjugation for dna nucleotides. ii) wormhole magnetic flux tubes having wormhole contact and its cp conjugate at its ends with wormhole contact carrying quark and anti-quark at its throats. the latter are predicted to appear in all length scales in tgd universe. 2. how to split the braid strands in a controlled manner? high tc super conductivity provides a possible mechanism: braid strand can be split only if the supra current flowing through it vanishes. a suitable voltage pulse induces the supra-current and its negative cancels it. the conformation of the lipid controls whether it it can follow the flow or not. 3. how magnetic flux tubes can be cut without breaking the conservation of the magnetic flux? the notion of wormhole magnetic field could save the situation now: after the splitting the flux returns back along the second space-time sheet of wormhole magnetic field. an alternative solution is based on reconnection of flux tubes. since only flux tubes of same color can reconnect this process can induce transfer of color: ”color inheritance”: when applied at the level of aminoacids this leads to a successful model of protein folding. reconnection makes possible breaking of flux tube connection for both the ordinary magnetic flux tubes and wormhole magnetic flux tubes. 4. how magnetic flux tubes are realized? the interpretation of flux tubes as correlates of directed attention at molecular level leads to concrete picture. hydrogen bonds are by their asymmetry natural correlates for a directed attention at molecular level. also flux tubes between acceptors of hydrogen bonds must be allowed and acceptors can be seen as the subjects of directed attention and donors as objects. examples of acceptors are aromatic rings of nucleotides, o = atoms of phosphates, etc.. a connection with metabolism is obtained if it is assumed that various phosphates xmp,xdp,xtp , x = a, t,g,c act as fundamental acceptors and plugs in the connection lines. the basic metabolic process atp → adp + pi allows an interpretation as a reconnection splitting flux tube connection, and the basic function of phosphorylating enzymes would be to build flux tube connections as also of breathing and photosynthesis. 1 introduction large values of planck constant makes possible all kinds of quantum computations [47, 41, 48, 50]. what makes topological quantum computation (tqc) [51, 45, 42, 43, 49] so attractive is that the computational operations are very robust and there are hopes that external perturbations do not spoil the quantum coherence in this case. the basic problem is how to create, detect, and control the dark matter with large ~. the natural looking strategy would be to assume that living matter, say a system consisting of dna and cell membranes, performs tqc and to look for consequences. there are many questions. how the tqc could be performed? does tqc hypothesis might allow to understand the structure of living cell at a deeper level? what does this hypothesis predict about dna itself? one of the challenges is to fuse the vision about living system as a conscious hologram with the dna as tqc vision. the experimental findings of peter gariaev [57, 59] might provide a breakthrough in this respect. in particular, the very simple experiment in which one irradiates dna sample using ordinary light in uv-ir range and photographs the scattered light seems to allow an interpretation as providing a photograph of magnetic flux tubes containing dark matter. if this is really the case, then the bottle neck problem of how to make dark matter visible and how to manipulate it would have been issn: issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal| january 2011 | vol. 1 | issue 1 | pp. 110-145 112 pitkänen m. dna as topological quantum computer: part i resolved in principle. the experiment of gariaev and collaborators [59] also show that the photographs are obtained only in the presence of dna sample. this leaves open the question whether the magnetic flux tubes associated with instruments are there in absence of dna and only made visible by dna or generated by the presence of dna. 1.1 basic ideas of tqc the basic idea of topological quantum computation (tqc) is to code tqc programs to braiding patterns (analogous to linking and knotting). a nice metaphor for tqc is as dance. dancing pattern in time direction defines the tqc program. this kind of patterns are defined by any objects moving around so that the universe might be performing topological quantum computation like activities in all scales. one assigns to the strands of the braid elementary particles. the s-matrix coding for tqc is determined by purely topological consideration as a representation for braiding operation. it is essential that the particles are in anyonic phase: this means in tgd framework that the value of planck constant differs from its standard value. tqc as any quantum computation halts in state function reduction which corresponds to the measurement of say spins of the particles involved. as in the case of ordinary computers one can reduce the hardware to basic gates. the basic 2-gate is represented by a purely topological operation in which two neighboring braid strands are twisted by π. 1-particle gate corresponds to a phase multiplication of the quantum state associated with braid strand. this operation is not purely topological and requires large planck constant to overcome the effects of thermal noise. in tgd framework tqc differs somewhat from the ordinary one. 1. zero energy ontology (zeo) means that physical states decompose into pairs of positive and negative energy states at the ”upper” and ”lower” light-like boundaries boundaries of cd×cp2, where cd denotes causal diamond identified as the intersection of the future and past directed lightcones (in the sequel cd is used for cd×cp2 in order to make notations more elegant). positive and negative energy states have opposite values of conserved quantum numbers. the interpretation is as an event, say particle scattering, in positive energy ontology. the time like entanglement coefficients define s-matrix, or rather m -matrix, and this matrix can be interpreted as coding for physical laws in the structure of physical state as quantum superposition of statements ”a implies b” with a and b represented as positive and negative energy parts of quantum state. the halting of topological quantum computation would select this kind of statement. 2. the new view about quantum state as essentially 4-d notion implies that the outcome of tqc is expressed as a four-dimensional pattern at space-time sheet rather than as time=constant final state. all kinds of patterns would provide a representation of this kind. in particular, holograms formed by large ~ photons emitted by josephson currents, including eeg as a special case, would define particular kind of representation of outcome. 1.2 identification of hardware of tqc and tqc programs one challenge is to identify the hardware of tqc and realization of tqc programs. 1. living cell is an excellent candidate in this respect. the lipid layers of the cell membrane is 2-d liquid crystal and the 2-d motion of lipids would define naturally the braiding if the lipids are connected to dna nucleotides. this motion might be induced by the self organization patterns of metabolically driven liquid flow in the vicinity of lipid layer both in interior and exterior of cell membrane and thus self-organization patters of the water flow would define the tqc programs. 2. this identification of braiding implies that tqc as dancing pattern is coded automatically to memory in the sense that lipids connected to nucleotides are like dancers whose feet are connected to the wall of the dancing hall define automatically space-like braiding as the threads connected to their feet get braided. this braiding would define universal memory realized not only as tissue memory but related also to water memory [29]. issn: issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal| january 2011 | vol. 1 | issue 1 | pp. 110-145 113 pitkänen m. dna as topological quantum computer: part i 3. it is natural to require that the genetic code is somehow represented as property of braids strands. this is achieved if strands are ”colored” so that a,t,c,g correspond to four different ”colors”. this leads to the hypothesis that flux tubes assignable to nucleotides are wormhole magnetic flux tubes such that the ends of the two sheets carry quark and antiquark (resp. antiquark and quark) quantum numbers. this gives mapping a,t,c,g to u, uc, d, dc. these quarks are not ordinary quarks but their scaled variants predicted by the fractal hierarchy of color and electro-weak physics. chiral selection in living matter could be explained by the hierarchy of weak physics. the findings of topologist barbara shipman about mathematical structure of honeybee dance led her to proposed that the color symmetries of quarks are in some mysterious manner involved with honeybee cognition and this model would justify her intuition [39]. 4. one should identify the representation of qubit. ordinary spin is not optimal since the representation of 1-gates would require a modification of direction of magnetic field in turn requiring modification of direction of flux tubes. a more elegant representation is based on quark color which means effectively 3-valued logic: true, false, and undefined, also used in ordinary computers and is natural in a situation in which information is only partial. in this case 1-gates would correspond to color rotations for space-time sheets requiring no rotation of the magnetic field. in this framework genes define the hardware of tqc rather than genetic programs. this means that the evolution takes place also at the level of tqc programs meaning that strict genetic determinism fails. there are also good reasons to believe that these tqc programs can be inherited to some degree. this could explain the huge differences between us and our cousins in spite of almost the identical genetic codes and explains also cultural evolution and the observation that our children seem to learn more easily those things that we have already learned [60]. it must be added that dna as tqc paradigm seems to generalizeddna, lipids, proteins, water molecules,... can have flux tubes connecting them together and this is enough to generate braidings and tqc programs. even water could be performing simple tqc or at least building memory representations based on braiding of flux tubes connecting water molecules. 1.3 how much tqc resembles ordinary computation? if god made us to his own image one can ask whether we made computers images of ourselves in some respects. taking this seriously one ends up asking whether facts familiar to us from ordinary computers and world wide web might have counterparts in dna as tqc paradigm. 1. can one identify program files as space-like braiding patterns. can one differentiate between program files and data files? 2. in ordinary computers electromagnetic signalling is in key role. the vision about living matter as conscious holograms suggests that this is the case also now. in particular, the idea that entire biosphere forms a tqc web communicating electromagnetically information and control signals looks natural. topological light rays (mes) make possible precisely targeted communications with light velocity without any change in pulse shape. gariaev’s findings [57] that the irradiation of dna by laser light induces emission of radio wave photons having biological effects on living matter at distances of tens of kilometers supports this kind of picture. also the model of eeg in which the magnetic body controls the biological body also from astrophysical distances conforms with this picture. 3. the calling of computer programs by simply clicking the icon or typing the name of program followed by return is an extremely economic manner to initiate complex computer programs. this also means that one can construct arbitrarily complex combinations from given basic modules and call this complex by a single name if the modules are able to call each other. this kind of program call mechanism could be realized at the level of tqc by dna. since the intronic portion of genome increases with the evolutionary level and is about 98 per cent for humans, one can ask whether introns would contain representations for names of program modules. if so, introns would express themselves electromagnetically by transcribing the nucleotide to a temporal pattern of electromagnetic radiation activating desired subprogram call, presumably the conjugate of intronic issn: issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal| january 2011 | vol. 1 | issue 1 | pp. 110-145 114 pitkänen m. dna as topological quantum computer: part i portion as dna sequence. a hierarchical sequence of subprogram calls proceeding downwards at intronic level and eventually activating the tqc program leading to gene expression is suggestive. gariaev [57] has found that laser radiation scattering from given dna activates only genomes which contain an address coded as temporal pattern for the direction of polarization plane. if flux tubes are super-conducting and there is strong parity breaking (chiral selection) then faraday rotation for photons traveling through the wormhole flux tube code nucleotide to an angle characterizing the rotation of polarization plane. user id and password would be kind of immune system against externally induced gene expression. 4. could nerve pulses establish only the connection between receiver and sender neurons as long magnetic flux tubes? real communication would take place by electromagnetic signals along the flux tube, using topological light ray (me) attached to flux tube, and by entanglement. could neural transmitters specify which parts of genomes are in contact and thus serve as a kind of directory address inside the receiving genome? 1.4 basic predictions of dna as tqc hypothesis dna as tqc hypothesis leads to several testable predictions about dna itself. 1.4.1 anomalous em charge the model for dna as tqc assigns to flux tubes starting from dna an anomalous em charge. this means that the total charge of dna nucleotide using e as unit is q = −2 + q(q), where -2 is the charge of phosphate group and q(q) = −/+ 2/3,+/− 1/3 is the electromagnetic charge of quark associated with ”upper” sheet of wormhole magnetic flux tube. if the phosphate group is not present one has q = q(q). in the presence of phosphate bonds the anomalous charge makes possible the coding of nucleotides to the rotation of angle of polarization plane resulting as photon travels along magnetic flux tube. the anomalous em charge should be visible as an anomalous voltage created by dna. it would be relatively easy to test this prediction by using various kinds of dna:s. 1.4.2 does breaking of matter antimatter and isospin symmetries happen at the level of dna and mrna? the nice feature of the model is that it allows to interpret the slightly broken a-g and t-c symmetries of genetic code with respect to the third nucleotide z of codon xy z in terms of the analog of strong isospin symmetry at quark level at wormhole magnetic flux tubes. also matter-antimatter dichotomy has a chemical analog in the sense that if the letter y of codon corresponds to quark u, d (antiquark uc, dc), the codon codes for hydrophobic (hydrophilic) aminoacid. it is also known that the first letter x of the codon codes for the reaction path leading from a precursor to an aminoacid. these facts play a key role in the model for code of protein folding and catalysis. the basic assumption generalizing base pairing for dna nucleotides is that wormhole flux tubes can connect an aminoacid inside protein only to molecules (aminoacids, dna, mrna, or trna) for which y letter is conjugate to that associated with the aminoacid. this means that the reduction of planck constant leading to the shortening of the flux tube can bring only these aminoacids together so that only these molecules can find each other in biocatalysis: this would mean kind of code of bio-catalysis. the fact that matter-antimatter and isospin symmetries are broken in nature suggests that the same occurs at the level of dna for quarks and anti-quarks coding for nucleotides. one would expect that genes and other parts of genome differ in the sense that the anomalous em charge, isospin, and net quark number (vanishes for matter antimatter symmetric situation) differ for them. from wikipedia [58] one learns that there are rules about distribution of nucleotides which cannot be understood on basis of chemistry. the rules could be understood in terms of new physics. chargaff’s rules state that these symmetries hold true in one per cent approximation at the level of entire chromosomes. szybalski’s rules [58] state that they fail for genes. there is also a rule stating that in good approximation both strands contain the same portion of dna transcribed to mrna. this implies that at mrna level the sign of issn: issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal| january 2011 | vol. 1 | issue 1 | pp. 110-145 115 pitkänen m. dna as topological quantum computer: part i matter antimatter asymmetry is always the same: this is analogous to the breaking of matter antimatter asymmetry in cosmology (only matter is observed). it would be interesting to study systematically the breaking of these symmetries for a sufficiently large sample of genes and also other in parts of genome where a compensating symmetry breaking must occur. that the irradiation of dna by laser light induces emission of radio wave photons having biological effects on living matter at distances of tens of kilometers supports this kind of picture. also the model of eeg in which magnetic body controls biological body from astrophysical distances conforms with this picture. the articles published in prespacetime journal[34] and journal of consciousness exploration & research [35, 36, 37] provide a conscise summary about tgd and tgd inspired theory of consciousness and biology and is recommended as a background besides the online books and articles at my homepage. i have divided the article to two parts. in the first part the basic concepts and ideas behind dna as tqc hypothesis are described. 1. a brief summary about what happens in quantum jump structurally analogous to quantum computation in zero energy ontology is given and a generalization of thermodynamics to take into account negentropic entanglement crucial for understanding living matter identified as something residing in the intersection of real world describing matter and p-adic worlds describing cognition. 2. in tgd framework the standard positive energy ontology is replaced with zero energy on. this implies that quantum computation in tgd universe differs from that in standard model world and these differences are summarized. one of the basic differences is temporal non-locality and top down nature of the computation and 4-d character of the ensemble coding for the outcome of the computation statistically. 3. a model for dna as topological quantum computer is formulated at the general level but details of the model are left to the second part of the article. 2 basic concepts and ideas the following represents a brief overall view about the notions of quantum jump, unitary process described by unitary u -matrix between zero energy states having as its orthogonal rowsm -matrices between positive and negative energy parts of zero energy states identifiable as counterpart of ordinary s-matrix and of negentropy maximization principle (nmp) governing the dynamics of state function reduction cascade. 2.1 what happens in quantum jump? quantum jump involves u process and state function reduction cascade. negentropy maximization principle implies second law for the standard view about state function reduction: second law states that the ensemble entropy increases by the randomness of the outcome of the state function reduction process. when negentropic entanglement possible in what might be called intersection of the real and various p-adic worlds is present the situation is not so clear. before proceeding to consider the modification of the second law one must define more precisely what u process is. the simplest view about quantum jump is as a unitary u -process followed by as a cascade of state function reductions proceeding from top to bottom. but what is the top? 1. in positive energy ontology it would be entire universe. quantum classical correspondence suggests that one should be able to assign to quantum jump a duration of geometric time. for this proposal this time is most naturally infinite. 2. the vision about fractal hierarchy of selves and quantum jumps together with zeo suggests a more refined view about quantum jump in which. u -process and subsequence state function reduction cascade could occur independently for disjoint cds. for a given cd the new sub-cds (representing mental images of the corresponding self) can be created and old destroyed so that the only constraint would be that only disjoint cds can perform quantum jumps independently. for this option the duration of geometric time assignable to the quantum jump would naturally correspond to the issn: issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal| january 2011 | vol. 1 | issue 1 | pp. 110-145 116 pitkänen m. dna as topological quantum computer: part i temporal distance between the tips of cd: p-adic length scale hypothesis and number theoretical vision suggest that this distance comes as an octave of cp2 time scale (prime or integer multiple is the more general option). for infinitely large cd this would mean infinite duration. this picture is consistent with the tgd view about how the arrow of subjective time induces the arrow of geometric time [22]. 2.2 m-matrix the unitary u -matrix characterizing the unitary process has as its rows orthogonal m -matrices characterized by in general non-unitarity m -matrices. m -matrix decomposes into a product of positive definite diagonal square roots of density matrix and unitary s-matrix measurent in particle physics experiment. m -matrix represents both the time-like entanglement between positive and negative energy parts of zero energy states with opposite quantum numbers and space-like entanglement for the positive and negative energy states. 2.2.1 time-like and space-like entanglement in zero energy ontology m -matrix for each summand is product of hermitian square root of density matrix and unitary smatrix multiplied by a square root of probability having interpretation as analog for boltzmann weight or probability defined by density matrix (note that it is essential to have tr(id) = 1 for factors of type ii1. if factor of type i∞ are present situation is more complex. this means that quantum computations are highly universal and m-matrices are characterized by the inclusion n ⊂ m in each summand defining measurement resolution. hermitian elements of n act as symmetries of m -matrix. the identification of the reducible entanglement characterized by boltzmann weight like parameters in terms of thermal equilibrium would allow to interpret quantum theory as square root of thermodynamics. if the entanglement probabilities defined by s-matrix and assignable to n rays do not belong to the algebraic extension used then a full state function reduction is prevented by nmp. ff the generalized boltzmann weights are also algebraic then also thermal entanglement is irreducible. in p-adic thermodynamics for virasoro generator l0 and using some cutoff for conformal weights the boltzmann weights are rational numbers expressible using powers of p-adic prime p. 2.2.2 effects of finite temperature usually finite temperature is seen as a problem for quantum computation. in tgd framework the effect of finite temperature is to replace zero energy states formed as pairs of positive and negative energy states with a superposition in which energy varies. one has an ensemble of space-time sheets which should represent nearly replicas of the quantum computation. there are two cases to be considered. 1. if the thermal entanglement is reducible then each space-time sheet gives outcome corresponding to a well defined energy and one must form an average over these outcomes. 2. if thermal entanglement is irreducible each space-time sheet corresponds to a quantum superposition of space-time sheets, and if the outcome is represented classically as rates and temporal field patterns, it should reflect thermal average of the outcomes as such. if the degrees of freedom assignable to topological quantum computation do not depend on the energy of the state, thermal width does not affect at all the relevant probabilities. the probabilities are actually affected even in the case of tqc since 1-gates are not purely topological and the effects of temperature in spin degrees of freedom are unavoidable. if t grows the probability distribution for the outcomes flattens and it becomes difficult to select the desired outcome as that appearing with the maximal probability. 2.3 hyper-finite factors of type ii1 and quantum measurement theory with a finite measurement resolution the realization that the von neumann algebra known as hyper-finite factor of type ii1 is tailor made for quantum tgd has led to a considerable progress in the understanding of the mathematical structure issn: issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal| january 2011 | vol. 1 | issue 1 | pp. 110-145 117 pitkänen m. dna as topological quantum computer: part i of the theory and these algebras provide a justification for several ideas introduced earlier on basis of physical intuition. hyper-finite factor of type ii1 has a canonical realization as an infinite-dimensional clifford algebra and the obvious guess is that it corresponds to the algebra spanned by the gamma matrices of wcw. also the local clifford algebra of the imbedding space h = m4 × cp2 in octonionic representation of gamma matrices of h is important and the entire quantum tgd emerges from the associativity or coassociativity conditions for the sub-algebras of this algebra which are local algebras localized to maximal associative or co-associate sub-manifolds of the imbedding space identifiable as space-time surfaces. the notion of inclusion for hyper-finite factors provides an elegant description for the notion of measurement resolution absent from the standard quantum measurement theory. 1. the included sub-factor creates in zero energy ontology states not distinguishable from the original one and the formally the coset space of factors defining quantum spinor space defines the space of physical states modulo finite measument resolution. 2. the quantum measurement theory for hyperfinite factors differs from that for factors of type i since it is not possible to localize the state into single ray of state space. rather, the ray is replaced with the sub-space obtained by the action of the included algebra defining the measurement resolution. the role of complex numbers in standard quantum measurement theory is taken by the non-commutative included algebra so that a non-commutative quantum theory is the outcome. 3. this leads also to the notion of quantum group. for instance, the finite measurement resolution means that the components of spinor do not commute anymore and it is not possible to reduce the state to a precise eigenstate of spin. it is however perform a reduction to an eigenstate of an observable which corresponds to the probability for either spin state. 4. the realization for quantum measurement theory modulo finite measurement resolution is in terms of m -matrices defined in terms of connes tensor product which essentially means that the included hyper-finite factor n takes the role of complex num bers. as already explained, the topology of the many-sheeted space-time encourages the generalization of the notion of quantum entanglement in such a manner that unentangled systems can possess entangled sub-systems. one can say that the entanglement between subselves is not visible in the resolution characterizing selves. this makes possible sharing and fusion of mental images central for tgd inspired theory of consciousness. these concepts find a deeper justification from the quantum measurement theory for hyper-finite factors of type ii1 for which the finite measurement resolution is basic notion. also the notions of resolution and monitoring pop up naturally in this framework. p-adic probabilities relate very naturally to hyper-finite factors of type ii1 and extend the expressive power of the ordinary probability theory. p-adic thermodynamics with conformal cutoff is very natural for hyper-finite factors of type ii1 and explains p-adic length scale hypothesis p ' 2k, k prime characterizing exponentially smaller p-adic length scale. 2.4 nmp and biology the notion of self is crucial for the understanding of bio-systems and consciousness. it seems that the negentropic entanglement is the decisive element of life and that one can say that in metaphoral sense life resides in the intersection of real and p-adic worlds. 2.4.1 generalization of the notion of information tgd inspired theory of consciousness, in particular the formulation of negentropy maximization principle (nmp) in p-adic context, has forced to rethink the notion of the information concept. in tgd state preparation process is realized as a sequence of self measurements and state preparation for next quantum jump is state reduction for the previous quantum jump. in zero energy ontology one can interpret the state preparation for positive and negative energy parts of the state as reduction and preparation in the sense of standard physics. each self measurement means a decomposition of the sub-system involved to issn: issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal| january 2011 | vol. 1 | issue 1 | pp. 110-145 118 pitkänen m. dna as topological quantum computer: part i two unentangled parts unless the system is bound state. the decomposition is fixed highly uniquely from the requirement that the reduction of the entanglement entropy is maximal. bound state entanglement is stable against self measurement simply because energy conservation prevents the decay to a pair of free (uncorrelated) subsystems. the generalized definition of entanglement entropy allows to assign a negative value of entanglement entropy to rational and algebraic entanglement, so that this kind of entanglement would actually carry information, in fact conscious information (experience of understanding). this kind of entanglement cannot be reduced in state function reduction. macro-temporal quantum coherence could correspond to a generation of either bound state entanglement or negentropic entanglement, and is indeed crucial for ability to have long lasting non-entropic mental images. generation of negentropic entanglement would involve experience about expansion of consciousness and that of bound states entanglement a loss of consciousness. the mathematical models for quantum computers typically operate with systems for which entanglement probabilities are identical. also rational numbers are involved. does this mean that negentropic entanglement makes possible quantum computation? this does not seem to be the case. state function reduction with random outcomes is a central element of quantum computation which suggests that quantum computation must be based on entropic entanglement with large enough value of ~ to overcome the restrictions caused by the interactions with the external world. the negentropic entanglement in turn would relate to conscious information processing involving experience of understanding represented by negentropic entanglement. negentropic entanglement would make possible conscious cellular automaton type information processing much closer to that carried out by ordinary computers and this information processing might be equally important in living systems. 2.4.2 life as islands of rational/algebraic numbers in the seas of real and p-adic continua? rational and even algebraic entanglement coefficients make sense in the intersection of real and p-adic words, which suggests that life and conscious intelligence reside in the intersection of the real and p-adic worlds. this would mean that the mathematical expressions for the space-time surfaces (or at least 3surfaces or partonic 2-surfaces and their 4-d tangent planes) make sense in both real and p-adic sense for some primes p. same would apply to the expressions defining quantum states. in particular, entanglement probabilities would be rationals or algebraic numbers so that entanglement can be negentropic and the formation of bound states in the intersection of real and p-adic worlds generates information and is thus favored by nmp. the identification of intentionality as the basic aspect of life seems to be consistent with this idea. 1. the proposed realization of the intentional action has been as a transformation of p-adic spacetime sheet to a real one. also transformations of real space-time sheets to p-adic space-time sheets identifiable as cognitions are possible. algebraic entanglement is a prerequisite for the realization of intentions in this manner. essentially a leakage between p-adic and real worlds is in question and makes sense only in zero energy ontology. the reason is that various quantum numbers in real and p-adic sectors are not in general comparable in positive energy ontology so that conservation laws would be broken or even cease to make sense. 2. the transformation of intention to action can occur if the partonic 2-surfaces and their 4-d tangent space-distributions are representable using rational functions with rational (or even algebraic) coefficients in preferred coordinates for the imbedding space dictated by symmetry considerations. intentional systems must live in the intersection of real and p-adic worlds. 3. for the minimal option life would be also effectively 2-dimensional phenomenon and essentially a boundary phenomenon as also number theoretical criticality suggests. there are good reasons to expect that only the data from the intersection of real and p-adic partonic two-surfaces appears in u -matrix so that only the data from rational and some algebraic points of the partonic 2-surface dictate u -matrix. this means discretization at parton level and something which might be called number theoretic quantum field theory should emerge as a description of intentional action. a good guess is that algebraic entanglement is essential for quantum computation, which therefore might correspond to a conscious process. hence cognition could be seen as a quantum computation like issn: issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal| january 2011 | vol. 1 | issue 1 | pp. 110-145 119 pitkänen m. dna as topological quantum computer: part i process, a more approriate term being quantum problem solving [27]. living-dead dichotomy could correspond to rational-irrational or to algebraic-transcendental dichotomy: this at least when life is interpreted as intelligent life. life would in a well defined sense correspond to islands of rationality/algebraicity in the seas of real and p-adic continua. life as a critical phenomenon in the number theoretical sense would be one aspect of quantum crticality of tgd universe besides the criticality of the space-time dynamics and the criticality with respect to phase transitions changing the value of planck constant and other more familiar criticalities. how closely these criticalities relate remains an open question [26]. the view about the crucial role of rational and algebraic numbers as far as intelligent life is considered, could have been guessed on very general grounds from the analogy with the orbits of a dynamical system. rational numbers allow a predictable periodic decimal/pinary expansion and are analogous to one-dimensional periodic orbits. algebraic numbers are related to rationals by a finite number of algebraic operations and are intermediate between periodic and chaotic orbits allowing an interpretation as an element in an algebraic extension of any p-adic number field. the projections of the orbit to various coordinate directions of the algebraic extension represent now periodic orbits. the decimal/pinary expansions of transcendentals are un-predictable being analogous to chaotic orbits. the special role of rational and algebraic numbers was realized already by pythagoras, and the fact that the ratios for the frequencies of the musical scale are rationals supports the special nature of rational and algebraic numbers. the special nature of the golden mean, which involves √ 5, conforms the view that algebraic numbers rather than only rationals are essential for life. that only algebraic extensions are possible is of course only a working hypothesis. also finitedimensional extensions of p-adic numbers involving transcendentals are possible and might in fact be necessary. consider for instance the extension containing e, e2, .., ep−1 as units (ep is ordinary p-adic number. infinite number of analogous finite-dimensional extensions can be constructed by taking a function of integer variable such that f(p) exists both p-adically and as a real transcendental number. the powers of f(p)1/n for a fixed value of n define a finite-dimensional transcendental extension of p-adic numbers if the roots do not exist p-adically. numbers like log(p) and π cannot belong to a finite-dimensional extension of p-adic numbers [21]. one cannot of course take any strong attitude concerning the possibility of infinite-dimensional extensions of p-adic numbers but the working hypothesis has been that they are absent. the phases exp(i2π/n) define finite dimensional extensions allowing to replace the notion of angle in finite measurement resolution with the corresponding phase factors in finite measurement. the functions exp(i2πq/n), where q is arbitrary p-adic integers define in a natural manner the physical counterparts of plane waves and angular momentum eigenstates not allowing an identification as ordinary p-adic exponential functions. they are clearly strictily periodic functions of q with a finite value set. if n is divisible by a power of p, these functions are continuous since the values of the function for q and q + kpn are identical for large enough values of n. this condition is essential and means in the case of plane waves that the size scale of a system (say one-dimensional box) is multiple of a power of p. 2.4.3 evolution and second law evolution has many facets in tgd framework. 1. a natural characterization of evolution is in terms of p-adic topology relating naturally to cognition. p-adic primes near powers of two are favored if cds have the proposed discrete size spectrum. from the point of view of self this would be essentially cosmic expansion in discrete jumps. cds and can be characterized by powers of 2 and if partonic 2-surfaces correspond to effective p-adic p-adic topology characterized by a power of two, one obtains the commeasurability of the secondary p-adic time scale of particle and that of cd in good approximation. 2. the notion of infinite primes motivates the hypothesis that the many-sheeted structure of spacetime can be coded by infinite primes[20]. the number of primes larger than given infinite prime p is infinitely larger than the number of primes than p . the infinite prime p characterizing the entire universe decomposes in a well defined manner to finite primes and p-adic evolution at the level of entire universe is implied by local p-adic evolution at the level of selves. therefore maximum entanglement negentropy gain for p-adic self increases at least as log(p) with p in the long run. issn: issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal| january 2011 | vol. 1 | issue 1 | pp. 110-145 120 pitkänen m. dna as topological quantum computer: part i this kind of relationship might hold true for real selves of p-adic physics is physics of cognitive representations of real physics as suggested by the success of p-adic mass calculations. thus it should be possible to assign definite p-adic prime to each partonic 2-surface. 3. a further aspect of evolution relates to the hierarchy of planck constants implying that at dark matter levels rational or at least integer multiples of the favored p-adic time scales are realized. the latter option is favored by the idea that the book like structure with pages consisting of many-sheeted coverings of cd and cp2, and correlates with the emergence of algebraic extensions of p-adic numbers defined by the roots exp(i2π/n) of unity. for the latter option evolution by quantum jumps would automatically imply the drifting of the partonic 2-surfaces to the pages of books labelled by increasing values of planck constant. for more general option one might argue that drifting to pages with small values of planck constant is also possible. this would give kind of antizooms of long length scale physics to short scales. both kind of temporal zooms could be crucial for conscious intelligence building scaled models about time evolution in various scales. 4. the generation of negentropic entanglement between different number fields would of course be the fundamental aspect of evolution. it would give rise to increasingly complex and negentropic sensory perceptions and cognitive representations based on conscious rules coded by negentropic entanglement. this would justify the association concept as it used in neuro-science. negentropic entanglement could be also crucial for the basic mechanism of metabolism and make possible conscious co-operation even in nano-scales. just for fun one can play also with numbers. 1. the highest dark matter level associated with self corresponds to its geometric duration which can be arbitrarily long: the typical duration of the memory span gives an idea about the level of dark matter hierarchy involved if one assumes that the time scale .1 seconds assignable to electrons is the fundamental time scale. if the time scale t of human life cycle corresponds to a secondary p-adic time scale then t = 100 years gives the rough estimate r ≡ ~/~0 = 233 if this time scale corresponds to that for dark electron. the corresponding primary p-adic time length scale corresponds to k = 160 and is 2.2× 10−7 meters. 2. if human time scale -taken to be t = 100 yearscorresponds to primary p-adic time scale of electron, one must have roughly r = 297. i have already discussed the second law in tgd framework and it seems that its applies only when the time scale of perception is longer than the time scale characterizing the level of the p-adic and dark matter hierarchy. second law as it is usually stated can be seen as an unavoidable implication of the materialistic ontology. 2.4.4 stable entanglement and quantum metabolism as different sides of the same coin the notion of binding has two meanings. binding as a formation of bound state and binding as a fusion of mental images to larger ones essential for the functioning of brain and regarded as one the big problems of consciousness theory. only bound state entanglement and negentropic entanglement are stable against the state reduction process. hence the fusion of the mental images implies the formation of a bound entropic statein this case the two interpretations of binding are equivalentor a negentropic state, which need not be bound state. 1. in the case of negentropic entanglement bound state need not be formed and the interesting possibility is that the negentropic entanglement could give rise to stable states without binding energy. this could allow to understand the mysterious high energy phosphate bond to which metabolic energy is assigned in atp molecule containing three phosphates and liberated as atp decays to adp and phosphate molecule. negentropic entanglement could also explain the stability of dna and other highly charged biopolymers. in this framework the liberation of metabolic (negentropic) energy would involve dropping of electrons to a larger space-time sheets accompanying the process atp → adp + pi. a detailed model of this process is discussed in [29]. issn: issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal| january 2011 | vol. 1 | issue 1 | pp. 110-145 121 pitkänen m. dna as topological quantum computer: part i 2. the formation of bound state entanglement is expected to involve a liberation of the binding energy and this energy might be a usable energy. this process could perhaps be coined as quantum metabolism and one could say that quantum metabolism and formation of bound states are different sides of the same coin. it is known that an intense neural activity, although it is accompanied by an enhanced blood flow to the region surrounding the neural activity, does not involve an enhanced oxidative metabolism [73] (that is atp → adp process and its reversal). a possible explanation is that quantum metabolism accompanying the binding is involved. note that the bound state is sooner or later destroyed by the thermal noise so that this mechanism would in a rather clever manner utilize thermal energy by applying what might be called buy now–pay later principle. if these interpretations are correct, there would be two modes of metabolism corresponding to two different kinds of fusion of mental images. 2.5 generalization of thermodynamics allowing negentropic entanglement and a model for conscious information processing the possibility of negetropic entanglement in tgd framework means that the second law of thermodynamics must be modified. the most obvious modification means only the replacement s → s−n , where s is thermodynamical entropy and n the negentropy associated with negentropic entanglement. hence the basic formulas of thermodynamics remain formally as such. the generalization leads to a thermodynamical model for how conscious information is generated and how metabolism relates to this. one can also understand why living matter is so effective entropy producer as compared to inanimate matter and the characteristic decomposition of living systems to highly negentropic and entropic parts. 2.5.1 modification of thermodynamics to take into account negentropic entanglement what does the presence of the negentropic entanglement mean from the point of view of thermodynamics? there are two obvious options to consider. the optimistic option is just the standard thermodynamics saying nothing about negentropy generation. the pessimistic option is that the generation of negentropy must be accompanied by a generation of at least the same amount of entropy: the good news is that this entropy can be carried by different system and it is possible to have genuinely negentropic systems. the following consideration is restricted to the pessimistic option which seems to be more realistic view about the world we live in. 1. one must generalize the basic expression for energy differential de = tds − dw → t (ds − dn)− dw . (2.1) this means that there are two kinds of energies given out by the system. the useful work dw and negentropic energy tdn . for steam engine only dw is present. for ideal system only negentropic energy would be present. 2. what happens to the second law? the pessimistic guess is that generation of negentropy requires a generation of at least same amount of entropy so that one would have ∆s −∆n ≥ 0 . (2.2) here s can be interpreted as a sum of two terms. the first part corresponds to the ensemble entropy generated by the randomness of ordinary quantum jumps, and second part to the entropy assignable as maximal entanglement entropy assignable to the decompositions of bound state to two parts. n corresponds to maximal negentropy for the decompositions of negentropic sub-system to pairs. one can criticize these definitions and a possible modification of could be as as the average for the entanglement entropies over this kind of decompositions. issn: issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal| january 2011 | vol. 1 | issue 1 | pp. 110-145 122 pitkänen m. dna as topological quantum computer: part i 3. quite generally, clausius inequality allowing to deduce extremization conditions for various thermodynamical potentials generalizes to t0(∆s −∆n)−∆e − p0∆v ≥ 0 . (2.3) where t0 and p0 and temperature and pressure of heat bath. living systems would be entropy producers and this seems to conform with what we see around us. for instance, for a system in constant volume one would have ∆s −∆n − ∆e t ≥ 0 . (2.4) so that systems developing negentropy would also generate thermodynamics entropy. for a system in heat bath one has t = t0 and clausius inequality gives ∆f = −∆w (2.5) stating that increase of free energy at constant temperature requires work done on the system (dw < 0): otherwise ∆f ≤ 0 holds true. by using the variable s − n instead of s all formulas reduce formally to standard thermodynamics except that s can be negative. 2.5.2 the analog of carnot cycle as a simple model for information processing in living matter carnot engine transforms heat to work. costa de beauregard [52] has proposed a modification of carnot engine as a model for information processing. one can consider carnot engine and its information theoretic analog in this framework. 1. the basic equation for carnot engine is dw = dqin − dqout ≥ 0 . (2.6) optimal efficiency corresponds to dsout = dsin. 2. the information theoretic analog of carnot engine proposed by beauregard does not perform work and one would have dw = 0 , (2.7) and dn = dsout − dsin ≥ 0 . (2.8) the interpretation would be that incoming entropy flow leaves the computer in a state of higher entropy and the difference corresponds to information dn feeded to say printer. the increase of entropy would have interpretation in terms of erasing of data from computer memory. issn: issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal| january 2011 | vol. 1 | issue 1 | pp. 110-145 123 pitkänen m. dna as topological quantum computer: part i the problematic aspect of the model is that it requires tin > tout in order to have dn > 0. for living systems one has however typically tin < tout. already for tin = tout the situation trivializes since one has dn = 0 (2.9) by dw = 0 and ds = dq/t . 3. in the recent case however a more general condition tind(sin −nin)− toutd(sout −nout) ≥ 0 (2.10) holds true and allows to generate conscious information provided it is compensated by thermodynamical entropy. note that the temperature of the environment can be even lower than the temperatures of the system. it is also possible to transform information to work as the expression for the differential df = −sdt − tdn − dw of the generalized free energy e = e − ts shows. the increase of dw for the work done by the system is compensated by the reduction of information dn so that system loses negentropy in the process keeping df constant. the loss of negentropy couild be interpreted in terms of a loss of metabolic energy which corresponds to negentropic entanglement for amp, adp, and atp molecules. 2.5.3 basic biological implications some clarifying comments about biological implications are in order. 1. there is no need to restrict the consideration to equilibrium systems. first of all, the environment and living system are in general at different temperatures and temperature difference is typically of wrong sign for the model of beauregard to work in this context. beauregard’s model is of course a model for computation, not for the generation of negentropic mental images. maybe cognitive machine might be proper term for what the modified model could describe. 2. quite generally, self-organization requires a feed of energy to the system so that one has flow equilibrium. in the case of living system this feed of energy is metabolic energy associated with the negentropic entanglement transferred to the system in the atp-adp process. self-organization driven by negentropic entanglement leads to standardized negentropic mental images automatically as asymptotic self-organization patterns in 4-d sense (cds within cds within ... : cd denotes causal diamond defined as cartesian produc to the intersection of the future and past directed light-cones with cp2, which is the key notion in zero energy ontology). 3. no explicit assumptions about computational aspects of the process has been made. just a generation of conscious information identified in terms of negentropic entanglement is assumed. the basic character quantum jump as u -process followed by the cascade of state function reductions represents a fractal hierarchy of what can be seen as quantum computations and are distinguished from classical computations in that the process proceeds from top to bottom rather than being a local process. the result of computation is represented using statistical ensembles defined by subcds at various levels of the hierarchy and is in principle communicable by classical fields (say eeg patterns in the case of brain) to higher levels of self hierarchy which in turn can induces the same distributions so that communication of the objective aspects of the experience with the mediation of ”medium” is possible. the presence of the ”medium” seems unavoidable. magnetic body would be this medium in tgd inspired biology. issn: issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal| january 2011 | vol. 1 | issue 1 | pp. 110-145 124 pitkänen m. dna as topological quantum computer: part i living matter involves also another aspect made possible by the generalized second law obtained by the replacement s → s − n . subsystem can have also negative net entropy and split to two highly negentropic and entropic pieces. in the extreme situation this is nothing but excretion, which is absolutely essential element of being alive but sometimes forgotten from the lists of properties distinguishing living matter from inanimate matter. it is not at all clear whether this is possible for standard non-equilibrium systems defining information as a reduction of disorder. at all levels of the fractal hierarchy division into negentropic and entropic subsystems is expected. this picture seems to be in accordance with basic chemistry of energy metabolism. 1. the process creating both negentropy and entropy would be standardized in living matter and mean a generation of high energy phosphate bonds assignable to amp, adp, and atp containing 1, 2, and 3 phosphates respectively besides the sugar residue. sugar residue is basic nutrient and would provide the stored metabolic energy transformed to the negentropic energy of the high energy phosphate bonds if the proposed view is correct. also other dna nucleotides such as g can appear besides a but in metabolism a has a preferred role. 2. the basic metabolic cycle provides adp with an additional phosphate energizing it to atp and the reverse process transfers the metabolic energy and also negentropic entanglement to the acceptor molecule. also adp can provide metabolic energy by transforming to amp when atp is not available in sufficient amounts. that the catabolism of amp creates urea excreted out of the system fits with the general picture. the catabolism for nutrients would create the entropy compensating for the negentropy of the high energy phosphate bonds. 3. the backbone of dna is made of sugar and phosphate residues and corresponds to a sequence of xmp , x = a, t,c,g with each xmp presumably containing single high energy phosphate bond serving as a storage or potential source of negentropy. this conforms with the view that dna carries conscious information. negentropic and entropic entanglement are assumed to generate mental images with opposite emotional colors. this connects information processing with emotions. from neuroscience point of view this is not a news: peptides are molecules of emotions on one hand and molecules of information on the other hand [76]. the well-known specialization of the left and right hand sides of the amygdala to experience positive and negatively colored emotions could be seen as one instance of this connection and representing also an example about fractal negentropic-entropic differentiation. 3 how quantum computation in tgd universe differs from standard quantum computation? many problems of quantum computation in standard sense might relate to a wrong view about quantum theory. if tgd universe is the physical universe, the situation would improve in many respects. there is the new fractal view about quantum jump and observer as ”self”; there is p-adic length scale hierarchy and hierarchy of planck constants as well as self hierarchy; there is a new view about entanglement and the possibility of irreducible entanglement carrying genuine information and making possible quantum superposition of fractal quantum computations and quantum parallel dissipation; there is zero energy ontology, the notion of m -matrix allowing to understand quantum theory as a square root of thermodynamics, the notion of measurement resolution allowing to identify m -matrix in terms of connes tensor product; there is also the notion of magnetic body providing one promising realization for braids in tqc, etc... this section gives a short summary of these aspects of tgd. there is also a second motivation for this section. quantum tgd and tgd inspired theory of consciousness involve quite a bundle of new ideas and the continual checking of internal consistency by writing it through again and again is of utmost importance. this section can be also seen as this kind of checking. i can only represent apologies to the benevolent reader: this is a work in rapid progress. issn: issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal| january 2011 | vol. 1 | issue 1 | pp. 110-145 125 pitkänen m. dna as topological quantum computer: part i 3.1 general ideas related to topological quantum computation topological computation relies heavily on the representation of tqc program as a braiding. there are many kinds of braidings. number theoretic braids are defined by the orbits of minima of vacuum expectation of higgs at lightlike partonic 3-surfaces (and also at space-like 3-surfaces). there are braidings defined by kähler gauge potential (possibly equivalent with number theoretic ones) and by kähler magnetic field. magnetic flux tubes and partonic 2-surfaces interpreted as strands of define braidings whose strands are not infinitely thin. a very concrete and very complex time-like braiding is defined by the motions of people at the surface of globe: perhaps this sometimes purposeless-looking fuss has a deeper purpose: maybe those at the higher levels of dark matter hierarchy are using us to carry out complex topological quantum computations)! 3.1.1 general vision about quantum computation in tgd universe the hierarchy of planck constants gives excellent prerequisites for all kinds of quantum computations. the general vision about quantum computation (tqc) would result as a special case and would look like follows. 1. time-like entanglement between positive and negative energy parts of zero energy states would define the analogs of qc-programs. space-like quantum entanglement between ends of strands whose motion defines time-like braids would provide a representation of q-information. 2. both timeand space-like quantum entanglement would correspond to connes tensor product expressing the finiteness of the measurement resolution between the states defined at ends of space-like braids whose orbits define time like braiding. the characterization of the measurement resolution would thus define both possible q-data and tq-programs as representations for ”laws of physics”. 3. the braiding between dna strands with each nucleotide defining one strand transversal to dna realized in terms of magnetic flux tubes was my first bet for the representation of space-like braiding in living matter. it turned out that the braiding is more naturally defined by flux tubes connecting nucleotides to the lipids of nuclear-, cell-, and endoplasma membranes. also braidings between other microtubules and axonal membrane can be considered. the conjectured hierarchy of genomes giving rise to quantum coherent gene expressions in various scales would correspond to computational hierarchy. 3.1.2 about the relation between space-like and time-like number theoretic braidings the relationship between spaceand time-like braidings is interesting and there might be some connections also to 4-d topological gauge theories suggested by geometric langlands program discussed in the previous posting and also in [16]. 1. the braidings along light-like surfaces modify space-like braiding if the moving ends of the space-like braids at partonic 3-surfaces define time-like braids. from tqc point of view the interpretation would be that tqc program is written to memory represented as the modification of space-like braiding in 1-1 correspondence with the time-like braiding. 2. the orbits of space-like braids define codimension two sub-manifolds of 4-d space-time surface and can become knotted. presumably time-like braiding gives rise to a non-trivial ”2-braid”. could also the ”2-braiding” based on this knotting be of importance? do 2-connections of n-category theorists emerge somehow as auxiliary tools? could 2-knotting bring additional structure into the topological qft defined by 1-braidings and chern-simons action? 3. the strands of dynamically evolving braids could in principle go through each other so that time evolution can transform braid to a new one also in this manner. this is especially clear from standard representation of knots by their planar projections. the points where intersection occurs correspond to self-intersection points of 2-surface as a sub-manifold of space-time surface. topological qft:s are also used to classify intersection numbers of 2-dimensional surfaces understood as homological equivalence classes. now these intersection points would be associated with ”braid cobordism”. issn: issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal| january 2011 | vol. 1 | issue 1 | pp. 110-145 126 pitkänen m. dna as topological quantum computer: part i 3.1.3 quantum computation as quantum superposition of classical computations? it is often said that quantum computation is quantum super-position of classical computations. in standard path integral picture this does not make sense since between initial and final states represented by classical fields one has quantum superposition over all classical field configurations representing classical computations in very abstract sense. the metaphor is as good as the perturbation theory around the minimum of the classical action is as an approximation. in tgd framework the classical space-time surface is a preferred extremal of kähler action so that apart from effects caused by the failure of complete determinism, the metaphor makes sense precisely. besides this there is of course the computation associated with the spin like degrees of freedom in which one has entanglement and which one cannot describe in this manner. for tqc a particular classical computation would reduce to the time evolution of braids and would be coded by 2-knot. classical computation would be coded to the manipulation of the braid. note that the branching of strands of generalized number theoretical braids has interpretation as classical communication. 3.1.4 the identification of topological quantum states quantum states of tqc should correspond to topologically robust degrees of freedom separating neatly from non-topological ones. 1. the generalization of the imbedding space inspired by the hierarchy of planck constants suggests an identification of this kind of states as elements of the group algebra of discrete subgroup of so(3) associated with the group defining covering of m4 or cp2 or both in large ~ sector. one would have wave functions in the discrete space defined by the homotopy group of the covering transforming according to the representations of the group. this is by definition something robust and separated from non-topological degrees of freedom (standard model quantum numbers). there would be also a direct connection with anyons. 2. an especially interesting group is dodecahedral group corresponding to the minimal quantum phase q = exp(2π/5) (golden mean) allowing a universal topological quantum computation: this group corresponds to dynkin diagram for e8 by the ale correspondence. interestingly, neuronal synapses involve clathrin molecules [70] associated with microtubule ends possessing dodecahedral symmetry. 3.1.5 some questions a conjecture inspired by the inclusions of hffs is that these states can be also regarded as representations of various gauge groups which tgd dynamics is conjectured to be able to mimic so that one might have connection with non-abelian chern-simons theories where topological s-matrix is constructed in terms of path integral over connections: these connections would be only an auxiliary tool in tgd framework. 1. do these additional degrees of freedom give only rise to topological variants of gaugeand conformal field theories? note that if the earlier conjecture that entire dynamics of these theories could be mimicked, it would be best to perform tqc at quantum criticality where either m4 or cp2 dynamical degrees of freedom or both disappear. 2. could it be advantageous to perform tqc near quantum criticality? for instance, could one construct magnetic braidings in the visible sector near q-criticality using existing technology and then induce phase transition changing planck constant by varying some parameter, say temperature. 3.2 fractal hierarchies fractal hierarchies are the essence of tgd. there is hierarchy of space-time sheets labelled by preferred p-adic primes. there is hierarchy of planck constants reflecting a book like structure of the generalized imbedding space and identified in terms of a hierarchy of dark matters. these hierarchies correspond at the level of conscious experience to a hierarchy of conscious entities selves: self experiences its sub-selves as mental images. issn: issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal| january 2011 | vol. 1 | issue 1 | pp. 110-145 127 pitkänen m. dna as topological quantum computer: part i fractal hierarchies mean completely new element in the model for quantum computation. the decomposition of quantum computation to a fractal hierarchy of quantum computations is one implication of this hierarchy and means that each quantum computation proceeds from longer to shorter time scales tn = t02−n as a cascade like process such that at each level there is a large number of quantum computations performed with various values of input parameters defined by the output at previous level. under some additional assumptions to be discussed later this hierarchy involves at a given level a large number of replicas of a given sub-module of tqc so that the output of single fractal sub-module gives automatically probabilities for various outcomes as required. 3.3 irreducible entanglement and possibility of quantum parallel quantum computation the basic distinction from standard measurement theory is irreducible entanglement not reduced in quantum jump. 3.3.1 nmp and the possibility of irreducible entanglement negentropy maximimization principle (nmp) states that entanglement entropy is minimized in quantum jump. for standard shannon entropy this would lead to a final state which corresponds to a ray of state space. if entanglement probabilities are rational or even algebraic one can replace shannon entropy with its number theoretic counterpart in which p-adic norm of probability replaces the probability in the argument of logarithm: log(pn) → log(|pn|p). this entropy can have negative values. it is not quite clear whether prime p should be chosen to maximize the number theoretic negentropy or whether p is the p-adic prime characterizing the light-like partonic 3-surface in question. obviously nmp favors generation of irreducible entanglement which however can be reduced in u process. irreducible entanglement is something completely new and the proposed interpretation is in terms of experience of various kinds of conscious experiences with positive content such as understanding. quantum superposition of unitarily evolving quantum states generalizes to a quantum superposition of quantum jump sequences defining dissipative time evolutions. dissipating quarks inside quantum coherent hadrons would provide a basic example of this kind of situation. 3.3.2 quantum parallel quantum computations and conscious experience the combination of quantum parallel quantum jump sequences with the fractal hierarchies of scales implies the possibility of quantum parallel quantum computations. in ordinary quantum computation halting selects single computation but in the recent case arbitrarily large number of computations can be carried out simultaneously at various branches of entangled state. the probability distribution for the outcomes is obtained using only single computation. one would have quantum superposition of space-time sheets (assignable to the maxima of kähler function) each representing classically the outcome of a particular computation. each branch would correspond to its own conscious experience but the entire system would correspond to a self experiencing consciously the outcome of computation as intuitive and holistic understanding, and abstraction. emotions and emotional intellect could correspond to this kind of non-symbolic representation for the outcome of computation as analogs for collective parameters like temperature and pressure. 3.3.3 delicacies there are several delicacies involved. 1. the above argument works for factors of type i. for hffs of type ii1 the finite measurement resolution characterized in terms of the inclusionn ⊂mmean is that state function reduction takes place to n -ray. there are good reasons to expect that the notion of number theoretic entanglement negentropy generalizes also to this case. note that the entanglement associated with n is below measurement resolution. issn: issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal| january 2011 | vol. 1 | issue 1 | pp. 110-145 128 pitkänen m. dna as topological quantum computer: part i 2. in tgd inspired theory of consciousness irreducible entanglement makes possible sharing and fusion of mental images. at space-time level the space-time sheets corresponding to selves are disjoint but the space-time sheets topologically condensed at them are joined typically by what i call join along boundaries bonds identifiable as braid strands (magnetic flux quanta). in topological computation with finite measurement resolution this kind of entanglement with environment would be below the natural resolution and would not be a problem. 3. state function reduction means quantum jump to an eigen state of density matrix. suppose that density matrix has rational elements. number theoretic vision forces to ask whether the quantum jump to eigen state is possible if the eigenvalues of ρ do not belong to the algebraic extension of rationals and p-adic numbers used. if not, then one would have number theoretically irreducible entanglement depending on the algebraic extension used. if the eigenvalues actually define the extension there would be no restrictions: this option is definitely simpler. 4. fuzzy quantum logic [18] brings also complications. what happens in the case of quantum spinors that spin ceases to be observable and one cannot reduce the state to spin up or spin down. rather, one can measure only the eigenvalues for the probability operator for spin up (and thus for spin down) so that one has fuzzy quantum logic characterized by quantum phase. inclusions of hffs are characterized by quantum phases and a possible interpretation is that the quantum parallelism related to the finite measurement resolution could give rise to fuzzy qubits. also the number theoretic quantum parallelism implied by number theoretic nmp could effectively make probabilities as operators. the probabilities for various outcomes would correspond to outcomes of quantum parallel state function reductions. 3.4 possible problems related to quantum computation at least following problems are encountered in quantum computation. 1. how to preserve quantum coherence for a long enough time so that unitary evolution can be achieved? 2. the outcome of calculation is always probability distribution: for instance, the output with maximum probability can correspond to the result of computation. the problem is how to replicate the computation to achieve the desired accuracy. or more precisely, how to produce replicas of the hardware of quantum computer defined in terms of classical physics? 3. how to isolate the quantum computer from the external world during computation and despite this feed in the inputs and extract the outputs? 3.4.1 the notion of coherence region in tgd framework in standard framework one can speak about coherence in two senses. at the level of schrödinger amplitudes one speaks about coherence region inside which it makes sense to speak about schrödinger time evolution. this notion is rather defined. in tgd framework coherence region is identifiable as a region inside which the modified dirac equation holds true. strictly speaking, this region corresponds to a light-like partonic 3-surface whereas 4-d spacetime sheet corresponds to coherence region for classical fields. p-adic length scale hierarchy and hierarchy of planck constants means that arbitrarily large coherence regions are possible. the precise definition for the notion of coherence region and the presence of scale hierarchies imply that the coherence in the case of single quantum computation is not a problem in tgd framework. decoherence time or coherence time correspond to the temporal span of space-time sheet and a hierarchy coming in powers of two for a given value of planck constant is predicted by basic quantum tgd. p-adic length scale hypothesis and favored values of planck constant would naturally reflect this fundamental fractal hierarchy. issn: issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal| january 2011 | vol. 1 | issue 1 | pp. 110-145 129 pitkänen m. dna as topological quantum computer: part i 3.4.2 de-coherence of density matrix and replicas of tqc second phenomenological description boils down to the assumption that non-diagonal elements of the density matrix in some preferred basis (involving spatial localization of particles) approach to zero. the existence of more or less faithful replicas of space-time sheet in given scale allows to identify the counterpart of this notion in tgd context. de-coherence would mean a loss of information in the averaging of m -matrix and density matrix associated with these space-time sheets. topological computations are probabilistic. this means that one has a collection of space-time sheets such that each space-time sheet corresponds to more or less the same tqc and therefore the same m matrix. if m is too random (in the limits allowed by connes tensor product), the analog of generalized phase information represented by its ”phase” s-matrix is useless. in order to avoid de-coherence in this sense, the space-time sheets must be approximate copies of each other. almost copies are expected to result by dissipation leading to asymptotic self-organization patterns depending only weakly on initial conditions and having also space-time correlates. obviously, the role of dissipation in eliminating effects of de-coherence in tqc would be something new. the enormous symmetries of m -matrix, the uniqueness of s-matrix for given resolution and parameters characterizing braiding, fractality, and generalized bohr orbit property of space-time sheets, plus dissipation give good hopes that almost replicas can be obtained. 3.4.3 isolation and representations of the outcome of tqc the interaction with environment makes quantum computation difficult. in the case of topological quantum computation this interaction corresponds to the formation of braid strands connecting the computing space-time sheet with space-time sheets in environment. the environment is four-dimensional in tgd framework and an isolation in time direction might be required. the space-time sheets responsible for replicas of tqc should not be connected by light-like braids strands having time-like projections in m4. length scale hierarchy coming in powers of two and finite measurement resolution might help considerably. finite measurement resolution means that those strands which connect space-time sheets topologically condensed to the space-time sheets in question do not induce entanglement visible at this level and should not affect tqc in the resolution used. hence only the elimination of strands responsible for tqc at given level and connecting computing space-time sheet to space-time sheets at same level in environment is necessary and would require magnetic isolation. note that super-conductivity might provide this kind of isolation. this kind of elimination could involve the same mechanism as the initiation of tqc which cuts the braid strands so the initiation and isolation might be more or less the same thing. strands reconnect after the halting of tqc and would make possible the communication of the outcome of computation along strands by using say em currents in turn generating generalized eeg, nerve pulse patterns, gene expression, etc... halting and initiation could be more or less synonymous with isolation and communication of the outcome of tqc. 3.4.4 how to express the outcome of quantum computation? the outcome of quantum computation is basically a representation of probabilities for the outcome of tqc. there are two representations for the outcome of tqc. symbolic representation which quite generally is in terms of probability distributions represented in terms ”classical space-time” physics. the rates for various processes having basically interpretation as geometro-temporal densities would represent the probabilities just as in the case of particle physics experiment. for tqc in living matter this would correspond to gene expression, neural firing, eeg patterns,... a representation as a conscious experience is another (and actually the ultimate) representation of the outcome. it need not have any symbolic counterpart since it is felt. intuition, emotions and emotional intelligence would naturally relate to this kind of representation made possible by irreducible entanglement. this representation would be based on fuzzy qubits and would mean that the outcome would be true or false only with certain probability. this unreliability would be felt consciously. the proposed model of tqc combined with basic facts about theta waves [75, 74] to be discussed in the subsection about the role of supra currents in tqc suggests that eeg rhythm (say theta rhythm) and issn: issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal| january 2011 | vol. 1 | issue 1 | pp. 110-145 130 pitkänen m. dna as topological quantum computer: part i correlated firing patterns correspond to the isolation at the first half period of tqc and random firing at second half period to the sub-sequent tqc:s at shorter time scales coming as negative powers of 2. the fractal hierarchy of time scales would correspond to a hierarchy of frequency scales for generalized eeg and power spectra at these scales would give information about the outcome of tqc. synchronization would be obviously an essential element in this picture and could be understood in terms of classical dynamics which defines space-time surface as a generalized bohr orbit. tqc would be analogous to the generation of a dynamical hologram or ”conscious hologram” [31]. eeg rhythm would correspond to reference wave generated by magnetic body as control and coordination signal and the contributions of spikes to eeg generated by neurons would correspond to the incoming wave interfering with the reference wave. 3.4.5 how data is feeded into submodules of tqc? scale hierarchy obviously gives tqc a fractal modular structure and the question is how data is feeded to submodules at shorter length scales. there are certainly interactions between different levels of scale hierarchy. the general ideas about master-slave hierarchy assigned with self-organization support the hypothesis that these interactions are directed from longer to shorter scales and have interpretation as a specialization of input data to tqc sub-modules represented by smaller space-time sheets of hierarchy. the call of submodule would occur when the tqc of the calling module halts and the result of computation is expressed as a 4-d pattern. the lower level module would start only after the halting of tqc (with respect to subjective time at least) and the durations of resulting tqc’s would come as tn = 2−nt0 that geometric series of tqc’s would become possible. there would be entire family of tqc’s at lower level corresponding to different values of input parameters from calling module. one of the ideas assigned to hyper-computation [44] is that one can have infinite series of computations with durations comings as negative powers of 2 (zeno paradox obviously inspires this idea). in tgd framework there can be however only a finite series of these tqc’s since cp2 time scale poses a lower bound for the duration of tqc. one might of course ask whether the spectrum of planck constant could help in this respect. 3.4.6 the role of dissipation and energy feed dissipation plays key role in the theory of self-organizing systems [46]. its role is to serve as a darwinian selector. without an external energy feed the outcome is a situation in which all organized motions disappear. in presence of energy feed highly unique self-organization patterns depending only very weakly on the initial conditions emerge. in the case of tqc one function of dissipation would be to drive the braidings to static standard configurations, and perhaps even effectively eliminate fluctuations in non-topological degrees of freedom. note that magnetic fields are important for 1-gates. magnetic flux conservation however saves magnetic fields from dissipation. external energy feed is needed in order to generate new braidings. for the proposed model of cellular tqc the flow of intracellular water induces the braiding and requires energy feed. also now dissipation would drive this flow to standard patterns coding for tqc programs. metabolic energy would be also needed in order to control whether lipids can flow or not by generating cis type unsaturated bonds. obviously, energy flows defining self organization patterns would define tqc programs. 3.4.7 is it possible to realize arbitrary tqc? the 4-d spin glass degeneracy of tgd universe due to the enormous vacuum degeneracy of kähler action gives good hopes that the classical dynamics for braidings allows to realize every possible tqc program. as a consequence, space-time sheets decompose to maximal non-deterministic regions representing basic modules of tqc. similar decomposition takes place at the level of light-like partonic 3-surfaces and means decomposition to 3-d regions inside which conformal invariance eliminates light-like direction as dynamical degree of freedom so that the dynamics is effectively that of 2-dimensional object. since these 3-d regions behave as independent units as far as longitudinal conformal invariance is considered, one can say that light-like 3-surfaces are 3-dimensional in discretized sense. in fact, for 2-d regions standard conformal issn: issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal| january 2011 | vol. 1 | issue 1 | pp. 110-145 131 pitkänen m. dna as topological quantum computer: part i invariance implies similar effective reduction to 1-dimensional dynamics realized in terms of a net of strings and means that 2-dimensionality is realized only in discretized sense. 4 dna as topological quantum computer braids [38] code for topological quantum computation. one can imagine many possible identifications of braids but this is not essential for what follows. what is highly non-trivial is that the motion of the ends of strands defines both time-like and space-like braidings with latter defining in a well-defined sense a written version of the tqc program, kind of log file. the manipulation of braids is a central element of tqc and if dna really performs tqc, the biological unit modifying braidings should be easy to identify. an obvious signature is the 2-dimensional character of this unit. 4.1 conjugate dna as performer of tqc and lipids as quantum dancers in this section the considerations are restricted to dna as tqc. it is however quite possible that also rna and other biomolecules could be involved with tqc like process. 4.1.1 sharing of labor the braid strands must begin from dna double strands. precisely which part of dna does perform tqc? genes? introns[72]? or could it be conjugate dna which performs tqc? the function of conjugate dna has indeed remained a mystery and sharing of labor suggests itself. conjugate dna would do tqc and dna would ”print” the outcome of tqc in terms of rna yielding amino-acids in the case of exons. rna could the outcome in the case of introns. the experience about computers and the general vision provided by tgd suggests that introns could express the outcome of tqc also electromagnetically in terms of standardized field patterns. also speech would be a form of gene expression. the quantum states braid would entangle with characteristic gene expressions. this hypothesis will be taken as starting point in the following considerations. 4.1.2 cell membranes as modifiers of braidings defining tqc programs? the manipulation of braid strands transversal to dna must take place at 2-d surface. the ends of the space-like braid are dancers whose dancing pattern defines the time-like braid, the running of classical tqc program. space-like braid represents memory storage and tqc program is automatically written to memory during the tqc. the inner membrane of the nuclear envelope and cell membrane with entire endoplasmic reticulum included are good candidates for dancing hall. the 2-surfaces containing the ends of the hydrophobic ends of lipids could be the parquets and lipids the dancers. this picture seems to make sense. 1. consider first the anatomy of membranes. cell membrane [65] and membranes of nuclear envelope [71] consist of 2 lipid [63] layers whose hydrophobic ends point towards interior. there is no water here nor any direct perturbations from the environment or interior milieu of cell. nuclear envelope consists of two membranes having between them an empty volume of thickness 20-40 nm. the inner membrane consists of two lipid layers like ordinary cell membrane and outer membrane is connected continuously to endoplasmic reticulum [61], which forms a highly folded cell membrane. many biologists believe that cell nucleus is a prokaryote, which began to live in symbiosis with a prokaryote defining the cell membrane. 2. what makes dancing possible is that the phospholipid layers of the cell membrane are liquid crystals [55]: the lipids can move freely in the horizontal direction but not vertically. ”phospho” could relate closely to the metabolic energy needs of dancers. if these lipids are self-organized around braid strands, their dancing patterns along the membrane surface would be an ideal manner to modify braidings since the lipids would have standard positions in a lattice. this would be like dancing on a chessboard. note that the internal structure of lipid does not matter in this picture since it is braid color dicated by dna nucleotide which matters. as a matter fact, living matter is full issn: issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal| january 2011 | vol. 1 | issue 1 | pp. 110-145 132 pitkänen m. dna as topological quantum computer: part i of self-organizing liquid crystals and one can wonder whether the deeper purpose of their life be running and simultaneous documentation of tqc programs? 3. ordinary computers have an operating system [54]: a collection of standard programs the system and similar situation should prevail now. the ”printing” of outputs of tqc would represent example of this kind of standard program. this tqc program should not receive any input from the environment of the nucleus and should therefore correspond to braid strands connecting conjugate strand with strand. braid strands would go only through the inner nuclear membrane and return back and would not be affected much since the volume between inner and outer nuclear membranes is empty. this assumption looks ad hoc but it will be found that the requirement that these programs are inherited as such in the cell replication necessitates this kind of structure (see the section ”cell replication and tqc”). 4. the braid strands starting from the conjugate dna could traverse several time through the highly folded endoplasmic reticulum but without leaving cell interior and return back to nucleus and modify tqc by intracellular input. braid strands could also traverse the cell membrane and thus receive information about the exterior of cell. both of these tqc programs could be present also in prokaryotes [66] but the braid strands would always return back to the dna, which can be also in another cell. in multicellulars (eukaryotes [67]) braid strands could continue to another cell and give rise to ”social” tqc programs performed by the multicellular organisms. note that the topological character of braiding does not require isolation of braiding from environment. it might be however advantageous to have some kind of sensory receptors amplifying sensory input to standardized re-braiding patterns. various receptors in cell membrane would serve this purpose. 5. braid strands can end up at the parquet defined by ends of the inner phospholipid layer: their distance of inner and outer parquet is few nanometers. they could also extend further. i) if one is interested in connecting cell nucleus to the membrane of another cell, the simpler option is the formation of hole defined by a protein attached to cell membrane. in this case only the environment of the second cell affects the braiding assignable to the first cell nucleus. ii) the bi-layered structure of the cell membrane could be essential for the build-up of more complex tqc programs since the strands arriving at two nearby hydrophobic 2-surfaces could combine to form longer strands. the formation of longer strands could mean the fusion of the two nearby hydrophobic two-surfaces in the region considered. in fact, tqc would begin with the cutting of the strands so that non-trivial braiding could be generated via lipid dance and tqc would halt when strands would recombine and define a modified braiding. this would allow to connect cell nucleus and cell membrane to a larger tqc unit and cells to multicellular tqc units so that the modification of tqc programs by feeding the information from the exteriors of cells essential for the survival of multicellulars would become possible. 4.1.3 gene expression and other basic genetic functions from tqc point of view it is useful to try to imagine how gene expression might relate to the halting of tqc. there are of course myriads of alternatives for detailed realizations, and one can only play with thoughts to build a reasonable guess about what might happen. 1. qubits for transcription factors and other regulators genetics is consistent with the hypothesis that genes correspond to those tqc moduli whose outputs determine whether genes are expressed or not. the naive first guess would be that the value of single qubit determines whether the gene is expressed or not. next guess replaces ”is ” with ”can be”. indeed, gene expression involves promoters, enhancers and silencers [62]. promoters are portions of the genome near genes and recognized by proteins known as transcription factors [68]. transcription factors bind to the promoter and recruit rna polymerase, an enzyme that synthesizes rna. in prokaryotes rna polymerase itself acts as the transcription factor. for eukaryotes situation is more complex: at least seven transcription factors are involved with the recruitment of the rna polymerase ii catalyzing issn: issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal| january 2011 | vol. 1 | issue 1 | pp. 110-145 133 pitkänen m. dna as topological quantum computer: part i the transcription of the messenger rna. there are also transcription factors for transcription factors and transcription factor for the transcription factor itself. the implication is that several qubits must have value ”yes” for the actual expression to occur since several transcription factors are involved with the expression of the gene in general. in the simplest situation this would mean that the computation halts to a measurement of single qubit for subset of genes including at least those coding for transcription factors and other regulators of gene expression. 2. intron-exon qubit genes would have very many final states since each nucleotide is expected to correspond to at least single qubit. without further measurements that state of nucleotides would remain highly entangled for each gene. also these other qubits are expected to become increasingly important during evolution. for instance, eukaryotic gene expression involves a transcription of rna and splicing out of pieces of rna which are not translated to amino-acids (introns). also the notion of gene is known to become increasingly dynamical during the evolution of eukaryotes so that the expressive power of genome increases. a single qubit associated with each codon telling whether it is spliced out or not would allow maximal flexibility. tqc would define what genes are and the expressive power of genes would be due to the evolution of tqc programs: very much like in the case of ordinary computers. stopping sign codon and starting codon would automatically tell where the gene begins and ends if the corresponding qubit is ”yes”. in this picture the old fashioned static genes of prokaryotes without splicings would correspond to tqc programs for which the portions of genome with a given value of splicing qubit are connected. 3. what about braids between dna, rna, trna and amino-acids this simplified picture might have created the impression that amino-acids are quantum outsiders obeying classical bio-chemistry. for instance, transcription factors would in this picture end up to the promoter by a random process and ”print” would only increase the density of the transcription factor. if dna is able to perform tqc, it would however seem very strange if it would be happy with this rather dull realization of other central functions of the genetic apparatus. one can indeed consider besides the braids connecting dna and its conjugate crucial for the success of replication also braids connecting dna to mrna and other forms of rna, mrna to trna, and trna to amino-acids. these braids would provide the topological realization of the genetic code and would increase dramatically the precision and effectiveness of the transcription and translation if these processes correspond to quantum transitions at the level of dark matter leading more or less deterministically to the desired outcome at the level of visible matter be it formation of dna doublet strand, of dna-mrna association, of mrna-trna association or trna-amino-acid association. for instance, a temporary reduction of the value of planck constant for these braids would contract these to such a small size that these associations would result with a high probability. the increase of planck constant for braids could in turn induce the transfer of mrna from the nucleus, the opening of dna double strand during transcription and mitosis. also dna-amino-acid braids might be possible in some special cases. the braiding between regions of dna at which proteins bind could be a completely general phenomenon. in particular, the promoter region of gene could be connected by braids to the transcription factors of the gene and the halting of tqc computation to printing command could induce the reduction of planck constant for these braids inducing the binding of the transcription factor binds to the promoter region. in a similar manner, the region of dna at which rna polymerase binds could be connected by braid strands to the rna polymerase. 4.1.4 how braid color is represented? if braid strands carry 4-color (a,t,c,g) then also lipid strands should carry this kind of 4-color. the lipids whose hydrophobic ends can be joined to form longer strand should have same color. this color need not be chemical in tgd universe. only braid strands of the same color can be connected as tqc halts. this poses strong restrictions on the model. 1. do braid strands appear as patches possessing same color? issn: issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal| january 2011 | vol. 1 | issue 1 | pp. 110-145 134 pitkänen m. dna as topological quantum computer: part i color conservation is achieved if the two lipid layers decompose in a similar manner into regions of fixed color and the 2-d flow is restricted inside this kind of region at both layers. a four-colored map of cell membrane would be in question! liquid crystal structure [65] applies only up to length scale of l(151) = 10 nm and this suggests that lipid layer decomposes into structural units of size l(151) defining also cell membrane thickness. these regions might correspond to minimal regions of fixed color containing n ∼ 102 lipids. the controversial notion of lipid raft [69] was inspired by the immiscibility of ordered and disordered liquid phases in a liquid model of membrane. the organization to connected regions of particular phase could be a phenomenon analogous to a separation of phases in percolation. many cell functions implicate the existence of lipid rafts. the size of lipid rafts has remained open and could be anywhere between 1 and 1000 nm. also the time scale for the existence of a lipid raft is unknown. a line tension between different regions is predicted in hydrodynamical model but not observed. if the decomposition into ordered and disordered phases is time independent, ordered phases could correspond to those involved with tqc and possess a fixed color. if disordered phases contain no braid strands the mixing of different colors is avoided. the problem with this option is that it restricts dramatically the possible braidings. if one takes this option seriously, the challenge is to make patches and patch color (a,t,c,g) visible. perhaps one could try to mark regions of portions of lipid layer by some marker to find whether the lipid layer decomposes to non-mixing regions. quantum criticality suggests that that the patches of lipid layer have a fractal structure corresponding to a hierarchy of tqc program modules. the hydrodynamics would be thus fractal: patches containing patches.... moving with respect to each other would correspond to braids containing braids containing ... such that sub-braids behave as braid strands. in principle this is also a testable prediction. 2. does braid color corresponds to some chemical property? the conserved braid color is not necessary for the model but would imply genetic coding of the tqc hardware so that sexual reproduction would induce an evolution of tqc hardware. braid color would also make the coupling of foreign dna to the tqc performed by the organism difficult and realize an immune system at the level of quantum information processing. the conservation of braid color poses however considerable problems. the concentration of braid strands of the same color to patches would guarantee the conservation but would restrict the possible braiding dramatically. a more attractive option is that the strands of same color find each other automatically by energy minimization after the halting of tqc. electromagnetic coulomb interaction would be the most natural candidate for the interaction in question. braid color would define a faithful genetic code at the level of nucleotides. it would induce long range correlation between properties of dna strand and the dynamics of cell immediately after the halting of tqc. the idea that color could be a chemical property of phospholipids does not seem plausible. the lipid asymmetry of the inner and outer monolayers excludes the assignment of color to the hydrophilic groups ps, pi, pe, pch. fatty acids have n = 14, ..., 24 carbon atoms and n = 16 and 18 are the most common cases so that one could consider the possibility that the 4 most common feet pairs could correspond to the resulting combinations. it is however extremely difficult to understand how long range correlation between dna nucleotide and fatty acid pair could be created. 3. does braid color correspond to neutral quark pairs? it seems that the color should be a property of the braid strand. in tgd inspired model of high tc super-conductivity [24] wormhole contacts having u and d and d and u quarks at the two wormhole throats feed electron’s gauge flux to larger space-time sheet. the long range correlation between electrons of cooper pairs is created by color confinement for an appropriate scaled up variant of chromo-dynamics which are allowed by tgd. hence the neutral pairs of colored quarks whose members are located the ends of braid strand acting like color flux tube connecting the nucleotide to the lipid could code dna color to qcd color. for the pairs ud with net em charge the quark and anti-quark have the same sign of em charge and tend to repel each other. hence the minimization of electro-magnetic coulomb energy favors the neutral configurations uu, dd and uu, and dd coding for a,t,c,g in some order. after the halting of tqc only these pairs would form with a high probability. the reconnection of the issn: issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal| january 2011 | vol. 1 | issue 1 | pp. 110-145 135 pitkänen m. dna as topological quantum computer: part i strands would mean a formation of a short color flux tube between the strands and the annihilation of quark pair to gluon. note that single braid strand would connect dna color and its conjugate rather than identical colors so that braid strands connecting two dna strands (conjugate strands) should always traverse through an even (odd) number of cell membranes. the only plausible looking option is that nucleotides a,t,g,c are mapped to pairs of quark and anti-quarks at the ends of braid strand. symmetries pose constraints on this coding. 1. by the basic assumptions charge conjugation must correspond to dna conjugation so that one a and t would be coded to quark pair, say qq and its conjugate qq. same for c and g. 2. an additional aesthetically appealing working hypothesis is that both a and g with the same number of aromatic cycles (three) correspond to qq (or its conjugate). this would leave four options: (a,g)→ (uu, dd) , (t,c)→ (uu, dd) , (a,g)→ (dd, uu) , (t,c)→ (dd), uu) , (t,c)→ (uu, dd) , (a,g)→ (uu, dd) , (t,c)→ (dd, uu) , (a,g)→ (dd), uu) . (4.1) it is an experimental problem to deduce which of these correspondences if any is realized. 4.1.5 some general predictions during tqc the lipids of the two lipid layers should define independent units of lipid hydrodynamics whereas after halting of tqc they should behave as single dynamical unit. later it will be found that these two phases should correspond to high tc superconductivity for electrons (cooper pairs would bind the lipid pair to form single unit) and its absence. this prediction is testable. the differentiation of cells should directly correspond to the formation of a mapping of a particular part of genome to cell membrane. for neurons the gene expression is maximal which conforms with the fact that neurons can have very large size. axon might be also part of the map. stem cells represent the opposite extreme and in this case minimum amount of genome should be mapped to cell membrane. the prediction is that the evolution of cell should be reflected in the evolution of the genome-membrane map. 4.1.6 quantitative test for the proposal there is a simple quantitative test for the proposal. a hierarchy of tqc programs is predicted, which means that the number of lipids in the nuclear inner membrane should be larger or at least of the same order of magnitude that the number of nucleotides. for definiteness take the radius of the lipid molecule to be about 5 angstroms (probably somewhat too large) and the radius of the nuclear membrane about 2.5 µm. for our own species the total length of dna strand is about one meter and there are 30 nucleotides per 10 nm. this gives 6.3 × 107 nucleotides: the number of intronic nucleotides is only by few per cent smaller. the total number of lipids in the nuclear inner membrane is roughly 108. the number of lipids is roughly twice the number nucleotides. the number of lipids in the membrane of a large neuron of radius of order 10−4 meters is about 1011. the fact that the cell membrane is highly convoluted increases the number of lipids available. folding would make possible to combine several modules in sequence by the proposed connections between hydrophobic surfaces. 4.2 how quantum states are realized? quantum states should be assigned to the ends of the braid strands and therefore to the nucleotides of dna and conjugate dna. the states should correspond to many-particle states of anyons and fractional electrons and quarks and anti-quarks are the basic candidates. issn: issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal| january 2011 | vol. 1 | issue 1 | pp. 110-145 136 pitkänen m. dna as topological quantum computer: part i 4.2.1 anyons represent quantum states the multi-sheeted character of space-time surface as a 4-surface in a book like structure having as pages covering spaces of the imbedding space (very roughly, see the appendix) would imply additional degrees of freedom corresponding to the group algebra of the group g ⊃ zn defining the covering. especially interesting groups are tedra-hedral, octahedral, and icosahedral groups whose action does not map any plane to itself. group algebra would give rise to n(g) quantum states. if electrons are labeled by elements of group algebra this gives 2n(g)-fold additional degeneracy corresponding to many-electron states at sheets of covering. the vacuum state would be excluded so that 2n(g) − 1 states would result. if only cooper pairs are allowed one would have mn = 2n(g)−1 − 1 states. this picture suggests the fractionization of some fermionic charges such as em charge, spin, and fermion number. this aspect is discussed in detail in the appendix. single fermion state would be replaced by a set of states with fractional quantum numbers and one would have an analogy with the full electronic shell of atom in the sense that a state containing maximum number of anyonic fermions with the same spin direction would have the quantum numbers of the ordinary fermion. one can consider two alternative options. 1. the fractionization of charges inspired the idea that catalytic hot spots correspond to ”half” hydrogen bonds containing dark fractionally charged electron meaning that the fermi sea for electronic anyons is not completely filled [25]. the formation of hydrogen bond would mean a fusion of ”half hydrogen bond” and its conjugate having by definition a compensating fractional charges guaranteing that the net em charge and electron number of the resulting state are those of the ordinary electron pair and the state is stable as an analog of the full electron shell. half hydrogen bonds would assign to bio-molecules ”names” as sequences of half hydrogen bonds and only molecules whose ”names” are conjugates of each other would form stable hydrogen bonded pairs. therefore symbolic dynamics would enter the biology via bio-catalysis. concerning quantum computation the problem is that the full shell assigned to hydrogen bond corresponds to only single state and cannot carry information. 2. the assignment of braids and fractionally charged anyonic quarks and anti-quarks would realize very similar symbolic dynamics. one cannot exclude the possibility that leptonic charges fractionize to same values as quark charges. this suggest the following picture. 1. one could assign the fractional quantum numbers to the quarks and anti-quarks at the ends of the flux tubes defining the braid strands. this hypothesis is consistent with the correspondence between nucleotides and quarks and assigns anyonic quantum states to the ends of the braid. wormhole magnetic fields would distinguish between matter in vivo and in vitro. this option is certainly favored by occam’s razor in tgd universe. 2. hydrogen bonds connect the dna strands which suggests that fractionally charged quantum states at the ends of braids might be assignable to the ends of hydrogen bonds. the model for plasma electrolysis of kanarev [17] leads to a proposal that new physics is involved with hydrogen bonds. the presence of fractionally charged particles at the ends of bond might provide alternative explanation for the electrostatic properties of hydrogen bonds usually explained in terms of a modification electronic charge distribution by donor-acceptor mechanism. there would exists entire hierarchy of hydrogen bonds corresponding to the increasing values of planck constant. dna and even hydrogen bonds associated with water might correspond to a larger value of planck constant for mammals than for bacteria. 3. the model for protein folding code [28] leads to a cautious conclusion that flux tubes are prerequisites for the formation of hydrogen bonds although not identifiable with them. the model predicts also the existence of long flux tubes between acceptors of hydrogen bonds (such as o =, and aromatic rings assignable to dna nucleotides, amino-acid backbone, phosphates, xy p , x = a, t,g,c, y = m,d, t ). this hypothesis would allow detailed identification of places to which quantum states are assigned. issn: issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal| january 2011 | vol. 1 | issue 1 | pp. 110-145 137 pitkänen m. dna as topological quantum computer: part i 4.2.2 hierarchy of genetic codes defined by mersenne primes the model for the hierarchy of genetic codes inspires the question whether the favored values of n(g)− 1 correspond to mersenne primes [40]. the table below lists the lowest hierarchies. most of them are short. {mn} {n(g)} {nb} {2, 7, 127, 2127 − 1, ?} {4, 8, 128, 2127, ?} {2, 6, 126, 2126, ?} {5, 31, 231 − 1} {6, 32, 231} {4, 30, 230} {13, 213 − 1} {14, 213} {12, 212} {17, 217 − 1} {18, 217} {16, 216} {19, 219 − 1} {20, 219} {18, 218} {61, 261 − 1} {62, 261} {60, 260} {89, 289 − 1} {90, 289} {88, 288} {107, 2107 − 1} {108, 2107} {106, 2106} (4.2) the number of states assignable to mn is mn = 2n − 1 which does not correspond to full n bits: the reason is that one of the states is not physically realizable. 2n−1 states have interpretation as maximal number of mutually consistent statements and to nb = n− 1 bits. the table above lists the values of nb for mersenne primes. notice that micro-tubules decompose into 13 parallel helices consisting of 13 tubulin dimers. could these helices with the conformation of the last tubulin dimer serving as a kind of parity bit realize m13 code? there would be a nice connection with the basic phenomenology of ordinary computers. the value of the integer n− 1 associated with mersenne primes would be analogous to the number of bits of the basic information unit of processor. during the evolution of pcs it has evolved from 8 to 32 and is also power of 2. 4.3 the role of high tc superconductivity in tqc a simple model for braid strands leads to the understanding of how high tc super conductivity assigned with cell membrane [32] could relate to tqc. the most plausible identification of braid strands is as magnetic or wormhole magnetic flux tubes consisting of pairs of flux tubes connected by wormhole contacts whose throats carry fermion and anti-fermion such that their rotational motion at least partially generates the antiparallel magnetic fluxes at the two sheets of flux tube. the latter option is favored by the model of tqc but one must of course keep mind open for variants of the model involving only ordinary flux tubes. both kinds of flux tubes can carry charged particles such as protons, electrons, and biologically important ions as dark matter with large planck constant and the model for nerve pulse and eeg indeed relies on this assumption [33]. 4.3.1 currents at space-like braid strands if space-like braid strands are identified as idealized structures obtained from 3-d tube like structures by replacing them with 1-d strands, one can regard the braiding as a purely geometrical knotting of braid strands. the simplest realization of the braid strand as magnetic flux tube would be as a hollow cylindrical surface connecting conjugate dna nucleotide to cell membrane and going through 5and/or 6cycles associated with the sugar backbone of conjugate dna nucleotides. the free electron pairs associated with the aromatic cycles would carry the current creating the magnetic field needed. for wormhole magnetic flux one would have pair of this kind of hollow cylinders connected by wormhole contacts and carrying opposite magnetic fluxes. in this case the currents created by wormhole contacts would give rise to the antiparallel magnetic fluxes at the space-time sheets of wormhole contact and could serve as controllers of tqc. i have indeed proposed long time ago that so called wormhole bose-einstein condensates might be fundamental for the quantum control in living matter [23]. in this case the presence of supra currents at either sheet would generate asymmetry between the magnetic fluxes. issn: issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal| january 2011 | vol. 1 | issue 1 | pp. 110-145 138 pitkänen m. dna as topological quantum computer: part i there are two extreme options for both kinds of magnetic fields. for b-option magnetic field is parallel to the strand and vector potential rotates around it. for a-option vector potential is parallel to the strand and magnetic field rotates around it. the general case corresponds to the hybrid of these options and involves helical magnetic field, vector potential, and current. 1. for b-option current flowing around the cylindrical tube in the transversal direction would generate the magnetic field. the splitting of the flux tube would require that magnetic flux vanishes requiring that the current should go to zero in the process. this would make possible selection of a part of dna strand participating to tqc. 2. for a-option the magnetic field lines of the braid would rotate around the cylinder. this kind of field is created by a current in the direction of cylinder. in the beginning of tqc the strand would split and the current of electron pairs would stop flowing and the magnetic field would disappear. also now the initiation of computation would require stopping of the current and should be made selectively at dna. the control of the tqc should rely on currents of electron pairs (perhaps cooper pairs) associated with the braid strands. supra currents would have quantized values and they are therefore very attractive candidates. the (supra) currents could also bind lipids to pairs so that they would define single dynamical unit in 2-d hydrodynamical flow. one can also think that cooper pairs with electrons assignable to different members of lipid pair bind it to a single dynamical unit. 4.3.2 do supra currents generate magnetic fields? energetic considerations favor the possibility that supra currents create the magnetic fields associated with the braid strands defined by magnetic flux tubes. in the case of wormhole magnetic flux tubes supra currents could generate additional magnetic fields present only at the second sheet of the flux tube. supra current would be created by a voltage pulse ∆v , which gives rise to a constant supra current after it has ceased. supra current would be destroyed by a voltage pulse of opposite sign. therefore voltage pulses could define an elegant fundamental control mechanism allowing to select the parts of genome participating to tqc. this kind of voltage pulse could be collectively initiated at cell membrane or at dna. note that constant voltage gives rise to an oscillating supra current. josephson current through the cell membrane would be also responsible for dark josephson radiation determining that part of eeg which corresponds to the correlate of neuronal activity [32]. note that tgd predicts a fractal hierarchy of eegs and that ordinary eeg is only one level in this hierarchy. the pulse initiating or stopping tqc would correspond in eeg to a phase shift by a constant amount ∆φ = ze∆v t/~ , where t is the duration of pulse and ∆v its magnitude. the contribution of josephson current to eeg responsible for beta and theta bands interpreted as satellites of alpha band should be absent during tqc and only eeg rhythm would be present. the periods dominated by eeg rhythm should be observed as eeg correlates for problem solving situations (say mouse in a maze) presumably involving tqc. the dominance of slow eeg rhythms during sleep and meditation would have interpretation in terms of tqc. 4.3.3 topological considerations the existence of supra current requires that the flow allows for a complex phase exp(iψ) such that supra current is proportional to ∇ψ. this requires integrability in the sense that one can assign to the flow lines of a or b (combination of them in the case of a-b braid) a coordinate variable ψ varying along the flow lines. in the case of a general vector field x this requires ∇ψ = φx giving ∇×x = −∇φ/φ as an integrability condition. this condition defines what is known as beltrami flow [19]. the perturbation of the flux tube, which spoils integrability in a region covering the entire cross section of flux tube means either the loss of super-conductivity or the disappearance of the net supra current. in the case of the a-braid, the topological mechanism causing this is the increase in the dimension of the cp2 projection of the flux tube so that it becomes 3-d [19], where i have also considered the possibility issn: issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal| january 2011 | vol. 1 | issue 1 | pp. 110-145 139 pitkänen m. dna as topological quantum computer: part i that 3-d character of cp2 projection is what transforms the living matter to a spin glass type phase in which very complex self-organization patterns emerge. this would conform with the idea that in tqc takes place in this phase. 4.3.4 fractal memory storage and tqc if josephson current through cell membrane ceases during tqc, tqc manifests itself as the presence of only eeg rhythm characterized by an appropriate cyclotron frequency. synchronous neuron firing might therefore relate to tqc. the original idea that a phase shift of eeg is induced by the voltage initiating tqc although wrong was however useful in that it inspired the question whether the initiation of tqc could have something to do with what is known as a place coding by phase shifts performed by hippocampal pyramidal cells [75, 74]. the playing with this idea provides important insights about the construction of quantum memories and demonstrates the amazing explanatory power of the paradigm once again. the model also makes explicit important conceptual differences between tqc a la tgd and in the ordinary sense of wordin particular those related to different view about the relation between subjective and geometric time. 1. in tgd tqc corresponds to the unitary process u taking place following by a state function reduction and preparation. it replaces configuration space (”world of classical worlds”) spinor field with a new one. configuration space spinor field represent generalization of time evolution of schrödinger equation so that a quantum jump occurs between entire time evolutions. ordinary tqc corresponds to hamiltonian time development starting at time t = 0 and halting at t = t to a state function reduction. 2. in tgd the expression of the result of tqc is essentially 4-d pattern of gene expression (spiking pattern in the recent case). in usual tqc it would be 3-d pattern emerging as the computation halts at time t. each moment of consciousness can be seen as a process in which a kind of 4-d statue is carved by starting from a rough sketch and proceeding to shorter details and building fractally scaled down variants of the basic pattern. our life cycle would be a particular example of this process and would be repeated again and again but of course not as an exact copy of the previous one. 1. empirical findings the place coding by phase shifts was discovered by o′reefe and recce [75]. in [74] y. yamaguchi describes the vision in which memory formation by so called theta phase coding is essential for the emergence of intelligence. it is known that hippocampal pyramidal cells have ”place property” being activated at specific ”place field” position defined by an environment consisting of recognizable objects serving as landmarks. the temporal change of the percept is accompanied by a sequence of place unit activities. the theta cells exhibit change in firing phase distributions relative to the theta rhythm and the relative phase with respect to theta phase gradually increases as the rat traverses the place field. in a cell population the temporal sequence is transformed into a phase shift sequence of firing spikes of individual cells within each theta cycle. thus a temporal sequence of percepts is transformed into a phase shift sequence of individual spikes of neurons within each theta cycle along linear array of neurons effectively representing time axis. essentially a time compressed representation of the original events is created bringing in mind temporal hologram. each event (object or activity in perceptive field) is represented by a firing of one particular neuron at time τn measured from the beginning of the theta cycle. τn is obtained by scaling down the real time value tn of the event. note that there is some upper bound for the total duration of memory if scaling factor is constant. this scaling down story telling seems to be a fundamental aspect of memory. our memories can even abstract the entire life history to a handful of important events represented as a story lasting only few seconds. this scaling down is thought to be important not only for the representation of the contextual information but also for the memory storage in the hippocampus. yamaguchi and collaborators have also found that the gradual phase shift occurs at half theta cycle whereas firings at the other half cycle show no correlation [74]. one should also find an interpretation for this. issn: issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal| january 2011 | vol. 1 | issue 1 | pp. 110-145 140 pitkänen m. dna as topological quantum computer: part i 2. tgd based interpretation of findings how this picture relates to tgd based 4-d view about memory in which primary memories are stored in the brain of the geometric past? 1. the simplest option is the initiation of tqc like process in the beginning of each theta cycle of period t and having geometric duration t/2. the transition t → t/2 conforms nicely with the fundamental hierarchy of time scales comings as powers defining the hierarchy of measurement resolutions and associated with inclusions of hyperfinite factors of type ii1 [18]. that firing is random at second half of cycle could simply mean that no tqc is performed and that the second half is used to code the actual events of ”geometric now”. 2. in accordance with the vision about the hierarchy of planck constants defining a hierarchy of time scales of long term memories and of planned action, the scaled down variants of memories would be obtained by down-wards scaling of planck constant for the dark space-time sheet representing the original memory. in principle a scaling by any factor 1/n (actually by any rational) is possible and would imply the scaling down of the geometric time span of tqc and of light-like braids. one would have tqc’s inside tqc’s and braids within braids (flux quanta within flux quanta). the coding of the memories to braidings would be an automatic process as almost so also the formation of their zoomed down variants. 3. a mapping of the time evolution defining memory to a linear array of neurons would take place. this can be understood if the scaled down variant (scaled down value of ~) of the space-time sheet representing original memory is parallel to the linear neuron array and contains at scaled down time value tn a stimulus forcing nth neuron to fire. the 4-d character of the expression of the outcome of tqc allows to achieve this automatically without complex program structure. to sum up, it seems that the scaling of planck constant of time like braids provides a further fundamental mechanism not present in standard tqc allowing to build fractally scaled down variants of not only memories but tqc’s in general. the ability to simulate in shorter time scale is a certainly very important prerequisite of intelligent and planned behavior. this ability has also a space-like counterpart: it will be found that the scaling of planck constant associated with space-like braids connecting bio-molecules might play a fundamental role in dna replication, control of transcription by proteins, and translation of mrna to proteins. a further suggestive conclusion is that the period t associated with a given eeg rhythm defines a sequence of tqc’s having geometric span t/2 each: the rest of the period would be used to perceive the environment of the geometric now. the fractal hierarchy of eegs would mean that there are tqc’s within tqc’s in a very wide range of time scales. 4.4 codes and tqc tgd suggests the existence of several (genetic) codes besides 3-codon code [30, 29]. the experience from ordinary computers and the fact that genes in general do not correspond to 3n nucleotides encourages to take this idea more seriously. the use of different codes would allow to tell what kind of information a given piece of dna strand represents. dna strand would be like a drawing of building containing figures (3-code) and various kinds of text (other codes). a simple drawing for the building would become a complex manual containing mostly text as the evolution proceeds: for humans 96 per cent of code would corresponds to introns perhaps obeying some other code. the hierarchy of genetic codes is obtained by starting from n basic statements and going to the meta level by forming all possible statements about them (higher order logics) and throwing away one which is not physically realizable (it would correspond to empty set in the set theoretic realization). this allows 2n−1 statements and one can select 2n−1 mutually consistent statements (half of the full set of statements) and say that these are true and give kind of axiomatics about world. the remaining statements are false. dna would realize only the true statements. the hierarchy of mersenne primes mn = 2n − 1 with mn(next) = mmn starting from n = 2 with m2 = 3 gives rise to 1-code with 4 codons, 3-code with 64 codons, and 3× 21 = 63-code with 2126 codons [30] realized as sequences of 63 nucleotides (the length of 63-codon is about 2l(151), roughly twice the issn: issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. dna decipher journal| january 2011 | vol. 1 | issue 1 | pp. 110-145 141 pitkänen m. dna as topological quantum computer: part i cell membrane thickness. it is not known whether this combinatorial hierarchy continues ad infinitum. hilbert conjectured that this is the case. in the model of pre-biotic evolution also 2-codons appear and 3-code is formed as the fusion of 1and 2-codes. the problem is that 2-code is not predicted by the basic combinatorial hierarchy associated with n = 2. there are however also other mersenne hierarchies and the next hierarchy allows the realization of the 2-code. this combinatorial hierarchy begins from fermat prime n = 2k + 1 = 5 with m5 = 25 − 1 = 31 gives rise to a code with 16 codons realized as 2-codons (2 nucleotides). second level corresponds to mersenne prime m31 = 231 − 1 and a code with 230=15×2 codons realized by sequences of 15 3-codons containing 45 nucleotides. this corresponds to dna length of 15 nm, or length scale 3l(149), where l(149) = 5 nm defines the thickness of the lipid layer of cell membrane. l(151) = 10 nm corresponds to 3 full 2π twists for dna double strand. the model for 3-code as fusion of 1and 2-codes suggests that also this hierarchy which probably does not continue further is realized. there are also further short combinatorial hierarchies corresponding to mersenne primes [40]. 1. n = 13 defines mersenne prime m13. the code would have 212=6×2 codons representable as sequences of 6 nucleotides or 2 3-codons. this code might be associated with microtubuli. 2. the fermat prime 17 = 24+1 defines mersenne prime m17 and the code would have 216=8×2 codons representable as sequences of 8 nucleotides. 3. n = 19 defines mersenne prime m19 and code would have 218=9×2 codons representable as sequences of 9 nucleotides or three dna codons. 4. the next mersennes are m31 belonging to n = 5 hierarchy, m61 with 260=30×2 codons represented by 30-codons. this corresponds to dna length l(151) = 10 nm (cell membrane thickness). m89 (44-codons), m107 (53-codons) and m127 (belonging to the basic hierarchy) are the next mersennes. next mersenne corresponds tom521 (260-codon) and to completely super-astrophysical p-adic length scale and might not be present in the hierarchy. this hierarchy is realized at the level of elementary particle physics and might appear also at the level of dna. the 1-, 2-, 3-, 6-, 8-, and 9-codons would define lowest combinatorial hierarchies. references books about tgd [1] m. pitkänen (2006), topological geometrodynamics: overview. http://tgd.wippiespace.com/public_html/tgdview/tgdview.html. [2] m. pitkänen (2006), quantum physics as infinite-dimensional geometry. http://tgd.wippiespace.com/public_html/tgdgeom/tgdgeom.html. [3] m. pitkänen (2006), physics in many-sheeted space-time. http://tgd.wippiespace.com/public_html/tgdclass/tgdclass.html. [4] m. pitkänen (2006), p-adic length scale hypothesis and dark matter hierarchy. http://tgd.wippiespace.com/public_html/paddark/paddark.html. [5] m. pitkänen (2006), quantum tgd. http://tgd.wippiespace.com/public_html/tgdquant/tgdquant.html. [6] m. pitkänen (2006), tgd as a generalized number theory. http://tgd.wippiespace.com/public_html/tgdnumber/tgdnumber.html. [7] m. pitkänen (2006), tgd and fringe physics. http://tgd.wippiespace.com/public_html/freenergy/freenergy.html. issn: issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. http://tgd.wippiespace.com/public_html/tgdview/tgdview.html http://tgd.wippiespace.com/public_html/tgdgeom/tgdgeom.html http://tgd.wippiespace.com/public_html/tgdclass/tgdclass.html http://tgd.wippiespace.com/public_html/paddark/paddark.html http://tgd.wippiespace.com/public_html/tgdquant/tgdquant.html http://tgd.wippiespace.com/public_html/tgdnumber/tgdnumber.html http://tgd.wippiespace.com/public_html/freenergy/freenergy.html dna decipher journal| january 2011 | vol. 1 | issue 1 | pp. 110-145 142 pitkänen m. dna as topological quantum computer: part i books about tgd inspired theory of consciousness and quantum biology [8] m. pitkänen (2006), tgd inspired theory of consciousness. http://tgd.wippiespace.com/public_html/tgdconsc/tgdconsc.html. [9] m. pitkänen (2006), bio-systems as self-organizing quantum systems. http://tgd.wippiespace.com/public_html/bioselforg/bioselforg.html. [10] m. pitkänen (2006), quantum hardware of living matter. http://tgd.wippiespace.com/public_html/bioware/bioware.html. [11] m. pitkänen (2006), bio-systems as conscious holograms. http://tgd.wippiespace.com/public_html/hologram/hologram.html. [12] m. pitkänen (2006), genes and memes. http://tgd.wippiespace.com/public_html/genememe/genememe.html. [13] m. pitkänen (2006), magnetospheric consciousness. http://tgd.wippiespace.com/public_html/magnconsc/magnconsc.html. [14] m. pitkänen (2006), mathematical aspects of consciousness theory. http://tgd.wippiespace.com/public_html/mathconsc/mathconsc.html. [15] m. pitkänen (2006), tgd and eeg. http://tgd.wippiespace.com/public_html/tgdeeg/tgdeeg.html. references to the chapters of the books about tgd [16] the chapter langlands program and tgd of [6]. http://tgd.wippiespace.com/public_html/tgdnumber/tgdeeg/tgdnumber.html#langlandia. [17] the chapter nuclear string model of [4]. http://tgd.wippiespace.com/public_html/paddark/paddark.html#nuclstring. [18] the chapter was von neumann right after all of [5]. http://tgd.wippiespace.com/public_html/tgdquant/tgdquant.html#vneumann. [19] the chapter basic extremals of kähler action of [3]. http://tgd.wippiespace.com/public_html/tgdclass/tgdclass.html#class. [20] the chapter tgd as a generalized number theory: infinite primes of [6]. http://tgd.wippiespace.com/public_html/tgdnumber/tgdnumber.html#visionc. [21] the chapter fusion of p-adic and real variants of quantum tgd to a more general theory of [6]. http://tgd.wippiespace.com/public_html/tgdnumber/tgdnumber.html#mblocks. references to the chapters of the books about tgd inspired theory of consciousness and quantum biology [22] the chapter about nature of time of [8]. http://tgd.wippiespace.com/public_html/tgdconsc/tgdconsc.html#timenature. [23] the chapter wormhole magnetic fields of [10]. http://tgd.wippiespace.com/public_html/bioware/bioware.html#wormc. issn: issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. http://tgd.wippiespace.com/public_html/tgdconsc/tgdconsc.html http://tgd.wippiespace.com/public_html/bioselforg/bioselforg.html http://tgd.wippiespace.com/public_html/bioware/bioware.html http://tgd.wippiespace.com/public_html/hologram/hologram.html http://tgd.wippiespace.com/public_html/genememe/genememe.html http://tgd.wippiespace.com/public_html/magnconsc/magnconsc.html http://tgd.wippiespace.com/public_html/mathconsc/mathconsc.html http://tgd.wippiespace.com/public_html/tgdeeg/tgdeeg.html http://tgd.wippiespace.com/public_html/tgdnumber/tgdeeg/tgdnumber.html#langlandia http://tgd.wippiespace.com/public_html/paddark/paddark.html#nuclstring http://tgd.wippiespace.com/public_html/tgdquant/tgdquant.html#vneumann http://tgd.wippiespace.com/public_html/tgdclass/tgdclass.html#class http://tgd.wippiespace.com/public_html/tgdnumber/tgdnumber.html#visionc http://tgd.wippiespace.com/public_html/tgdnumber/tgdnumber.html#mblocks http://tgd.wippiespace.com/public_html/tgdconsc/tgdconsc.html#timenature http://tgd.wippiespace.com/public_html/bioware/bioware.html#wormc dna decipher journal| january 2011 | vol. 1 | issue 1 | pp. 110-145 143 pitkänen m. dna as topological quantum computer: part i [24] the chapter bio-systems as super-conductors: part i of [10]. http://tgd.wippiespace.com/public_html/bioware/bioware.html#superc1. [25] the chapter about the new physics behind qualia of [10]. http://tgd.wippiespace.com/public_html/bioware/bioware.html#newphys. [26] the chapter quantum theory of self-organization of [9]. http://tgd.wippiespace.com/public_html/bioselforg/bioselforg.html#selforgac. [27] the chapter dna as topological quantum computer of [12]. http://tgd.wippiespace.com/public_html/genememe/genememe.html#dnatqc. [28] the chapter a model for protein folding and bio-catalysis of [12]. http://tgd.wippiespace.com/public_html/genememe/genememe.html#foldcat. [29] the chapter evolution in many-sheeted space-time of [12]. http://tgd.wippiespace.com/public_html/genememe/genememe.html#prebio. [30] the chapter genes and memes of [12]. http://tgd.wippiespace.com/public_html/genememe/genememe.html#genememec. [31] the chapter bio-systems as conscious holograms of [11]. http://tgd.wippiespace.com/public_html/hologram/hologram.html#hologram. [32] the chapter dark matter hierarchy and hierarchy of eegs of [15]. http://tgd.wippiespace.com/public_html/tgdeeg/tgdeeg.html#eegdark. [33] the chapter quantum model for nerve pulse of [15]. http://tgd.wippiespace.com/public_html//tgdeeg/tgdeeg/tgdeeg.html#pulse. articles related to tgd [34] m. pitkänen (2010), article series about topological geometrodynamics in prespacetime journal vol 1, issue 4. http://www.prespacetime.com/file/pstj_v1(4).pdf. [35] m. pitkänen (2010), tgd inspired theory of consciousness. journal of consciousness exploration & research, march 2010, vol. 1, issue 2, pp. 135-152. http://www.jcer.com/file/jcer_v1(2).pdf. [36] m. pitkänen (2010), quantum mind in tgd universe, journal of of consciousness exploration & research, november 2010, vol 1, issue 8, pp. 971-991. quantum dream inc.. http://www.jcer. com/file/jcer_v1(8).pdf. 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[39] b. shipman (1998) the geometry of momentum mappings on generalized flag manifolds, connections with a dynamical system, quantum mechanics and the dance of honeybee.http://math.cornell.edu/~oliver/shipman.gif. b. shipman (1998), on the geometry of certain isospectral sets in the fullkostant-toda lattice.http: //nyjm.albany.edu:8000/pacj/1997/shipman.html. b. shipman (1998), a symmetry of order two in the full kostant-toda lattice.http://www.math. rochester.edu:8080/u/shipman/symmetrypaper/. issn: issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. http://tgd.wippiespace.com/public_html/bioware/bioware.html#superc1 http://tgd.wippiespace.com/public_html/bioware/bioware.html#newphys http://tgd.wippiespace.com/public_html/bioselforg/bioselforg.html#selforgac http://tgd.wippiespace.com/public_html/genememe/genememe.html#dnatqc http://tgd.wippiespace.com/public_html/genememe/genememe.html#foldcat http://tgd.wippiespace.com/public_html/genememe/genememe.html#prebio http://tgd.wippiespace.com/public_html/genememe/genememe.html#genememec http://tgd.wippiespace.com/public_html/hologram/hologram.html#hologram http://tgd.wippiespace.com/public_html/tgdeeg/tgdeeg.html#eegdark http://tgd.wippiespace.com/public_html//tgdeeg/tgdeeg/tgdeeg.html#pulse http://www.prespacetime.com/file/pstj_v1(4).pdf http://www.jcer.com/file/jcer_v1(2).pdf http://www.jcer.com/file/jcer_v1(8).pdf http://www.jcer.com/file/jcer_v1(8).pdf http://www.jcer.com/file/jcer_v1(8).pdf http://en.wikipedia.org/wiki/braid_theory http://math.cornell.edu/~oliver/shipman.gif http://nyjm.albany.edu:8000/pacj/1997/shipman.html http://nyjm.albany.edu:8000/pacj/1997/shipman.html http://www.math.rochester.edu:8080/u/shipman/symmetrypaper/ http://www.math.rochester.edu:8080/u/shipman/symmetrypaper/ dna decipher journal| january 2011 | vol. 1 | issue 1 | pp. 110-145 144 pitkänen m. dna as topological quantum computer: part i [40] mersenne prime.http://en.wikipedia.org/wiki/mersenne_prime. 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[76] c. b. pert (1997), molecules of emotion. simon & schuster inc.. issn: issn: 2159-046x dna decipher journal www.dnadecipher.com published by quantumdream, inc. http://en.wikipedia.org/wiki/endoplasmic_reticulum http://en.wikipedia.org/wiki/promoter http://en.wikipedia.org/wiki/lipid http://en.wikipedia.org/wiki/phospholipid http://en.wikipedia.org/wiki/cell_membrane http://en.wikipedia.org/wiki/prokaryote http://en.wikipedia.org/wiki/eukaryote http://en.wikipedia.org/wiki/transcription_factors http://en.wikipedia.org/wiki/lipid_raft http://en.wikipedia.org/wiki/clathrin http://en.wikipedia.org/wiki/nuclear_envelope http://en.wikipedia.org/wiki/introns http://www.brain.riken.jp/reports/annual_reports/2003/2003-doc/0243.pdf http://www.brain.riken.jp/reports/annual_reports/2003/2003-doc/0243.pdf http://www3.interscience.wiley.com/cgi-bin/abstract/109711451/abstract http://www3.interscience.wiley.com/cgi-bin/abstract/109711451/abstract introduction basic ideas of tqc identification of hardware of tqc and tqc programs how much tqc resembles ordinary computation? basic predictions of dna as tqc hypothesis anomalous em charge does breaking of matter antimatter and isospin symmetries happen at the level of dna and mrna? basic concepts and ideas what happens in quantum jump? m-matrix time-like and space-like entanglement in zero energy ontology effects of finite temperature hyper-finite factors of type ii1 and quantum measurement theory with a finite measurement resolution nmp and biology generalization of the notion of information life as islands of rational/algebraic numbers in the seas of real and p-adic continua? evolution and second law stable entanglement and quantum metabolism as different sides of the same coin generalization of thermodynamics allowing negentropic entanglement and a model for conscious information processing modification of thermodynamics to take into account negentropic entanglement the analog of carnot cycle as a simple model for information processing in living matter basic biological implications how quantum computation in tgd universe differs from standard quantum computation? general ideas related to topological quantum computation general vision about quantum computation about the relation between space-like and time-like number theoretic braidings quantum computation as quantum superposition of classical computations? the identification of topological quantum states some questions fractal hierarchies irreducible entanglement and possibility of quantum parallel quantum computation nmp and the possibility of irreducible entanglement quantum parallel quantum computations and conscious experience delicacies possible problems related to quantum computation the notion of coherence region in tgd framework de-coherence of density matrix and replicas of tqc isolation and representations of the outcome of tqc how to express the outcome of quantum computation? how data is feeded into submodules of tqc? the role of dissipation and energy feed is it possible to realize arbitrary tqc? dna as topological quantum computer conjugate dna as performer of tqc and lipids as quantum dancers sharing of labor cell membranes as modifiers of braidings defining tqc programs? gene expression and other basic genetic functions from tqc point of view how braid color is represented? some general predictions quantitative test for the proposal how quantum states are realized? anyons represent quantum states hierarchy of genetic codes defined by mersenne primes the role of high tc superconductivity in tqc currents at space-like braid strands do supra currents generate magnetic fields? topological considerations fractal memory storage and tqc codes and tqc login dna decipher journal open journal systems journal help subscription login to verify subscription give a gift subscription user username password remember me notifications view subscribe journal content search search scope all authors title abstract index terms full text browse by issue by author by title other journals font size ~ advertisements hot products at amazon information for readers for authors for librarians home about login register search current archives home > login login subscription or article purchase required to access item. to verify subscription, access previous purchase, or purchase article, log in to journal. username password remember my username and password not a user? register with this site forgot your password? issn: 2159-046x 