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 exper- iment 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 experi- ment 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 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 gen- eration 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 chem- istry 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 particles- at least electrons and protons- in 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 self- organization 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 proteins- would 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 case- have this double role. 4. The process occurs also both for hydrogen cyanide and mineral oil and and this raises obvious ob- jections 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 de- fect 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 long- of 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 pro- tocell 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 and- would 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 molecules- also lipids- serve 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 Mat- ter 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 Mat- ter 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