



































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 re-

stated 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. 


