February 2014: Revisiting in IMAGES the "EQUATION of LIFE" and the "MASTER CODE" Great UNIFICATION of BIOLOGY

1/ a two images abstract...

2/ All this basic research main discovery is described by the book CODEX BIOGENESIS (chapter 20 and annexe)

3/ step 1: the EQUATION of LIFE... applied to eny biological compound ATOMIC MASS: C O N H S P bioatoms, DNA, RNA, Amino acids, others complementary organic compounds...

4/ result is a common scale language based on PI/10 token steps...

5/ The MASTER CODE result: patterned images for DNA genomic and amino acids patterned images are SIMILAR and CORRELATED...

6/ Example of correlated GENOMICS and PROTEOMICS images: a real "J.S. BACH" MUSIC...

7/ idem on whole human chromosome4

8/ idem on whole Chimpanze chromosome4

9/ A big mystery: this PERFECT fine-tuned BALANCE is destroyed by small CHANGES or VARIATIONS atomic mass of bioatoms ISOTOPES...

The Main QUESTION is now:  

relating the BIOMATHEMATICAL great UNIFICATION of LIFE compounds: bioatoms, DNA, RNA, amino acids chains, chromosomes and genomes (1997, 2009, 2011):

The following abstract provides an overview of this basic research discovery:

.../... 

            Meanwhile, the main question interesting this group is the following:

            We discovered a formula unifying ALL biological components from C O N H S P bioatoms to DNA RNA amino acids then genes proteins and genomes.

             But this perfect balance is optimal only when atom atomic mass is the % mix from our atmosphere: i.e %C12 C13 C14 etc... This fine tuning is destroyed by example                  when all isotopes are C12 only... or also in case of environmental disorders.

             My question: Is this the result of James LOVELOCK GAIA theory?

             OR

              Isotopes does not exists but are a quantum, views of a meta multiple isotopes quantum atom structure?

              BUT this condition of atmosphere like %mix balancing of isotopes within C O N H S P bioatoms is a necessary condition for earth like LIFE on other planets...

.../...

This basic research discovery is also described in :

http://fr.scribd.com/doc/57828784/jcperezBeijing032011

and in the book CODEX BIOGENESIS (2009), chapter 20 and annexes:

http://www.amazon.fr/product-reviews/2874340448

http://www.resurgence.be/90-codex-biogenesis-9782874340444.html

website : https://sites.google.com/site/codexbiogenesis/

October 2013: the first proof that complete human genome codon triplets population DNA single strand is a WHOLE: the 3 genomic numbers discovery article

October 2013 APPLIED MATHEMATICS 
(special issue BIOMATHEMATICS)

The “3 Genomic Numbers” discovery:

How our genome single-stranded DNA sequence

 is “self-designed” as a numerical whole

Jean-claude Perez

Email: jeanclaudeperez2@gmail.com

Received May 22, 2013; revised June 10, 2013; accepted June 14, 2013

===============================
Note:

All results presented in this article are REPRODUCIBLE by other researchers from the following basic information:

[3] International Human Genome Project Sequencing Centers

and Verified by NCBI and UCSC, “Human Genome Finalized

BUILD34. Build 34 Finished Human Genome

Assembly,” 2003.

http://genome.ucsc.edu/FAQ/FAQreleases.html

and

Table 3 of the article pp 40.

===============================

The article is now available in OPEN ACCESS on line:

details access:

access:

http://www.scirp.org/journal/PaperInformation.aspx?PaperID=37457

from SCIRP scientific research APPLIED MATHEMAICS website http://www.scirp.org/journal/AM/

===================================

The “3 Genomic Numbers” discovery:

How our genome single-stranded DNA sequence

 is “self-designed” as a numerical whole

Copyright © 2013 Jean-claude Perez. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

"The beginning (1) is the middle (2) of the whole (Phi)"  

Here is my interpretation of this famous sentence from Pythagoras[2]...

Abstract

This article proves the existence of a hyper-precise global numerical meta-architecture unifying, structuring, binding and controlling the billion triplet codons comprising the sequence of single-stranded DNA of the entire human genome. Beyond the evolution and erratic mutations like transposons within the genome, it's as if the memory of a fossil genome with multiple symmetries persists. This recalls the "intermingling" of information characterizing the fractal universe of chaos theory. The result leads to a balanced and perfect tuning between the masses of the two strands of the huge DNA molecule that constitute our genome. We show here how codon populations forming the single-stranded DNA sequences can constitute a critical approach to the understanding of junk DNA function. Then, we suggest revisiting certain methods published in our 2009 book “Codex Biogenesis”. In fact, we demonstrate here how the universal genetic code table is a powerful analytical filter to characterize single-stranded DNA sequences constituting chromosomes and genomes. We can then show that any genomic DNA sequence is featured by three numbers, that characterize it and its 64 codon populations with correlations greater than 99%. The number "1" is common to all sequences, expressing the second law of Chargaff. The other 2 numbers are related to each specific DNA sequence case characterizing life species. For example, the entire human genome is characterized by three remarkable numbers 1, 2, and Phi = 1.618 the golden ratio. Associated with each of these three numbers, we can match three axes of symmetry, then "imagine" a kind of hyperspace formed by these codon populations. Then we revisit  the value (3-Phi) / 2 which is probably universal and common to both the scale of quarks and atomic levels, balancing and tuning the whole human genome codon population. Finally, we demonstrate a new kind of duality between “form and substance” overlapping the whole human genome : we will show that - simultaneously with the duality between genes and junk DNA - there is a second layer of embedded hidden structure overlapping all the DNA of the whole human genome, dividing it into a second type of duality information / redundancy involving golden ratio proportions.

Keywords : genetic code; codon populations; junk DNA; cancer genomics chromosomal translocations; genomes diversity; chromosomes diversity; whole human genome DNA sequence; “Phi” the golden ratio; Fibonacci numbers;  information theory;  symmetry; cellular automata; Chargaff’s  codon  level symmetry principle; fractal self-similarity; “e” Euler's number; “Pi”; form and substance; redundancy; encryption.

[1]
      This article publishing was supported by Professor Luc Montagnier, Fondation Mondiale Recherche et Prévention SIDA

                UNESCO 1, rue Miollis 75732 Paris Cedex 15 Web site: http://montagnier.org/index.php

[2]    “1”, ”2” and “Phi the golden ratio” are the 3 genomic numbers characterizing codon populations of the whole human genome.

==============================================

FULL TEXT other link (PDF):
http://fr.scribd.com/doc/169323556/7401586of18september2013

published 4 october 2013 in open access by http://www.scirp.org/journal/am/

10B access

"FORM AND SUBSTANCE" ("Le FOND et la FORME" i.e ESCHER) memories of a former conference by jean-claude perez on the mysteries of DNA and genomes ...

Now I propose to discuss on 

FORM and SUBSTANCE:

-in Arts and photos,

-then in Spheres and Geometry,

-then in GENETICS 
and the HUMAN GENOME !!!

these photos were realized by the french professional 

photograph and filmmaker FLORENT MARCIE

   http://fr.wikipedia.org/wiki/Florent_Marcie

a conference of JC PEREZ on DNA mystery background...

followed by a conference of jc perez on POINCARE fractal chaos background...

followed by a conference of... DNA on ... jc perez shadow background !!!!!

Now, more on

"FORM and SUBSTANCE"...

in HUMAN GENOME DNA...

and PLATONIC "MUSIC of the SPHERES...

http://en.wikipedia.org/wiki/Music_of_the_Spheres_(disambiguation)

http://www.musicofthespheres.org/

     
      In ( Perez J.-C. (2010). Codon populations in single-stranded whole human 
     genome       DNA are fractal and fine-tuned by the golden ratio 1.618. - 

      Interdisciplinary Sciences: Computational Life Sciences, 2: 1–13.

      http://www.ncbi.nlm.nih.gov/pubmed/20658335 , full text in:

      ( http://fr.scribd.com/doc/95641538/Codon-Populations-in-Single

      -stranded-Whole-Human-Genome-DNA-Are-Fractal-and-Fine-

      tuned-by-the-Golden-Ratio-1-618 ).  ),

      we showed that the population of the 64 codons of the whole human 
      genome,       when reorganizing the universal genetic table using the 
     successive transformed fractal “dragon curve”, self-organized codons 
     populations around 2 atttractors: 1 and (3-phi) / 2. When publishing 
     this paper, I, of course, been very interested in the presence of the golden 
     ratio phi in this rule seemed to be a real tuning of our genome.You 
     understand my surprise when I discovered that my paper and especially 
     the value 0.6909830056 is quoted in a web site dedicated 

      to the intimate structure of atoms, quarks or Higgs boson (Gielen, 2012)

       … (please visit http://quarks-divided.over-blog.fr/pages/Pi_e_Phi_and_

      1381976-7937512.html ).

      But let us now look at the value 

      VOLUME SPHERE = 4 × PI (R * 3) / 3 = 1.381944838 ... 

      We see that it is very close to 3-phi = 1.381966011. We deduce a 
      remarkable discovery: if the radius of a sphere is (3-phi) / 2 then the volume 
      of this sphere is 3-phi ... The error is only 0.0000211732501. Secondly, 
      we note also that 

      the SECTION of the SPHERE is PI×R*2 = 1.499977019 = 3/2. The error 

      is 0.000022981. Thirdly, we note that the surface of this 

      same sphere is 
      = SURFACE SPHERE = 4×PI×R*2 = 5.999908074 = 6 = 2x3 

       with an error = 6-5.999908074 = 0.000091926. Finally, the circumference 
       of the sphere is equal to 2 × PI × R = 4.341574268. Which is very close to 

      3 times the reverse of (3-phi) / 2, effectively: 6 ÷ (3-phi) = 

      4.341640786 then, the error is = 0.00006651754558.

      In conclusion: “A sphere of volume 3-phi has radius (3-phi / 2) 

      which is half the same volume”.

      Corollary: a sphere whose volume is equal to the diameter, 

      the section is 3/2, the circumference is 3 times the reverse of (3-phi) / 2 

      and the surface is equal to 6 has a radius = (3-phi) / 2.

      Finally, if the radius of a specific sphere is (3-phi)/2

      then:

      the diameter is 3-phi

      the circumference is 3 x ( 2/(3-phi)) ) 6 / (3-phi)

      the section is 3/2 = 6/4

      the surface is 6=2x3

      and the volume is … 3-phi

      Then to resume: 

                                               

	Sphere geometry						Human genome single stranded DNA
formula	(3-phi)/2	3-phi	6/(3-phi)	3/2=6/4	6	3-phi	(3-phi)/2	(3-phi)/2
error	0	0	0.000066517	0.000022981	0.000091926	0.000021173	¯0.000993038463	¯0.000908846295

     recall:

                                Sphere geometry
                                ==========                                                 
      geometry: radius     diameter circumf.   section     surface      volume
      formula:  (3-phi)/2  3-phi      6/(3-phi)  3/2=6/4   6              3-phi 
      error:      0             0           0.000066  0.000023 0.000092  0.000021            

                     Human genome single stranded DNA
                     ======================
      DNAkind   nucleotides     codons 
      formula:   (3-phi)/2        (3-phi)/2

      error:       ¯0.000993     ¯0.000909

      Figure: The (3-phi)/2 ratio in sphere geometry and human genome.

       We note particularly a kind of “NUMERICAL RESONANCE”: 
      effectively,  ALL ratios are related to the same 3 basic initial numbers: 
      2, 3, and phi.Yes (3-phi) / 2 looks good on a universal value! Here are 
      the proportions of codons and nucleotides populations within the whole 
      single stranded human genome DNA !!!

      YES!!!! (3-Phi) / 2 is probably a major 

      UNIVERSAL VALUE...

      First I recall you that DNA is constitued by the 4 nucleotides T C A 
      and G...

      Finally, I could say you this confidence:

      In the human genome I could demonstrate that the unique coding 
      nucleotide is 
      the "G" base... of the double strand of DNA...

      Then the C or G bases of the single stranded DNA...

      C and G are the...FORM...

        but,

         What about T and A ?

         They play the same rôle that 
         "the white of the paper sheet" 
         or "silence to music"...
      
         T and A are the... SUBSTANCE...

      Then in the whole single stranded DNA, the ratio between C+G and 
      T+A is... 
      (3-Phi)/2...

      Here is the discovered and fabulous ratio between FORM and 
     SUBSTANCE... 
      between C+G and T+A in the billion codon of our whole human 
     genome... 
      or in the 3 billion TCAG nucleotides of this same human genome...

      Like in this magic SPHERE of 3-Phi Diameter and volume !!!!!!!!!!!!!!

Last PUBLICATIONS and CONFERENCES of JC Perez on the "NUMERICAL ARCHITECTURE OF DNA AND GENOMES"...

Towards a big UNIFICATION of BIOLOGY:

Long range GENOMES T C A G scale level:

Is the whole HUMAN GENOME a meta WAVEFORMS FRACTAL HOLOGRAPHIC-like field ?

Local bio-atomic C O N H scale level:

2012: Paper of jc perez in "The Cerebellum"

publication of a main paper in

"The Cerebellum" 
Handbook of the Cerrebelum and cerrebelar disorders

: with Dr Andras Pellionisz (silicon valley)

" RECURSIVE GENOME FUNCTION OF THE CEREBELLUM: GEOMETRIC UNIFICATION OF NEUROSCIENCES AND GENOMICS"

(to be published in 2012)

references: 2013, Andras J. Pellionisz, Roy Graham, Peter A. Pellionisz and Jean-Claude Perez. Recursive Genome Function of the Cerebellum: Geometric Unification of Neuroscience and Genomics. In: Springer Handbook; "The Cerebellum and Cerebellar Disorders",
Ed. by M. Manto.  M. Manto, D.L. Gruol, J.D. Schmahmann, N. Koibuchi, F. Rossi (eds.),  Handbook of the Cerebellum and Cerebellar Disorders, pp.  1381-1423, DOI 10.1007/978-94-007-1333-8_61, Science+Business Media Dordrecht   http://www.junkdna.com/pellionisz_unification/ full .pdf  http://www.scribd.com/doc/111439455/BOOK-Unification-of-Neuroscience-andGenomics-Pellionisz-Et-Al-in-Section-4-Springer-theCerebellum-Handbook-2012

2011:

Conference in Espacio interdisciplinar Universited de la Republica MONTEVIDEO URUGUAY: invitation Pr Claudio MARTINEZ-DEBAT: "CAMINANDO INTERDISCIPLINARIO" charts...

"CAMINANDO INTERDISCIPLINARIO" (paper)

2011:

Conference in BEIJING CHINA (BIT Life SCIENCES Vaccines congress) :

"Decoding non-coding Dna Codes:Human GenomeMeta-Chromosomes Architecture"

support Pr Luc Montagnier FMPRS World AIDSFoundation UNESCO and Jean-rené Fourtou Vivendi Universal chairman

2010:

paper in INTERDISCIPLINARY SCIENCE (China)(chairman Pr Luc Montagnier) :
Interdiscip Sci Comput Life Sci (2010) 2: 228–240DOI: 10.1007/s12539-010-0022-0
Codon Populations in Single-stranded Whole Human Genome DNAAre Fractal and Fine-tuned by the Golden Ratio 1.618

2009:

Publishing my 5th book "CODEX BIOGENESIS - The 13 codes of DNA" (french): references in the dedicaced website and in editor house 
and also... ON-LINE access by AMAZON: http://www.amazon.co.uk/Codex-Biogenesis-harmonies-g%C3%A9nome-latome/dp/2874340448#reader_2874340448


... and a lot of years ago: 1994

THE CD "The First Music of Genes": overview...

overview of a sample music from the CD "The first music of genes": the KI-RAS Oncogene

The FULL CONFERENCE CHARTS of JC PEREZ BEIJING WORLD VACCINES CONGRESS March 2011

BIT Life Science VACCINE world Congress Beijing China
FULL PROGRAM...
detailed Full Program sessions chapter 2... 

1 2 3 ...clic... 
The 3 PDFs (clic please)
PART IA  BACKGROUND A
  PARTIB  BACKGROUND B 

PART II   RESULTS


PART III   FUTURES

The full conference by jean-claude perez ( PDF format ) is now available here !!!!!!

Part 2.2: Novel Vaccine Discovery Technology
Section 2-2-1: Bioinformatics, Antigen Design, and Vaccine Development
Time: March 23, 2011 13:30-17:10

Part 2.2: Novel Vaccine Discovery Technology

Section 2-2-1: Bioinformatics, Antigen Design, and Vaccine Development Time: March 23, 2011 13:30-17:10
Chair:	Dr. Vidadi M. Yusibov, Executive Director, Fraunhofer USA Center for Molecular Biotechnology, USA
Co-Chair:	Dr. Yongqun ”Oliver” He, Assistant Professor, University of Michigan Medical School, USA
13:30-13:55	Title: Using Comparative Bacterial Genomics to Identify Novel Vaccine Targets Dr. Garth D. Ehrlich, Director, Department at Allegheny Singer Research Institute, Center for Genomic Sciences, USA
13:55-14:20	Title: VLP-based Vaccine against MalariaDr. Vidadi M. Yusibov, Executive Director, Fraunhofer USA Center for Molecular Biotechnology, USA
14:20-14:45	Title: Computational Antibody Vaccine Discovery by Conformational Epitope Prediction and Design of Novel Protein Scaffolds Dr. Vaikuntanath Samudrala, Associate Professor, Computational Biology Group, University of Washington, USA
14:45-15:10	Title: Systematic Analysis of Vaccine Targets of Bacterial Pathogens Using Vaxign Reverse Vaccinology Dr. Yongqun ”Oliver” He, Assistant Professor, University of Michigan Medical School, USA
15:10-15:30	Coffee Break
15:30-15:55	Title: Decoding Non-coding Dna Codes: Human Genome Meta-chromosomes ArchitectureDr. Jean-Claude Perez, Individual Researcher, Bordeaux, France (support from Pr Luc Montagnier FMPRS World AIDS Foundation UNESCO and Jean-rené Fourtou Vivendi Universal chairman)

BIT Life Sciences’ 3rd World Congress of Vaccine Beijing·China

Session Name: Section 2-2-1: Bioinformatics, Antigen Design, and Vaccine Development
Decoding non-coding Dna Codes: Human Genome Meta-Chromosomes Architecture
Dr. Jean-Claude Perez* support from Pr Luc Montagnier World AIDS Foundation UNESCO  
and Jean-René Fourtou Vivendi Universal chairman

Abstract

The question of the hypothetical function of the 98% non-coding DNA of the human genome remains one of the major open problems of Genetics. In 2010, we prooved that the entire human genome codon population is fine-tuned around the "Golden ratio" ("Codon Populations in single-stranded DNA Whole Human Genome Are fractal and fine-tuned by the Golden Ratio 1618" , 2010, Interdisciplinary Science). We show how, across the entire human genome, there appears to be an overall balance in the whole single-stranded DNA. This digital balance fits neatly around 2 attractors whose predominant values are 1 and (3-Phi)/2, where Phi is the Golden Ratio. Yet, the same analysis applied to each of our 24 chromosomes and to each of the 25 chromosomes of the chimpanzee (book “Codex Biogenesis”, 2009), will reveal a strange phenomenon: while this study shows that populations of the respective genome codons of humans and chimpanzees are 99.99% correlated. It appears, also, that some human chromosomes are more similar to chimpanzee chromosomes than other human chromosomes. And vice versa. We then identified two clusters of chromosomes in humans and two other clusters in the chimpanzee chromosomes that correlated. Some human chromosomes (16 17 19 20 and 22) will appear at the extremity. Simultaneously, a study of the affinities of integrating HIV type genomes within various human chromosomes (Mitchell et al, 2004) have demonstrated a permeability 2 to 3 times that of all other chromosomes for chromosomes 16 17 19 and 22 which appear exactly in this extremity cluster. Thus, we are confronted with a paradox: the same analysis shows a global unity across the genome, whereas, applied to each of the constituent chromosomes of this same genome a great heterogeneity between these chromosomes is revealed. The objective of this study is, precisely, to analyse this paradox in greater depth. Then, we discovered a meta-structure that overlaps all 24 human chromosomes. It is based on a set of strong numerical constraints based particularly on Pi, Phi and integers numbers such as 2, 3 etc. A functionality of this fine-tuned structure appears: the structure is 90% correlated with the density of genes per chromosome from the Human Genome project. It is 89% correlated with the chromosome's permeability to intrusion by retroviruses like HIV, 94% with CpG density and 62% with SNP inserts/deletes. Finally, we discovered a classification network of the 24 human chromosomes, including one measuring scale, ranging from 1/Phi (chromosome 4) to 1/Phi + 1/Pi (chromosome 19), which is both correlated with the increasing density of genes and permeability to the insertion of external viruses or vaccines. To close this speech, we speculate on a powerful basic Pi, Phi based numerical projection law of the C O N H S P bio-atoms average atomic weights. We will reveal an integer number based code which unifies the 3 worlds of genetic information: DNA, RNA and amino acids. Correlating, synchonizing and matching Genomics/Proteomics global patterned images in all coding/noncoding DNA sequences, all biologic data is unified from bioatoms to genes, proteins and genomes. This code applied to the whole sequence of human genome, produces generalized discrete waveforms. We will show that, in the case of the whole double-stranded human genome DNA, the mappings of these waves fully correlate with the well known Karyotype alternate dark/grey/light bands.

Biography

Jean-Claude Perez, Ph.D. (Bordeaux university), is a French interdisciplinary scientist born in 1947 in Bordeaux (France). Perez worked with IBM in both Biomathematics and Artificial Intelligence research, inventing the "Fractal Chaos" neural network, his holographic-like memory « deja vu » novelty detector. In 1990, Perez published research showing strong links between both the worlds of fractals and Fibonacci numbers, which are based on the Golden ratio. In this last area, with "dna supracode", he proved that the DNA coding for genes is structured by proportions related to Fibonacci numbers. He verified this discovery in the field of the HIV genome, in partnership with Nobel Prize-winner Luc Montagnier. Perez has worked for 20 years in the fields of whole-genome numerical analysis and the numerical decoding of genes as coding or non-coding DNA sequences. Perez has also published five books, notably: L'ADN décrypté – 1997 and Codex Biogénésis, (Resurgence, Belgium – 2009.), registered an international Patent for high temperature superconductors (1994) and produced an audio CD entitled “The first music of genes” (1994). Awards: 1991 "Denis Guichard" prizewinner from the "Fondation de France".

* Dr. Jean-Claude Perez, Independent researcher, Bordeaux, France jeanclaudeperez2@free.fr http://golden-ratio-in-dna.blogspot.com/

SECTION 1: The 3 PDFs (clic please)

PART IA  BACKGROUND A
  PARTIB  BACKGROUND B 

PART II   RESULTS


PART III   FUTURES




SECTION 2: THE 52 CHARTS...
==>  PLEASE CLIC ON FOLLOWING  IMAGES TO ZOOM THEM....

 

 

BINARY CODE =0  LOW FREQUIENCIES  DARK banding

BINARY CODE =1  HIGHT FREQUENCIES  WHITE banding

LOW FREQUENCIES  =  Montagnier's Electromagnetic WAVES=ON exp BORRELIA or HIV

HIGH FREQUENCIES = Montagnier's Electromagnetic WAVES = OFF exp: LACTOBACILLUS