more on SCRIBD... and in the book CODEX BIOGENESIS...


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

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

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

read the book on AMAZON here...

...a research starting then published 20 years ago...please, clic here...

October 2013: a new publication demonstrating why human genome is a WHOLE...


clic please on the peace symbol then access: ... AUTOUR DU LIVRE "CODEX BIOGENESIS"

mardi 7 juillet 2015

July 2015: A main article: "Deciphering Hidden DNA Meta-Codes -The Great Unification & Master Code of Biology"

July 2015: published open access in Glycomics § Lipidomics

My main article revealing the methods to compute the "Master Code of Biology", great unification between DNA, RNA and amino acids chains sequences...

on ACADEMIA:
==> ==> Full text of the article "Decyphering Hidden DNA Meta-codes: The Great Unification § Master Code of Biology" accessed from ACADEMIA

and

on Journal of Glycomics and Lipidomics:
http://www.omicsonline.org/open-access/deciphering-hidden-dna-metacodes-the-great-unification--mastercode-of-biology-2153-0637-1000131.php?aid=55261


mercredi 8 avril 2015

April 2015: From Artificial Neural Networks towardsDecyphering DNA and Genomes Hidden CODES

Numerical, Binary and Undulatory Hidden CODES
that organize DNA, chromosomes and whole genomes

Jean-claude PEREZ - April 2015 jeanclaudeperez2@gmail.com

"The numbers are objects in its own right, like the atoms or molecules. Although their nature differs, they exist independently of the mind that studied them, the brains of mathematicians creating only the theoretical tools to apprehend the"
Jacques de schryver in "Le réincarné" Amazon french ebook 2013

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

July 2015:
The main peer-review article on J.C. Perez's research on the Numerical hidden codes of DNA and Genomes is now published:
"Deciphering Hidden DNA Meta-Codes -The Great Unification & Master Code of Biology"

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

CODEX BIOGENESIS: major french language book (2009)


By Jacques de Schryver (Strasbourg, France Al) - See all my reviews
(TOP 1000 REVIEWER) (REAL NAME)
This review is from: Codex Biogenesis - 13 DNA codes (Paperback)
Jean-Claude Perez hypothesized that the redundancy of the genetic code might contain a meaning. Structure of redundancy or hidden meaning? Armed with extensive knowledge in the humanities, Jean-Claude Perez is a talented mathematician who has devoted over twenty years to understand that if life is characterized by the ability to achieve a goal, methodical decoding DNA can reveal several levels of meaning. Codex Genesis is a unique book that deserves a Fields Medal (the Nobel of mathematics) and which also is able to make us dream. The rigorous poetry serving a meaning to life? This epistemological book might as well be in store shelves philosophy, religion than math. A kind of Sherlock Holmes novel as interesting as the works of Stephen Hawking.

Jean-ClaudePerez is a French interdisciplinary researcher . Researcher in Artificial Intelligence and Robotics at IBM, he was a pioneer of artificial neural networks in the 1980s, he published the first two French books on Artificial Neural Networks .



He primarily explores the emergence of "sub-Artificial Intelligence" such as pattern recognition based on self-organizing properties. Exploiting the findings of the French mathematician Benoit Mandelbrot IBM Yortown Heights Thomas J. Watson basic research Laboratory (fractals), the Belgian Nobel Prize Ilya Prigogine (order far from equilibrium) and Chilean biologists Humberto Maturana and Francisco Varela (autopoiesis), he discovers the "Fractal Chaos " network, a real gifted holographic-like memory type providing "déjà vu" memory compressing thousands learned images in a small 3x3 Fractal Chaos neurons cells network.

He discovered a remarkable attractor at the heart of its fractal: point of the famous « golden ratio » and just around a hyper-sensitive region to the proportions of consecutive Fibonacci numbers. 

We are in 1990, Jean-Claude perez then has a famous intuition: "If we were looking for in the DNA sequences of nucleotides TCAG relative proportions as the proportions of Fibonacci? " (Eg if 89 consecutive nucleotides are divided into 34 T bases and 55 bases A, C, or G, we say that there is here a "resonance" because 34, 55 and 89 are three successive Fibonacci numbers. In a small genome such as the HIV AIDS 9000 nucleotides long, then we discover thousands of "resonances" the longest of which cover the 2/3 of the genome ( 6765 bases resonance as Fibonacci sequence = 0, 1, 1, 2, 3, 5, 8, 13, 21, 34, 55, 89, 144, 233, 377, 610, 987, 1597, 2584, 4181, 6765, ... / ...). In 1991, jean-Claude Perez published the first and the oldest scientific article demonstrating the proof of the golden section and Fibonacci numbers in the DNA sequences and especially in the DNA coding for genes, there is his main article on the « Supracode of DNA ».



In the 25 years that followed, Jean-Claude Perez then abandoned research in Artificial Intelligence to devote himself exclusively to research digital structures controlling the DNA of genes, chromosomes, and whole genomes.

Particularly, he publish 2 french books :
1997 : « L 'ADN décrypté » (DNA decyphered .

He also discovered two amazing universal formulas:



The « Formula for Life » unifying all organic compounds from C O N H isotopes towards whole genomes providing "The MASTER CODE of BIOLOGY", a common meta-language unifying the 3 languages of Life : DNA, RNA and Amino Acids.



Then, the main scientific articles published during this period are particularly :

2010 : Perez J.C. Codon Populations in Single-Stranded Whole Human Genome DNA AreFractal and Fine-Tuned by the Golden Ratio 1.618,. Interdisciplinary Sciences: Computational Life Sciences, Vol. 2, No. 3, 2010, pp. 1-13. http://www.ncbi.nlm.nih.gov/pubmed/20658335 2010.

2011 : Perez J.C. Decoding Non-Coding DNA Codes: Human Genome Meta-ChromosomesArchitecture. BIT Life Sciences’ 3rd Annual World Vaccine Congress, Beijing, 23-25 March 2011. 

2012 : Pellionisz A.J., Graham R., Pellionisz P.A. and Perez J.C. Recursive GenomeFunction of the Cerebellum: Geometric Unification of Neuroscience andGenomics. In: M. Manto, D. L. Et al. Eds., Handbook of the Cerebellum and Cerebellar Disorders, 2012, pp. 1381-1423. 


2015 : to be published : «  Deciphering hidden DNA meta-codes -
The Great Unification & Master Code of Biology ».

Finally in this long research trip, we discovered in various ways the Golden Ratio, Numerical structures, Biobits binary codes, waveforms interferences, and resonances.
We have here the proof that DNA is not only Biology but also Field numbers, waves and finally... Mathematics.






RECALL...
CODEX BIOGENESIS: major french language book (2009)




By Jacques de Schryver (Strasbourg, France Al) - See all my reviews
(TOP 1000 REVIEWER) (REAL NAME)
This review is from: Codex Biogenesis - 13 DNA codes (Paperback)
Jean-Claude Perez hypothesized that the redundancy of the genetic code might contain a meaning. Structure of redundancy or hidden meaning? Armed with extensive knowledge in the humanities, Jean-Claude Perez is a talented mathematician who has devoted over twenty years to understand that if life is characterized by the ability to achieve a goal, methodical decoding DNA can reveal several levels of meaning. Codex Genesis is a unique book that deserves a Fields Medal (the Nobel of mathematics) and which also is able to make us dream. The rigorous poetry serving a meaning to life? This epistemological book might as well be in store shelves philosophy, religion than math. A kind of Sherlock Holmes novel as interesting as the works of Stephen Hawking.

Foreword by Carl Johan Calleman PhD author of "The Purposeful Universe" 

There are certain times in history when our world view undergoes fundamental shifts and the theories that may have previously seemed to be cut in stone are suddenly questioned and at the very least considered as inadequate. An obvious such point in time is the scientific revolution in the early 17th century when Galileo and Kepler introduced a totally new approach to gaining knowledge. Experiments and instruments were introduced and the first mathematical laws of nature were formulated resulting in Descartes philosophy of rational empiricism, which meant that theories had to corroborate the actual observation of nature. The broader philosophy underlying this may be said to have been deism, in other words the idea that the universe was like a clockwork which God had started, never intervened in and so would operate according to the laws of nature until the end of time.

A second significant shift in the scientific world view may be said to have come with the introduction of the concept of evolution notably through Darwin’s theory. This was not only a reflection of a new notion of time, but also a view of our origins that excluded any role of a creative intelligence behind the workings of the universe. This atheist approach to science has since then become somewhat of a dogma and has profoundly influenced the kind of questions that scientists have been asking. While the good side of this may be that much religious bias have been removed from science, the negative aspect is that it has excluded holistic approaches to it that would explain how everything in nature is connected. Thus, only if you accept that there is a unified plan behind the existence of the universe do you have any reason to consider a holistic approach.

I want to encourage the reader to consider the possibility that the work of Jean-Claude Perez belongs to a new and fundamentally different paradigm of science, one that uses the established methods of rational empiricism to elucidate significant relationships, but does not reject the possibility that our universe has an intelligent origin. This, I believe, is the kind of science that is at its forefront in our own particular time. Fascinating in this respect is Dr Perez re-contextualization of Mendeleïev’s periodic system of the elements, a typical example of how a theory attains a new meaning even though its previous formulation had been perceived as cut in stone. Hence, Perez work entices us to explore intelligent causes underlying the relationships of nature without putting in question the empirical facts that have been gathered about it.

Fascinating are also Dr Perez studies of the presence of the so-called Golden Ratio in the nucleic acids. The Golden Ratio and its associated Fibonacci numbers have been known to play a role in the geometry of nature for at least 800 years, but what is fundamentally new in Perez treatise is that he studies the information content of the DNA in light of the Golden Ratio rather than merely its geometry. This leads us to various relationships pointing to an order behind the emergence of the biological organisms the study of which may now only have started. A fundamental conclusion that can be drawn from the relationships that Dr Perez has discovered is that the DNA sequences of all organisms must have emerged, or have been created, as a whole. They have in other words not emerged through random chemical reactions. I believe Dr Perez has here discovered something that simply cannot be accommodated by the previous scientific paradigm that looks upon biological evolution as a whim of nature. This discovery alone has so wide-ranging ramifications for all of biology, and especially molecular biology, that it should prompt researchers either to refute his claims or to widen the framework of their own analysis.

It is through this holism that it becomes clear that Dr Perez’ work is part of a new scientific revolution, one that brings us back to a meaningful view of the universe, which has a source that we may call “intelligent”. While much of his work requires quite a degree of specialized knowledge to understand these conclusions by themselves are important enough to deserve the attention of the entire scientific community, as well as the broadly interested public. In a sense Dr Perez work thus means a return to a science, which acknowledges as meaningful some of the numerological relationships that were typical of many ancient peoples of our planet. Yet, this return to seeing a higher meaning and purpose of nature here takes place at a new level where the methodology and mathematical means of analysis of science are recognized as necessary for the new quest. Ultimately, any understanding of a higher purpose of the universe will have to rely on such reality checks and it is only if it does so that there will be a true value of this new wave of science in helping us understand what it means to be a human being.

Seattle, August 22, 2009
Carl Johan Calleman, Ph.D.

Carl Johan Calleman holds a Ph.D. in physical biology from the University of Stockholm. He has been a senior researcher at the University of Washington and has served as a cancer expert for the World Health Organization. He is also a leading expert on the Mayan Calendar and is the author of The Mayan Calendar and the Transformation of Consciousness and The Mayan Calendar. He lives in Seattle.In 2009, he will publish The Purposeful Universe How Quantum Theory and Mayan Cosmology Explain the Origin and Evolution of Life”, Bear & Company USA (December 15, 2009 – ISBN-10 : 1591431042 ISBN-13: 978-1591431046).



samedi 8 février 2014

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







mardi 13 août 2013

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
===============================
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:


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.



==============================================
Inline image 1


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

lundi 8 avril 2013

"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


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

Photo

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


Photo

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


Now, more on


"FORM and SUBSTANCE"...


in HUMAN GENOME DNA...




     
      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.
      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)
      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 !!!!!!!!!!!!!!