2 Interdiscip Sci Comput Life Sci (2010) 2: 1–13
Genomes Conference, Sept. 14–17, 2009).Secondly, in January 2010, the journal
re-ported that the golden ratio is present in the atomicscale of the magnetic resonance of spins of cobalt nio-bate atoms (Coldea
., 2010). When applying amagnetic ﬁeld at right angles to an aligned spin, themagnetic chain shifts into a new state called “quantumcritical.” New properties emerge from
’s Un-certainly Principle.For the last 20 years, whole genomes have revealedtraces of fractal behavior as various publications stud-ied the logical level of both elementary gene-coding ornon-coding TCAG single DNA sequences. In
found trace evidence of fractals inanalyzing DNA sequences (Peng
., 1992).Models of fractal integer patterns, like
numbers, have been proposed:In 1991 we proposed that Golden Ratio Fi-bonacci/Lucas integer numbers deﬁne strong relation-ships between DNA gene-coding region sequences andFibonacci’s embedded TCAG gene sequence patterns(Perez, 1991). We also prove the optimality of thesepatterns (Perez, 1997) in the book
L’ADN d´ecrypt´e(“Deciphering DNA”)
. Examples involving evolutionand pathogen analysis include genes or small genes-richgenomes
especially the HIV genome.Then, in 2008, Yamagishi proposed evidence of
based organization and veriﬁed it at a statisti-cal global level across the whole human genome. (Ya-magishi
., 2008).For several years, other researchers like
advocated ways to analyze and detect fractal defectswithin whole genomes. This is based on recursive frac-tal exploration methods and artiﬁcial neural networktechnologies (Pellionisz, 2008).Then ﬁnally, simultaneously with the (Lander, 2009)October 2009 paper, we showed in the book
(Perez, 2009) a convergence of evidence for
This book explores a numerical property called “
” consisting of an exhaustive combinatorialresearch of “
” within gene-coding DNA se-quences: a resonance is an exact Fibonacci/Lucas nu-cleotide number harmonious proportion. For example:144 contiguous TCAG nucleotides have exactly 55 Tnucleotides and 89 A or C or G nucleotides. Then aresonance exists with an exact Golden ratio proportionas deﬁned in the Methods section: 55, 89 and 144 areconsecutive Fibonacci numbers following the Golden Ra-tio. Gene-rich genomes like HIV have thousands “reso-nances”, where the longer ones are overlapping 2/3rdsof the whole genome length.
Research on HIV-SIV isolates genomic diversity with thesupport of Pr
, FMPRS (World Founda-tion for AIDS research and Prevention (UNESCO), 1 rueMiollis, 75015, Paris, France).
whole genome fractal organization. This comes fromanalyzing whole genomes not at a physical level, butat the logical level of TCAG single stranded sequencedDNA. These ﬁndings were obtained primarily by an-alyzing the ﬁnalized human genome sequence (Balti-more, 2001).The goal of the present paper is show fractal behaviorin the genome at the
DNA analysis level. Weprovide an exhaustive analysis of codon frequencies ona whole human genome scale.This analysis classiﬁes the 64 codon populations com-bined with various embedded foldings of the universalgenetic code map. This is based on the DRAGON curve(Gardner, 1967) also called the “folding paper curve”(Fig. 1). It reveals the fractal structure of the whole hu-man genome at the DNA sequential information scale.This analysis reveals that codon frequencies are ori-ented around 2 numerical attractors. The distance sep-arating the attractors is “1/2Phi”, where Phi is the“Golden ratio”. These discoveries simultaneously ex-tend the reach of
’s second rule for single-stranded DNA of the whole Human Genome.
Fig. 1 The Dragon curve or “paper folding” embeddedfractal dynamics
2.1 Human genome release analysed withDragon curve folding
We analyzed the entirety of the whole human genomefrom the 2003 “BUILD34” ﬁnalized release
. We con-sidered only the main single strand of the DNA se-quence. Within this sequence, we computed, for eachof the 3 possible codon reading frames, the cumulativenumber of each of the 64 genetic code codons
Human genome ﬁnalized BUILD34. Build 34 ﬁn-ished human genome assembly (hg16, Jul 2003).http://hgdownload.cse.ucsc.edu/goldenPath/hg16/chromosomes/
The full detailed data relating codon populations for the3 codon reading frame and for the 24 human chromo-somes is available in supplementary materials.