Many thanks to Gordon Davisson and Joe Felsenstein for review and criticism of my UD article

_{Salvador Cordova

April 28, 2014

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I previously highlighted the work of Jean Claude Perez in my Vodka! essay. I had encountered Perez work in my google searches related to the 3-base periodicity pattern in DNA.

The 3-base pattern seems widely acknowledged in the literature as On the origin of three base periodicity in genomes.

Genomes of almost all organisms have been found to exhibit several periodicities, the most prominent one is the three base periodicity. It is more pronounced in the gene coding regions and has been exploited to identify the segments of a genome that code for a protein. The reason for this three base periodicity in the gene-coding region has been attributed to inhomogeneous nucleotide compositions in the three codon positions. However, this reason cannot explain the three base periodicity present at the level of the whole genome where the codon concept is not applicable. Even though the distribution of each nucleotide is uniform at the positions 0(mod 3), 1(mod 3) and 2(mod 3) when the whole genome data is considered, our analysis reveals that the three base periodicity is arising because of higher correlations among the nucleotides separated by three bases.

Biosystems. 2012 Mar;107(3):142-4. doi: 10.1016/j.biosystems.2011.11.006. Epub 2011 Nov 12.
http://www.ncbi.nlm.nih.gov/pubmed/22100873

The 3-base periodicity pattern seems to be widely accepted as evidence on non-randomness, but not the work of Perez.

Gordon Davisson and Joe Felsenstein raised many red flags with Perez work and caused me to reconsider if Perez findings are of any value. In light of their analysis, I’m forced to conclude it would not be in the best interest of the ID movement to cite Perez work favorably at this time. And so I offer my retraction and errata.

I’m indebted to Gordon Davisson especially and also Joe Felsenstein for their criticism of my article at UD. I’m especially thankful to Gordon for his very meticulous review of Perez work.

But possible missteps by Perez do not invalidate the possibility of non-randomness in DNA. Codon bias for example, is a non-random feature of DNA, not to mention the ability to code for functional proteins. At issue is whether any given patterns claimed to be discovered is really non-random or figment of after-the-fact pattern projection and imagination.

I am continuing to search for non-random patterns in DNA. I would welcome getting good leads on the matter. I’m now currently trying to understand the 3-base periodicity pattern and duplicate some of the work so I can better understand it. If my work has bugs in my computer code, poor methodology, bad DNA data files, I would welcome correction. My current exploration is here:

Request for Help Verifying non-Random 3mer pattern in human chromosome 3

Thanks in advance to all who offer help and constructive criticism.

NOTES
Gordon’s comments: Vodka!…Comments

Joe Felsenstein’s comments: Sandwalk, Cordova tries and fails

Comments

Dear Eric Anderson OK well here complete links: http://fr.scribd.com/doc/205337844/jcperezLINKSresearchs-pdfjean-claude perez_{May 5, 2014
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Dr. Perez: Thank you for your comments. I was outlining general principles that hold across all known systems, whether DNA or otherwise. As a result, it is unlikely there would be anything to contradict those principles, but if I get a chance I'll try to peruse the article you linked to see what other interesting information it may contain.Eric Anderson_{May 4, 2014
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Eric ANDERSON more... in french: https://plus.google.com/+jeanclaudePerez/posts/a5EYNdK3vBT and http://www.amazon.co.uk/Codex-Biogenesis-harmonies-g%C3%A9nome-latome/dp/2874340448jean-claude perez_{May 3, 2014
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Eric ANDERSON, for your last topic on "patterns" discussion: —– Well, that is much too long, but hopefully lays out a few points worth considering. My caution would be that (i) there will be many patterns in DNA — it is a given — particularly if we define “pattern” broadly enough to include stochastic statistical properties, (ii) but unless and until the “pattern” can be clearly identified as (1) not the result of a law-like process and (2) not a statistical reflection of the underlying code or cellular mechanisms, and (3) matching some independent specification, then we should not conclude, indeed, should not even suggest, that the “pattern” we have discovered is itself evidence of design. I suggest expressely you to read the EQUATION OF LIFE and MASTER CODE great UNIFICATION of the 3 languages DNA RNA amino acids PLEASE read: http://fr.scribd.com/doc/57828784/jcperezBeijing032011jean-claude perez_{May 3, 2014
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Sal complementary data: .../... 3/ but BUT I think to day there is a royal way: the human chromosome4 differenciation relating 23 other human chromosomes and relating chr4 in other primates I could send you some data unformal on this… for this task, could you send me an email adresse for this purpose? send to jeanclaudeperez2@gmail.comjean-claude perez_{May 3, 2014
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finally, the problem of this discussed entry provides from this reason: You published my results from the intelligent design oriented analysis of my frien perry Marshall : http://www.cosmicfingerprints.com/mathematics-of-dna/ unstead the native original article which details METHODS and DISCUSSION: http://fr.scribd.com/doc/95641538/Codon-Populations-in-Single-stranded-Whole-Human-Genome-DNA-Are-Fractal-and-Fine-tuned-by-the-Golden-Ratio-1-618jean-claude perez_{May 3, 2014
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meanwhile layer 3 is result of layer 2 and layer 1...jean-claude perez_{May 3, 2014
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Sal, There was a "prejuje" on these discussions around my papers... which were not read slowly before discussing about! see last discussions on http://sandwalk.blogspot.fr/2014/04/sal-cordova-tries-and-fails-to.html?showComment=1399095899611#c392249966776270900 meanwhile: if we research possible design trace, after 25 years of continue research of numerical patterns in DNA (see my 1st peer review article on this in 1990 about http://fr.scribd.com/doc/183925484/Jc-Perez-in-Speculations-in-Science-and-Technology-1991 ).... I think that: 1/ the discussed 2 articles on human genome codon populations are potentially interesting for design trace (but we must consider this statistically and not son sequential dna as your people discuss here)... 2/ certainly the EQUATION of LIFE and MASTER CODE is a way to design: see my Beijing conference http://fr.scribd.com/doc/57828784/jcperezBeijing032011 3/ but BUT I think to day there is a royal way: the human chromosome4 differenciation relating 23 other human chromosomes and relating chr4 in other primates I could send you some data unformal on this... for this task, could you send me an email adresse for thsis purpose?jean-claude perez_{May 3, 2014
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Sal: "I was in a day-long conference with Dr. Sanford this week . . ." I'm jealous! Thanks for all you have done. Hopefully you'll be able to swing by UD from time to time to highlight (even if you don't have time for a lot of detail) some new find or ideas. In the meantime, please shoot me an email so we can stay in touch. Thanks, EricEric Anderson_{May 2, 2014
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Eric and friends, I was in a day-long conference with Dr. Sanford this week and there is a subtlety to the 3-base periodicity pattern which my superficial statistical analysis didn't reveal, namely it is highly concentrated in certain regions. I'm still indebted to Gordon for finding a bug in my java code, and that was sloppy work on my part. I presented the statistics to Dr. Sanford on Chromosome 1 and he immediately stopped me and said the issue is the high concentration in certain regions which my superficial analysis didn't bear out. I'm am not still not sure I will find anything of significance, but we just sat together for a day looking chromosome after chromosome. I conveyed to him my concerns that we might not find anything, that it was high risk research. He smiled and said, "I know what high risk research is, this isn't high risk." Here was a photo of Dr. Sanford in a Time/Life magazine issue that featured his gene gun. That was a high risk research gamble that paid-off. The Young Dr. Sanford He spent much of his life re-engineering genes and now he is studying the original engineering in the gene. At one time most of the GMO's in the grocery store were made through the gene gun. That says to me if a line of inquiry has nothing to lose, but much to gain, then go for it. Unbelievable that he thought to put some DNA on a bullet made of gold and just aim and shoot it into the center of a cell and see if does anything! Amazing that he was able to do so much re-engineering without really understanding the original engineering! So for him, ID isn't high risk research. He's quite confident continued research in the genes will reveal meaningful patterns, we just have to be persistent. That said, I really have to bow out of participating so much at UD. I have to go back and learn things like organic chemistry, biochemistry, molecular biology. UD has been a chance to put forward ideas, get feedback and correction. Though Gordon, Joe Felsenstien, and Larry Moran have a different view than I on intelligent design, their feed back has been incredibly valuable. So I must now bow out of the internet debate and now start being a little more focused in my personal quest and building out the material on the CEU website. Dr. Perez, We are honored you visited us. Thank you for joining our discussion. My very best wishes to you, and I'm sorry I probably won't be making many appearances at UncommonDescent or elsewhere on the internet for quite some time.scordova_{May 2, 2014
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Sal, Two points, one procedural and one substantive. On the procedural side, I'm not sure you have to "retract" anything. I read your prior thread as exploring some ideas. They didn't pan out, at least not yet. That's OK. But anyway, thanks for being willing to come out and acknowledge that. Patterns in Nature On the substantive side, I think we need to be extremely cautious in attributing "patterns" (in this case, in DNA) to design. Patterns are everywhere in nature. Many are produced by law-like processes. Indeed, that is, in a very real sense, what law-like processes do -- produce repetitive patterns. Furthermore, patterns can be produced by random processes. Particularly when we define "pattern" so loosely, as in the present case, as to pick up not just those things that produce a regular sequence or those things that correspond to an independent specification, but things that are merely stochastic in nature. Such a "pattern" can be found in random noise. It isn't meaningful by itself and in most cases is just a statistical artifact. So the search for a "pattern", in my view, is on very shaky ground. The vast majority of patterns that we may discover are the result of either (i) law-like processes that don't indicate design, or (ii) statistical artifacts. What we are looking for is a meaningful, independent specification. I realize "pattern" is a word sometimes used to describe this, but I'm not sure it is even a helpful word in most cases. Intelligent design is not primarily about identifying "patterns" broadly speaking; it is about identifying complex independent specification (many times precisely anathema to a "pattern"). We need to be careful not to conflate the two. Finally, there are many statistical "patterns" (if we want to call them that) which are the result of an intelligently-designed system, but which, in and of themselves, aren't necessarily indicative of design. For example, if I am looking at Java code I will quickly discover a "pattern" that lines end with a semi-colon. The existence of a semi-colon is meaningful and is part of the syntax of the coding system, but outside such a coding system seeing a bunch of semi-colons isn't meaningful. As another example, in English we are much more likely to find a 'u' after a 'q' than any other letter; we will often find an 'n' after the letters 'tio'; and so on. These are true and objective observations, but they can't be divorced from the code itself; they are in essence artifacts of the code. Every code, every language, will have some of these structural, syntactic artifacts -- things that are statistically true, but that have meaning only in the context of the particular code or language. Thus, if we discover a code we can infer that it was designed. But we should not then assume that all the structural and statistical artifacts that flow from that code are themselves, independently, designed. Yes, they result from the rules governing the expression of the code, but they don't have independent significance outside of the code. This is why, for example, we can have a computer put together perfectly grammatical sentences in English -- sentences that follow all the rules of the code, but that are meaningless gibberish. And in that case, all the "patterns" normally associated with English would still be there and we could discover those "patterns" through statistical analysis, but it would not mean that the particular sentence had been intelligently designed. The Genetic Code. As I mentioned on the other thread, the genetic code also has (as any code must have) some of these built-in statistical artifacts. For example, it is not the case that each of the four nucleotides has an equal probability of occurrence under the code. So finding, hypothetically, that there are more A's than C's may not be any more meaningful than the fact that we are seeing the code implemented. There may not be anything independently meaningful about it. Furthermore, if we ever get to the point of understanding proteomics better we may well find that other rules of the system dictate a tendency toward this or that amino acid or even toward particular triplets that code for an amino acid. These would also produce a tendency toward specific nucleotides showing up more than others and will, as a purely statistical artifact, produce many "patterns" that can be seen but that have no particular independent meaning. The genetic code was no doubt designed. And the system of amino-acid translation was no doubt designed. And it may be the case that protein construction itself was designed. All of these will impact, to a greater or lesser extent, the nucleotide sequence we see in DNA. All of them will leave artifacts or statistical "patterns". But those patterns may not have any independent significance, other than being a reflection of the designed code and cellular apparatus. ----- Well, that is much too long, but hopefully lays out a few points worth considering. My caution would be that (i) there will be many patterns in DNA -- it is a given -- particularly if we define "pattern" broadly enough to include stochastic statistical properties, (ii) but unless and until the "pattern" can be clearly identified as (1) not the result of a law-like process and (2) not a statistical reflection of the underlying code or cellular mechanisms, and (3) matching some independent specification, then we should not conclude, indeed, should not even suggest, that the "pattern" we have discovered is itself evidence of design.Eric Anderson_{May 2, 2014
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Dear Salvador CORDOVA, After analysing a bit various discussions, my feeling is that all coments particularly from Pietr, Joe or Gordon, are UNFUNDED and cannot be used to make an objective decision on your nice post. The reasons: Their unapropried comments on SANDWALK of your Sal Cordova entry entitled Vodka! Jean Claude Perez, the golden ratio, dragon curve fractals and musical design in “junk DNA”... The reason is that all (ALL) their comments were done without reading the basic original article: I suggest you reading the original basic peer review article of 2010 published in Interdisciplinary Science: 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 and my 2013 peer review article: http://www.scirp.org/journal/PaperInformation.aspx?paperID=37457#.U2Mwlfl_trAjean-claude perez_{May 2, 2014
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Dears Pietr, Joe or Gordon, I'm sorry for your unapropried comments on SANDWALK of the Sal Cordova entry entitled Vodka! Jean Claude Perez, the golden ratio, dragon curve fractals and musical design in “junk DNA”... The reason is that all (ALL) their comments were done without reading the basic original article: I suggest you reading the original basic peer review article of 2010 published in Interdisciplinary Science: 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 and my 2013 peer review article: http://www.scirp.org/journal/PaperInformation.aspx?paperID=37457#.U2Mwlfl_trAjean-claude perez_{May 1, 2014
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SCORDOVA, in other post, GORDON said: “Finally, is there any reason to regard the similarity between the GC/AT ratio and (3–Phi)/2 as anything other than a numeric coincidence? Especially since it varies a great deal between different regions of the genome, different chromosomes, and different species? Especially since there are many other formulae involving Phi that it could have come out close to (e.g. Phi/3, Phi/2, Phi-1, 4-2*Phi, 2*Phi/5, etc…)” my 2 responses: 1/ In my 2013 article, it is show the universal nature of this value ‘quarks etc…° 2/ applying this same analysis to: -whole human genome ==> (3-Phi)/2 -lower scale chromosome is chr4: ratio = 1/Phi -highter scale chromosome is chr19: ratio = 1/Phi + 1/Pi strange no? Then analysing by others approachs chr4 shows that – if there is “design” – the right research way must be… HUMAN CHROMOSOME4: https://plus.google.com/103572438711329205534/posts/26WczM9aQbS and http://fr.scribd.com/doc/186894835/jcperezEvolutionFibonacciPrimatesChromosomes4UKjean-claude perez_{April 30, 2014
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Dr. Perez, Thank you for your kind visit to UD. Your work with Nobel Prize winner Dr. Luc Montagnier is certainly noteworthy. I will continue researching all areas, and best of luck to you. I am deeply sorry at this time I'm not able to endorse some of your ideas, but I will support you getting an audience for your work, and I will encourage people to hear what you have to say. I thank you for your many years of service to science, and if you and Dr. Pellionisz are able to find ways to improve detection and treatment of diseases related to junk DNA, then I most certainly wish you the best. I certainly think DNA is non-random, the question is which patterns are genuinely there. If there are Fibonacci numbers anywhere in the DNA, then there will be golden ratios not far behind. This is well-known in mathematics. I remember studying the phenomenon many years ago when studying math and recursion relations. I most certainly see the Fibonacci relation and golden ratio in this photo of a flower. :-) http://www.mathsisfun.com/numbers/nature-golden-ratio-fibonacci.html I would also suppose the human visual field is basically the proportion of a golden ratio, and that is why we like watching movies on theater screens that accord with the golden ratio and why Greeks liked architecture with the golden ratio. Thank you again for you kindness in visiting our tiny weblog. I'm honored you'd take time to post here.scordova_{April 29, 2014
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sorry, here the right BEIJING CONFERENCE link: http://www.scribd.com/doc/57828784/jcperezBeijing032011jean-claude perez_{April 29, 2014
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sorry, here the right BEIJING CONFERENCE link: http://www.scribd.com/doc/57828784/jcperezBeijing032011jean-claude perez_{April 29, 2014
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I understand your cepticism: please read slowly this BEIJING full presentation of parts of my 25 years research... then you 'll reonsidere probably your feeling on these basic/experimental breakthought pionnering research... http://fr.scribd.com/doc/57828.....jing032011jean-claude perez_{April 29, 2014
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Gordon all this work was reproduced by Dr Jordi sola soler http://www.sacred-geometry.es/.....-music-dna for human chromosome1 I have all data results… details in my book CODEX BIOGENESIShttp://www.amazon.co.uk/Codex-.....2874340448 and particularly in my last article in APPLIED MATHEMATICS : http://file.scirp.org/Html/4-7401586_37457.htm more details in: Welcome… http://golden-ratio-in-dna.blogspot.com/ https://sites.google.com/site/codexbiogenesis/ http://fr.scribd.com/doc/57828.....jing032011 http://www.scribd.com/jean_claude_perez/documents http://file.scirp.org/Html/4-7401586_37457.htm http://www.scribd.com/doc/9564.....atio-1-618 https://plus.google.com/u/0/+jeanclaudePerez/aboutjean-claude perez_{April 29, 2014
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I went over to that sandwalk article and I found nothing more than a lot of name calling. Really. That was it.Jehu_{April 28, 2014
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