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.
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:
Thanks in advance to all who offer help and constructive criticism.
Gordon’s comments: Vodka!…Comments
Joe Felsenstein’s comments: Sandwalk, Cordova tries and fails