Refutation of a Statistical Argument Supporting Coevolution (Origins)

by David Turell , Tuesday, February 23, 2010, 23:03 (5385 days ago) @ xeno6696


> http://www.pnas.org/content/97/25/13690.full
> 
> For the uninitiated, "Coevolution theory claims that the conserved pathways of amino acid biosynthesis in modern organisms (i.e., those found in all three domains of life) can be used to infer the historical precursor-product relationships between amino acids."
> 
> This paper demolishes this line of questioning, showing that chance can account for 23-64% of the amino acid combinations we see today. > 
> You lost an important weapon, David!-
No way! this article is investigating a previous theory. IT assumes some type of original DNA existed, how they don't say, and then that DNA was enlarged and modified. We still don't know how DNA started and the article itself is filled with presumptions and provisos: copied from the abstract and conclusions:-It has long been conjectured that the canonical genetic code evolved from a simpler primordial form that encoded fewer amino acids [e.g., Crick, F. H. C. (1968) J. Mol. Biol. 38, 367...379].-
A conservative correction for these errors reveals a surprisingly high 23% probability that apparent patterns within the code are caused purely by chance. Finally, even this figure rests on post hoc assumptions about primordial codon assignments, without which the probability rises to 62% that chance alone could explain the precursor-product pairings found within the code. Thus we conclude that coevolution theory cannot adequately explain the structure of the genetic code.-
It is also noteworthy that other patterns of biosynthetic relatedness have been reported within the code (e.g., refs. 40 and 41). Specifically, amino acids from the same biosynthetic pathway tend to be assigned to codons that begin with the same first base. Although the generality of this observation (lacking specific precursor/product pairs) removes problems with unrealistic pathways and lends strong statistical support (20), the pattern cannot be explained in terms of any known biological process. Furthermore, the lack of specific predictions about individual codon assignments appears to require the additional intervention of natural selection (for error minimization) to adequately explain the structure of the genetic code (10, 42). -With such considerations in mind, we word our conclusion with extreme care. Biochemical considerations and statistical reanalysis show that the product-precursor pairings at the heart of code coevolution theory are unreliable markers for a putative evolutionary process of code expansion. Subsequent analyses that used these pairings to predict the intermediate steps of code evolution, and to infer the evolutionary forces at work (27), are therefore speculative at best. It is plausible (if not probable) that the genetic code arose from a simpler form encoding fewer amino acids. However, it remains an open question whether any patterns of biosynthetic relatedness in the modern code can inform us of this process.