Wednesday, November 24, 2010

Kimura said that the strongest evidence for the neutral theory is the molecular clock

A recent comment from a reviewer of my primate phylogeny manuscript again said the same thing as Scott Page has said over at Nature Precedings where my manuscript is posted that “the concept of the moleculr clock has little bearing on molecular phylogenetic studies that do not enforce a molecular clock criterion in their analyses.” Thus, there is a strong consensus in the field that even if the molecular clock is implausible which nearly everyone admits, one can still use other methods to infer molecular phylogeny within the overall paradigm originally started by the molecular clock concept. It is a self-deceiving illusion in my opinion, and I have just inserted the following into my revised manuscript (under review) to dispel it in the clearest way possible.

All traditional molecular phylogeny methods are based on the neutral theory. Early methods made explicit use of the molecular clock idea. But since the molecular clock has been widely known as implausible today, other methods have also been developed that are supposed to not to depend on the molecular clock. However, these methods are still based on the neutral theory and the neutral theory is in turn based on the molecular clock, as admitted by Kimura and Ohta: “Probably the strongest evidence for the theory is the remarkable uniformity for each protein molecule in the rate of mutant substitutions in the course of evolution.” (1). Therefore, we can conclude that all traditional molecular phylogeny methods are either explicitly or implicitly based on the molecular clock. The non-existence of the molecular clock in macroevolution as demonstrated by the overlap feature of the genetic equidistance result is sufficient to deem all traditional molecular phylogeny methods invalid for macroevolution.

Ref:
1. Kimura M, Ohta T (1971) Protein polymorphism as a phase of molecular evolution. Nature 229: 467-479.

1 comment:

Anonymous said...

Hi there,

You write:

"Thus, there is a strong consensus in the field that even if the molecular clock is implausible which nearly everyone admits,"

This is inaccurate. What nearly everyone admits is that there is little evidence for a universal, aka global, molecular clock. So-called local molecular clocks have been and are being used for a variety of reasons. You should look into it.

" one can still use other methods to infer molecular phylogeny within the overall paradigm originally started by the molecular clock concept.

This is just ludicrous. Molecular phylogenetic analyses were performed decades before the notion of a molecular clock was put on paper. If analyses can be performed without reference to molecular clocks, how on earth can such methods be part of some "overall paradigm originally started by the molecular clock concept"?


It is a self-deceiving illusion in my opinion,

I wouldn't put much stock in your opinion. You have claimed to have single-handedly overturned the Neutral Theory and the conclusions of all molecular phylogeny publications that did not produce arrangements that you think are correct. Yet here we are, 3-4 years later, and none of your amazing paradigm busting papers has made it into print.

One cannot overturn the relevance of methods that have actually been tested -

Gene trees and the origins of inbred strains of mice

Experimental phylogenetics: generation of a known phylogeny

- premised on their desires.

sorry.