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genetic code & mutation rates

Keith Robison robison at nucleus.harvard.edu
Wed Aug 2 13:07:26 EST 1995

In article <3vauce$obv at newsbf02.news.aol.com>,
HPYockey <hpyockey at aol.com> wrote:
>Tom Jukes is my Mentor. I owe a lot to him. If we always agreed there
>would be no need for both of us.
>I look forward to comment on Chapter 7 by someone AFTER he reads Part I
>and Chapter 7. 

I've done a quick read of Yockey's book, and while I find his
arguments well-constructed and sound, they still must face
the evidence.  Yockey's theory, crudely paraphrased, is
that the genetic code had not yet "solidified" (my word, not his) 
during many of the early divergences of species, and in genomes such
as mitochondria it "solidified" differently than elsewhere.  I.e.,
the genetic code was still plastic, but is not any longer.  The
competing Jukes theory is that the genetic code had settled down
at the time of the last common ancestor of all known life, but
later events allowed small changes in some lineages.

> I believe in solving coding problems by coding theory and
>chemical problems by chemistry.

This evidence is neither -- it is history.  By looking at the
phylogenies of organisms we can infer a history.  The inferred
history of mitochondria is that they evolved from purple bacteria,
which in turn share common ancestors with all other eubacteria, and
the eubacteria can be joined to archeans and eukaryotes at or near
the last common ancestor of all life (urgenote).  For Yockey's
theory to be correct, there was massive convergence to the
"universal" code in almost every other line other than 
the mitochondria.  

Again, I feel the data is in favor of Jukes hypothesis, because
unusual genetic codes are rare and are restricted to clades
at the tips of the tree.  If unusual codes were common and
present in deeper-branching clades, then I would be more
in favor of Yockey's hypothesis.

Keith Robison
Harvard University
Department of Cellular and Developmental Biology
Department of Genetics / HHMI

robison at mito.harvard.edu 

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