genetic code & mutation rates

S. LaBonne labonnes at csc.albany.edu
Fri Jul 28 19:08:16 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 believe in solving coding problems by coding theory and
>chemical problems by chemistry.

Protein synthesis _is_ a chemical process and the chemistry cannot be
safely neglected.  "Changing the code" requires only changing the
sequence of an anticodon, generally by just a single nucleotide. Only
the obvious selection pressure resulting from screwing up many
proteins simulataneously prevents much larger and more frequent
deviations from the "universal" code. Furthermore, it looks as though
the anticodon stem-loop evolved _after_ the acceptor-TUC minihelix,
which is probably the older part of the tRNA and originally had
nothing at all to do with "coding" (Schimmel and Ribas de Pouplana
(1995), Cell 81: 983-86).  In that case, I think the burden of proof
is on anyone who claims that the assignment of amino acids to codons
is anything more than a "frozen accident".  Even if one of the many
(contradictory) schemes for rationally associating amino acids with
base triplets should turn out to be true, that again would involve a
_chemical_ interaction, inacessible to understanding by "coding
theorists".

Finally, the attempt to think about "coding" in purely abstract terms
should be deja vu to anyone who knows the history of molecular biology
(and Yockey must know this at first hand): remember the wonderful
theoretical constructs like Crick's "comma-free" code, that turned out
to be entirely unhelpful because nature just wasn't as clever as
Francis Crick?  The moral is that too high a level of abstraction
produces thinking that just doesn't connect with the everyday reality
of experimental biology.
-- 
Steve LaBonne ******************* (labonnes at cnsunix.albany.edu)
"It can never be satisfied, the mind, never." - Wallace Stevens



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