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Frequency/distribution of nucleotides/amino acids before selection

Dr. Peter Gegenheimer PGegen at UKans.nolospamare.edu
Fri Oct 23 20:45:42 EST 1998

On Wed, 21 Oct 1998 17:53:14, Dr.Ram Samudrala <ram.samudrala at stanford.nojunkemail> 

> Have there been any estimates published on the frequency/distribution
> of nucleotides/amino acids in DNA/protein sequences PRIOR to
> selection, i.e., before selection kicks in? I can get the frequencies
> of amino acids in known protein sequences, but these proteins have
> generally arisen through natural selection.

Isn't this really the $64K question? In general, it's hard to find proteins _before_ 
selection has acted on them. I'm aware of a study (Hillis, in Science, maybe 1 yr 
ago?) on nucleotide sequence changes over generations of bacteriophage growth. 

I should think it would be difficult even to determine whether or not "selection" has
"acted" on a given stretch of genetic information. I contend (as a nucleic acid 
biochemist, not an evolutionist) that since we don't know the function (or, all the 
functions) of large stretches of DNA, or even of amino acids in well-characterized 
proteins, we have no way of knowing whether amino acid or nucleotide changes are 
fixed as a result of selection or not. 

I would certainly appreciate informed comment on this topic!

| Dr. Peter Gegenheimer      | Vox:785-864-3939  FAX:785-864-5321 |
| Dept Molecular Biosciences |   PGegen at UKans.edu                 |
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