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Frequency/distribution of nucleotides/amino acids before selection

Arlin Stoltzfus arlin at is.dal.ca
Thu Nov 5 11:08:12 EST 1998


On 4 Nov 1998, Donald Forsdyke wrote:

> But surely, as soon as a piece of DNA "thinks" of encoding a protein,
> selection becomes operative on the protein. Can there really be a period
> prior to selection kicking in?

Ok, can we stop being pedantic now and help this person express 
his idea?  Of course it is a mistake to say that non-coding DNA
represents DNA "before" selection, and coding DNA represents DNA "after"
it.  Nevertheless, we can make a comparison of amount of variation 
or rates of evolution between coding and non-coding, and this 
will tell us something about the influence of selection relating 
to specifically to coding.  This is an obvious method that is 
used repeatedly by professionals in experimental population 
genetics.  

>    What you seem to be missing out is that selection may have acted on
> the piece of DNA before it "thinks" of becoming a protein-encoding gene,
> (and even after it becomes a protein-encoding gene selection may be
> acting on it for genomic reasons discussed elsewhere:

Yes, and if these are truly "genomic" factors, they will
constitute a "background" set of conditions that applies to 
coding and non-coding DNA, and will be factored out in the 
coding-vs-non-coding comparison, so that your point is moot.

Arlin

Arlin Stoltzfus, Ph.D. 
email arlin at carb.nist.gov; phone 902 494-2968; fax 902 494-1355
mailing addresses: 
 current: Biochemistry, Dalhousie U., Halifax, NS, B3H 4H7 Canada
 near-future: CARB, 9600 Gudelsky Drive, Rockville, MD, 20850 USA





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