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 

>    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 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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