Re: Junk DNA: A hypothesis

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Date: Sun, 23 Jan 2005 22:55:05 -0500 (EST)

On Sun, 23 Jan 2005 15:18:44 -0500 (EST),
lamoran@bioinfo.med.utoronto.ca (Larry Moran) wrote:

>On Sat, 22 Jan 2005 13:01:49 -0500 (EST),
>Perplexed in Peoria <jimmenegay@sbcglobal.net> wrote:

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>> This is probably a good place to interject a question to Larry
>> about terminology, rather than theory. My reading of the OP
>> was that he was assuming that most junk consisted of pseudo-genes.
>> Your response seemed to be based on a different reading; in fact,
>> you used the existence of pseudo-genes as evidence that he didn't
>> understand evolution. My question is this: are pseudo-genes commonly
>> classified among the junk, or does the technical term "junk" only
>> include repeat sequences, introns, and other stuff that is not
>> translated and apparently has never been translated?
>
>Pseudogenes are excellent examples of junk DNA.
>
>> Another question: Are (untranslated) transcription promoter sequences
>> junk, simply because they are not transcribed or translated?
>
>Of course not. Any DNA that has a function is, by definition, not
>junk DNA. Telomeres aren't junk and neither are centromeres, promoters,
>restriction/modification sites, DNA replication origins, and a host of
>other sequences.
>
>> Clearly, these are functional. Isn't it possible that some
>> "junk" has a (not yet understood) role in the control of gene
>> expression in eukariotes?
>
>Yes. No respectable scientist is going to say that every single
>bit of DNA that we now think is junk has been correctly identified.
>That part of the argument against junk DNA is just plain silly.
>>From time to time we find a role for some small pieces of DNA that
>were thought to be junk. Every time it happens there are newspaper
>headlines about the demise of junk DNA. By my calculation, those
>of us who believe in junk DNA have been "refuted" every three months
>for the past twelve years.
>
>> And now for another opinion: While the hypothesis that junk is
>> functional is unproven, and while many of the specific functions
>> that have been proposed are fatuous, I am not sure that we can
>> reject all functional roles for the junk out of hand. There is
>> still a lot we don't know about molecular biology, especially for
>> eukariotes. We have only learned of the existence of snRNAs within
>> the last decade, and we are still deciphering their function. Not
>> too long ago, the "genes" coding these things would have been
>> dismissed as junk.
>
 I'll just interject a comment on what constitutes "junk" and how one
can recognize a sequence that is not junk.
 With more and more genomes being sequenced, one can compare the
divergence of sequences in related species. If a sequence is less
divergent than the neutral rate it is being maintained via selection
and is not "junk", if it is diverging at the neutral rate it is junk.
You may have no clue what the function of the sequence is, but if it
is being maintained it is not junk. Some have gone looking in these
vast deserts where nothing seemed to have any function. Sure enough,
they sometimes find small areas where the lower sequence divergence
jumps out at them. These sequences are being maintained via selection.
They are not junk even though one may know what there function is. But
these sequences are few and far between, they are not finding anything
to greatly reduce these estimates of the amount of junk in a genome.
 William L Hunt
 
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• In reply to: Larry Moran: "Re: Junk DNA: A hypothesis"
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