Re: Article: On the Origins of Chemical Biodefense

lamoran@xxxxxxxxxxxxxxxxxxxxxxx (Larry Moran) wrote in news:diu8pu$7bb$1
@darwin.ediacara.org:

> On Sun, 16 Oct 2005 01:41:04 -0400 (EDT),
> Robert Karl Stonjek <rstonjek@xxxxxxxxxxxxxx> wrote:
>
>> On the Origins of Chemical Biodefense
>>
>> The following points are made by R. Liddington and L. Bankston
>> (Nature 2005 437:484):
>
> [snip]
>
>> Random mutations occurring over hundreds of millions of years mean
>> that the component amino-acid sequences of individual domains no
>> longer share any similarity; nevertheless, their evolutionary origin
>> is preserved in their three-dimensional structure.
>
> The other possibiity is that the motifs/domains in different
> proteins do not share a common ancestor. Their structural similarity
> is due to convergence on a common structural motif. In that case,
> the absence of any sequence similarity is evidence that they are not
> evolutionarily related.
>
> There is a controversy in the field of molecular evolution. Some
> people, like me, believe that convergence explains many common
> sequence motifs. We believe it's very unlikely that all traces
> of sequence similarity could be lost in regions that must preserve
> structural integrity while randomly changing all the amino acids
> in order to wipe out sequence similarity. That just doesn't make
> a lot of sense.


It's very strange to hear Larry arguing for convergence - this is the
adaptationist stance. Convergence on a common protein structure from
diverse lineages over millions of years? Surely that cannot be due to
neutral evolution - the odds against are astronomical. But I agree that
the alternative explanation of retention of structural similarity absent
sequence similarity is sketchy (based on my rather limited knowledge),
examples in evolution of structural invariance are always associated with
sequence invariance - e.g. the strongly conserved structure of hemoglobin
is associated with a strongly conserved sequence.


> Others believe that structural similarity trumps sequence similarity
> when it comes to making decisions about homology. Those people
> believe that all similar structures have evolved from a common
> ancestor. In extreme cases they'll even argue that all zinc
> fingers and all leucine zippers are homologous.

I don't have a clue what you are talking about with zinc fingers and
leucine zippers - but I can see a problem with maintaining structural
similarity while varying sequences, unless the sequences being changed
are outside of the binding site. At some point as you vary sequences you
are moving rapidly downhill on the fitness landscape (not just sideways
as in neutral evolution), and as you note above that doesn't make a lot
of sense.

Yours,

Bill Morse



> It doesn't really matter to which camp you belong. Both views have
> strong evidence to support them and neither one can explain all
> of the data. It's very likely that there are some cases of descent
> from a common ancestor where structural similarity has been
> preserved while sequence similarity has been lost. On the other
> hand, there are some very well-known "models" of this that are
> certainly wrong. They are really examples of convergence.
>
> The sad thing is that many of the "structural" group are completely
> unaware of the controversy. They tend to come from the structural
> biologists and not from those who study molecualr evolution. They
> publish papers as if their viewpoint was the only possible
> interpretation and they don't even bother paying lip service to
> any other explanation. The authors should have, at the very least,
> mentioned that their similar motifs may not be related by evolution
> and that's the real reason why they don't show any sequence
> similarity.
>
> (The ironic thing about this paper is that the structure of
> C3 may actually be a good example of exactly what the authors
> claim. In that case, if the authors were aware of the controversy,
> they would have put a more thorough discussion in their paper -
> except that it's a Nature paper and such discussions are forbidden.)
>
>
>
>
> Larry Moran
>
>
>
>
>
>
>

.

Relevant Pages

  • Re: Article: On the Origins of Chemical Biodefense
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    (sci.bio.evolution)
  • Re: Complex Specified Information - Pitman Formula
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    (talk.origins)
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