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Opponents of 3-domain hypoth.?

S. LaBonne labonnes at csc.albany.edu
Thu Oct 20 20:18:41 EST 1994

In article <382l17$abr at mserv1.dl.ac.uk>,
JAMES O. MCINERNEY <James.Mcinerney at UCG.IE> wrote:
>There was a discussion of this subject in april of this year. If you wish to
>find out about it, either gopher or ftp to net.bio.net and look in the 
>molecular-evolution folder in 9404.  That discussion, however, focussed on
>the monophyletic nature of the archaea more than anything else, so maybe this
>is a different discussion.

Thanks- I've taken a look at that. There were some interesting things,
but the scope of the discussion and the range of participants was
rather limited.  It was interesting that apart from Larry Moran, even
the strongest opponents of Woese's tree seemed to be quite unequivocal
about the distinctness of the Archaea and Bacteria- perhaps the
proposal (I forget who originally published it)of archaeal and
bacterial kingdoms within a prokaryotic "empire" would be a reasonable
alternative to Woese in the current state of the data (though as
you'll see below I do find some of the evidence for the closeness of
Archaea and Eukarya rather compelling.)

One thing that disturbs me (as a non-taxonomist) about some of these
discussions is what seems to an outsider like a failure to see the
forest for the "trees" (if you'll forgive a feeble pun).  I find it
hard to give the same weight to a tree based on an enzyme of secondary
importance as to, say, the organization of the transcriptional
machinery (i.e. the presence in archaea of TBP and TF-IIB homologues).
The latter are the sort of thing that seem most likely to be ancestral
and least likely to have been acquired via horizontal transfer, but
maybe that's just a molecular biologist's prejudice. I do think some
taxonomists in this area are really insufficiently aware of the amount
of gene-swapping that goes on among bacteria (sensu latu!) in the
environment (I believe Lynn Margulis has published some provocative
speculations on the evolutionary significance of this).

There also seems to be an unwarranted bias in some quarters against
rRNA data; I even recall one post that questioned the justification
for aligning secondary structure before doing a sequence alignment,
which would appear to indicate a serious lack of understanding of the
differences between protein-coding sequences and RNA's that are
themselves the functional gene product.
There now, that ought to be enough flame bait to get a discussion
going! :-)  Comments, anyone?

Steve LaBonne *********************** (labonnes at csc.albany.edu)
"It can never be satisfied, the mind, never." - Wallace Stevens

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