But how do we establish phylogeny? - Based on simple similarity!
ah! the old rhetorical trick of changing the problem or question a posteriori!
all i pointed out was that things can't be "25% homologous" (well, i can think
of a contrived example in which two four-domain proteins have one homologous
domain in common, but that's not how the concept is normally (ab)used)
current thinking about support for a hypothesis of common ancestry is
summarised here (thank you, Wayback Machine! the prime source of webpages you
want to find again but that have disappeared from the web altogether - see:
http://www.archive.org/web/web.php):
http://web.archive.org/web/20061020081239/http://opbs.okstate.edu/~melcher/ProtEvolOut.html
"# Summary of current views
* Statistically significant sequence and structural similarity strongly
imply common ancestry
* Statistically significant sequence or structural similarity
o weakly imply common ancestry;
o could result from convergent evolution, often not considered
seriously enough. (It's still evolution, though!)
* Functional similarity supports a common ancestry hypothesis, but is not
sufficient to prove it. Functional dissimilarity does not disprove common
ancestry.
* Intelligent design is a near-sighted and unrealistic argument,
inconsistent with known properties of chemical and biological systems."
IMHO, the phylogenetic concept of homology in biology does not buy you much
of anything useful. It seems to be just a leftover from pre-Darwinian days -
redefined since but still lacking solid foundation.
i'm glad your opinion is humble here, because it has much to be humble about
:-) do you really think that property (e.g., structure and function)
prediction is not useful? and i can't even begin to understand how you can
think that 'homology' in its present-day meaning is a pre-darwinian concept.
okay, so can we all agree now that we won't be saying and writing things like
"the two proteins are X% homologous" anymore from now on?
--dvd
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Gerard J. Kleywegt
[Research Fellow of the Royal Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology University of Uppsala
Biomedical Centre Box 596
SE-751 24 Uppsala SWEDEN
http://xray.bmc.uu.se/gerard/ mailto:[EMAIL PROTECTED]
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The opinions in this message are fictional. Any similarity
to actual opinions, living or dead, is purely coincidental.
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