RE: Gaia theropod follow-up: a "new" phylogeny

[chris brochu <cbrochu@fieldmuseum.org>]

>
>It changes and changes and changes, over and over again. I'm going to keep
>tabs on how many matrix's needed to be twiked to work at the SVP.
>Tracy

But DOES it really change and change and change fundamentally?  We have
statistical tests to show whether two trees are fundamentally different or
not.  Tom used them in his '99 poster, and they're not - a few taxa bounce
around here and there, but that's all.  Moreover, support for nodes where
these taxa lie is low, so it's no surprise they bounce around.  That
happens.  The gross structure of the tree is stable.  When I teach/taught
my Age of Dinos course, I usually used some sort of consensus tree that
reflected the disparate views of different workers for the labile taxa
(many of which have names beginning with "T"), and the tree was still
well-resolved (we have stats to measure degree of resolution as well).

If you're looking for a perfectly stable, perfectly dichotomous tree,
you'll have to found a metaphysics based on systematics - the science of
systematics accepts that some aspects of phylogeny will be labile, for the
simple reason that our understanding of biodiversity is imperfect (and is
likely to remain so as long as bipedal primates are the primary executors
of phylogenetic analysis).  I don't like homoplasy or missing information
any more than the fact that I can't pinpoint a particle's location in space
and time, but like Heisenberg's principle, homoplasy and missing
information are just the way things are, and we have to live with them.

Regarding the last sentence - ALL matrices need to be tweaked to "work."
All of us are professional tweakers.  I'm at home with my oatmeal now, but
I'm on my way to the museum to tweak the day away.  Every paper in Syst Bio
has some tweaking in it.  Why is this a problem?




chris

------------------------
Christopher A. Brochu
Department of Geology
Field Museum
1400 S. Lake Shore Drive
Chicago, IL 60605

phone 312-665-7633
fax 312-665-7641
electronic cbrochu@fmppr.fmnh.org