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The "debates" on phylogenetics on this list brought to mind Sisyphus,
the legendary king of Corinth. Sisyphus was condemned by the gods to
forever roll a boulder to the top of a hill, from which it always
rolled back to the bottom. Tom Holtz, Chris Brochu and others deserve
sainthood for the continual patience they show. My attitude is simply
to plug for objectivity and repeatability.
That said, there are independent ways of "testing" phylogenies. For
example, the recent tripartite bilaterian animal phylogeny based on
mitochondrial sequences conflicts in several very important respects to
the "traditional" tree, which was based on a speculative assessment of
the order in which body plans may have evolved. I've just taught the
new tripartite tree to first year students. Anticipating the comment
"Why should we believe this tree over the other" from students who were
not totally au fait with phylogenetic methodology, I described the
pattern of hox clusters amongst bilaterians. Each of the three great
clades of bilaterians has a distinct hox cluster, a result
which independently supports the new molecular tree.
Dinosaurs are extinct, so perhaps there is not much hope of a similar
independent source of information. But perhaps developmental studies of
birds may offer some hope (I've got to say I'm in no doubt here - but
it might silence the doubters). I raised the issue of paedomorphosis
earlier, to deafening silence!