From: "David Marjanovic" <david.marjanovic@gmx.at>
Reply-To: david.marjanovic@gmx.at
To: "DML" <dinosaur@usc.edu>
Subject: Combined answer 1: cladistics
Date: Sun, 1 Feb 2004 11:26:40 +0100
> >:-) The hypothesis is not unscientific anymore. But before the advent
of
> >cladistics -- the method to make phylogenetic hypotheses and to test
how
> >well they fit the totality of the data -- it was. "Unscientific"
doesn't
> >mean "wrong". It just means "if it's wrong, we can't find that out with
> >certainty".
>
> Nor was it unscientific when it was presented.
I think it was, and Mickey has explained why.
> Occam's Razor is one thing, but naive adherence to parsimony is another.
It
> is a central tenet of cladistic analysis that convergence, paralellisms,
and
> reversals are very rare
Oh no. Not at all. IT is a central tenet of cladistic analysis using
parsimony that homoplasies are a bit rarer than synapomorphies -- just a
bit.
> Indeed within Aves we see astonishing convergences, time and again.
This means that we should be very careful before giving a character high
weight. It also means that, if we get a cladogram of good size but a high
consistency index, we have to assume that there's a bias in the data set
(e.
g. the CIs of Sereno's cladograms are 2 and 3 times those of other people's
cladograms, implying that -- as he AFAIK says anyway -- he omits characters
which he thinks are "prone to convergence").
> To claim for instance that anything which calls for convergence
> and so on is ad hoc fails to distinguish between ad hoc hypotheses, and
> auxiliary hypotheses.
:-) May well be, because I've never seen the latter term. -- See above, we
don't expect to need zero ad hoc assumptions, or anywhere near that few. We
just expect that we need as few as possible.
> While we almost all agree that shared derived characters ought to be
used,
> this idea that cladistic analysis in the solitary scientific method of
> phylogenetic reconstruction, with a monopoloy on accuracy and
objectivity,
> is simply farcical.
Obviously it doesn't have a monopoly on accuracy -- or if it does, we can't
find that out, because to do so we'd have to compare cladograms to The True
Tree. But... what other scientific methods are there for phylogenetic
reconstruction? I know none.