"Logic of Cladistics"

Mark Siddall mes at zoo.toronto.edu
Sat Jun 11 10:06:13 EST 1994


Bruce Rannala (rannala at minerva.cis.yale.edu) writes:

... much interesting and cogent food for thought.

But...
Unlike him I would not discourage posting re: cladistics.  True, we 
cladists are not unknown for vitriol and venom, but perhaps through reasoned
discussion, suggested here by Joe Felsenstein, I can help dispell the
myth that we are all painted with the same brush.

Notwithstanding references to Buddhism, Christianity and near-condescending
references to young cladists not hitching to trains (Bruce - I forgot
how much I've missed your unique brand of discourse!)  I would
in fact suggest that one thoroughly investigate all lines, BUT do not
be a fence-sitter.  Not all approaches are philosophically reconcileable
and one must have conviction.

On this thread, and more pertinent to this group perhaps, I am increasingly
concerned with a tendency to crank off sequences, fire them into some
phylogenetic software like PHYLIP, PAUP, MEGA or Hennig86 without
full understanding of what's going on.  The argument can be made that
it is an awkward, if not dangerous, thing to simply pump out a
parsimony tree, a Fitch-Margoliash distance tree, a UPGMA, and whatever
and publish them all side by side. There appears to be in some arenas
a fundemental ignoring of the issues, as though phylogenetic investigation
was so-much recipe work.  It is not.  There are issues that need to be
addressed by all practitioners in their analyses regarding multiple
trees, assumptions, defensibility of a chosen approach, and so much
more...

Just a thought.

Mark

-- 
Mark E. Siddall                "I don't mind a parasite...
mes at vims.edu                    I object to a cut-rate one" 
Virginia Inst. Marine Sci.                     - Rick
Gloucester Point, VA, 23062



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