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"Logic of Cladistics"

Juan Carlos Morales jcm19 at COLUMBIA.EDU
Sun Jun 12 09:48:56 EST 1994

On Sat, 11 Jun 1994, Mark Siddall wrote:

> 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

I think that a more dangerous thing is when people run all these programs
and then select for presentation the one that most pleases their
preconceptions.  I rather have them show me all the options and allow me
to make my own judgement.  Furthermore, I think that by analysing
differences in tree topologies generated with different sets of
assumptions one can learn more about the data set.

Juan Carlos Morales

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