The attitrion of taxonomic expertise

Tom DiBenedetto tdib at UMICH.EDU
Fri Oct 18 13:45:45 CDT 1996


On Fri, 18 Oct 1996 12:19:51 -0700 (PDT), James Lyons-Weiler wrote:

>On Fri, 18 Oct 1996, Tom DiBenedetto wrote:
> No need to apologize; the circularity is most certainly in my head, which
>I recognize the problem.  The method itself (cladistic parsimony) does not
>proceed in any such manner; parsimony algorithms first calcluate a
>pairwise distance (purely a phenetic),

HUH? Parsimony programs evaluate the number of state-tranformations
necessary to account for the data on each topology. They do not
evaluate alternative trees on the basis of phenetic distances.

 and then go about finding the
>shortest route possible between terminal taxa.  The problem is the same as
>finding a Steiner graph.  Character transformations are then reported as
>ticks on the tree.  The parsimony tree is the tree with the shortes
>possible internodes.

You are missing the concepts by trying to impose a  terribly
misleading rewording of
the details. There is no criterion for "shortest possible
internodes".
 The criterion is to minimize the number of state-transformations,
tree-wide, necessary to account for the data.

>That is what amounts to "best fit".  The tree
>itself is derived from the data, and then the tree is used to infer
>something about the data.  Sounds circular to me.

Except that this is not what happens.....the tree is not used to
infer anything about the data, the tree merely displays the results
of the test of congruence. Congruence is a necessary test for
hypotheses of homology, for truly homologous characters are congruent
by definition. The parsimony algorithm merely constrains our
statements of generality to the extent necessary in light of the
requirement of congruence.

>If you expect to find homology, you'll find it.

HUH? We expect to find congruence between statements of
generality,,and we often dont.

* But you won't know if
>other hypotheses of homology have been rejected because you're accepting
>erroneous synapomorphies when the tree is wrong.  It's not a good test,
>but it is a rather nice way to summarize the data.

It is an excellent test of what it is trying to test; that your
hypotheses of homology fit into the expectation of congruence;
something essential within the evolutionary paradigm.
It is not an absolute test, which is what your question seems to beg;
of course at some level NO test will assure you that your tree or the
"facts" which it displays are TRUE.

tom


---------------------------------------------
Tom DiBenedetto
Fish Division
Museum of Zoology
University of Michigan




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