[Taxacom] Pasimony and base alignment

[J. Kirk Fitzhugh]

If one carefully reads what I said, they will notice I was not 
'pooh-poohing' parsimony or posteriors, as Dr. Zander deftly contends.  I 
merely pointed out that the parsimony criterion as applied in the inference 
of phylogenetic hypotheses provides no relation to truth.  This is not idle 
philosophical double speak, but rather a reality of the mechanics of 
hypothesis inference. The 'middle ground' Dr. Zander seeks has existed for 
quite some time, but is in fact no middle ground at all, but rather 
recognizing the proper testing of explanatory hypotheses, which has been 
routinely misapplied in phylogenetics. Phylogenetic inference does not 
generate knowledge, but rather very vague, incomplete explanatory accounts 
with modest potential to provide causal understanding. The issue is to 
correctly assess the explanatory veracity of hypotheses. For one to then 
judge the truth, plausibility, or confidence in a given hypothesis requires 
properly testing that hypothesis. Problem is, however, shared similarities 
can never serve as test evidence. Ergo, Bayesian methods are irrelevant for 
they deal not with the inference of hypotheses but with their subsequent 
confirmation, and confirmation requires test evidence, which cannot be 
shared similarities.

Kirk

At 10:45 AM 9/8/2006 -0500, Richard Zander wrote:
>Kirk F. has shifted the problem to something else again, pooh-poohing
>parsimony and posteriors alike in a rather absolute philosophical
>fashion. Somewhere there is a judicious mesocosm between joyous
>overconfidence in phylogenetic analysis as a process generating
>knowledge (or at least hypotheses that someone else will confirm
>someday), and dour condemnation of the whole bit. Are there any comments
>along the lines of a middle view?

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J. Kirk Fitzhugh, Ph.D.
Curator of Polychaetes
Invertebrate Zoology Section
Research & Collections Branch
Los Angeles County Museum of Natural History
900 Exposition Blvd
Los Angeles CA 90007

Phone:   213-763-3233
FAX:       213-746-2999
e-mail:   kfitzhug at nhm.org
http://www.nhm.org/research/annelida/staff.html
http://www.nhm.org/research/annelida/index.html
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