[Annelida] re: eunicid phylogeny

J. Kirk Fitzhugh kfitzhug at nhm.org
Fri Mar 24 16:52:20 EST 2006

Since Torsten continues to insist that I am operating in the realm of 
metaphysics, rather than the philosophy of science, it might be instructive 
that we know what is meant by the term "metaphysics":

"Metaphysics is the study of the most general concepts used in science and 
ordinary life, through the study of the internal structure of the language 
used in different fields" (from: Harré, R.  The Philosophies of Science, 
pg. 30).

Clearly, the issues I have raised fall within the realm of the metaphysical 
only because metaphysics is a vital component of the philosophy of science, 
just as is logic (the theory of reasoning) and epistemology (the theory of 
knowledge).  It would be impossible to discuss the merits of science 
without invoking all three components.  But, as we can see, the arguments I 
have presented are not "purely metaphysical," contrary to Torsten's attempt 
to misapply that term.  It is within the philosophy of science that we 
critically evaluate what we do as scientists, which has been the realm in 
which I have been operating, under the recognized principles of logic, 
epistemology, and metaphysics.  To deny such an activity is to deny the 
very justification for doing science.  None of us should find that acceptable.

There are three recognized classes of reasoning: deduction, induction, and 
abduction.  Since phylogenetic inference is a form of abduction, we must 
seriously examine the consequences that has for phylogenetic methods.  This 
is not a simple matter of likelihood versus parsimony, since the concepts 
of likelihood and parsimony must be examined in relation to abduction and 
the nature of our causal questions.  When one does examine those relations, 
it is found that so-called "maximum likelihood" and "maximum parsimony" 
methods are founded on defective premises.

Let's keep in mind that throughout the development of phylogenetic methods 
no one has clearly and cogently identified the nature of the abductive 
inferences we employ.  No one has clearly and cogently outlined the formal 
framework of abduction as used in phylogenetics.  Rather, we see methods of 
phylogenetic inference said to be "hypothetico-deductive," "Popperian," 
"statistical," "probabilistic," "Bayesian," or "inductive."  All of these 
labels apply to either deduction or induction, not abduction.  The 
consequence is that when methods that are deductive or inductive are 
applied to abduction, then the manner in which those methods are applied is 
scientifically unacceptable.  If parsimony and likelihood are incorrectly 
applied to abductive inference, then those methods are scientifically 
unacceptable, just as it is scientifically unacceptable to apply Bayesian 
inference to the abduction of hypotheses, or bootstrapping to 
non-statistical hypotheses, or partitioning of relevant data.

To claim that a method is "well proven by empirical data" is a defense 
devoid of merit if the very basis for the method is derived from incorrect 
premises.  Since phylogenetic methods have been developed without 
consideration of the fact that they are constrained by the abductive nature 
of hypothesis formation, the acceptability of those methods is seriously 
compromised.  To defend a method without understanding the basis for using 
the method is a false defense.

I thank you for your kind attention ;-)


"To become a standard authority is, sooner or later, to become an obstacle 
to knowledge."

D.R. Dudley, The Civilization of Rome

J. Kirk Fitzhugh, Ph.D.
Curator of Polychaetes
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
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