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 ;-)
Kirk
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"To become a standard authority is, sooner or later, to become an obstacle
to knowledge."
D.R. Dudley, The Civilization of Rome
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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.orghttp://www.nhm.org/research/annelida/index.html
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