Lobo,
I am very glad to hear of your interest in this subject. The book on
abduction you mention in your message is a very good one. Interest in
abduction has especially grown in recent years in the field of artificial
intelligence. But, excellent reading can be found in the 19th century
writings of Charles Sanders Peirce, who has until recently been very much
ignored in the area of scientific methods and philosophy of
science. Peirce was a brilliant, although tormented, individual.
Regarding your question about abduction and Bayesian priors, it is first
important to recognize that it would only be in the context of p(H) that
our phylogenetic hypotheses have any relevance. This means that one starts
with their observations of shared similarities among organisms, then
abductively infers phylogenetic hypotheses, subsequent to which they could
if they wish assign some measure of plausibility, i.e., p(H), to
these. Now, how one can possibly assign priors to all these minimum-length
cladograms is absolutely beyond me! But, even if you DO assign priors, you
must then contend with the actual and proper approaches to testing any of
those hypotheses such that you might later determine a posterior
probability. Therein is one of the biggest problems: the correct testing
of phylogenetic hypotheses. I discuss this matter extensively in my
Zootaxa and Biosystema papers. So, the problem with the phylogenetics
application of what is claimed to be Bayesianism is that Bayes theorem is
not correctly applied to any hypothesis, especially to correctly interpret
the notion of 'evidence' for moving from prior to posterior probabilities.
Kirk
-----------------------------------------------------
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.orghttp://www.nhm.org/research/annelida/staff.htmlhttp://www.nhm.org/research/annelida/index.html
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