[Annelida] re: eunicid phylogeny

J. Kirk Fitzhugh kfitzhug at nhm.org
Fri Mar 24 22:02:20 EST 2006


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.org
http://www.nhm.org/research/annelida/staff.html
http://www.nhm.org/research/annelida/index.html
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