[Taxacom] Reproducibility of phylogenetic analysis

J. Kirk Fitzhugh kfitzhugh at nhm.org
Wed Jan 27 11:54:33 CST 2010

Interesting. We've returned to Philosophy of Science 101. If only this 
had been the emphasis all along in systematics.


J. Kirk Fitzhugh, Ph.D.
Curator of Polychaetes
Invertebrate Zoology Section
Research & Collections Branch
Natural History Museum of Los Angeles County
900 Exposition Blvd
Los Angeles CA 90007
Phone: 213-763-3233
FAX: 213-746-2999
e-mail: kfitzhug at nhm.org

Richard Jensen wrote:
> I couldn't agree more. We have to assume that there are patterns (e.g., 
> regularities that can be detected, whether with respect to morphological 
> features, nucleotide sequences, atomic structure, response to light 
> photons, etc.) that represent the consequences of real phenomena (my 
> words are fraught with loaded meanings - no apology for that). After 
> all, if every event is unique, and every event requires an independent 
> explanation, then we can never have hypotheses, laws and theories, 
> except for the conclusion that we can never know how or why anything 
> happens!). So, if we want to explain why things are the way they are, we 
> start with observations, notice patterns (regularities) and then, given 
> whatever assumptions we use to organize our thinking, try to find out if 
> we can explain these patterns and if our explanation is useful for 
> interpreting other patterns.
> Cheers,
> Dick J
> Richard Jensen, Professor
> Department of Biology
> Saint Mary's College
> Notre Dame, IN 46556
> Tel: 574-284-4674
> Richard Zander wrote:
>> Well, Dick, I think we need to go beyond patterns. The particular
>> processes and the particular historical events that lead to patterns and
>> clustering in nature should be a focus. Doubtless patterns lead to and
>> guide study that might reveal processes and historical events. Patterns
>> also are convenient for classification, but surely knowledge (when such
>> can be had) of a process and/or an historical event should also inform
>> classification. Also, patterns of what? With morphological data we get
>> inferred clusters of shared homologous traits fixed at nodes in a
>> gradualist model of evolution, with molecular data we get inferred
>> genetic continuity and isolation events without relevance to taxa. Of
>> course, compared to these bad interpretations in phylogenetic analysis,
>> phenetics is refreshingly clean in what it is doing.
>> *****************************
>> Richard H. Zander 
>> Voice: 314-577-0276
>> Missouri Botanical Garden
>> PO Box 299
>> St. Louis, MO 63166-0299 USA
>> richard.zander at mobot.org
>> Web sites: http://www.mobot.org/plantscience/resbot/
>> and http://www.mobot.org/plantscience/bfna/bfnamenu.htm
>> Modern Evolutionary Systematics Web site:
>> http://www.mobot.org/plantscience/resbot/21EvSy.htm
>> *****************************
>> -----Original Message-----
>> From: Richard Jensen [mailto:rjensen at saintmarys.edu] 
>> Sent: Wednesday, January 27, 2010 9:54 AM
>> To: Richard Zander
>> Cc: Stephen Thorpe; Bob Mesibov; TAXACOM
>> Subject: Re: [Taxacom] Reproducibility of phylogenetic analysis
>> I think the key is that analytic methods produce results that we wish to
>> interpret according to some set of a priori 
>> assumptions/hypotheses/guesses. What we get, as Stephen noted, is a 
>> function of what those assumptions etc. are. Are they a function of some
>> explicit process, or are they just one possible reflection of a 
>> particular set of assumptions? There are patterns in nature - the 
>> questions are: Can we detect them? If so, how do we detect them? How do 
>> we know when we have detected them? Can we explain them?
>> Dick J
>> Richard Jensen, Professor
>> Department of Biology
>> Saint Mary's College
>> Notre Dame, IN 46556
>> Tel: 574-284-4674
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