[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.

Kirk

-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
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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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