[Taxacom] Reproducibility of phylogenetic analysis

Richard Zander Richard.Zander at mobot.org
Wed Jan 27 13:01:23 CST 2010


Philosopher of science Lakatos indicated that we need not reexamine the
fundamentals of our science every time we engage in research, but merely
need only plunge ahead into a standard Research Program, which pretty
much guarantees generation of results since it using the same methods on
similar data. Systematics, however, has always struggled with its
fundamentals because the results cannot be directly checked against
history or easily checked against evolution which is a process but damn
well-hidden. 

Systematics is famed for its arguments and battles. This is as it should
be. We seem to have a different standard Research Program every 40 years
or so. (Time for a change? What now?)

*****************************
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: taxacom-bounces at mailman.nhm.ku.edu
[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of J. Kirk
Fitzhugh
Sent: Wednesday, January 27, 2010 11:55 AM
To: TAXACOM
Subject: Re: [Taxacom] Reproducibility of phylogenetic analysis

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
http://www.nhm.org/site/research-collections/polychaetous-annelids
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


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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