[Taxacom] Reproducibility of phylogenetic analysis

J. Kirk Fitzhugh kfitzhugh at nhm.org
Wed Jan 27 13:18:50 CST 2010

A standard research program for Lakatos was one that actively engages in 
theory/hypothesis formation and testing. Nothing remarkable about that. 
Explanatory hypotheses, by their very nature are reactions to effects in 
the present. What causes actually did occur in the past are rarely 
available to us, even as eye witness accounts. This is just the plain 
reality for all facets of explanation, not just systematics. We struggle 
no more or less than anyone else seeking to explain the present by way 
of the past. As in all the sciences, the mechanics of testing 
explanatory hypotheses is rather straightforward, regardless of the 
difficulty of actually doing it. The problem in systematics and 
evolutionary biology is that the subject is either ignored, in lieu of 
seeing cladograms as the end point, or testing is misrepresented, as is 
often seen with the notion of 'throw in more characters.'

You're correct, systematics has had a rather different sort of research 
program. One that isn't particularly in accord with how science is done 
in other fields. That seems like a good basis for making a change from 
the status quo of cladograms being the means to the end.


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 Zander wrote:
> 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
> 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

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