[Taxacom] Reproducibility of phylogenetic analysis

Richard Jensen rjensen at saintmarys.edu
Wed Jan 27 09:54:29 CST 2010

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

Richard Zander wrote:
> Interesting exchange here. It reflects the difficulty of checking
> results in systematics. If we could test a process against examples of
> the process, bob's your uncle. But only part of systematics is process
> (evolution) the rest consists of a series of one-time historical events
> (speciation events and the like). Evolution we can test, with
> difficulty, as a process, but cladograms and phenograms are usually
> treated as things in themselves, the ends of analysis.
> *****************************
> 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 Dick Jensen
> Sent: Tuesday, January 26, 2010 6:54 PM
> To: Stephen Thorpe
> Cc: Bob Mesibov; TAXACOM
> Subject: Re: [Taxacom] Reproducibility of phylogenetic analysis
> Gosh, Stephen,that sounds amazingly like the criticisms of phenetics
> that lead (in part) to the cladistic revolution - too many ways to
> determine similarity and find clusters.
> The more things change, the more they stay the same!
> Dick J
> Richard Jensen, Professor
> Department of Biology
> Saint Mary's College
> Notre Dame, IN 46556
> tel: 574-284-4674

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