[Taxacom] Reproducibility of phylogenetic analysis

Wed Feb 3 12:51:05 CST 2010

Sorry to have just gotten back to checking my 
emails and thus responding to this thread later than most.

Some might find the following interesting with 
regard to it.  I even have some extra reprints available:

Intraspecific Variation in Pavetta rigida 
(Rubiaceae):  Estimates of Reliability of 
Taxonomic Information.  Ann. Missouri Bot. Gard. 78: 535-538.  1991.

Steve

At 01:32 PM 1/26/2010, J. Kirk Fitzhugh wrote:
>'Abduction' has it's origin with Aristotle (the history of which can be
>found in the extensive writings of Charles Sanders Peirce). 'Inference
>to the best explanation' (IBE) was a creation of Gilbert Harman in 1965,
>and a good modern exposition of it can be found in Peter Lipton's book
>by the same title.
>
>Abductive inference, however, allows for concluding mulitple, mutually
>exclusive hypotheses, much in the way phylogenetics (cladistics)
>computer programs produce multiple cladograms. IBE attempts to go
>further by implementing criteria that might aid in narrowing down
>candidate hypotheses. This could have the benefit of saving time, money,
>etc., if one were to pursue the process of testing. Albeit, my
>recollection is that some have claimed that IBE is a surrogate to
>testing, I'm not sold on that idea.
>
>It's been recognized at least since the 19th century that abduction in
>human reasoning includes that 'intuitive' step. To his credit, C.S.
>Peirce (see also N.R. Hanson's 'Patterns of Discovery') largely
>demystified that intuitive notion by carefully outlining the nature of
>abductive reasoning as we apply it to our sense perceptions to infer
>observation statements, theories, and hypotheses. Peirce then related
>the fundamental importance of abduction to de- and induction in the
>sciences. My personal view is that Peirce preempted Popper in many ways.
>Indeed, in his biography on Peirce, Joseph Brent comments: "To read
>Popper or Carl Hempel on the logic of science after reading [Peirce]
>shows how little has been added to the model first proposed by Peirce
>over a century ago, and may also show that some elements, particularly
>the essentiality of hypothetical inference, has been removed with
>damaging effect to our understanding of science."
>
>I've discussed this subject as it relates to biological systematics in
>these papers:
>
>Fitzhugh, K. 2005a. Les bases philosophiques de l'inférence
>phylogénétique: une vue d'ensemble. Biosystema  24: 83-105.
>
>Fitzhugh, K. 2005b. The inferential basis of species hypotheses: the
>solution to defining the term 'species'.  Marine Ecology 26: 155-165.
>
>Fitzhugh, K. 2006a. The abduction of phylogenetic hypotheses. Zootaxa
>1145: 1-110.
>
>Fitzhugh, K. 2006b. The 'requirement of total evidence' and its role in
>phylogenetic systematics. Biology & Philosophy 21: 309-351.
>
>Fitzhugh, K. 2006c. The philosophical basis of character coding for the
>inference of phylogenetic hypotheses. Zoologica Scripta 35: 261-286.
>
>Fitzhugh, K. 2008a. Fact, theory, test and evolution. Zoologica Scripta
>37: 109-113.
>
>Fitzhugh, K. 2008b. Abductive inference: implications for 'Linnean' and
>'Phylogenetic' approaches for representing biological systematization.
>Evolutionary Biology 35: 52-82.
>
>Fitzhugh, K. 2008c. Clarifying the role of character loss in
>phylogenetic inference. Zoologica Scripta 37: 561-569.
>
>Fitzhugh, K. 2009. Species as explanatory hypotheses: refinements and
>implications. Acta Biotheoretica 57: 201-248.
>
>Fitzhugh, K. in review. 'Evidence' for evolution versus 'evidence' for
>intelligent design: parallel confusions. Acta Biotheoretica.
>
>Richard Zander wrote:
> > I think the fancy term is "abduction" nowadays, Don. Fitzhugh can
> > comment on such with familiarity.
> > R.
> >
> > *****************************
> > 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
> > Don.Colless at csiro.au
> > Sent: Tuesday, January 26, 2010 12:13 AM
> > To: jcclark-lists at earthlink.net
> > Cc: taxacom at mailman.nhm.ku.edu
> > Subject: Re: [Taxacom] Reproducibility of phylogenetic analysis
> >
> >
> > It's worth noting that Karl Popper, while insisting that science
> > advances by the testing of hypotheses, steered clear of just how we
> > should arrive at those hypotheses. Indeed, I seem to recall that he
> > admitted intuition there. The most respectable these days seems to be
> > the process of "inference to the best explanation" - which, surely,
> > requires just the intuition of a highly trained, talented expert.
> >
> > Donald H. Colless
> > CSIRO Div of Entomology
> > GPO Box 1700
> > Canberra 2601
> > don.colless at csiro.au
> > tuz li munz est miens envirun
> >
> > ________________________________________
> > From: taxacom-bounces at mailman.nhm.ku.edu
> > [taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Curtis Clark
> > [jcclark-lists at earthlink.net]
> > Sent: 26 January 2010 01:49
> > To: TAXACOM
> > Subject: Re: [Taxacom] Reproducibility of phylogenetic analysis
> >
> > On 2010-01-24 14:58, Richard Zander wrote:
> >
> >> "     A third method of scientific analysis is intuition, long
> >> lambasted as illogical and subjective though often defended as "common
> >> sense."
> >>
> >
> > In my estimation, science only progresses through intuition, and the
> > purpose of the scientific method is to provide post-hoc evaluation of
> > intuitive insights.
> >
> > --
> > Curtis Clark                  http://www.csupomona.edu/~jcclark/
> > Director, I&IT Web Development                   +1 909 979 6371
> > University Web Coordinator, Cal Poly Pomona
> >
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