[Taxacom] Reproducibility of phylogenetic analysis

J. Kirk Fitzhugh kfitzhugh at nhm.org
Tue Jan 26 13:32:42 CST 2010


'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
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> richard.zander at mobot.org
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> Modern Evolutionary Systematics Web site:
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> *****************************
>
> -----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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