[Taxacom] Reproducibility of phylogenetic analysis

Richard Zander Richard.Zander at mobot.org
Tue Jan 26 14:43:25 CST 2010


Intuitions are Bayesian only in the sense that they may be connected
with a probabilistic analysis in terms of the Bayes equation. That
equation requires assigning an exact prior probability, but intuitions
need no exact probability. They could be just "best guesses" or
compelling notions or bright ideas that encourage further work with more
data. Empiric priors (from previous analyses) have a place, but these
are not intuitions. 

On the other hand, you are right, Derek, IMO, in calling attention to
Bayes' theorem. Particularly I like the transcendence of the Bayesian
idea that the key point for credibility is exactly when you choose to
act on a theory and accept the consequences if wrong, instead of just
issue a ukase on whether some theory is right or wrong based on
attractive a priori mental criteria. Systematics is unfortunately liable
to academic cowboys riding theories off into the sunset because the
predicted or retrodicted results can't be checked directly. 

*****************************
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 Derek Sikes
Sent: Tuesday, January 26, 2010 12:54 AM
To: Taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] Reproducibility of phylogenetic analysis

intuition & inference to the best explanation leads us to hypotheses
with
the highest prior probability; these are then tested to obtain a
posterior
probability for each. All science is Bayesian in this broad sense. Few
test
hypotheses that have extremely low prior probabilities because most are
wrong.

-Derek



On Mon, Jan 25, 2010 at 9:13 PM, <Don.Colless at csiro.au> wrote:

>
> 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/<http://www.csupomona.edu/%7Ejcclark/>
> Director, I&IT Web Development                   +1 909 979 6371
> University Web Coordinator, Cal Poly Pomona
>
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+++++++++++++++++++++++++++++++++++
Derek S. Sikes, Curator of Insects
Assistant Professor of Entomology
University of Alaska Museum
907 Yukon Drive
Fairbanks, AK   99775-6960

dssikes at alaska.edu
http://users.iab.uaf.edu/~derek_sikes/sikes_lab.htm

phone: 907-474-6278
FAX: 907-474-5469

University of Alaska Museum of the North -
http://www.uaf.edu/museum/collections/ento/
+++++++++++++++++++++++++++++++++++
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