[Taxacom] Reproducibility of phylogenetic analysis

Richard Zander Richard.Zander at mobot.org
Tue Jan 26 16:06:06 CST 2010

Popper got, rightly, knighted for his defense of democracy's foundation
in respect for the past and for reason (kind of Burkeian conservatism,
but what do you expect from the Queen, it's better than President's
Medals from the neocons (IMO)). He of course overemphasized
nomological-deductivism and sloughed off intuition, perhaps because of
what are not historical reasons for us, such as Nazi Aryanism and
Mussolini's superman "First do, then think!" Popper is understandable in
context, and the times were sad.

I'm tried to struggle with his formal logic re evidence and hypothesis,
and found (I think) that somewhere in the middle of some pages of
"proof" that he switches e and H without telling. Blink and suddenly
evidence and hypothesis are no longer what they seem. No I don't really
understand it, but I am really doubtful. Anybody else get a similar
feeling about this?

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:

-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu
[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Sergio Vargas
Sent: Tuesday, January 26, 2010 12:28 PM
To: taxacom at mailman.nhm.ku.edu
Subject: [Taxacom] Reproducibility of phylogenetic analysis

If I'm not wrong, Popper insisted that our brains are theory-based. So
we propose theories pretty much by nature... I guess. Testing them
allow us to reject the wrong ones. This is pretty much the same as to
say that we all have a non-flat prior distribution for the possible
explanations of a phenomenon. I think, however, Popper demonstrated
that the ratio between the prior and the posterior probability of an
hypothesis doesn't change after testing the hypothesis... not sure
though, is in the first postscriptum to the logik.

anyways... he did said that all we have is Conjectures and their
Refutations... if a conjecture is not intuition, what is it?


> 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.


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