Cladistic hypotheses

[Richard.Zander at MOBOT.ORG]

Someone wrote the program, as has been pointed out by others in this thread,
and the computer's algorithm is pretty simplistic. There is a difference
between data and assumptions. Someone should therefore interpret the results
in light of the assumptions to distinguish scientific advances from vagaries
and piffle.

One of the assumptions that has been laid on us is about likelihood: that,
given that the likelihood of the hypothesis is the likelihood of the data,
therefore the data is all that one needs to evaluate the correctness of a
hypothesis.

Nonsense. This ignores assumptions. It's been noted that about 4 or 5
nucleotides are wrong per every 10,000 bases in a dataset, even when checked
in the usual manner. In a common-sized database of about 2,000 sites, one
might expect one wrong nucleotide. Does it matter for a given branch
arrangement of interest? Small chance. When using computerized sequence
alignment, one can set the probability of being correct at 95%. Does this
small chance of misalignment matter? Small chance. Et cetera, etc. Add up
the small chances and what do you get? Perhaps a factor that will be
significant when you multiply 1 minus probability of being wrong and the
posterior probability.

The probability of being correct must be acted upon only in light of the
risk. There are two risks, (1) your science is wrong, and (2) the
assumptions are wrong. We can deal with the first by setting high acceptable
significance levels (or pleading mere speculation), but everyone ignores
assumptions because phylogenetic speculation and having to actually use the
results (e.g. in biogeography, evolution studies) are conflated.

______________________
Richard H. Zander
Bryology Group, Missouri Botanical Garden
PO Box 299, St. Louis, MO 63166-0299 USA
richard.zander at mobot.org <mailto:richard.zander at mobot.org>
Voice: 314-577-5180;  Fax: 314-577-0828
Websites
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-----Original Message-----
From: E. Parmasto [mailto:e.parmasto at ZBI.EE]
Sent: Wednesday, November 23, 2005 2:56 PM
To: TAXACOM at LISTSERV.NHM.KU.EDU
Subject: Re: [TAXACOM] Cladistic hypotheses


Richard Zander, 23 Nov 2005 14:25:38:
   > A cladogram is produced from reasonable data
by a computer using a
> particular reasonable evolutionary model and some assumptions...
>
   A cladogram is a *metahypothesis* based on
hypotheses-based computer programs, on
taxonomists' hypotheses on homologies of
characters (character states) used, on a hypothetical
evolutionary model, on hypotheses-based selection
of (sometimes numerous) cladograms by the
taxonomists, &c. Consequently, a (published,
released) cladogram is a hypothesis proposed by
taxonomists, not by a PC.
*************
Erast Parmasto
Institute of Agricultural and Environmental Sciences
181 Riia St.,  51014 Tartu, Estonia
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