3TA (was Human and ape phylogeny)

[Richard Jensen]

Kirk,



Kirk Fitzhugh wrote:

> Thanks Dick. I'm not saying that hypothesis (B,C) cannot be tested. What
> I'm saying is that those effects which were used to infer the hypothesis in
> the first place cannot also be tests of the hypothesis.

Are you referring to characters as effects or the hypothesized origins of
characters as effects.  In an earlier post you refer to two classes of effects:
"Such consequences must be of a class of effects [consequences of the causal events
claimed by (A(B,C))] independent from the class of effects, i.e., characters, the
hypothesis is intended to address."  As I read this, you are treating the
historical events that lead to (A(B,C)) as one class of effects and the characters
as a second class of effects.  Because the characters (known and yet to be
discovered) are the result of the first set of effects, they cannot be used to test
hypotheses about the first set of effects.

If I have this right, then I agree.

Here, then, is the crux of our disagreement.  My classification [recognition of
(B,C) as a natural subset of (A,B,C)] makes no assumptions about the historical
effects (events) that might have given rise to (B,C).  For me, each character is
simply an observation and whether or not I can recognize synapomorphies is not
germane to the problem at hand.  I simply want to know what arrangement of taxa is
most consistent with the information contained in the data I have at hand.  That
arrangement may not (and I don't expect it to) reflect the phylogenetic
(historically determined) relationships among the three taxa.

I believe my view is analogous to that of Mendeleyev.  His original periodic table
had gaps.  Based on the patterns he perceived, he was able to make predictions
about what was missing.  Each discovery of a new element was a test of his periodic
table.  Similarly, a newly discovered set of characters can be used to test my
classification.  These characters are independent of the initial set of characters
because I make no assumptions about causal links among the characters.

It seems that the bottom line is that you are expecting the classification to
reflect what we cannot know (the pattern of historical events that lead to the
observed character distributions) and I am expecting the classification to reflect
patterns derived solely as a function of what we do know (the characters that each
OTU has).

Cheers,

Dick

--
Richard J. Jensen              | tel: 574-284-4674
Department of Biology      | fax: 574-284-4716
Saint Mary's College         | e-mail: rjensen at saintmarys.edu
Notre Dame, IN 46556    | http://www.saintmarys.edu/~rjensen