3TA (was Human and ape phylogeny)

[Kirk Fitzhugh]

Dick,

The clarity of your points is refreshing. To answer your question: am I
referring to characters as effects or the hypothesized origins of
characters as effects, my answer definitely would be the former. What we
perceive in the present are objects, or organisms, with properties. I ask
why some organisms have one sort of property in contrast to some other
property. I am asking a causal question, for which I infer an explanatory
hypothesis, as a cladogram, as a tentative answer.

So, I do not regard (A(B,C)) as an effect, but as a summary of causal
events accounting for the shared similarities, as effects, I observe. You
are correct that one set of effects are shared similarities, which are the
basis for inferring some explanatory hypothesis. What I mean by the second
class of effects, which stand as tests of the hypothesis, are
extra-organismal effects stemming directly from the past hypothesized
causal events stipulated by my explanatory hypothesis. For instance, a
homicide detective might formulate a hypothesis of who killed a person
based on a set of effects, "evidence." In essence, they then test their
hypothesis by searching for effects wholly independent of the body. These
other effects are traces of the past causal event(s) which narrow down the
likelihood that their suspect is the culprit. Finger prints are a classic
example of such effects. In our field, biogeographic "evidence" comes to
mind as one component of independent tests to be used against a cladistic
hypothesis. As a result, you are very correct when you said, "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."

I appreciate your candidness in describing the "crux of our disagreement,"
and agree with you that we have very different motivations for our
respective inferences of cladograms. It is true that any explanatory or
historical hypothesis proceeds from what is known to invoking the unknown.
But, this pervades all realms of science and everyday living, including the
inferences leading to the periodic table. "Here is a glass of water," is an
inference of the same standing as a cladogram, as an explanatory
hypothesis. It is not my position to criticize you or anyone else for
holding the position that cladograms should be non-historical constructs. I
do, however, have disdain for those who find it necessary to claim one or
the other point of view is the only acceptable avenue. My only intent was
to outline the requirements for proper testing of historical hypotheses,
which have traditionally not been correctly conveyed in the cladistic
literature.

Best,
Kirk

At 01:01 PM 4/10/03 -0500, you wrote:
>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