Nature September 1 issue

John Grehan jgrehan at SCIENCEBUFF.ORG
Sat Sep 10 09:03:57 CDT 2005

More response to Kirk below:


From: Taxacom Discussion List on behalf of J. Kirk Fitzhugh
Sent: Fri 9/9/2005 4:51 PM
Subject: Re: [TAXACOM] Nature September 1 issue

Thanks, John. Just a couple of comments on what you say.

There is no reason to consider observations (evidence) in terms of value or
being comparative if the context in which one is dealing with those
observations is explanatory. 

Perhaps, perhaps not.

And, morphological/molecular observations
cannot be regarded as independent research programs unless one is willing
to stipulate that the causal questions associated with each class of
observations are not of the same basic form.  

>From my perspective they are not. It seems to me that equence studies involve the replacement in different combinations of four bases and deriving phylogenetic inferences from those combinations according to tree building procedures while morphology involves hypotheses of homology for each individual character in order to make three taxon statements. The methdological procedures are different in each case. 

If, on the other hand, our
interest as systematists is to causally account for shared similarities
distributed among members of two or more species, then the causal theory of
choice would be that of descent with modification.  The theory is being
applied to all of these observations, if one is willing to accept that the
nature of the causal questions are the same across those observations, such
that the requirement of total evidence cannot be circumvented.  This is not
an illusion of a solution - it is the only solution given the basic
principle that scientific reasoning should be rational.

It seems to me that what is being said here is that if one conforms to a particular belief about the cause of similarities then one cannot be selective about characters. We would have to agree to disagree here. Shared primitive characters, for example, are not of the same status as shared derived. Combining the two in a way that would not allow their respective identification would produce illusary groupings.

To speak of observations as misleading is irrelevant to the inference of
any explanatory hypothesis that is phylogenetic.  To judge the integrity of
observations in terms of our willingness to trust our own perceptions is a
matter to be dealt with prior to explaining those observations.  This is
the criterion that needs to be applied in order to determine whether or not
descent with modification is to be applied to observations across
species.  If descent with modification is the choice, then again, separate
phylogenetic inferences will be irrational.  I would be more concerned
about someone deciding to actively exclude observations without any viable
excuse for why observations of the same properties among members of two or
more species are not to be explained by phylogeny in lieu of other
properties deserving such explanation.

Fair enought. Reasons for excluding DNA sequence simialrities in the case of the orangutan and human affinitiy have been stated. Of course not everyone agrees with them.

I would not agree that the problem in science is the suppression of
exploration of conflict by editors.  

I will agree to disagree with you on that.

Again, conflict is not the issue, per
the requirement of total evidence.  The problem starts with scientists who
either do not understand or are willing to ignore the requirement of total
evidence and the mechanics of causal inference that is the basis for

Perhaps, and perhaps not

I do agree with you that there exists a sociological
problem relative to funding agencies and their lack of understanding of the
principles of Science.

Or that they just have a different understanding of the principles of science (if there are really any such principles)

John Grehan

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