[Taxacom] DNA homologies

[J. Kirk Fitzhugh]

John,

Regarding the requirement of total evidence, you stated, "Combining DNA and 
macro-biological characters may provide total evidence if the characters 
are of the same kind."  What do you mean by "same kind?" Unfortunately, 
such a condition has nothing at all to do with why the requirement stands 
as part of our rational reasoning. If you wish to maintain that sequence 
data are not to be considered in a phylogenetic context along with any 
other types of observations of organisms, then you will have to show that 
those data are not amenable to being explained by way of descent with 
modification. Otherwise, you commit the same error so often seen of 
inferring separate phylogenetic hypotheses for partitioned data, wherein 
those distinct hypotheses are irrelevant to one another and cannot be 
rationally compared. Are you willing to claim that sequence data must be 
explained by causal conditions other than descent with modification?

You stated, "Interesting about comparison of molecular and macro-biological 
data being nonsensical since that would seem to be what one is doing when 
combining data."  I did not state that it is nonsensical to compare the 
data.  I stated that it is nonsensical to compare phylogenetic hypotheses 
derived from separate sets of data.  Keep in mind that a cladogram is 
nothing but a very vague explanatory hypothesis. It suggests events of 
character origin among members of common ancestral species and speciation. 
Such events are only relevant to the data in need of being explained by 
that hypothesis. What one might have in the way of some other hypothesis 
invoking the same classes of events cannot be compared to the other 
hypothesis. But, to make the mistake of engaging in such comparisons shows 
that the data are explanatorily relevant to one another, thereby precluding 
the exercise of partitioning.

You stated, "I would think similarity is all about the distribution of same 
or different properties. At least I do not see at this time sufficient 
reason not to use the term so I will stick to it for now."  Your emphasis 
on similarity as a way to critique the explanations of observations is 
incorrect.  Similarity is only relevant at the point that you infer and 
defend your perceptual beliefs and present your observation 
statements.  Similarity has nothing to do with phylogenetic 
inference.  More fundamentally, if phylogenetic hypotheses present causal 
explanations of shared characters, then one should be able to articulate 
the causal questions that prompted inference of those hypotheses.  This is 
the real focal point that needs to be addressed with regard to sequence data.

You stated, "Perhaps you are right about total evidence, but this is not 
what molecular geneticists and almost all primate systematists believe. 
They believe that DNA similarities (or whatever) cannot be 
challenged...."  Yes well, one of the grand failures of our education 
system has been the lack of emphasis on the philosophical principles needed 
to justify the processes of doing science.  And one of those principles is 
that of rational reasoning, and the requirement of total evidence is one of 
the uncontested hallmarks of such reasoning.

Kirk

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J. Kirk Fitzhugh, Ph.D.
Curator of Polychaetes
Invertebrate Zoology Section
Research & Collections Branch
Los Angeles County Museum of Natural History
900 Exposition Blvd
Los Angeles CA 90007

Phone:   213-763-3233
FAX:       213-746-2999
e-mail:   kfitzhug at nhm.org
http://www.nhm.org/research/annelida/staff.html
http://www.nhm.org/research/annelida/index.html
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