Nature September 1 issue

J. Kirk Fitzhugh kfitzhug at NHM.ORG
Mon Sep 12 16:29:10 CDT 2005

John, just a comment on your following statement:

At 09:03 AM 9/10/2005 -0400, you wrote:
> From my perspective [morphological and molecular observations] are not
> [equivalent]. It seems to me that sequence 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.

Nucleotide sequences are no different from any other characters of
organisms. All are properties observed of those organisms, stimulating
causal questions to account for shared properties. Regardless of the class
of property observed, causal questions can have the form: 'Why do members
of species B & C have property 1 in contrast to property 0 in A (or all
other species)?' The form of this question applies to nucleotide sequences
just as it does to any morphological observations.  Sequence studies do not
involve replacement, as this is an hypothesized event, not an observation.
Sequence studies, in a phylogenetic context, start with observations of
properties among members of two or more species. Note that the form of the
causal question encapsulates any three-taxon statement. So, it is the
nature of the causal questions as applied to the relevant observations that
dictates the need to invoke phylogenetic inference for the purposes of
answering those questions. The inference of explanatory hypotheses
accounting for morphological and nucleotide characters by way of descent
with modification are identical, per the form of the causal questions
asked, hence the imposition of the requirement of total evidence.

On the matter of homology, once one recognizes the distinction between
homologue and homology, both concepts can be applied to molecular or
morphological observations.  Homologues, as pointed out by Richard Owen,
are conditions to which the same name is applied.  Homology involves the
causal explanation of those homologues.  E. Ray Lankester (1871), however,
correctly suggested replacing the one term homology with two new terms,
homogeny and homoplasy, because of the switch from the archetype theory to
descent with modification.  Unfortunately, while use of the term homoplasy
(for homoplasts) eventually became popular, homogeny (for homogens) did not
catch on to complete the replacement, leaving the term homology with
multiple, inaccurate connotations that do not make a clear distinction
between the effects in need of explanation and the hypotheses causally
accounting for those effects.



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

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