[Taxacom] DNA homologies

[John Grehan]

> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
> bounces at mailman.nhm.ku.edu] On Behalf Of pierre deleporte
> >This correlation between similarity and
> >relationship fails to recognize that the two concepts are not
> >necessarily identical.
> 
> = classic notion of the "pitfall of clustering on the basis of
> simplesiomorphies", an objection addressed to phenetic analyses, which
is
> applicable to molecular and morphological data analysis as well,
> hence this assertion is WRONG if applied to ALL molecular analyses,
> because
> parsimony analyses of molecular data avoid this problem

All I was saying that similarity and relationship are not necessarily
identical. One needs to determine what kind of similarities are
informative about relationships. But in molecular studies there seems to
be an emphasis on similarity (of DNA bases) being a direct indicator of
relationship.

> This is a particularly dangerous illusion. There is nothing like "pure
> empirical observation" in comparative morphology - there is simply no
> "theory-free empirical observation" in science. A morphological
homology
> statement is necessarily loaded with theory (see below).

In a philosophical sense that is true, but I can observe each character
claim directly, whereas in molecular systematics the character claims
are generated by an alignment algorithm (i.e. I could empirically see
each base, but the match between bases of different species is
constructed by an algorithm.

> 
> >This match is accomplished by shuffling the DNA
> 
> NOT for nuclear DNA: no gaps, no 'shuffleable' data - there are much
more
> "gaps" in morphological data than in nuclear DNA sequences, see below

> nobody can decently ignore such "squeleton shuffling and morphological
gap
> coding", unless ignorant, or ideologically biased against molecular
> analyses

This is an interesting point although I am not sure that it is entirely
the same situation in that morphologist do not rely on algorithms to
make the homology choices, and the problem does not arise in all
character comparisons. I'll certainly retain the thought, although I
will leave it to others to make your case.
> 
> [overall similarity I presume?]
yes

> it is strange that you don't mention obvious problems of difference in
> structure of the data, like the limitation of number of states in
> molecular
> sequence characters (increased statistical risk of "saturation"
compared
> with morphological traits with more numerous states or slower
evolution)
> 
> otherwise you keep on reiterating indefinitely the same misconceptions
> about how morphological and molecular data are analysed (= obviously
the
> same way in fact, if you apply the same methods, e.g. maximum
parsimony)

Whether they are misrepresentations or not I will leave to our
respective opinions. But yes, I could raise the limitations on number of
states, but in the current draft I had not. There may be plenty of other
problems as well. The point is that if morphology is problematic in one
or more ways, then so too is DNA analysis.

> >Other theoretical assumptions include a continuous clock like
divergence
> >of DNA,
> 
> this is utterly WRONG for maximum parsimony analysis of molecular
data,
> i.e. under the "NO COMMON MECHANISM" model of character evolution -
can't
> be farther away from molecular clocks (strictly no regular common
> evolutionary process is involved - there are potential problems with
long
> branch attraction / repulsion, but this - strangely enough - is not
your
> point)

The technical issues of algorithmic procedures do not come under my
expertise so I will leave that to others to argue about. However, I do
point out that there seems to be a contradiction between cladistic
requirements for primitive states in outgroups and the assumption of
continuous molecular divergence in all lineages that seems to be the
underlying principle for viewing molecular similarity as a measure of
phylogenetic relationship.

> what do you mean ? "primitive group" is hardly a "cladistic"
(parsimony)
> notion, 

Outgroup then - whatever you like.

> again, can you explain what do you mean ? is it you, or is it still
> "Schwarz talking" ? 

Me talking. Molecular biologist refer to random mutations, so given that
they are random there seems to be no necessary basis for the
distribution of differences between taxa to track the sequence of
speciation.

provided that you include the generally implicit (but
> necessary)
> theoretical assumptions underlying morphological phylogenetic analyses
> 
> "relevant data" are not facts, they are theory-loaded hypotheses (a
> classic
> in modern epistemology)

Good - we seem to agree that both molecular and morphological approaches
can be open to question.
> 
> this illusion of theory-free scientific observations when it comes to
> morphology seems to be underlying your strongly biased charge against
> molecular analyses - you cannot change your philosophy when you change
> data
> sets

I did not indicate that morphology was theory-free - I just proposed
that there were less theoretical layers involved.

> the general answer to inconsistencies (inside molecular analyses as
well
> as
> between molecular and other approaches) is effectively; combined
analysis
> of all relevant evidence

Yes, except that I my current position is that the data are not
equivalent.

> 
> >He argues that where molecular and morphological
> >data disagree, both must be re-examined carefully.
> 
> no objection - just apply this to morphological analyses as well,
> including
> tracking implicit "models" / assumptions, i.e. rejecting the illusion
of
> "theory-free" morphological analyses

It seems that you jump to some unnecessary conclusions about what I am
saying, but the general proposition - that contradictory results do not
automatically lead to the molecular result being correct is the
principle point of agreement here. Excellent!

> 
> you're also talking of "passing the censors", I suggest that your
first
> concern should be "passing the pertinent reviewers" you will likely
> encounter in any good journal

Unfortunately some reviewers, even for good journals, act as censors
opposing publication of views they themselves do not hold. It's a real
problem.

John Grehan