parsimony/biology

[Thomas DiBenedetto]

-----Original Message-----
From: Zdenìk Skála [mailto:skala at INCOMA.CZ]
>...which source of information you use to distinguish homology from
>non-homology? 

Your knowledge of biology provides the initital tests. Congruence, an
expectation of theory, is another test.

>Is a glandular hair of a plant leaf homologous with a similar
>one on another plant? 

If you judge it to be so, then you propose the hypothesis.

>If a cladogram is used to distinguish homologies from
>homoplasies, the method seems to be clear. 

I think so.

>And vice versa: if the "true homologies" are defined at the level of data
>matrix, how can part of them turn to homoplasies (non-homologies) during 
>cladogram construction? 

"True homologies" are not defined in the matrix, homologies are hypothesized
in the matrix. They can "turn to homoplasies" by failing the test of
congruence.

>(1) the parsimony itself (as already stated by others) does not 
>necessarily invoke the use of character congruence criterion in the 
>cladistic sense.

I think it does. I agree that parsimony is a general principle, but its
specific application is given meaning by the context of the analysis. The
context for our analysis is that we have assembled a set of grouping
hypotheses (characters), and we have a finite set of overall-relationship
schemes (trees). This gives the general parsimony principle a particular
meaning in these analyses - one (or possibly more) of the trees is the
simplest summary of the grouping hypotheses.

>(2) to "efficiently summarize the evidence" means to summarize under a
>particular evolutionary model (also stated by others already). 

No. Why do you think this necessarily must be true? 

>Cladogram can summarize the evidence (in the sense of phylogen. tree 
>topology approximation) if and only if its construction principles apply
> also to the phylogeny 

The phylogeny was "constructed" by the divergence of taxa. We assume that
characters are passed from ancestors to descendants within these diverging
lineages. We reconstruct the phylogeny by identifying the characters that
are shared by the descendants. 

>Imagine, e.g., the evolutionary model in which each character would change
>each 10th generation. Do yo mean that cladogram "efficiently summarize the
>evidence" even under such conditions?

The cladogram efficiently summarizes the evidence irrespective of any model.
I dont understand your question. No such model is incorporated into a
cladistic analysis. Are you asking whether the cladistic summary would be
efficient if life really had evolved as your model indicates? The answer is
yes, - the cladogram is still the most efficient summary of the evidence.
Whether it is correct is another matter.

>(3) hence, not only that the "parsimony" (cladistic) is biology as well as
>logic; 

I dont think so,

>moreover the underlying hypotheses about the character change pattern
>... are basically untestable hypotheses (the "picture of evolution" 
>depends on the methodology which in turn depends on our assumed "picture
>of evolution").

Yes, this is problem of basing phylogenies on evolutionary models, and why
we dont do that.