parsimony/biology

[Kirk Fitzhugh]

Zdenìk Skála stated,
"...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").

To which Tom DiBenedetto replied,

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

If we take Skála's statement at face value, then the testing of all 
explanatory hypotheses in all fields of inquiry are impossible. Since this 
clearly is not the case, why must we think so for phylogenetics? Tom's 
statement as well dooms all explanation in the sciences. In the inference 
of cladograms, one actually does not use a "model," rather one uses a 
specific causal theory applied to observed effects to infer a set of causal 
conditions. Models are themselves stipulations of specific causal 
conditions, which must be inferred from some more basic causal theory. 
Cladograms, as hypotheses of some set of causal conditions cannot therefore 
be derived from the same set of causal conditions. It is as well impossible 
not to employ a causal theory in the inference of some set of causal 
initial conditions.

Kirk