corroboration

[Doug Yanega]

John Trueman wrote:

>2.  that *after* the hypothesis was constructed we subjected it to
>such-&-such *critical* tests, and in so far as it did not fail those tests
>it is corroborated.
>
>Here, the key words are 'after' and 'critical'.
>
>Re After:   A hypothesis cannot be corroborated using the very data from
>which it was constructed.  In this I disagree with certain well-known
>cladists who see 'corroboration' of a parsimonious tree merely in the fact
>it is parsimonious. These cladists argue that "the most parsimonious tree
>is the least falsified tree", meaning it is the tree least falsified by
>homoplasy.  Out of the set of all possible trees it is the tree least in
>need of protection from falsification by the addition of ad-hoc hypotheses.

As I have always understood it, the tree is NOT the hypothesis being tested
in cladistics. Each set of character states is a separate hypothesis of
homology. When one performs a cladistic analysis, all of the hypotheses of
homology are compared to one another simultaneously, and the most
parsimonious tree is the resulting hierarchy which results in the smallest
total number of rejected hypotheses. Trees are not falsifiable nor
corroborated in any sense, only the individual hypotheses of homology upon
which the tree is based, and they are only rejected *in* the context of
constructing the tree, not *after* the tree is constructed. In this sense,
your argument about corroboration appears to be a red herring. At the
least, one cannot assign probabilities of being right or wrong to these
individual hypotheses either before or after the analysis.

>Do changes to our character set change the tree?  We might try a character
>jackknife.  We might try resampling from the available characters as in a
>nonparametric bootstrap: which of the nodes are supported and which have no
>support (which are corroborated and which are refuted) by this test?  If we
>have an explicit model we may try a parametric bootstrap technique.

To quote Wenzel's recent paper, after he gives a list of known (published)
limitations and problems with the bootstrap, he concludes; "It is also
important to note that the ordinary application of bootstrapping procedures
is to derive a confidence interval for the estimate of a parameter of a
distribution (Manly, 1991), and that statistical mean and variance do not
apply to unique historical identity of the phylogeny (Wenzel & Carpenter,
1994). So, although the bootstrap values mean something, it is not clear
what they mean exactly, and it is clear that they do not mean the same
thing when compared across different trees. It would seem that these
objections would suffice to exile the bootstrap from its current place of
honor." He suggests that Bremer support values are more informative, but
notes; "...these are not intended to serve as statistical confidence
tools."

I think it would be fair to say that cladists do not view ANY of this
process as having or requiring statistical properties, and therefore view
attempts to include probabilistic or statistical approaches in phylogeny
reconstruction as misguided at best, and misleading at worst, stemming from
a preoccupation with *process*-based models (e.g. max-like) which are NOT
compatible with parsimony-based cladistics. Parsimony is not a process
model - it is Occam's Razor applied to a nested set of hypotheses of
homology. The kinds of tests you want to apply appear to be inappropriate
for cladistic analyses.

Peace,

Doug Yanega    Depto. de Biologia Geral, Instituto de Ciencias Biologicas,
Univ. Fed. de Minas Gerais, Cx.P. 486, 30.161-970 Belo Horizonte, MG   BRAZIL
phone: 031-449-2579, fax: 031-441-5481  (from U.S., prefix 011-55)
                  http://www.icb.ufmg.br/~dyanega/
  "There are some enterprises in which a careful disorderliness
        is the true method" - Herman Melville, Moby Dick, Chap. 82