Who is the postivist?

[Richard Zander]

Ted Schultz wrote:
>

> I think many good points are being made on all sides in this thread and I
> hesitate to get too involved.  Nonetheless, I will say that there are any
> number of reasons why Zander's critique of phylogenetic methods above is
> not fully justified.  In a post long past, I described one of them: All
> possible topologies for a given set of taxa are not a priori equally
> probable, i.e., in a Bayesian sense the prior probability is not evenly
> distributed across all possible trees.  Depending on how skewed this
> distribution is, the posterior probability of a given tree may be quite
> high.

Wonderful! I would like to see statistical phylogeneticists deal more
knowledgeable with priors in such a way that we get better results. I do
think, however, that they already are being lenient in assuming a
neutralist selection position for all genes, as well as a number of
other (somewhat outrageous) assumptions.

>
> Two other reasons that blunt Zander's critique are:
>
> 1. An entire tree is not really a single hypothesis.  Instead, it is the
> conjunction of multiple hypotheses of monophyletic groups.  Some of these
> monophyletic groups may appear in many of the suboptimal trees surrounding
> the optimal (most likely/most parsimonious) tree, i.e., they may be very
> well supported and thus highly "probable."  Judging the probability of
> subtrees rather than trees is certainly more fair to phylogenetic
> methodology.

Okay. Bremer support is fine. How much Bremer support is needed to make
a subclade a probabilistic reconstruction of phylogeny? Now, I am not
talking about obvious relationships like ((man chimp) dog). That's a
nicely parsimonious subclade. It is the fine structure of big trees,
dealing with very similar taxa differing by simple characters that I
question.

>
> 2. This relates to the Bayesian reason given above, but is phrased in
> 20th-century statistical terms: When trees or subtrees are framed as a
> priori null hypotheses, and when they are subsequently corroborated because
> they appear in the optimal tree or in the "confidence-set" of
> optimal+suboptimal trees in some specified confidence interval, then we
> have failed to reject these null groupings and, again, a probability is
> conferred upon them that is greater than what is implied by Zander above.

They are not corroborated. Coincidence may be due to convergence among
daughter lines. There is no independent test. Failing to reject a null
hypothesis confers ... what? A probability higher than something else?
Failing to reject a null hypothesis just means it could be true.

>
> In non-statistical terms, impugning phylogenetics because complex trees
> consisting of many taxa are rarely entirely "true" or "false" ignores the
> fact that phylogeneticists have discovered and continue to discover real,
> highly corroborated monophyletic groups.

No, no. Complex trees usually include disparate taxa that you don't need
a computer to arrange in a reasonable tree vis-a-vis a shared ancestor
with some outgroup. Phylogeneticists have not "discovered" these trees.
They are guesses based on like produces like (mostly). It is when there
are lots of alternative trees (optimal+suboptimal as above) that
parsimony methods fail and should be impugned most vigorously.


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Richard H. Zander, Buffalo Museum of Science
1020 Humboldt Pkwy, Buffalo, NY 14211 USA bryo at commtech.net
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