Striking a balance, weighting and Cladistics

[Richard Zander]

Tom:
You cling tenaciously to the idea that a single tree or a bunch of equally
parsimonious trees must be a "result" or a "preference." I suggest that only
when the output of a computer program has demonstrably high support is a
admissible as a "result" or a "preference." It is otherwise nothing.

Take a coin. Somebody says it may be loaded. You toss it fairly 100 times
and it comes up 51 tails and 49 heads. What is the scientific "preference"
here? That it is loaded? Shared phylogeny is assumed to load the cladogram
towards a particular result. Exactly when is the amount of loading
distinguishable from tossing a coin?

Richard

---------
From:
Richard H. Zander
Curator of Botany
Buffalo Museum of Science
1020 Humboldt Pkwy
Buffalo, NY 14211 USA
email: rzander at sciencebuff.org
voice: 716-896-5200 x 351



----- Original Message -----
From: "Thomas DiBenedetto" <TDibenedetto at DCCMC.ORG>
To: <TAXACOM at USOBI.ORG>
Sent: Tuesday, February 20, 2001 4:26 PM
Subject: Re: Striking a balance, weighting and Cladistics


> -----Original Message-----
> From: Richard Zander [mailto:rzander at SCIENCEBUFF.ORG]
>
> >Those who reject statistics but use philosophy to guide their choices
must
> >often make Type I errors. They almost always get publishable results,
> >because an exact solution is (philosophically) always acceptable (if only
> >"poorly supported").
>
> Richard,
> I am a little confused as to the relevance of your point. Let me try to
> respond with a few points of my own.
> 1. The focus of my argument was on the method for selecting a preferred
> tree. Your point seems to address the issue of the "strength" of the
result,
> an issue that seems to have a general relevance, not limited to any
> particular procedure for arriving at the result.
> 2. Cladistic results are always accompanied by a set of indices or metrics
> of the "strength" of the results; most notably the decay index. So
> cladistics certainly recognizes that some results are weakly supported,
and
> supplies the numbers by which that can be ascertained. I think that most
> everyone in the field gives the appropriate amount of respect to a weakly
> supported result.
> 3. It is also happens very frequently that the result of a cladistic
> analysis is a set of equally most parsimonius trees, so I don think that
it
> is fair to say that the method always produces some specific result.
> 4. Ironically, it is the most common statistical method (max-like, the
> method I was discussing) that tends to always generate a single result
(the
> tree of maximum likelihood) no matter how weakly supported. As a
statistical
> method, the procedure is certainly amenable to generating a confidence
set,
> but how often do we see this? How often do we see a max-like result with
> collapsed branches, representing a consensus of all trees not
significantly
> different from the tree of maximum likelihood? I recognize that it is
> standard to approach this issue after the analysis, by use of a bootstrap,
> but it doesnt seem to me that that obviates the need to represent the
> results of the max-like analysis itself in a responsible manner.
> 5. Your use of statistical concepts to describe non-statistical methods is
a
> bit confusing. The 'null hypothesis" of no support is not part and parcel
of
> a cladistic analysis. We are simply trying to select one or more patterns
> from a finite set of patterns, and reporting explicitly the evidentiary
base
> for that choice. As I said above, this does not preclude a result that
> effectivly accepts your null hypothesis (by indicating that all patterns
> have equal levels of support - i.e. a bush).