Circularity & testing.

James Lyons-Weiler weiler at ERS.UNR.EDU
Sun Oct 20 16:17:24 CDT 1996

On Sun, 20 Oct 1996, Tom DiBenedetto wrote:

> I had written:
> >> > The argument revolves around what one considers to be a
> >> >critical test; I simply reject that whatever you mean by congruence
> >> >provides anything resembling a critical test.
> >>
> >> Well, that is your problem.
> >
> >I don't think so; it would be my problem if I continued to use
> >phylogenetic argumentation despite its very obvious flaws and limitations.
> It would also be your problem if what seems obvious to you now were
> really not so obvious, and you never bothered to discover that.
Obviously, but that is not so.

> > An analogy would be to continue to use parametric statistics when you
> >the distribution of the population or sample is not normal.
> Well then since you use statistics, I am sure you have a cogent and
> well delimited sense of what are and are not statsitical questions.


> > > > The rest of the biological
> >> >sciences see the danger of circular reasoning, and Hull (in
1967!) warned
> >> >us about the limitations of the same within the context of phylogenetic
> >> >systematics.
> >>
> >> and yet for the past thirty years this approach has become nearly
> >> paradigmatic in systematics. Now either thousands of practicing
> >> systematists are too dumb to notice a fundamental flaw in their
> >> logic, or perhaps you have not yet arrived at the point of fully
> >> understanding what the approach is all about.
> >
> >You're commiting the fallacy of consensus gentium, and relying on the
> >beliefs and behaviors of a majority to make you point.  This holds no
> >water.
> nah, it was just a semi-polite way of suggesting that you might
> consider holding off on the grand assertions until you fully
> understood the approach. It would save us from having to conduct the
> discussion on different levels at the same time.

I think I understand the approach far better than you do.  Its circularity
is clear to me, and I have yet to hear a reasoned argument to the
contrary.  Proponents of metholodologies bear the responsibility of
communicating the limitations of those methods these days, because it is
commonly known that all methods of inference have limitations.  Why
someone would ever act like a method does not have a limitation so
blatantly obvious as circular reasoning escapes me.

> >> If the homology is "dead on", I guess you mean that it is really
> >> really true. Could you please tell me how you can combine a set of
> >> really really true hypotheses of homology and get a really reallly
> >> false tree?
> >
> >Homoplasies can be entirely homologous.
> ??? I am at a total loss to understand this assertion. First of all
> you discussed a set of "dead on" homologies. A cladogram of such a
> set would exhibit no homoplasy, by definition. Furthermore, if all
> the homologies were true, the tree would have to be true, contra your
> original assertion. Now we have homoplasies? On that tree? and they
> are entirely homologous? What do you mean?
Your plastic definition of homology can't save the inference from being
circular.  Completely convergent states can neverthess be homologous.
Homoplasy in state can cause the cladogram to be wrong.

Now that we have relived the past three decades of discussion in
Systematic Biology (nee Zoology), I (again) offer a statistical analysis
of discrete character data (morphological or molecular), that circumvents
the problem(s) of the circular reasoning inherent to phylogenetic
argumentation (when used alone).  The software for the Mac can be gotten

James Lyons-Weiler

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