Circularity & testing.

James Lyons-Weiler weiler at ERS.UNR.EDU
Sun Oct 20 11:39:40 CDT 1996

On Sun, 20 Oct 1996, Tom DiBenedetto wrote:

> On Sat, 19 Oct 1996 16:02:11 -0700 (PDT), James Lyons-Weiler wrote:
> >On Sat, 19 Oct 1996, Tom DiBenedetto wrote:
> >> One more time....the tree itself is not turned back to test the
> >> hypotheses, the test is a test of congruence; the tree is the result.
> >> What is so difficult about this?
> >
> >What is so difficult about it is that there the test you describe does not
> >manifest itself in any measureable manner. Tree length does not provide
> >any measure of congruence;
> ??? Of course it does. The number of steps, over and above the
> minimum number implied by the uncombined set of characters, is a
> direct measure of the number of instances in which a character
> generality must be fractured in order to fit to the particular
> topology. Thats what incongruence is.
> >
A cladogram will result from random data, and shortes trees do exist for
random data.  Because cladistic parsimony alone cannot provide a
distinction between random data and data generated by a phylogenetic
process, it cannot possibly be testing anything at all.

 > > homoplasy indices are unreliable. >
> ??? Unreliable? What are you relying on them for? They are merely
> descriptions of the number of steps relative to some other measure
> deemed relevant by the person using the index.
By your argument, homoplasy is the measure of incongruence.  Adding
additional taxa alone results in a decrease in congruence (i.e.,
homoplasy ratios go up).

 > > Again, where is the test?
> What test are you looking for?

If I recall, the discussion is on whether or not reciprocal illumination
provides a reciprocal test, or is simply circular.  Somewhere in there the
hypotheses of homology came up, and you're offering congruence as a
critical test for homology.  What's the mystery?

 > >> Do you know what a hypothesis of homology is? > > > >Wiley (p. 139)
> >
> >"  the "problem of homology" can be broken by simply realizing that
> >homologies can be treated as hypotheses that are tested by other
> >hypotheses of homology and their associated phylogenetic hypotheses".
> >Like I said, hypotheses can't be tested by other hypotheses;
> Mere assertion doesnt count for much. I think you are simply wrong.

Popper demonstrated with elegance that if a test statement for a
particular hypopthesis includes the background information used to
construct the hypothesis, the test requires inductive, probabilistic
support.  He then (with Miller in 1983) went on to show that inductive
probabilistic support does not exist.  Hardly a mere assertion; it is a
proof.  Now, that's logic, and not science.  Science can occur in any
number of ways imaginable.  It does help to be explicit (and honest) about
the nature of the inferences one makes as they go about their day.

> As I explained twice now, the real test is made in reference to the
> assumption that true homologies must be congruent. Thus when you
> combine character A (with its set of state-generalities) and
> character B (with its set of state-generalities), both of which are
> considered truly homologous, to the best of our knoweldge, you have
> an expectation that they will be congruent. If they are not, then you
> have decisive reason to believe that they cannot both be truly
> homologous, despite your best knowledge. The cladogram is simply the
> grouping scheme which presents the arrangement of homologies which
> minimizes the need for abandoning character generality statements;
> statements which we have no other reason to abandon.
> >
As I have responded twice now, that's not much of a test, expecially when
the reason why you might end up abandoning correct character generality
statement is because other character generality statements are erroneous.

> >where are the critical values? Where are the probability distributions?
> > Where are error terms?
> I think you are confusing this approach with a statsitical estimation
> analysis. Despite the assertions of some statisticians, the two
> approaches are fundamentally different.
Yes; one is inductive. (Max lik is inductive, too, by the way).

> > 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.
An analogy would be to continue to use parametric statistics when you know
the distribution of the population or sample is not normal.

 > > 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

> I must say that I find
> a lot of evidence for the latter argument, but I ask you,,,which do
> you think is the most parsimonious explantaion :), or the maximally
> liley one, for that matter?

If we relied on dogma and common practice (conventions) as guides for
sensible scientific inquiry, who would have listened to Hennig?  or
Galileo? Kepler? Copernicus? Planck? Morgan? Darwin? and on and on...

> >> > No, when homology is dead on, the trees can be dead wrong. Where is
> >> > the test?
> >>
> >> HUH? That is absurd.
> >
> >How?  Why?
> 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.

James Lyons-Weiler

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