Circularity & testing.

Tom DiBenedetto tdib at UMICH.EDU
Sun Oct 20 10:56:24 CDT 1996


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.

>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.

> Again, where is the test?

What test are you looking for?

>>  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.
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.

> 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.

>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.

> 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.  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?

>> > 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?
---------------------------------------------
Tom DiBenedetto
Fish Division
Museum of Zoology
University of Michigan




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