Circularity & testing.

Tom DiBenedetto tdib at UMICH.EDU
Sun Oct 20 13:47:40 CDT 1996


On Sun, 20 Oct 1996 11:39:40 -0700 (PDT), James Lyons-Weiler wrote:

>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.

???? Once again again again, it is testing the congruence of the
elements which are entered into the analysis, under the constraint of
combining them into a hierarchy. If the units are data arrived at
randomly, then you might feel inclined to explain why this data set
exhibits pattern. The algorithm simply displays the pattern that is
there. The meaning of the pattern is a separate matter, being a
function of the meaning of the units.

>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).

???not necessarily. If the new taxa have sets of characters which are
fully congruent with the pattern emerging from the original analysis,
then the homoplasy ratio goes down. If their character sets have a
similar amount of incongruence as does the original analysis, the
ratios remain about the same. If they have more incongruence than the
"average" in the original set then the ratios go up. Ratios are
pretty simple things. None of this is relevant anyway,,the ratios are
only used to compare alternative topolgies for the same matrix, they
are meaningless when compared across two different matrices.

>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?

Well, then perhaps you should explain exactly what you think
"reciprocal illumination" means; there being plenty of room for
misunderstanding underneath our joint use of that term. I admit that
I have simply been responding to your individual blatent assertions
on various matters and letting the discussion wander. Reciprocal
illumination in systematics refers to testing phylogenetic hypotheses
against independant data-sets drawn from other research programs,
e.g. consilience with biogeographic or host/parasite patterns.
Obviously you are using the term in a different context, but I dont
see your point.

>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.

So translate this into systematics for me. I assert that the state
"presence of an amnion" has a generality encompassing all of my taxa;
the state "fusion of the first two intercentra" is general for the
turtle, the snake and the bird; the state "presence of hair" is
general for the platypus, the kangaroo and the bat; and the state
"presence of wings" is general for the bird and the bat. I will save
space by imaging a lot of other characters as well, that will be
congruent. I examine all possible topologies for these taxa and find
that the currently accepted one requires the least number of
modifications to my generality statements; I need only reject the
generality of wings in order for the data to be mapped on that tree.
All other trees require more modifications. Now, tell me what the
"test statement" is, the "background information", and where on earth
one is required to invoke induction or probabilities.

>>
>> 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.

Well, perhaps we are making progress; "not much of a test" is better
than "no test at all"! All that you are now demanding is some test
which will prevent us from ever being wrong! Hah!

>> 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).

Hmmm, "yes" they are fundamnetally different...one is
inductive,,,,and so is the other. I think I understand.......

>> > 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.

>An analogy would be to continue to use parametric statistics when you know
>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.

>>> 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?


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




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