Who is the postivist?

[Tom DiBenedetto]

James Francis Lyons-Weiler wrote:

>       Cladists and others are fond of stating that one of Hennig's
>       contributed influences was to standardize the way in which
>       phylogenetic and ultimately taxonomic inferences were made.  In
>       the dark ages, authoritarianism ruled, and folks created gestalt
>       taxonomies.Then came cladistics - a formal method.  The question is,
>       is that sufficient to make it scientific?  I think from
>       your question you might say "No.".

It was not parsimony per se which made cladistics non-authoritarian,
but you could say, in a sense, that its formalism helped it to be so.
The point was simply that character evidence should be explicitly
laid out, with detailed definitions, and an algorithmic approach to
combining evidence. This formalism did not presuppose any particular
stance on the relevant issues; for instance, it doesnt preclude
weighting characters; it merely asserts that one must lay out all the
evidence that was used to arrive at a conclusion, justify weighting
some characters more than others if that is what you do,,,,basically
make the whole procedure transparant. This is very much in line with
the notion of science as a critical process, open to any person or
any idea which can arrive at a more compelling explanation of the
data.

>         But just because
>       one group of people agree that parsimony is the best way
>       to perform a phylogenetic estimation problem doesn't make
>       the trees correct.

ah,,,yeah,,,so? Who ever claimed that? I merely assert that the most
parsimonious tree is the logically ordered set of corroborated
hypotheses. I dont see any method which does better.

>        Hennig moved the field to become
>       "more scientific", but others have helped to finish the
>       job to move phylogenetic science - beyond parsimony.

Ah yes, let us reject some of our homology hypotheses even when there
is no reason to do so! What a wonderful idea! It should prove to
everyone that we are passionate falsificationists!

>       Well, in modern phylogenetics as I have come to understand
>       it, synapomorphies as read from the tree are taken
>       "in support of" hypotheses of homology and monophyly -

A synapomorphy does not support a hypothesis of homology; it IS the
hypothesis, left standing after the test of congruence. Neither does
it "support" the hypothesis of monophyly, for it IS the hypothesis of
monophyly, left standing after the test of congruence.

>       Each is taken as a confirming instance.

No James, a coding match in a matrix is simultaneously a hypothesis
of homology (for the character) and of monophyly (of the groups which
possess it). After the test of congruence, they remain hypotheses,
only now a bit more corroborated. A cladogram merely represents the
logical ordering of individual corroborated hypotheses of
homology/monophyly. Dont get hung up in casual language.

>       The more synapomorphies, the better _confirmed_ (others
>       disagree and say "corroborated" but it's a loose usage
>       of the term).

Amen; may I direct you again to "Realism and the Aim of Science" in
which Popper goes on at length about the subtle differences between
the two terms, and why he prefers the latter to the former.
Breifly, "confirmation" is a term which arises from the
verificationist approach; those who try to validate hypotheses by
searching out confirming instances. "Corroboration" is meant to refer
to confirming instances which arise in the course of critical
testing, serious attempts to refute the hypothesis. Hypotheses gain
credence as a function of the testing they have endured. A hypothesis
of monophyly (a character) is tested against all other hypotheses of
monophyly (characters); the test being the expectation of congruence.
Confirming instances (congruent distributions) are thus rightly
referred to as sources of corroboration.

>         as such, after much debate, the
>       idea emerged that such inferences amount to "weak
>       corroboration" but not at all firmly within the realm of
>       falsificationism.

who was debating with whom?

>       And yet you state without reservation
>       as if it were entirely agreed upon that parsimony
>       corroborates.  As an inductive inference, it simply
>       cannot.

No James, the test of congruence leads to corroboration. Parsimony is
the principle behind the test, behind most scientific tests......am I
repeating myself here? Parsimony is not an inductive inference; it is
a logical standard which implements the test of congruence. We test
the set of hypotheses to see what congruence they have relative to
each other. The parsimony criterion merely refers us to the tree
which indicates those hypotheses which really are falsified by the
rest of the data. Less parsimonious trees imply more falsification
than actually exists in the data. It is important ot have powerful
tests, but accepting falsification when it is not indicated is just
silly.

>  The difference between molecular data and morphological data still eludes me.

On one level, they are not different; they are both sources of
heritable characters, and thus neither should be ignored. This is a
*very* important point.
Once we accept that both are valid sources of evidence, we can note
differences between them. Morphological structures are complex and
they have ontogenies, In general, morhological character evolution
tends not to erase the previous state - a stapes is recognizable as a
modified hyomandibula which in turn is recognizable as a modified
branchial arch part. Sequence evolution tends to erase information -
an "A" is not recognizable as a modifed "T". This difference tends to
make sequence data far more problematical.

>> Once again, and very briefly, cladistic parsimony utilizes a
>> parsimony criterion in the
>> implementation of the test of congruence. We do not use parsimony as
>> a test in itself.

>       That's like saying that final exams are a test for a subject
>       course, but that the exam is not a test.  ??????????

Not really.....its like saying that the exam (test of congruence)
will be graded (parsimony criterion), and the exam is not the same
thing as the principle of grading.

>       The hierarchy is tree-based, the tree
>       is based on the data, so when the data mislead the
>       tree, they also mislead the inferences of hierarchy.

yes james, if the coded similarities are not historical homologies,
then we will derive a hierarchy which is not phylogenetic.
Unfortunatly, we cannot know this absolutely, all we can do is study
hard and assure ourselves, through applying all our biological
knowledge and the tests they imply, that our set of hypotheses are as
legitimate as we can make them.

>> The result of a cladistic analysis is a set of character homologies
>> which have been corroborated both through the biological tests they
>> have endured, and the congruence test. Their logical combination
>> represents the sum of phylogenetic evidence from character
>> distributions, and our best overall reconstruction

>       I prefer "estimation"

As well you should, given your line of work. Estimation has meaning
in the realm of statistics; when one engages in a statistical
analysis of sequence data, estimation is the proper term. When one
does cladistics, which is a very different approach, then
reconstruction is a far more appropriate term

>> Verisimilitude is a notion of "closeness to truth"

>       "Successive approximation" in based on this notion,

That doesnt exhaust the potential of the notion. I am not entirely
comfortable with succesive approximation, and am not inspired to
defend it.

>       As we develop new and more critical tests of hypotheses of
>       homology (and there are many that have and well continue
>       to be developed), we should be moving farther along the
>       asymptote to truth.

Well fine!, I have NO problem with that. The more the better. I have
always thought that if the stats folks would translate thier max-like
trees into an explicit set of conclusions regarding the homology of
the various sites, that we might begin to speak the same language.
Then we could begin a debate on what makes a legitmate test of
homology.

>         For instance, parsimony
>       can be mislead by long branch attraction, and
>       no model of evolution is needed for that to be true (sparse
>       taxon sampling can lead to the same problem and guarantee
>       the wrong tree, and we are limited in our taxon sampling
>       via extinction),

Sparse taxon sampling is usually one of those new problems spawned by
the
generation of roving sequencers who have no committment to the study
of a particular group. The folks who are really interested in
organisms and their diversity have ususally gone to great lengths to
make sure they include every taxon available.
And although long branches can conceivably decieve parsimony in some
cases, it need not do so. Sister taxa can attract each other as well.
Furthermore, long branches can equally decieve every other method.
The fear of long branches has already spawned some ridiculous claims;
sister-group relationships are being denied because of the mere
possibility of long branches - even when the relationships are
heavily corroborated by many different character systems including
complex morphologies.
And of course, the existence of conditions which might lead to a long
branch situation can hardly indicate a preference for another tree.

>        new tests for the identification of
>       long edge taxa will prevent errors that would otherwise
>       have been made.

just be careful that you can isolate real instances

>       No philosophical justification of cladistic parsimony
>       will ever change the informativeness of a single data set -
>       that is predetermined by whatever processes of evolution have
>       already occured to the characters, to the biologcial prowess
>       of the investiagtor, and to a large extent by
>       taxon sampling.

So, to run throught your list backward: sample your taxa thoroughly
(this is not an argument you will probably have to make to cladists);
study biology (this is not an argument you will probably have to make
to cladists); and dont restrict yourself to single character systems,
to avoid cases where some evolutionary process has destroyed
information (this is not an argument you will probably have to make
to cladists).

>       More to the point of the thread, I consider it positivistic
>       (read: like positivism) to presume that parsimony (or any other
>       method of inference) will lead asymptotically to the truth when it
>       has been known for so long that it can be positively mislead under
>       some circumstances, and that adding more data will only
>       make things worse.  To continue the myth of the sufficiency of
>       parsimony is to say that it cannot be improved.

The improvements in our field will not come from abandoning the
preference for the result which represents the logical ordering of
those hypotheses which have survived critical testing.
Your comments here seem to contradict what you said a few paragraphs
above. You claimed there that we would move along the asymptote to
truth by further testing homology hypotheses. That is perfectly
consistent with parsimony - for parsimony is (one last time) the
logical ordering of tested homology hypotheses. Test 'em more,,,sure,
but eventually they will be combined in a matrix and submitted to a
congruence test to form the overall phylogenetic hypothesis.