Positivism vs Realism

James Francis Lyons-Weiler weiler at ERS.UNR.EDU
Fri Dec 12 20:43:55 CST 1997

On Fri, 12 Dec 1997, Tom DiBenedetto wrote:

> >         Bold hypotheses receive
> >        a higher dose of corroboration because they are not expected
> >        to survive a truly critical test; i.e., they represent
> >        hypotheses which may run counter to expectation.
> Once again, you make this almost sound like a psychological
> criterion, how much we are surprised by a result, because you fail to
> understand what Popper was driving at with his reference to
> expectation and surprise. THese are a function of information
> content. You can achieve a  high degree of corroboration when a
> hypothesis is unexpected RELATIVE TO BACKGROUND KNOWLEDGE, i.e. when
> the hypothesis has high information content relative to the
> underlying assumptions. It doesnt matter a hoot what you personally
> expect!

        Who does systematics - people, or some other entity?
> >         In the case
> >        of cladistics, if we have done our biology right, our set
> >        of hypotheses of homology is expected to be congruent.  This
> >        expectation diminishes the level of corroboration for those that
> >        are found to be congruent RELATIVE TO the level that which should
> >        be achieved under a truly critical test.

> 1. We propose a hypothesis.
> 2. We deduce a set of expectations/predictions from the hypothesis\
> 3. We test the hypothesis against the real world (observe, experiment
> etc.)
> 4. Even if it passes the test, it realy isnt corroborated, because we
> hoped/expected that it would pass the test, therefore we cant really
> pretend we are surprised.
> Now the end of this train of logic is, of course
> 5. since we expect the hypothesis to pass, our surprise  might be
> maximized if in fact it fails the test,,,so in James's world, perhaps
> a hypothesis is maximally corroborated when it is falsified!

        Hypotheses of homology that have failed the test, according
        to you, have risen from the ashes as hypotheses of convergence.

        If you are saying that hypotheses of convergence that
        are retained as result of a parsimony analysis are not
        corroborated as hypotheses of convergence by the parsimony "test",
        then you must also be saying that hypotheses of homology that
        are retained are also not corroborated.  If parsimony is not
        test in the sense that convergences are corrboraborated,
        then non-convergences (informative synapomorphies) can't
        be corroborated either.

        Popper and Miller's proofs in the early '80s show clearly
        that when a test only serves to restate the obvious, (1)
        no corroboration results, (2) the test was not a critical
        test, (3) time is better spent either thinking of new and
        bold hypotheses or devising more critical tests that
        surpass the no longer salient ones in their revelations.

> As I said above,,,the "amount of surprise" that Popper was referring
> to was not a personal psychological state, it was a casual way of
> making refernce to the relationship bvetween the hypothesis and
> background knowledge.

        This straw man is obvious - no psychologism is
        needed.  When I said "surprise" and background
        knowledge, I meant it in the same meaning as in
        Popper's model of epistemology.  Interestingly,
        he was charged with requiring a subjective knower,
        which he vehemently denied.

> Congruence reprents a minimal level of background knoweldge; it is a
> direct deduction from the notion of life as having evolved a single
> time through a process of descent with modification. James is correct
> that even this amount of background knowedge reduces the level of
> corroboration, and he seems to demand we abandon even that in order
> to have a "truly critical test". But by abandoning congruence we are
> left with nothing.

        Hardly.  We need only use tests that are set up to tell
        us if and when a significant level of congruence exists.
        Parsimony doesn't address this.

>. THe irony here is that all other methods seem
> determined to load up on background knowledge,,,whether it be by
> character weighting, or, at an extreme, by accepting a model of
> evolution as background knoweldge.

        I won't go on and on about it, but the tests I have
        devised require no modelling or character weighting.
        They are designed to to what parsimony should be doing,
        but doesn't.
> This is why the statistical methods can be seen as engaged in a
> retreat from the scientific method -  by building ever more factors
> into the background knowledge of their analysis, they end up saying
> nothing - basically simply deducing the phylogenetic consequences of
> the model, with no testing involved whatsoever.

        This is not a balanced representation of that literature.
> >        When hypotheses
> >        of homology are revised to account for those found to be
> >        discordant, either by calling them homoplasy or by
> >        re-examining the material, then Popperian corroboration is
> >        conveniently dismissed -
> huh? When something is labeled homoplasy and we are forced to accept
> an ad hod explanation for its presence in the data, we are
> acknowledging that it has failed to be corroborated by out test - it
> is a falsification. How can this be seen as dismissing Popperian
> corroboration?????

        Because if it to be dismissed as a hypothesis of homology,
        it must be a hypothesis of convergence.  If your pefectly
        objective system is really Popperian, then each hypothesis
        to which the data pertain receive the same dose of
        corroboration, whether we are interested in them (the
        hypotheses we might fail to recognize) or not.

> >        i.e., it is applied to the
> >        hypotheses of congruence homologies, but it is not allocated
> >        to the emergent hypotheses of discordant homologies, and
> >        yet they represent the archetype of bold hypotheses because
> >        they were unexpected.
> An ad hoc hypothesis is the archtype of bold hypotheis......buddy you
> are getting lost in space now!

        I don't think so.  Popper defines what he means as an
        ad-hoc hypoothesis in his famous paper on the problem of

        "I call a conjecture 'ad hoc' is it is introduced... to
        explain a particular difficulty, but if... it cannot
        be tested independently".

        (the deletions are trivial references to an example
        hypothesis "like this one" and "unlike this one".

        Popper is consistent in his use of the term, and
        never equates a bold hypothesis with an ad-hoc one;
        consider, for example, that bold hypotheses, when they
        survive a critical test, are afforded a great deal of
        corroboration because they, as originally formulated,
        go beyond the background knowledge.  How can a bold
        hypothesis be corroborated if it is ad-hoc, and cannot
        be tested?  At the same, bold hypotheses need not be
        testable - no definition of boldness is tied to
        falsifiability. Some bold hypotheses can be ad-hoc, and vice
        versa, but a hypotheses need not be ad-hoc to be bold,
        and you are entirely confused on this point, ergo your
        next misappropriation:

>And it all comes form not
> understanding the role of expectations in Popper's notions. Ad hoc
> hypotheses are the least bold, by definiton, for they are special
> hypotheses which account for particular cases, they say nothing
> beyond the particular case, and have minimal scientific value..

        This has nothing to do with how bold an ad-hoc hypothesis
        might or might not be.  It is clear that the only useful
        bold hypotheses are the testable ones, but that's
        only because they are hypotheses, and this is true of
        any hypothesis...
> >        (2)  The first position views parsimony as an inductive
> >        step in hypothesis formulation - which is fine.
> but inaccurate

> >        The position that
> >        parsimony is a test belies the fact that most consider
> >        published trees to be hypotheses in a long series of
> >        attempts to model the past - not as theories or
> >        truth, but mere hypotheses.
> Huh? How does this sentence hold together? First off, I told you
> several times that parsimony is a criterion, congruence is the test.
> And I never met a cladist who needed to be convinced that cladograms
> are hypotheses, they are corroborated hypotheses; everyone has always
> seen that.

        It is far better and more accurate to say that they are
        hypotheses - to be tested in the future by independent
        means - than to say that they are phylogenies, which
        is downright misleading.
> >       To expect otherwise is
> >        positivistic.  Some of the greatest contributors to phylogenetics
> >        have become skeptical of the utility of the trees that get
> >        published - Swofford and Maddison come to mind.
> Swofford is one of the......what??????? (you lookin' for a job
> buddy?)
> And he has become skeptical of the utility of the trees that get
> published?????????
> My god,,,,just imagine what the poor boy will be faced with once
> everyone starts using PAUP* !!

        The reference is Swofford, D.L. and W.P. Maddison. 1992
        Parsimony, character-state reconstrcutions, and evolutionary
        inferences.  pp 186-223 in R> Mayden (eds.), Systematics,
        Historical Ecology and North American Freshwater Fishes.
        Stanford Undiversity Press, Stanford.

        The *, by the way, means (* and other methods).
> >        This would not be problematic if parsimony did not provide
> >        a set of optimal trees for ANY data set with variable
> >        character states.
> Which is saying only that any data set can have some amount of
> congruence. So what? We are testing specific data sets for the
> congruent pattern that they have.

        You keep saying you are; but the "test" you rely on
        will pass any data matrix with variable states -
        with or without a remarkable degree of congruence
        (remarkable in the Popperian sense).

> I dont understand this. You think you can detect (e.g) convergence
> without a tree?


> If you can,,,,,and you can do it convincingly, then I wont propose it
> as a homology. Such concerns are addressed in the character defintion
> phase. Whats the problem?

        Great!  I'll send reprints and other materials.

        James Lyons-Weiler

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