Positivism vs Realism

James Francis Lyons-Weiler weiler at ERS.UNR.EDU
Thu Dec 11 10:08:49 CST 1997

On Thu, 11 Dec 1997, Byron Adams wrote:

>         I thought this was a clever way of illustrating the suboptimal
> position of trying to divorce science from metaphysics.  But isn't this
> what one of you is accusing some research programs of doing?

        My comments are not intended to place cladistics firmly into
        metaphysics, but rather to say as formulated it appears to
        be closer to the metaphysical end of the spectrum of
        perspectives on reality than I am comfortable with.
>         I get lost trying to keep track of who is saying what on taxacom as
> I follow the threads - but it seems to me that either James or Tom is
> accusing a particular research program of relying on the tenets of logical
> positivism (or something other than realism) as a part of its discovery
> operations.  In order to do this, it would be helpful if they (again, I
> can't remember who is accusing who of being a positivist) could show that a
> particular research program defies realism in some critical aspect of it's
> methodology or interpretation.  This means that you should be able to show
> that at some point, the discovery operations employed behave as if what is
> true is not independent of what we know, do, or believe as scientists.

        I think the fundamental point, and the one that seems to creep
        into any discussion between Tom and I, is whether parsimony
        represents a critical test as it is claimed to by (some) of
        its proponents.  Parsimony is a criterion, but the belief that
        the criterion will lead to meaningful estimates of the past
        requires a bolus of faith I'd rather not choke on.  The LEAST
        positivistic position, in my view, is the one that allows that
        more than we might expect could have happened - and this allows
        for numerous intrusions into the data that can mislead parsimony
        in particular, and other methods as well (some to a lesser
        degree).  Congruence is expected sometimes, but not always -
        descent with modification only partly explains the distribution
        of states among taxa, and it does not always occur in a clean
        manner.  The intrusions include homoplasy, of course, but
        also population-based processes during speciation such as
        differential lineage sorting. Parsimony from this position is a
        useful inductive tool for hypothesis formulation.  At the other
        end of the spectrum is the MOST positivistic position, that
        parsimony will provide the best estimate of the past, regardless
        of the number or scope of the possible intrusions, because it is
        so - and the tree itself (a set of relationship statements) is
        directly corroborated by the level of congruence found among
        individual hypotheses of homology.  This position is at odds with
        the first in that

        (1) Popper indicated that the degree of corroboration is
        inversely related to how expected a result is.  If we include
        too much "background knowledge" in the formulation of the
        hypothesis (i.e., winnow away unreasonable hypotheses of
        homology on other grounds, say, development), then the degree of
        corroboration afforded by the existence of congruence among
        the characters (individual sets of hypotheses of homology)
        is decreased, and approaced zero if we include all of the
        background knowledge that is in fact accurate and relevant
        (in which case we have a tautology).  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.  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.  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 - 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.  This reveals the positivism of the
        bare-bones parsimony approach - congruence is expected.

        (2)  The first position views parsimony as an inductive
        step in hypothesis formulation - which is fine.  Popper
        said that it doesn't matter how we formulate our hypotheses;
        what matters most is how we test them.  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.  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.

> > For example, I am now trying to recover the
> relationships among some insect parasitic nematodes.  My *opinion* of what
> happened is independent of the reality that cladogenetic events millions of
> years ago produced the diversity and relationships among nematodes I am
> trying to recover.  Or, as Ghiselin points out in his defense of realism,
> "How could any scientist's beliefs or opinions possibly affect whether or
> not chordates have a more recent common ancestor with echinoderms than they
> do with flatworms?"

        This is, I think, closer to my own position - how could any
        scientists' faith in parsimony possibly effect whether
        the data they have collected are informative or misleading?
        This would not be problematic if parsimony did not provide
        a set of optimal trees for ANY data set with variable
        character states.  Evolution has allocated various states to
        various organisms - and in this way can directly influence
        our ability to discern homology. Tom's opinion of parsimony is
        independent of whether or not, in a particular case, parsimony
        tests and provides corroboration, or has merely summarized the
        set of best hypotheses of homology in a congruent manner, which
        even then mau remain misleading.  The focus
        should be on the evidence present in the data, and not what the
        data look like after they have been structured on a tree.
>         It seems reasonable to me that any scientific research program or
> methodology employing discovery operations subservient to positivism should
> be exposed as such.  I think this is a very clever and valid way to
> criticise a research program or methodology, and I would like to see it
> continue.  So far (from reading the threads) I am not convinced that this
> argument has been clearly made or defended.
        You have outlined some rather decent criteria for demonstrating
        positivisitic thought.  I agree that the goal of the development
        of science should remain focused on identifying it whereever
        it exists, and then trying hard to fix things where they
        fall short.

        James L-W

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