Positivism vs Realism

[James Francis Lyons-Weiler]

On Sun, 14 Dec 1997, Tom DiBenedetto wrote:


>
> >        Parsimony clearly assumes model of
> >        lots of descent with little modification, whether it
> >        is used as a summary, a criterion, or test (the last
> >        bit there for completeness).
>
> gee, like maybe we should assume more modification even when we dont
> see it, eh?

        Depends on how you "see it". If you "see" modification as those
        positioned on the parsimony tree, you are sure to underestimate
        the degree of modification sometimes.

> Hey, anything COULD have happended! Cladistics, like science in
> general, is focussed on explaining the data we discover, not any set
> of data which could possibly be imagined.
> The hypothesis tested is that the distributions coded in the matrix
> are the result of descent. Logical violations of that are revealed as
> homoplasy.

        But isn't the backbone of the background knowlegde that
        characters are inherited?  What does this do to c?
>
> >        ....our ideas
> >        on the expected prevalence of homoplasy, its independence and
> >        its distribution have everything to do with whether we can be (I
> >        mean as individuals) confident about the use of the term "best".
>
> As if these ideas have any justification themselves! Where do they
> come from? What universal priniples allow you to claim that more
> homoplasy exists than what we find in a parsimony tree? What gives
> you the predictive power to claim that parsimony is underestimating
> homoplasy, or that  a particular synapomorphy is really an artifact
> of something?

        I can't imagine a world where processes of evolution
        and taxon sampling and chaarcter sampling don't cause
        parsimony to (sometimes) underestimate homoplasy.  How
        do the principles of evolutionary biology lead to the
        ridiculous conclusion that the processes of evolution will
        not render misleading data in specific cases???

        A major limitation of cladistics is the insistence that
        a synapomorphy is something that we get from a tree.
        It's not: they existed before humans evolved - before
        the term was coined.  Hence, _apparent_ synapomorphy...

>
> >       There are numerous
> >        types of analyses that take precedence over parsimony
> >        because they can predict, for a specific case, that parsimony
> >        is likely to fail.
>
> But it can be, and has been, demonstrated that a prediction of (e.g.)
> an unavoidable long branch problem, can be specious.
> How exactly do you propose to derive trees?

        With informative data that have survived critical tests.

James LW