[Re:] reweighting characters, few and many

[Don McAllister]

Thomas Schlemmermeyer wrote:

> Popper got to the point of applying Darwin´s theory of selection to the working
> of his own mind.
> That is Popper was astonished how often he had to write, delete and re-write a
> certain line of argument, before it got ready.
> This selection process of intelectual things is called learning by "trial and
> error".

Darwin, however, always wrote down criticisms of his work as soon as he heard/read
them - that way he didn't conveniently forget them!

don
Don McAllister

>
>
>           Thomas
>
> On (         Thu, 28 Oct 1999 16:51:02 +0200
> ),         Pierre Deleporte <Pierre.Deleporte at UNIV-RENNES1.FR> wrote:
>
> >Dear all,
> >
> >
> >first, a comment on Thomas Schlemmermeyer's message (maybe it was largely
> >a joke, but I just play it serious a little while)
> >
> >
> >asking for suggestions, Thomas wrote :
> >
> >
> >>In PAUP 4.0, I ran a matrix
> >
> >
> ><underline>suggestion</underline>:  expose your evolutionary assumptions
> >justifying the use this parsimony program for phylogeny reconstruction
> >
> >
> >>which gave 423 most parsimonious trees. As the
> >
> >>consensus tree was highly unresolved,
> >
> >
> ><underline>s</underline>:  ... you could very well have stopped here, and
> >went and look after more characters and more taxa, or try to improve
> >primary homology assessments...
> >
> >but I still follow you anyway
> >
> >
> >>I ran the command "reweight"
> >
> >
> ><underline>s</underline>:  justify reweighting
> >
> >
> >>which gave,
> >
> >>after a new search, 21 parsimonious trees, and a nice consensus tree,
> >but one
> >
> >>that I personally dislike. So,
> >
> >
> ><underline>s</underline>:  there is no shame in disliking (but have you
> >any biological justification for rejecting?)
> >
> >
> >>in the next step I widened up slightly, but only slightly, the upper
> >bound
> >
> >>of the trees to be kept and searched the unweighted characters again.
> >
> >>Excitingly, this enlargened the tree file from 423 trees to
> >approximately >25000 trees. Now, I reweighted those 25000 trees, and run
> >parsimony search >again.
> >
> >>I got only three trees, and Imagine!!!, the consensus tree corresponds
> >exactly
> >
> >>to the tree, which is my person favourite!!!
> >
> >>
> >
> >>  Any suggestions?   Thomas
> >
> >
> >
> >Well, you may convince some colleagues to accept the two consensus trees
> >as acceptable alternatives (if the results are very "close to one
> >another"), but surely not to prefer the second one... unless you provide
> >convincing external justification, but presumably your arguments are
> >already "coded in the data matrix" under the form of (possibly weighted)
> >characters and polarisation rules.
> >
> >Perhaps you could look after some possible external arguable reasons
> >supporting your "preference", but, in itself, this personal preference is
> >not an  argument, and not even a problem for biology.
> >
> >
> >
> >Further in this thread, Richard Zander wrote:
> >
> >
> >>What would Karl Popper say relevant to this exercise? Probably that
> >
> >>phylogenetic estimation is just historicism in reverse.
> >
> >>(...)
> >
> >>I guess he hadn't heard of cladistics yet.
> >
> >>Check out: Popper, K. R. 1957. The Poverty of Historicism.
> >
> >>Harper & Row, N.Y.
> >
> >
> >
> >It happens that I am presently reading this book (French translation,
> >sorry for possible errors), and, to my disappointment, as far as I
> >understand it it does not bear directly on the subject.
> >
> >
> >Popper condemned the possibility for <underline>social
> >sciences</underline> to scientifically make <underline>long-term
> >predictions</underline> about the future evolution of human societies
> >(and for physics to predict the long-term future of real, complex
> >situations as well). But he said nothing in this book about
> >retrodictions.
> >
> >His notion of "historicism in social sciences" should not be confused
> >with other "historical approaches" (reconstructions of the past), and
> >surely not with phylogeny reconstruction. The notion of "historicism in
> >reverse" is apparently Richard Zanders creation and should be defined.
> >
> >
> >More than this, Popper explicitly <underline>accepted</underline> the
> >notion of general tendencies in the evolution of organisms, namely the
> >tendency toward an increasing number and an increasing variety of
> >biological forms. He called them: <underline>explained</underline>
> >tendencies, which may be the basis for some general predictions given
> >that the conditions ("initial conditions") for the expression of this
> >tendency do not vary too much.
> >
> >Well, with the notions of multiplication and diversification, we are not
> >too far from "descent with modification", isn't it? And if this explained
> >tendency  is good for prediction, I think it may be useful for
> >retrodiction too...?
> >
> >
> >Of course we must assume some "general law of evolution" (however
> >careful, e.g. descent with modification with no imposed tempo) to
> >reconstruct the phylogeny, but... the whole story already happenned, was
> >unique, and left some traces behind it, thus we are NOT facing the
> >problem of guessing which of multiple ways evolution will follow in the
> >future, we are instead facing the more accessible problem of "reading"
> >the traces of a unique past, given the knowledge of explained
> >tendencies.
> >
> >
> >In conclusion, please let's not feign confusing phylogenetics with
> >Popper's "historicism", and Sherlock Holmes with Nostradamus.
> >
> >
> >
> >sincerely,
> >
> >Pierre
> >
> >
> >
> >
> >
> >Pierre Deleporte
> >
> >CNRS UMR 6552 - Station Biologique de Paimpont
> >
> >F-35380 Paimpont   FRANCE
> >
> >Téléphone : 02 99 61 81 66
> >
> >Télécopie : 02 99 61 81 88
> >
>
> ------------------------------------------------------------------------------
> Thomas Schlemmermeyer
> Museu de Zoologia, Universidade de São Paulo
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>
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> Thomas Schlemmermeyer
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>
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