Nicely summarized!
Cheers,
Ted
---- Original message ----
Date: Tue, 29 Sep 2009 11:30:23 -0700
From: Wayne Maddison <wmadd...@interchange.ubc.ca>
Subject: Re: [R-sig-phylo] is maximum likeyhood a
phylogenetic approach?
To: r-sig-phylo@r-project.org
>If you want some real fun, sign on to the Taxacom mailing
list and
>post an opinion about whether a particular method is
"cladistic" or
>not.
>
>But the heated exchange that might result is already
anachronistic.
>There's an expression in English, "It's all over but the
shouting."
>The shouting will go on for some time, but it's over.
Whether or not
>you agree with it, the matter's settled: the community
now very much
>considers that an organism's identity arises from its
genetic
>history, and that classification should as directly as
possible
>reflect that genetic history. Classification is about
words, and it
>helps very much to have the words we use reflect the
concepts that we
>think matter.
>
>Yes, the questions of evolutionary history and
classifications can be
>separated, but I wouldn't say that a confusion between
them hampered
>the progress of evolutionary biology. A battle *within*
evolutionary
>biology between older and newer paradigms as to what
emphasis
>mattered (adaptive zones versus genetic history) was
fought with
>classification as the prize to be won. The fact that most
adherents
>to the new paradigm weren't concerned about
classification, and many
>of the traditionalists were, made it seem to the younger
generations
>as if progress was being hindered by a focus on
classification. Of
>course, since the battle was won long before the shouting
stopped,
>it's understandable why the younger generations felt
burdened by the
>unnecessary shouting.
>
>Wayne
>
>
>At 10:43 AM -0700 29.9.2009, Joe Felsenstein wrote:
>>When I wrote:
>>
>>> >As what classifications should be, or whether methods
should be
>>> >considered as making phylogenetic or phenetic
classifications, I have my
>>> >own position, that no one else seems to back (in
public, anyway). I
>>> >think that we should not think of these trees as
classifications, and not
>>> >call them phylogenetic classifications or phenetic
classifications, but
>>> >consider them as estimates of the phylogeny. The
issue of how to classify
>>> >is less important anyway.
>>
>>Emmanuel Paradis responded -
>>
>>> I have the strong feeling that most users of R and its
[phylo]genetics
>>> packages are interested in the study of evolutionary
processes, not in
>>> classification (I rarely see questions about
classification or
>>> systematics here). So maybe most of us silently back
Joe's position.
>>>
>>> About the issue of how to classify, I think it is very
important. The
>>> point here is, in my view, that the confusion between
classification and
>>> evolution greatly hampered the progress of
evolutionary biology, but the
>>> situation has improved in recent years.
>>
>>I can't speak for most users of R, but I do suspect that
Emmanuel is
>>right in that there is agreement with this position
among many younger
>>evolutionary biologists. But it is a sufficiently
intimidating atmosphere
>>for them that they do not usually say that out loud. I
have stuck my neck
>>out, mostly for the fun of it. The reactions among many
systematists have
>>been strong -- they are really outraged, and figure that
this is just
>>some arbitrary opinion of mine, which they are (barely)
willing to tolerate.
>>I suppose the matter will become one of open discussion
some day.
>>
>>Anyway, back to R.
>>
>>J.F.
>>----
>>Joe Felsenstein j...@gs.washington.edu
>> Department of Genome Sciences and Department of
Biology,
>> University of Washington, Box 355065, Seattle, WA
98195-5065 USA
>>
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>>R-sig-phylo mailing list
>>R-sig-phylo@r-project.org
>>https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>
>
>--
>--------------------------------------------------------
>Wayne Maddison
> Professor and Canada Research Chair
> Depts. of Zoology and Botany and
> Biodiversity Research Centre
> & Director
> Beaty Biodiversity Museum
> 6270 University Boulevard
> University of British Columbia
> Vancouver, BC V6T 1Z4 Canada
>
>email: wmadd...@interchange.ubc.ca FAX: +1 604 822-2416
>
>Mesquite: http://mesquiteproject.org
>MacClade: http://macclade.org
>Salticidae: http://salticidae.org
>Tree of Life: http://tolweb.org
>Beaty Biodiversity Museum: http://beatymuseum.ubc.ca
>Home page: http://salticidae.org/wpm/home.html
>
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