[Taxacom] Usefulness vs. convenience (Protista)

[Stephen Thorpe]

well, it is a bit difficult to know exactly what you are saying sometimes 
(perhaps that's just me?), but I was objecting to what I thought you were 
saying, which was something like "artificial (=allowing paraphyly) 
classifications are not science and so nobody (scientist or bioinformatician) 
should use them". Maybe you aren't saying that? I agree that it would be bad for 
scientists to pass off artificial classifications as science, but I haven't 
really thought of that as a problem. On the other hand, you seem to reiterate 
that classification should go hand in hand with your conception of "science", 
but I say that would make bioinformatics too unstable to be useful. If you want 
to do "science", then do science, but I wouldn't say that people doing something 
slightly different, such as biodiversity information management, must follow 
your lead. "80% bootstrap support for clade X", or whatever, just isn't really 
that relevant to their activities ...

Stephen



________________________________
From: Richard Zander <Richard.Zander at mobot.org>
To: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>; Curtis Clark 
<lists at curtisclark.org>; taxacom at mailman.nhm.ku.edu
Sent: Tue, 21 December, 2010 12:11:51 PM
Subject: RE: [Taxacom] Usefulness vs. convenience (Protista)


So…Stephen you are saying “That’s not science” is an old (and apparently 
therefore unimpressive) accusation when I suggest that scientists are passing 
off artificial classifications as based on evolution? Passing them off because 
patterns of evidence of evolution are made to be neatly dichotomous and are 
often statistically well supported, rocket science, even though artificial? 

 
I think your response is an excellent example of shifting ground. I talk about 
science and you talk about classification, as though classification is not based 
on science. And I think you are right, phylogenetic classification is not based 
on science. I hear no theories, no induction, no discussion of taxa evolving 
from taxa, no discussion of differences just similarities. It’s like we are in 
the Agora again arguing over the Absolutes. 

 
I think once phylogenetic methods (innocent and powerful) have been let out of 
the bottle, lots of evolutionary theory can be generated from cladograms. 
Restricting phylogenetic results to mere classification is a disservice, 
certainly to biodiversity specialists and certainly to students who may value 
scientific use of induction to make theories about WHY there is paraphyly and 
polyphyly of taxonomically identical exemplars. Students? You hear this? 
Opportunity knocks for the bold.
 
* * * * * * * * * * * * 
Richard H. Zander 
Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299 USA 
Web sites: http://www.mobot.org/plantscience/resbot/ and 
http://www.mobot.org/plantscience/bfna/bfnamenu.htm
Modern Evolutionary Systematics Web site: 
http://www.mobot.org/plantscience/resbot/21EvSy.htm

________________________________

From:Stephen Thorpe [mailto:stephen_thorpe at yahoo.co.nz] 
Sent: Monday, December 20, 2010 4:58 PM
To: Richard Zander ; Curtis Clark; taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] Usefulness vs. convenience (Protista)
 
surely not the old "that's not science" argument!! Lots of things aren't science 
... in fact just about everything except science isn't science, like art, 
recreation, management, eating, ... Specifically, bioinformatics (=biodiversity 
information management) isn't science, but just like the other things that 
aren't science, that doesn't mean that it isn't worth doing ... So scientists 
can worry about the fact that the classification that bioinformaticians are 
using isn't science, but bioinformaticians and bioinformatic data users need not 
worry about that ...
 
Stephen
 

________________________________

From:Richard Zander <Richard.Zander at mobot.org>
To: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>; Curtis Clark 
<lists at curtisclark.org>; taxacom at mailman.nhm.ku.edu
Sent: Tue, 21 December, 2010 11:48:35 AM
Subject: RE: [Taxacom] Usefulness vs. convenience (Protista)

Stephen:

If you try to mix classifications based on patterns of evidence (phylogenetics) 
and classifications based on theories of evolution of a group (evolutionary 
systematics) you will always get a mish-mash of apples and oranges. A 
paraphyletic group is a synchronic (one-dimensional present-day) view of a 
diachronic (through time) evolutionary process. The phylogenetic view is from 
well-supported evidence and the evolutionary view is theory. Only the last is 
science. The first is artificial.

R. 
* * * * * * * * * * * * 
Richard H. Zander 
Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299 USA 
Web sites: http://www.mobot.org/plantscience/resbot/ and 
http://www.mobot.org/plantscience/bfna/bfnamenu.htm
Modern Evolutionary Systematics Web site: 
http://www.mobot.org/plantscience/resbot/21EvSy.htm


-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu 
[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Stephen Thorpe
Sent: Sunday, December 19, 2010 11:12 PM
To: Curtis Clark; taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] Usefulness vs. convenience (Protista)

>But name me an uncrackable paraphyletic group

basal Bilateria ... where do Acoela and Nematodermata fit in? Xenoturbellida?

>Certainly Reptilia seems well-cracked

then please point me to a fully-worked out published Linnean classification 
which is congruent with the phylogeny (i.e., with mammals and birds as 
subordinate to the class Reptilia, but still with Linnean ranks) ...

Stephen