[Taxacom] Was Reproducibility of phylogenetic analysis

Stephen Thorpe s.thorpe at auckland.ac.nz
Wed Jan 27 16:22:34 CST 2010


It is relevant here to note that one of the biggest hurdles (at least in this part of the world) facing systematics in the more "scientific" sense is lack of material of key taxa. The work that Mike and others do to locate good field sites for taxa is therefore very valuable. An example: a mite expert in New York received a handful of specimens of a new mite, collected in NZ by visiting American collectors. It turns out to be a new family, which may help to shed some light on the early evolution on the group. As far as anybody new, the mite was rare and localised. In fact, I am busy sending to New York as many of the literally HUNDREDS of specimens, from several widespread localities, that I am picking out of pitfall trap samples.

"Faunistics" = intensive systematic collecting, and underpins everything else in systematics. Whats the point in doing other stuff, like phylogeography for example, when you don't know which taxa are where in the field?

________________________________________
From: taxacom-bounces at mailman.nhm.ku.edu [taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of mivie at montana.edu [mivie at montana.edu]
Sent: Thursday, 28 January 2010 8:41 a.m.
To: TAXACOM
Subject: [Taxacom] Was Reproducibility of phylogenetic analysis

Historically, much of this series of arguments was rooted in an insecurity
as other areas of study became more obviously and clearly "scientific"
after the development of statistics, leaving the historically progressive
taxonomy/systematics/phylogenetics field to worry if we got the respect we
thought we deserved.

I struggle with this all the time, and especially now that I am in one of
our 5-year review programs.  As a Land Grant faculty member, I have to
present a 5-year proposal that lays out a research program that is
scientifically valid, geographically limited and can be linked to
practical results.  Yea Gods!  No one has ever gotten to picky about it
with me, but I always feel vulnerable and inadequate (probably lots of
reasons to feel inadequate, but I mean here in the sense of our field).
My more clearly scientific work is outside this series of requirements,
being either global or tropical, or on groups with no clear economic
connection to Montana.  My real local value is in teaching, curating the
collection and identifying things for my colleagues.  Thus, they want to
keep me around.  However, I still have qualms about the "science" I
propose for that particular program (which does cover a majority of my
salary).

Basically, faunistics of a state shaped like Montana is silly (completely
unnatural boundaries), and even if it were natural, faunistics is hardly
defensible in a Popperian sense.  So it comes down to "I will explore the
state, find new and interesting things, and report them."

How is exploratory discovery framed properly as good science?

Any (positive) suggestions would be greatly appreciated,

Mike Ivie



Mike Ivie> A standard research program for Lakatos was one that actively
engages in
> theory/hypothesis formation and testing. Nothing remarkable about that.
> Explanatory hypotheses, by their very nature are reactions to effects in
> the present. What causes actually did occur in the past are rarely
> available to us, even as eye witness accounts. This is just the plain
> reality for all facets of explanation, not just systematics. We struggle
> no more or less than anyone else seeking to explain the present by way
> of the past. As in all the sciences, the mechanics of testing
> explanatory hypotheses is rather straightforward, regardless of the
> difficulty of actually doing it. The problem in systematics and
> evolutionary biology is that the subject is either ignored, in lieu of
> seeing cladograms as the end point, or testing is misrepresented, as is
> often seen with the notion of 'throw in more characters.'
>
> You're correct, systematics has had a rather different sort of research
> program. One that isn't particularly in accord with how science is done
> in other fields. That seems like a good basis for making a change from
> the status quo of cladograms being the means to the end.
>
> Kirk
>
> --
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> J. Kirk Fitzhugh, Ph.D.
> Curator of Polychaetes
> Invertebrate Zoology Section
> Research & Collections Branch
> Natural History Museum of Los Angeles County
> 900 Exposition Blvd
> Los Angeles CA 90007
> Phone: 213-763-3233
> FAX: 213-746-2999
> e-mail: kfitzhug at nhm.org
> http://www.nhm.org/site/research-collections/polychaetous-annelids
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
>
> Richard Zander wrote:
>> Philosopher of science Lakatos indicated that we need not reexamine the
>> fundamentals of our science every time we engage in research, but merely
>> need only plunge ahead into a standard Research Program, which pretty
>> much guarantees generation of results since it using the same methods on
>> similar data. Systematics, however, has always struggled with its
>> fundamentals because the results cannot be directly checked against
>> history or easily checked against evolution which is a process but damn
>> well-hidden.
>>
>> Systematics is famed for its arguments and battles. This is as it should
>> be. We seem to have a different standard Research Program every 40 years
>> or so. (Time for a change? What now?)
>>
>> *****************************
>> Richard H. Zander
>> Voice: 314-577-0276
>> Missouri Botanical Garden
>> PO Box 299
>> St. Louis, MO 63166-0299 USA
>> richard.zander at mobot.org
>> 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 J. Kirk
>> Fitzhugh
>> Sent: Wednesday, January 27, 2010 11:55 AM
>> To: TAXACOM
>> Subject: Re: [Taxacom] Reproducibility of phylogenetic analysis
>>
>> Interesting. We've returned to Philosophy of Science 101. If only this
>> had been the emphasis all along in systematics.
>>
>> Kirk
>>
>>
>
>
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