[Taxacom] Was Reproducibility of phylogenetic analysis

Richard Zander Richard.Zander at mobot.org
Wed Jan 27 15:05:08 CST 2010


Occasionally there occurs some flack against those who contribute
articles that are data-rich but do not seem to have clear hypothesis,
methods, and conclusion in the standard experiment format.

I see floristic and faunistic papers as part of a 250-long research
program initiated by (or we can say initiated by) Linnaeus, to discover,
describe and name the world's living organisms. Along the way, we have
added an element of explanation according to the lights of current
process-based theory of evolution, geographic and climate change over
time, and other natural processes.

We do not have to restate the principles of this multi-participant,
multi-national, multi-decade project every time we find new data on
distribution and ecology for organisms. Results of the study are done
betimes with revisions, evolutionary study based on specimens collected
in the past, and explanatory evaluations of the distribution and
ecological descriptive papers. 

Excepting Deans. We have to explain the Linnaean Project to Deans. Deans
are not cretins but must be helped Get the Money. 

My essay on this:
http://www.mobot.org/plantscience/ResBot/Essa/EventHorizon.htm 



*****************************
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
mivie at montana.edu
Sent: Wednesday, January 27, 2010 1:41 PM
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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