[Taxacom] Usefulness vs. convenience (Protista)

Richard Zander Richard.Zander at mobot.org
Mon Dec 20 18:00:48 CST 2010

Again we have a little problem. "80% bootstrap support" is not science
in itself. It is a measure of the apparent certainty of a cluster (where
83% bootstrap is about 95% posterior probability from my simulations,
depending on branch length). We use the theory of evolution to make
scientific inferences about descent with modification of taxa. "80%
bootstrap" is about the evidence, not the theory. 


You say you have difficulty in understanding what I'm saying? Well, it's
partly me (editors have twice independently labeled my imperishable
prose as "dense and obscure"), but also partly the structuralist box of
"tree thinking" you can't quite break out of.


Bioinformatics naturally has a problem with reporting/recording the
results of science. The results change and are commonly controversial. A
theory of the macroevolution of a group is a result of science.
Well-supported patterns of EVIDENCE of macroevolution are not terribly
controversial, but that is all they are, evidence. _Of course_
phylogenetics fits bioinformatics better than that messy, controversial
science stuff.


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


From: Stephen Thorpe [mailto:stephen_thorpe at yahoo.co.nz] 
Sent: Monday, December 20, 2010 5:22 PM
To: Richard Zander; Curtis Clark; taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] Usefulness vs. convenience (Protista)


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 ...


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