[Taxacom] Reproducibility of phylogenetic analysis

Bob Mesibov mesibov at southcom.com.au
Sun Jan 24 16:27:49 CST 2010


This article

http://arstechnica.com/science/news/2010/01/keeping-computers-from-ending-sciences-reproducibility.ars

is relevant to systematics, as it highlights an aspect of algorithm-based phylogenetic analysis which troubles some systematists.

In the past, some Taxacomers have worried aloud that phylogenetic inference is a house of cards, implying (incorrectly, IMO) that if even one of the analytical steps is flawed, then the whole process is worthless. I and others have suggested here that algorithm-based phylogenetic inference is a closed, self-consistent process whose results are not tested by other means. Richard Zander has proposed an explicit statistical procedure to clarify the nature of Bayesian results, but I suspect his paper has been widely ignored.

I'm not sure that any of this skepticism will make systematists any less enthusiastic about filling the literature with analyses, because trees are very useful and systematists are keen to build them using whatever tools are acceptable to their peers and their editors. What's worth keeping in mind is that most (imagine your own percentage here) of animal and plant taxonomy has been built by morphologists who made 'non-reproducible' and subjective judgements about similarities and relationships.

Some of those judgements were wrong, and it's easy to feel superior to systematists who didn't have today's analytical tools. It would be a mistake, though, as the Ars Technica article implies, to try to escape responsibility for bad judgements by saying, 'Well, we used these data and these methods and got these results, so if they're wrong it's not our fault.'
-- 
Dr Robert Mesibov
Honorary Research Associate
Queen Victoria Museum and Art Gallery, and
School of Zoology, University of Tasmania
Home contact: PO Box 101, Penguin, Tasmania, Australia 7316
(03) 64371195; 61 3 64371195
Website: http://www.qvmag.tas.gov.au/mesibov.html




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