[Taxacom] molecular nonsense?

Robin Leech releech at telusplanet.net
Thu Nov 6 16:36:40 CST 2008


Bob,
Sounds like good sense.
Robin

----- Original Message ----- 
From: "Bob Mesibov" <mesibov at southcom.com.au>
To: <jgrehan at sciencebuff.org>
Cc: "TAXACOM" <taxacom at mailman.nhm.ku.edu>
Sent: Thursday, November 06, 2008 3:26 PM
Subject: Re: [Taxacom] molecular nonsense?


> 
> Hi, John.
> 
> I think the best way to understand 'this molecular stuff' is with
> analogies.
> 
> The kindest analogy is with the first microscopes. The optics were crap
> and people didn't have a clue what they were looking at. Reports
> appeared of dust mistaken for 'animalcules', and of tiny, complete
> animals packed into eggs (preformation). Over time, optics improved. The
> reports got better and you could begin to trust the results.
> 
> I'm old enough to remember (this is analogy 2) the early transmission
> SEM work and how people responded to it. One anatomist told this student
> "I believed it until I saw the actual SEMs."
> 
> Unkind analogy from my early days as a biochemist: For several decades
> surrounding the turn of the 20th century, the research program in
> leading biochemical labs was quantitative inorganic analysis. Numerous
> papers from that time carried huge tables giving the elemental
> compositions of tissues from all sorts of plants and animals. Why?
> 
> The reasons were partly sociological. Quantitative analysis generated
> numbers, often with lots of decimal places. Biology could now be seen as
> just as scientific as physics, or "proper" chemistry. Quantitative
> analysis dignified biology and its practitioners.
> 
> Second, it was an open-ended program. After you'd analysed liver vs
> kidney in sheep, you could do the same in cows, pigs and humans.
> Further, you could return to sheep liver vs. kidney when analytical
> methods for manganese or other trace elements had improved: better
> elemental resolution.
> 
> Third, the enormous effort put into the inorganic analysis of Life meant
> that vast quantities of data had been published which could be reviewed
> and compiled into books: "metapublishing" which gave even greater
> dignitas to the leading authorities in the field.
> 
> Looking back on this from the 1960s, it was hard for me to understand
> how intelligent scientists had got it so wrong. Inorganic composition of
> life was a dead end. You could write eminently plausible arguments about
> it in 1890, e.g. "There are no vital forces. Life is just chemistry.
> Chemistry is the elements. If we learn more about which elements are in
> which tissues, and in which proportions, we will move much closer to an
> understanding of how Life operates." But you would be wrong, and very
> badly wrong at that.
> 
> Well, that's what molecular phylogenetics looks like at the moment:
> lousy optics, poorly understood statistics and overweening pride. Give
> it time, John.
> 
> I recently reanalysed a GenBank set of 20 sequences. I used 3 maximum
> likelihood methods, 1 Bayesian inference, 2 maximum parsimony and 3
> distance-based, and got 14 different trees, all different from the one
> published using a 3rd maximum parsimony method. What's going on? Is it
> all just nutty?
> 
> No. There's a lot of non-phylogenetic noise in those 20 sequences, and
> *any* method struggles to get a signal out. Better now to reexamine the
> morphology or play with a few more genes, or both.
> -- 
> 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
> Ph (03) 64371195; 61 3 64371195
> Webpage: http://www.qvmag.tas.gov.au/mesibov.html
> 
> 
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