[Taxacom] molecular nonsense?

Richard Pyle deepreef at bishopmuseum.org
Thu Nov 6 21:03:52 CST 2008


I've said it before, and I'll say it again:

There is almost(*) NOTHING phylogentically informative in morphology, that
is not SOMEWHERE in the genome.

The problems with molecular analysis have to do with the "analysis" part,
not the "molecular" part.

As Bob so masterfully illustrated in his post (very nicely done, by the
way!), the real problems stem from limitations of our ability to properly
interpret molecular data in a phylogenetic context.  But we're getting there
(and it seems we're getting there mighty fast!).

Frankly (alluding to Ken's post forwarded by Robin), I'm not especially
impressed by the phylogenetically informative value of a lot of
morphological studies, either.  In fact, having been exposed to both
morphological and molecular approaches to formulating and testing
phylogenetic hypotheses throughout my (many) graduate student years, I
eventually found the entire business intellectually uninteresting.  Not the
notion of reconstructing evolutionary histories itself (which I think is one
of the most interesting aspects of all of biology), but rather the crude
(and oftentimes misleading, and/or over-confidence-inspiring) methodologies
that were (and, as far as I know, still are) available for trying to infer
phylogenies from morphological and/or molecular data.  

Don't get me wrong -- I applaud those who play in that sandbox, and I regard
them as true pioneers (at least the ones who apply appropriate levels of
caution when drawing conclusions).  Because of their efforts, we (humanity)
will eventually get to the point where we can extract robustly meaningful
conculsions about phylogeny from these myriad data.  But so far, it still
involves too much guesswork and too many layers of assumptions to give me
the intellectual satisfaction I'm looking for.

Instead, I derive much more satisfaction from exploring nature, encountering
previously undocumented organisms, and assigning new species names to those
sets of organisms for which I believe communication amongst humans would be
best enhanced by doing so.  It's not really science in the physics sense --
more in the early naturalist sense (i.e., describing nature in a more
qualified, rather than quantified, way).  But at the end of the day, at
least I have some degree of confidence that global human knowledge has
actually increased as a result of my efforts.

:-)

Aloha,
Rich

*I added "almost" to qualify "NOTHING" because, well, it's often dangerous
to make bold statements without such qualifiers.

> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu 
> [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Bob Mesibov
> Sent: Thursday, November 06, 2008 12:27 PM
> To: jgrehan at sciencebuff.org
> Cc: TAXACOM
> 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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