[Taxacom] Morphology vs Molecular

Wed Aug 19 16:32:56 CDT 2009

Yes hindsight may be 20:20 - but the point here is that is what molecular hindsight concluded.

John Grehan

> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
> bounces at mailman.nhm.ku.edu] On Behalf Of Jason Mate
> Sent: Wednesday, August 19, 2009 5:19 PM
> To: Taxacom
> Subject: Re: [Taxacom] Morphology vs Molecular
> 
> 
> And phrenology didn´t yield the desired results either. Hindsight is
> 20:20.
> 
> > Date: Wed, 19 Aug 2009 16:57:04 -0400
> > From: jgrehan at sciencebuff.org
> > To: Taxacom at mailman.nhm.ku.edu
> > Subject: Re: [Taxacom] Morphology vs Molecular
> >
> > Pierre is correct that counting occurs in morphology as well as
> molecules, but it's not a matter of just counting bases, but whether
> counting bases will necessarily give the correct phylogeny. This has
> already been recognized among molecular systematists who have recognized
> that some molecular techniques, such as DNA hybridization, are indeed
> measures of overall similarity that may give erroneous results due to the
> effects of shared primitive retention.
> >
> > John Grehan (the obstinate)
> >
> > Perhaps that will go on my gravestone.
> >
> > > -----Original Message-----
> > > From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
> > > bounces at mailman.nhm.ku.edu] On Behalf Of Deleporte Pierre
> > > Sent: Tuesday, August 18, 2009 5:02 PM
> > > To: Taxacom at mailman.nhm.ku.edu
> > > Subject: Re: [Taxacom] Morphology vs Molecular
> > >
> > > Richard,
> > >
> > > I suggest that you reconsider this line of argument "equal weighting
> is
> > > phenetic" (even if "some way"...)
> > > because it is highly confusing;
> > > for instance, 'standard' cladistic  analysis (i.e. parsimony analysis)
> > > traditionally makes use of equal weights for all character changes,
> at
> > > least for morphological characters,
> > > while phenetics is  classically (and better) defined as "classifying
> on
> > > the basis of an index of overall similarity"
> > >
> > > such a definition clearly rules out statements like "such and such
> > > characters (or data sets) are phenetic in themselves",
> > > only the analysis of the characters may be "phenetic", while any data
> > > matrix of characters may be analysed either cladistically or
> phenetically,
> > > or any other way you like
> > >
> > > ("phenetic characters" is an obstinate 'Grehanian' confusion,
> apparently
> > > used as a rhetoric trick for discarding any imaginable molecular
> analysis,
> > > because molecular sequence data would be "phenetic" in themselves, you
> > > know... and molecularits ar just "counting bases", when morphologist
> > > certainly never "count" morphological characters, which are not
> > > "phenetic", by the way...    not to mention the fact that Grehanian
> > > "cladistics" mean compatibility analysis, and anything that is not
> > > compatibility analysis seems to be classed as "phenetic"...   sigh...
> > > fortunately, nearly nobody on this list seems to follow such
> > > extraordinarily strange propositions)
> > >
> > > so, you know quite well that I have some serious doubts about the
> > > rationale underlying "equal weighing",
> > > but calling this "phenetics" cannot facilitate the discussion...
> > > we really need to share a common vocabulary - IMHO
> > >
> > > best,
> > > Pierre
> > >
> > > Richard Zander <Richard.Zander at mobot.org> a écrit :
> > >
> > > > In one way, molecular is indeed phenetic. There is no weighting for
> > > > phyletic importance. Well, there is one case, codon bias, in which
> > > > selection on a pool of messenger RNA emphasizes one synonymous codon
> > > > over another (if I have this right), but all other weighting (I
> > > > think) is purely part of the analysis, e.g. avoiding 3rd codon
> > > > positions because they may be over-saturated with changes. Basically
> > > > the Dirichlet priors are all 1 in Bayesian analysis. In some cases
> > > > certain site positions are weighted differently but I'm not sure how
> > > > this is part of pre-weighting for phyletic importance.
> > > >
> > > > (Now ask me what phyletic importance is.)
> > > >
> > > > *****************************
> > > > 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
> > > > Non-post deliveries to:
> > > > Missouri Botanical Garden, 4344 Shaw Blvd., St. Louis, MO 63110
> > > > *****************************
> > > >
> > > >
> > > > -----Original Message-----
> > > > From: taxacom-bounces at mailman.nhm.ku.edu
> > > > [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Jason Mate
> > > > Sent: Monday, August 17, 2009 7:09 PM
> > > > To: Taxacom
> > > > Subject: [Taxacom] Morphology vs Molecular
> > > >
> > > > Your counterargument is to say that molecular data is phenetic (how
> > > > you got here is anybody´s guess) and that
> > > > a unique and intimate knowledge of the characters (read, I have been
> > > > doing this for years so trust me) trumps any
> > > > amount of contradictory data (information that it not of the right
> > > kind).
> > > >
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