[Taxacom] molecular nonsense?

John Grehan jgrehan at sciencebuff.org
Thu Nov 6 10:46:06 CST 2008


Alan, thank you for some interesting observations. My comments inserted below. 

> -----Original Message-----
> From: Alan DAvid Forrest [mailto:aforrest at rjb.csic.es]
> Sent: Thursday, November 06, 2008 10:26 AM
> To: John Grehan
> Cc: TAXACOM
> Subject: Re: [Taxacom] molecular nonsense?
> 
> Please do not allow all researchers who use molecular data to address
> hypotheses to be tarred with the brush of poor quality science. There
> are many examples of the latter - I am aware of papers rejected due to
> poor quality science, only for them to be published soon afterwards
> despite any concerns. This does not invalidate molecular data in general
> terms.

So the question here is what are the high quality molecular papers supporting the human-chimpanzee relationship? Are there any? I do not know.

But even so, if the same methodological problems apply to molecular data in general then there may well be problems for molecular analysis in general.

> Molecular data (when of high quality and analysed appropriately) 

My question is what is 'high quality' molecular data? What is 'appropriate analysis'. As an apparently extremist cladist I have not yet seen any high quality molecular data or appropriate analysis.

can
> reveal additional insights, as the mode of inheritance of homologous
> nucleotides is well understood, 

I have not yet seen mode of inheritance as a critical aspect of molecular analyses of human and great ape relationships (not that I am excluding the possilbity).

which is not always the case for
> morphological character states: our knowkledge of the inheritance of the
> latter is patchy and does not conform to any over-riding rules. 
> example, in the following paper: Grehan (2001) Biogeography and
> evolution of the Galapagos: integration of the biological and geological
> evidence. Biol. J. Linn. Soc. 74, 267-287, a biogeographic track is
> analysed in the Galapagos, using as an example the plant genera Galvezia
> and Gambelia, which are assumed to be sister genera based upon a
> morphological taxonomic monograph and a study of the genera using
> allozymes - the absence of a tribal analysis to establish sister genus
> status is somewhat lacking in the literature. Our own (as yet
> unpublished) work has used four genes (both plastid and nuclear)
> alongside other biological and morphological data (including outgroups
> from across the included tribe, all other tribes in the family, and
> several taxa from related but increasingly distant families) to show
> that these 2 genera are completely unrelated. The key here is the
> diversity of data used, and the appropriate sampling and analyses which
> was not apparent from previous publications.

In terms of comparative biology I am in full agreement with the need for broad taxonomic comparison. I presume this also applied to your genetic comparison by including sequences of all species of the outgroups to maintain that standard?

> In this case molecular data are just another form of data. 

I agree, although as a cladist I would give more credence to cladistic data.

Incongruence
> between data types requires analysis of what causes the incongruence,
> not rejection of one data in favour of another based on a priori
> preferences.

Agreed! Unfortunately in the science of hominid origins this is not the response. Instead it is declared almost religiously that the molecular evidence has to be right and the morphology wrong.

> Remember, the most important thing in science is to get some good
> publications as this is how you obtain employment. 

Although the 'old boys' or 'old girls' network and be even more influential.

The quality of the
> science underlying those publications we can worry about at a later
> date. Chimps and humans are a hot topic.

But humans and orangutans are a very cold topic.

John Grehan
> 
> AD Forrest
> 
> 
> 
> 
> 
> 
> 
> 
> 
> John Grehan escribió:
> > Ebersberger et al (2007) Mapping human genetic ancestry. Mol. Biol.
> > Evol. 24: 2266-2276
> >
> >
> >
> > I am grateful for one list member sending me the above work as "rather
> > relevant for your questioning of the (human, chimp) relationship"
> >
> >
> >
> > It certainly is, and illustrates what I see as continuing illusion of
> > the putative chimpanzee-human clade. The paper uses a likelihood
> > approach (correct me if I am wrong, but I understand that this approach
> > sort of models what the true tree is supposed to be in the first place)
> > to "identify those sequence trees that significantly reject chimpanzees
> > as our closest relatives, that is, are incongruent with the species
> > tree". There you have it, anything that does not fit must be wrong. The
> > authors begin with the human-chimpanzee assumption and interpret
> > everything from there. This seems to me a continuance of the molecular
> > propaganda machine.
> >
> >
> >
> > Cladistically the taxonomic sampling is nonsense. To evaluate
> > relationships of humans and great apes the outgroup is just one monkey
> > species! The authors also admit that they have no information on the
> > quality of the individual aligned sequence reads! Amazing! Is this the
> > standard of systematic quality for molecular analyses? Imagine the
> > response if a morphologists tries to say that they had no information on
> > the quality of morphological homologies! The authors then proceed to
> > invent the quality through a series of computational manipulations to
> > somehow make the data good. They end up with 30,112 multiple sequence
> > alignments that are available upon request (I will be requesting).
> >
> >
> >
> > The authors "re-estimate the splitting times for the human and great ape
> > lineages." Hmmm - wonder why they have to do that. If molecules are
> > supposed to give the right answer, then why revisit what has already
> > been determined? On p. 2274 the authors node that "it is still unclear
> > when in our evolutionary history we split from the ancestral species
> > shared with the chimpanzees. Hmmm - maybe because the theory is wrong in
> > the first place!
> >
> >
> >
> > "Particularly puzzling in this context is the apparent discrepancy
> > between the dating of this split based on genetic evidences and the age
> > of fossils." Well, their answer in short is that the fossil record is
> > wrong because morphology is wrong! They state "The unequivocal
> > assignment of fossil remains to a species more closely related to humans
> > than to chimpanzees based on the presence of certain human-specific
> > apomorphies should, therefore, be taken with a grain of salt"!!!!! This
> > authoritative statement mirrors what Jeff and I have been saying for
> > some time - if only DNA can be relied upon to give the right answer then
> > the entire fossil record is scientifically meaningless, and now some
> > molecular experts are saying the same thing! All you morphological
> > systematists - you are going to be out of job.
> >
> >
> >
> > Anyway, they note that the "current interpretation of the fossil record
> > argues for the presence of hominids already at 5.8 MYBP" and possibly
> > earlier. The molecular study manages to come up with the 'right' answer
> > divergence estimate of 5.7 Ma (2270) Believe it or not.
> >
> >
> >
> > There is more! P. 2274 there is a general denouncement of morphological
> > cladistics! "The problem with using apomorphies for the reconstruction
> > of phylogenetic relationships, however, extends beyond the
> > classification of fossils".
> >
> >
> >
> > "Because gene products essentially defined the phenotype, we can expect
> > a certain proportion of derived morphological characters to support the
> > sister grouping of humans and gorillas, or chimpanzees and gorillas"
> > [but for some strange reason, not humans and orangutans!]
> >
> >
> >
> > So here you have it, on the authority of these expert molecular
> > systematists, morphological cladistics is dead!!! (As I have said
> > before, it baffles the boffin in my to understand why morphologists are
> > so willing (desperate) to make themselves slaves to molecular
> > authority)>
> >
> >
> >
> > Am I the only one on this list that thinks this molecular stuff is
> > nutty?
> >
> >
> >
> > John Grehan
> >
> >
> >
> >
> >
> > Dr. John R. Grehan
> >
> > Director of Science
> >
> > Buffalo Museum of Science1020 Humboldt Parkway
> >
> > Buffalo, NY 14211-1193
> >
> > email: jgrehan at sciencebuff.org
> >
> > Phone: (716) 896-5200 ext 372
> >
> >
> >
> > Panbiogeography
> >
> > http://www.sciencebuff.org/biogeography_and_evolutionary_biology.php
> >
> > Ghost moth research
> >
> > http://www.sciencebuff.org/systematics_and_evolution_of_hepialdiae.php
> >
> > Human evolution and the great apes
> >
> > http://www.sciencebuff.org/human_origin_and_the_great_apes.php
> >
> >
> >
> >
> >
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