[Taxacom] Molecular vs. morphological evidence

[John Grehan]

Please explain "multiple claims of homology" and also which concepts of homology you are referring to with respect to St Hilaire and Owen respectively? Are you saying that they had the same concept of homology and if so, what concept are you referring to, and in what way do you see that relating to genome analysis?

John Grehan


> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
> bounces at mailman.nhm.ku.edu] On Behalf Of Paul J. Morris
> Sent: Wednesday, July 01, 2009 12:59 PM
> To: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] Molecular vs. morphological evidence
> 
> On Wed, 1 Jul 2009 08:06:40 -0400
> "John Grehan" <jgrehan at sciencebuff.org> wrote:
> > Should? Whole 'genomes' (read entire sequence) is still the same kind
> > of data, and taking a chunk or taking the whole (and that would be
> > for all species) doesn't change the ingredients and the inherent
> > problems of molecular bean counting.
> 
> Wrong.
> 
> Many of the people working with whole genomes are identifying
> multiple classes of molecular homologies in addition to sequence
> similarity.  Read this paper and its supplemental material:
> 
> Sark A., et al., 2007. Discovery of functional
> elements in 12 Drosophila genomes using evolutionary signatures.
> Nature 450:203-218.
> 
> Among other things, based on patterns of which bases are changing
> amongst Drosophila species, they predicted the presence of previously
> unknown protein coding regions, identified regions of both
> pre-translational and post-translational regulation, and constructed a
> tentative map of regulatory interactions between several thousand
> genes.  The assertion that region X of the genomes of twelve fruit fly
> species is a protein coding exon, and that the protein gene product of
> this region regulates the production of another protein in region Y
> involves multiple claims of homology.  That is, homology in the
> classical senses of Saint-Hilaire and Richard Owen, though the
> language they are using to describe these are "functional elements".
> Each part of that assertion is inherently different from, and has
> different inherent problems from the molecular bean counting of
> sequence similarity.
> 
> This is one example of many.  Phylogenomics is a different world.
> 
> -Paul
> --
> Paul J. Morris
> Biodiversity Informatics Manager
> Harvard University Herbaria/Museum of Comparative Zoölogy
> mole at morris.net  AA3SD  PGP public key available
> 
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