[Taxacom] Robust argument

John Grehan jgrehan at sciencebuff.org
Sun Jun 28 08:40:26 CDT 2009

A college of mine made the following comment on sequence analysis and phylogeny that may be of interest: 

"comparing sequences in non-coding regions (basic to the regulation of development) just doesn't make sense as it might in the coding region (producing proteins/enzymes). In the non-coding regions multiple transcription factors (proteins) can affect a single promoter region (which "begins" a signaling pathway) and importantly it is RNA that alternatively splices introns (post-natally apparently inactive space fillers between exons) and puts together the exons it "needs" to make the protein necessary for a particular aspect of development. Sequence is meaningless. But what is, is the way in which DNA is chopped up and used differently/differentially by RNA and other molecules to produce the organism. So the concept of everything we need to know about an organism (although we really don't know) is not going to come merely from sequence data (in metazoans)."

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




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> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
> bounces at mailman.nhm.ku.edu] On Behalf Of bti at dsmz.de
> Sent: Sunday, June 28, 2009 6:39 AM
> To: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] Robust argument
> Bob,
> >
> > All three clauses are untrue. This kind of reasoning had a chemical
> > analogy in the 19th and early 20th century: organisms are only made
> > of atoms and molecules, there's no vital force; therefore everything
> > we can infer about how organisms work is inherent in atoms and
> > molecules, and if we could only completely understand the chemistry
> > we'd have the whole organismal story. Anyone still think that way?
> Genomes are composed of nucleic acid bases, which consist of a pentose
> sugar back bone, phosphate and the appropriate nitrogen bases. The
> helical structure depends on the absoute stereochemistry of the
> pentose, the base pairing due to the bonding between the complementary
> nucleosides. t-RNA mediates protein synthesis by the same base-pair
> chemistry and the structure of proteins depends upon the individual
> amino acids present and their interactions, and we are also talking
> about "molecular machines". Try explaining membrane structure and
> functon by looking at genes alone.
> Nearly forgot, the selection of D- or L-amino acids is by interaction
> of the t-RNA and the t-RNA amnio acid synthase. I have not been able
> to find any evidence that a codon specifies "L-amino acid" rather than
> "D-amino acid".
> Brian
> Dr.B.J.Tindall
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