Molecular taxonomy: on way out?

[Frederick W. Schueler]

Richard Jensen wrote:
>
> Richard Pyle wrote:

> >  "Is there any information useful for inferring evolutionary relationships that can be interpreted from morphology that is not, somewhere, somehow, also represented in the genome?"
>
> I guess the question is, does the interaction of genome with environment yield any emergent properties that cannot be directly inferred from knowledge of the genome itself.

* maybe the question here is whether by 'genome' you mean only the
formal 4-base sequence read off the DNA, or supporting models and
theories about what the genes, and subsequent proteins, do once they're
transcribed,  how they affect transcription of other sequences, et
cetera, et cetera.

As the simplest case, you could restrict the meaning of 'genome' to the
raw DNA sequence for a protein (ignoring all functional implications,
starting with synonymous codons), or you could feed the sequence data
into a model of protein folding, and use the shape or inferred activity
of the protein as characters. Both are equally determined by the genome,
but the second entrains a lot more chemical theory, and potentially says
a lot more about the biology of any apomorphies.

It's a question of how much theory you're going to inject before doing
the overall analysis. Maybe there's an analogy with panbiogoeography
here, with its analysis of raw distributions, as opposed to 'Darwinian'
injection of theory about dispersal mechanisms and geological history
before asking "what's going on?".

> Perhaps if we did know *everything* about each component of the genome, about all the interactions of these components with each other, and about all permutations of these interactions with environmental variation, from beginning to end, it may be that all morphology is predictable from the genome.

* and then you could model the morphology of every hypothetical
intermediate form, and we'd have reached the nirvana foreseen by Sokal
and Sneath in 'Numerical Taxonomy:' "if we could visualize the phenetic
position of all organisms, past and present, we would find that they
represent a dendrogram in hyperspace, outlining the phyletic history of
living creatures."

fred.
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