Re: Functional proteins from a random library

From: Preston Garrison (
Date: Tue Apr 10 2001 - 02:30:00 EDT

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    Tim Ikeda wrote:

    >Now a word on "strategy". Given that the passage of time increases
    >the difficulty of untangling past events, it seems to me that
    >those wishing to demonstrate proximate extra-natural assembly,
    >or at least hoping to make the best cases for it, would focus on
    >finding the most recent examples. These are the cases where the
    >tracks left behind would be the freshest and where breaks in
    >"normal" causality should be easier to document. I once mentioned
    >this in a discussion on the ARN site. One reply was that the
    >focus was on ancient, large and complex systems because they
    >wanted to provide an example of something that was obviously
    >"irreducibly complex." To me, this seems to be putting the
    >cart before the horse, and bad scientific strategy IMHO.
    >Scientists typically try to understand the simplest, most
    >experimentally tractable systems they can find, in hopes of
    >being able to apply their discoveries to more complex systems,
    >not the other way around. Certainly, to make a case that the
    >general scientific world would accept (and also one that would
    >fit within the pages of a journal), I'd be scrambling to work
    >on extra-naturally assembled systems which I though were the
    >most recent.

    Good point. The most useful systems are those which diverged
    recently AND where complete genome sequences for both (or better
    several) closely related species are available.

    >Any word yet on the comparison between human and chi(m)p genomes,
    >or between different species of Hawaii's fruit flies?

    One thing is clear at this point. There are thousands of
    transposable element sequences inserted at exactly the same
    positions in the chimp and human genomes. The number and age of
    specific types of elements shared between human and other
    mammalian species matches up with the expected time since the
    common ancestors, as expected. Those who want to continue denying
    that we have common ancestors with other mammals had best not
    look at this evidence.

    Another thing I find interesting is the surprising number of genes/
    proteins in each new completed genome that appear to be unrelated
    to any already known gene. And this with 15 billion nts in GenBank
    and the genome sequences of over 100 species either finished or
    soon to be finished.
    The paper covering the release of the Drosophila genome mentioned that
    something like a third of randomly chosen D. melanogaster cDNAs seemed
    to be absent in a closely related Drosophila species. This could of
    course just be due to gene loss or very rapid divergence of sequence,
    but the possibility that some of this is emergence of completely
    new classes of protein is tantalizing.

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