Re: Functional proteins from a random library

From: Preston Garrison (
Date: Tue Apr 10 2001 - 01:27:55 EDT

  • Next message: Preston Garrison: "Re: Functional proteins from a random library"

    I wrote:

    >We use synthesized reagants and artificial conditions
    >>to do all of biochemistry and genetics. Does that mean
    >>that biochemistry and genetics are biologically irrelevant?
    >>If intelligent control invalidates an experiment in this
    >>area, then _all_ experiments are invalidated.

    Paul Nelson wrote:


    It is you who are writing nonsense, although perhaps you are just not
    taking the trouble to write what you really mean.

    Paul Nelson wrote:

    Origin-of-life investigators routinely
    >debate the merits of each other's experiments in
    >terms of their prebiotic plausibility. I do not
    >think you would credit an experiment claiming to
    >show the natural or prebiotic (i.e., undirected)
    >synthesis of ribozymes, for instance, if the
    >investigators began with RNA from Sigma. Experiments can be more, or
    >less, illuminating
    >of any particular problem, depending on how
    >closely we take their conditions to mirror nature. Of course experiments
    >are "intelligently-designed," in the sense that we arrange what Francis
    >Bacon called "a trial," to understand how nature herself operates. But if
    >a *result* depends critically on the intervention of an agent -- i.e., if
    >we see that nature on her own would not achieve the same -- then it
    >is willfully naive to pretend that we didn't intervene.

    You appear to be claiming that any experiment short of a full re-enactmant
    of a natural origin under authentic conditions is useless. I agree that
    overblown claims have been made from many "pre-biotic" simulations, but
    that doesn't mean that all experiments that only address a segment of
    the problem are useless. The fact is that the specific objections you made
    would apply to any experiment.

    I wrote:

    >>The experiments are designed to begin answering the
    >>specific question, "How rare are foldable/functional
    >>protein sequences in sequence space?" This is an
    >>interesting question from the standpoint of protein
    >>biophysics alone, but it is obviously relevant to the
    >>question of whether and how completely new proteins
    >>can arise in non-functional or frame shifted sequences
    >>of existing organisms.
    >>The only reason I alluded to Bill Dembski in particular
    >>in my message is that I gather that, in contrast to Behe,
    >>he believes that even individual proteins cannot arise
    >>by chance.

    >The number I remember is 10^60 for the odds that he
    >>gives, which is too rare to find by chance. The results
    >>of these experiments begin to suggest that he is wrong
    >>about that one point, but obviously much remains to
    >>be done to see how rare different kinds of functions are.

    Paul Nelson wrote:

    >The number Bill estimates refers to a prebiotic context.

    In the stuff I have seen, Dembski uses the size of protein
    sequence space as a basis for defining a level of complexity
    that cannot be produced by anything but intelligent design.
    I don't see anything in his argument that is specific to
    the prebiotic context. As I said, I am under the impression
    that he doesn't think that even single proteins can arise by
    chance in any context.

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