Evolution of proteins in sequence space

From: pruest@pop.dplanet.ch
Date: Fri Aug 17 2001 - 15:28:02 EDT

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    Keith B Miller wrote:
    > Peter wrote:
    > >But can you specify any feasible scientific tests for the following
    > >propositions? (If not, why not?)
    > >
    > >(1) Life can emerge spontaneously by purely natural means.
    > >
    > >(2) Novel enzymatic activities (not slight modifications or new
    > >combinations of pre-existing ones) can emerge spontaneously by purely
    > >natural means.
    > Firstly, I am assuming that by "purely natural" you mean that matter has
    > the properties capable of organizing into living things without any breaks
    > or "gaps" in the continuity of casue-and-effect processes. However, if you
    > mean "without divine action or participation" then the answer in of course
    > no - as this is a not question that can conceivably be addressed by
    > scientific means. The existence or action of God is non amenable to
    > scientific test.


    Of course, I assume that God is providentially active in whatever
    occurs, whether the events are purely natural or not. I should have
    specified that by "purely natural", I meant events and processes
    amenable to scientific investigation. But I am not sure this is
    equivalent to your matter having "properties capable of organizing into
    living things without any breaks or 'gaps' in the continuity of
    cause-and-effect processes". I am not talking about "gaps" in the
    continuity of scientifically investigatable cause-and-effect processes.
    But how do we deal with quantum uncertainties and selection of outcomes
    from distributions of "random" events? In such cases, science is in
    principle unable to detect a possible "supernatural selection", so these
    are not "gaps" waiting to be closed by scientific advances.
    > Both of the questions your list are areas of extensive current research.
    > These are clearly scientific questions, even if we do not currently have a
    > solid handle on the most likely answers. I am excited by the current
    > discoveries being made - which show slow but continued progress in
    > addressing these questions. Much progress has been made in our
    > understanding of primordial Earth conditions,

    These are the conditions an origin of life has to respect, but they do
    not in themselves constitute any part of an explanation of biopoesis,
    existing _before_ this event.

    > on the environments and biology of extremophile archeobacteria,

    These are full-fledged living organisms, which do not in themselves
    constitute any part of an explanation of biopoesis, existing _after_
    this event.

    > on both terrestrial and space
    > environments conducive to the synthesis of organic molecules,

    These organic molecules may have been required for an origin of life,
    but they do not in themselves constitute any part of an explanation of
    biopoesis, existing _before_ this event.

    > on the autocatalysis of RNA,

    Strictly speaking, autocatalysis of RNA has not yet been found (an RNA
    molecule producing more of itself out of non-RNA precursors, in an
    infinite loop). Also, it is completely unknown how a first RNA could
    have arisen, and whether such an RNA world ever existed as an
    intermediate in biopoesis.

    > on the random generation of functional proteins,

    This is the subject of the two papers which I discussed when I started
    this thread. They indicate that functional proteins are an extremely
    small part of all possible amino acid sequences, and that such
    artificial selection experiments cannot be a valid model of natural
    selection of random mutants, much less of biopoesis.

    > on factors that can generate excesses of L- or D- amino acids. (With regard
    > to the latter I just recently ran onto a book called "Advances in
    > Biochirality" edited by G. Palyi, C. Zucchi, and L. Caglioti and published
    > by Elsevier (1999).)

    As far as I know, none of the proposed mechanisms for generating a
    chiral excess has been accepted as satisfactory by the research
    community. Saghatelian A., Yokobayashi Y., Soltani K., Ghadiri M.R., "A
    chiroselective peptide replicator", Nature 409 (2001), 797-801, write:
    "...none of the possible physicochemical processes considered can
    produce the significant imbalance required if homochiral biopolymers are
    to result from simple coupling of suitable precursor molecules. This
    implies a central role for either additional processes that can
    selectively amplify an initially minute enantiomeric difference in the
    starting material, or for a nonenzymatic process by which biopolymers
    undergo chiroselective molecular replication." They present a system
    employing fully chiral peptides of length 32, consisting of either all
    L-amino acids or all D-amino acids. Of course, no possible way of
    abiotic formation such molecules is known.
    > If such research continues to prove to be fruitful then our confidence that
    > the scientific hypothesis that matter does indeed have the requisite
    > capabilities to bring forth living things is in fact true would be
    > supported. That is how any scientific model works. It is never proven,
    > but either eventually abandoned for lack of fruitfull progress, modified to
    > accomodate novel discoveries, or increasing supported by new data.
    > Keith

    The point I wanted to make initially (10 Aug 2001 16:24:10 +0200) is
    that you require of Bert Massie (or of "progressive creationists") that
    they present a scientifically testable hypothesis of _how_ living
    organisms were formed (either in the origin of life or later), but you
    fail to mention that the scientific establishment is exactly in the same
    boat. To date no one is capable of presenting a testable model within
    the framework of scientific origin-of-life research or of biological
    evolution (as far as genuine novelty is concerned). I agree that there
    is no scientifically testable model of "progressive creationism", but
    neither is there any such model in the evolutionary establishment! You
    write that "we do not currently have a solid handle on the most likely
    answers". I think this is a serious understatement. It seems rather that
    we have no idea about how to approach the two questions I posed.


    Dr Peter Ruest, <pruest@dplanet.ch>
    CH-3148 Lanzenhaeusern, Switzerland
    Biochemistry - Creation and evolution
    Creative providence in biology (Gen.2:3):
    "..the work which God created (in order) to (actively) evolve it"

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