Re: the *fantastic* molecular machinery of the cell (was Obituaries William D. Hamilton; Biologist ...)

From: Stephen E. Jones (sejones@iinet.net.au)
Date: Sun Mar 19 2000 - 16:12:15 EST

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    Reflectorites

    On Thu, 16 Mar 2000 19:47:43 -0800, Cliff Lundberg wrote:

    >SJ>PS: I have been utterly blown away in my Biology classes over last two
    >>weeks by the *fantastic* molecular machinery of the cell, e.g. ATP
    >>synthase's proton pump motor.

    Please note my spelling mistake corrected.

    CL>The argument from personal incredulity will never mean anything
    >in science.

    Who is arguing "from personal incredulity"? If Cliff or anyone else can
    plausibly explain fully naturalistically the origins of the "molecular
    machinery of the cell," including "ATP synthase's proton pump motor," then
    I will accept it. But I will not be intimidated by materialist-naturalist
    slogans like "argument from personal incredulity"which have the effect of
    closing down minds so that the materialist-naturalist position can never be
    threatened, no matter what the evidence actually points to.

    Indeed, the boot is on the other foot. It is the *non*-theists who find the
    idea of an Intelligent Designer "incredible":

    "...the theory of evolution...a theory universally accepted not because it can
    be proved by logically coherent evidence to be true but because the only
    alternative, special creation, is clearly incredible." (Watson D.M.S.,
    "Adaptation," Nature, Vol. 124, 1929, p.233, in Bird W.R., "The Origin of
    Species Revisited," 1991, Vol. II, p.172).

    But to help Cliff (or anyone else) out to provide a fully naturalistic
    explanation, here are two web sites with details and pictures of the ATP
    synthase molecular machine:

    http://www.arn.org/docs/behe/mb_mm/atpmechanism.htm and
    http://www.nobel.se/announcement-97/chemistry97.html.

    Here briefly is what they say about it. The second one first: the Royal
    Swedish Academy of Sciences' 1997 Nobel Prize in Chemistry citation:

    "ATP synthase - an exceptional molecular machine ... Boyer has called
    ATP synthase a molecular machine. It may be compared to a water-driven
    hammer minting coins. The Fo part is the wheel, the flow of protons is the
    waterfall and the structural changes in F1 lead to three coins in the ATP
    currency being minted for each turn of the wheel.... Na+, K+-ATPase, the
    first molecular pump to be discovered... Following the discovery of Na+,
    K+-ATPase other ion pumps have been discovered with similar structures
    and functions."

    Next, the article "More about the ATP Synthase Molecule: ATP
    Mechanisms Revealed By Sean Henahan":

    "...New X-ray crystallographic studies have revealed the working of
    adenosine triphosphate synthase, the basis of energy transport in all living
    organisms. ..."It's one of the most complex molecules ever revealed, almost
    six times larger than the blood molecule hemoglobin," says Pedersen. It's
    also, the researchers agree, one of the tiniest and most powerful motors
    ever identified. "

    Note that this complex nanomachine is fundamental to the production of
    cellular energy in *all* living things. So it could not arise by natural
    selection among living organisms because it is required to be already
    present in all living organisms.

    [...]

    >SJ>If Darwinists cannot demonstrate how this absolutely *fundamental*
    >>molecular machinery which *all* known life needs to have each and every
    >>component working together as a total, integrated system, then their
    >>theory *has* absolutely broken down. Darwinists can of course invent
    >>imaginary `just-so' stories to explain just about anything (and its opposite)
    >>but I think even their imagination would fail here! Darwinism, as a general
    >>theory, is therefore either falsified or unfalsifiable.

    CL>Darwin's rigorous anti-saltationism is simply wrong, and has been protested
    >by many, beginning with his friend T.H.Huxley. So pure gradualism is rather
    >a straw man. If Stephen can convince people that evolution in general stands
    >or falls with pure gradualism, and if he can convince himself that this is a
    >valid argument, then I guess he's making progress.

    Despite all the hand-waving, neither Huxley or Gould has ever explained
    how complex biological organs could be built by saltation. I quoted Gould's
    sotto voce admission that: "I know of no scientific mechanism other than
    natural selection with the proven power to build structures of such
    eminently workable design." (Gould S.J., "Darwinian Fundamentalism",
    New York Review of Books, June 12, 1997.
    http://www.nybooks.com/nyrev/WWWfeatdisplay.cgi?19970612 34F@p3)

    Darwin simply thought far longer and harder about this problem than
    Huxley.

    Darwin realised what Huxley and his latter day disciples like Gould have
    never seriously considered, that the saltational origin of a complex organ
    would be indistinguishable from a miracle:

    "The idea of continuity in nature occurs in many places in the history of
    human thought. Natura non facit saltum-nature makes no jumps-was a
    guiding motto for generations of evolutionists and protoevolutionists. But
    Darwin encountered it in a sharp and interesting form, posed as an
    alternative of terrible import: nature makes no jumps, but God does.
    Therefore, if we want to know whether something that interests us is of
    natural origin or supernatural, we must ask: did it arise gradually out of
    that which came before, or suddenly without any evident natural cause?"
    (Gruber H.E., "Darwin on Man," 1974, p.125)

    CL>The symbiotic theory of the origin of cells has been around a while now.
    >Cells are ecosystems that became genomically integrated (except for the
    >complication of maternal mitochondrial DNA). If this basically simple
    >mechanistic theory is rejected out of hand as objectionably imaginary,
    >there must be prejudice involved.

    No. Cliff simply misunderstands the problem. The "fantastic molecular
    machinery of the cell" that I am referring to is found in *both* prokaryotes
    and eukaryotes, and therefore in *all* living things:

    "FIGURE 9.14 - ATP synthase, a molecular machine. This protein
    complex, which uses the energy of an H+ gradient to drive ATP synthesis,
    resides in mitochondrial and chloroplast membranes and in the plasma
    membranes of prokaryotes." (Campbell N.A., Reece J.B. & Mitchell L.G.,
    "Biology," 1999, p.159)

    "More than a dozen enzymes and other proteins participate in DNA
    replication. Much more is known about how this "replication machine"
    works in bacteria than in eukaryotes. However, most of the process seems
    to be fundamentally similar for prokaryotes and eukaryotes. In this section
    we take a closer look at the basic steps." (Campbell, et. al., 1999, p.286)

    So whether the endosymbiotic theory for the origin of eukaryotes from
    prokaryotes is true or not is therefore *irrelevant* to my argument.

    Steve

    --------------------------------------------------------------------------
    "Although a biologist, I must confess that I do not understand how life
    came about. Of course, it depends on the definition of life. To me,
    autoreplication of a macromolecule does not yet represent life. Even a viral
    particle is not a life organism, it only can participate in life processes when
    it succeeds in becoming part of a living host cell. Therefore, I consider that
    life only starts at the level of a functional cell. The most primitive cells may
    require at least several hundred different specific biological
    macromolecules. How such already quite complex structures may have
    come together, remains a mystery to me. The possibility of the existence of
    a Creator, of God, represents to me a satisfactory solution to this
    problem." (Arber, Werner [Professor of Microbiology at the University of
    Basel, Switzerland, shared Nobel Prize for Physiology/Medicine in 1978.],
    "The Existence of a Creator Represents a Satisfactory Solution," in
    Margenau H. & Varghese R.A., eds., "Cosmos, Bios, Theos: Scientists
    Reflect on Science, God, and the Origins of the Universe Life, and Homo
    Sapiens," [1992], Open Court: La Salle IL., 1993, Second Printing, pp.142-
    143)
    Stephen E. Jones | sejones@iinet.net.au | http://www.iinet.net.au/~sejones
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