Part II of reply to Stephen on my remarks about Johnson

From: Chris Cogan (
Date: Tue Jan 18 2000 - 16:05:08 EST

  • Next message: Chris Cogan: "Any strong challenges to Naturalistic Sufficiency?"

    This continues my last post on some of Stephen Jones' remarks. It is a
    continuation of the "Re: Why Phillip Johnson is a Dangerous Man 1/2" thread,
    but we should rename it now because we are no longer explicitly dealing with
    Johnson's demagoguery and misrepresentations of both facts and theories. We
    are back to the misrepresentations of Stephen Jones and Fred Hoyle now.

    Stephen Jones
    > It is one thing to talk *theoretically* of how Darwinian processes of
    > mutation and selection might be able to create new information. But it is
    > quite another to go to the *actual* history of life, as revealed in the
    > record, and claim that the same process, while it might be able to account
    > for changes at lower taxonomic levels like Species and Genera, can account
    > for the *massive* amounts of new genetic information required change a
    > member of a higher taxonomic category (like a Class and Order, let alone a
    > Phylum and Sub-phylum) into a member of another, within the timeframes
    > allowed by the fossil record.

    It can do it easily, because of the large populations involved and the
    variety of environments and because of the range of causes of variation
    (causes of mutation (such as chemicals), causes of inserting new information
    (such as viruses), and recombination via sexual union).

    Incidentally, as I've think I've said before, I don't believe truly new
    information is *ever* created. However, sometimes it "crystallizes" out of
    the general melee of information into specific forms that have a kind of
    resistance to major single-step modifications, at least in certain types of
    environments. Strictly speaking, I do not claim that *any* new information
    is ever created by genetic activity.

    But: I *do* think that the constant shuffling activity of genetic
    reproduction (which, in some cases is strong enough to require restraint, as
    Mike points out) *does* introduce information into genes, and not
    necessarily in tiny amounts, either, though probably nearly always in
    *relatively* small amounts (relative to the overall size of the genome).
    This is based on chemistry and genetics. Does Stephen wish to deny facts of
    genetics that are based on observation independent of evolution?

    > To claim that genes can duplicate, go off-line where selection cannot
    > them, accumulate new design information by random mutation, then come
    > back on-line with whole new design information ready to be slotted back
    > seamlessly into the system, is the equivalent of believing in genetic
    > miracles, yet this in fact what is now the orthodox Darwinian theory, even
    > though it is radically non-Darwinian:
    > "But all of evolution cannot consist of changes in genes that are already
    > present. Totally new functions have also been added to the biochemical
    > repertoires of organisms during evolution. Bacteria do not make muscle
    > fibers, bones, hormones, blood antigens, or the host of other structures
    > compounds that make up higher organisms. New genes, in addition to the
    > old ones, must be made. It is thought that this occurs as a two-step
    > process. First, a gene (or group of genes) is accidentally duplicated so
    > a chromosome now carries an extra copy of it. Because only one good
    > copy is needed to produce the original protein, the extra copy is free to
    > accumulate mutations without harming the organism. After a time, enough
    > changes may have accumulated in the duplicate to give it a new function."
    > (Lewontin R.C., "Human Diversity", 1995, p151).
    > But this is just hand-waving. It is compatible with an Intelligent
    > modifying genes while they are off-line, and then bringing them back
    > online, slotting them seamlessly back into the system (just as
    > designed computer program upgrades do), but not with a `blind
    > watchmaker'.

    As usual, you are misrepresenting your opponent's views, even after
    (apparently) accurately quoting them. They do not go "offline"; they merely
    become selectively neutral (if they don't produce any significant
    consequences). Since we know that large chunks of a many a genome can be
    removed without apparent harm to the resulting organism (at least relative
    to its normal habitat), this hypothesis is not as far-fetched as you make it
    seem. Keep in mind that all that's required is that such "genes" get
    themselves replicated in each new genome (possibly with modification).
    Selection doesn't "see" them because they don't interfere with the normal
    biology of the organism, and as a part of the DNA, are too small to impose a
    large biological cost on the organism during reproduction (either of cells
    or of the organism).

    Secondly, an entire gene does not need to be duplicated for this process to
    work. If only *part* of a functioning gene is duplicated, it may then either
    act as a new *functional* gene right from the start, or wait to be modified
    or recombined to become a functional gene.

    Finally, it is quite likely that, when such genes become functional, they do
    not do so "seamlessly." Many genes do not behave seamlessly as it is. They
    may provide a benefit, but at a significant cost (as does the gene for
    resisting Malaria, which also occasionally causes sickle-cell anemia, for
    example). Evolution cares only about *net* benefit to genome's
    survivability, and will not necessarily eliminate side-effects for a long
    time after the gene has become established (if ever; some anatomical
    "design" flaws remain essentially *permanently* precisely because they *are*
    such that there is no path to a better design that does not go through a
    "fitness valley," even though no *designer* in his right mind would allow
    such quirks to remain).

    > Hoyle critiques this "Evolution by Gene Duplication" theory first proposed
    > by the Japanese biochemist Susumu Ohno. First, duplication of genes does
    > not produce any markedly new functions and indeed may cause the genome
    > to be unable to change:
    > "It is possible that tandem duplication of one or several genes could
    > produce a marked increase in the amount of genetic material over only a
    > few thousand generations, but it is doubtful that any marked functional
    > diversity could arise in this way. Indeed, quite the reverse. In writing
    > the lungfish. S. Ohno remarks: `By establishing such a system [tandem
    > duplication] the organism effectively forfeited an opportunity for further
    > evolution. In a manner of speaking, the genome became frozen, while
    > containing enormous genetic redundancy. It is clear that in doing so such
    > lineage reached an evolutional dead end. It will be shown that what
    > happened to the lungfish also happened to salamanders and newts....
    > Indeed, this side branch stopped dead at the amphibian stage.' (Ohno S.,
    > "Evolution by Gene Duplication", 1970, in Hoyle F. & Wickramasinghe C.,
    > "Evolution from Space", 1983, p105).
    > In particular, Hoyle points out, gene duplications do not provide the
    > "sequence of 'quantum jumps' which are needed to account for the
    > observed changes "in the forms of plants and animals":
    > "At all events, tandem duplication does not solve the evolutionary
    > It might give a rapid increase in the quantity of genetic material, but it
    > does so by being highly repetitive, and this will not give a sequence of
    > 'quantum jumps' in the forms of plants and animals, such as is needed to
    > provide for the divergent evolutionary branches shown in Figures 6.6 to
    > 6.10. Repetitions will give some changes, of course, by altering the
    > quantities of certain proteins, but, as Ohno remarks in the above
    > the changes are much more likely to be stultifying than to lead to
    > adventurous new possibilities." (Hoyle F. & Wickramasinghe C., 1983,
    > p106).

    This is a vast overgeneralization, as I point out at the end of this post.

    > Indeed, if Ohno's Evolution by Gene Duplication theory was true, it
    > required that the duplications *anticipated* changes which would be later
    > needed down the track:
    > "To speed the fixing of neutral mutations, Dr Ohno requires the ancestral
    > breeding group to have been rather small. The free genes then go in
    > biochemical directions that have little to do with natural selection. In
    > way a gene can drift, even within a reptile, to a form that will be of
    > use to man. Indeed, the genes are supposed to have drifted to a
    > configuration which determined the later evolution of Figure 6.10, and the
    > still later evolution of Figure 7.2, not by the need to adapt to the
    > environment, but by chance. The chance anticipation of later need
    > continued even up the last stage of Figure 7.2. Thus in his concluding
    > pages Dr Ohno remarks: `Did the genome of our cave dwelling
    > predecessor contain a set or sets of genes which enable modern man to
    > compose music of infinite complexity and write novels with profound
    > meaning? One is compelled to give an affirmative answer .... It looks as
    > though the early Homo was already provided with the intellectual potential
    > which was in great excess of what was needed to cope with the
    > environment of his time.'

    It was *not* in great excess, *given* the lack of *knowledge*
    explicitly-worked-out thinking skills (i.e., logic, mathematics, scientific
    method, etc.). The "excess" potential was *needed* to compensate for the
    lack of such knowledge that was acquired *later.* If you aren't very
    educated, you had damnwell better be *intelligent*, particularly if you are
    also physically rather weak compared to other animals your size or larger.
    That "excess" intelligence enabled early man to make use of his "intuition"
    rather than modern conceptual thought. But, that intuitive ability also
    included the roots of conceptual thought (i.e., recognizing similarities and
    differences at a higher level of abstraction than do other animals).

    Given a sufficient modern education in the nature of the physical reality of
    the environments of early large-brained hominids, modern people could do
    *far* better than early man or other hominids did, because we not only have
    at least most of that large brain, we also have highly-developed language,
    abstract concepts statable in our languages, a knowledge of mathematics,
    physics, chemistry, nutrition, medicine, zoology, botany, structural
    engineering principles, a knowledge of meteorology, geology, evolution (so
    we could start breeding new varieties immediately), tools, tool-making,
    pumping water, hygiene, psychology, economics, division of labor, mass
    production, and even rules for more-efficient and effective social living.
    Early man had to make do *entirely* with "street smarts," because there was
    so little, if any, formal knowledge.

    But, even if, occasionally, genes *do* produce a function that is vastly
    beyond current needs (unlike early man's brain), so what? It does not mean
    that the genes were *trying* to produce such a result. It was just good
    fortune, that's all. Keep in mind that a major morphological or functional
    change does not necessarily need a major *genetic* change. It is
    conceivable, for instance, that the more-developed cerebral cortex of man
    arose as the result of a *small* change in genetic material, a change that
    basically said, "You know that little cerebral cortex we now have? Well, I'm
    tripling the production of it. So there." I doubt that it went this way, but
    major changes of this sort *can* be genetically trivial, amounting to little
    more than a small code that says to produce *more* of something, or to make
    something *longer* (e.g. okapi neckbones).

    > Dr Ohno was thus led by his resolute respect for the biological facts to
    > what seems to us a non-Darwinian position almost as marked as our own.
    > The facts, interpreted within a terrestrial theory of the origin and
    > of life, force one to suppose not only that chance faced up to the
    > minute probability of discovering the enzymes and other basic biochemical
    > substances, a probability we calculated in chapter 2 to be less than
    > 000, but that chance mutations also produced genes which were to prove
    > capable of writing the symphonies of Beethoven and the plays of
    > Shakespeare. This is the position to which one is inevitably led by
    > an Earth-bound theory, a position that we believe to constitute a reductio
    > ad absurdum disproof of that theory." (Hoyle F. & Wickramasinghe C.,
    > 1983, pp106-108).

    These kinds of arguments always make me suspicious. For one thing, they are
    attempts to generalize from what does *not* happen in a few cases to what
    allegedly does not happen in *all* cases. This is obviously unsound

    But, more importantly, probabalistic claims, such as those in the paragraph
    above, always rest on assumptions. In this case, what those assumptions are
    is not stated. But, if Hoyle's assumptions in this case is anything like his
    earlier argument from fine-tuning, and Behe's argument form "irreducible"
    complexity, this argument is probably just as bad.

    I think it's interesting that large amounts of redundancy can cause genetic
    inflexibility. I even find the claim plausible. But, it's essentially
    irrelevant to the main claim, which depends on a smallish amount of
    information being duplicated and then *changed* over time to have a new
    function. This is less likely in a large glob of redundancy because there is
    too much contextual constraint, which limits the ability of any part of it
    to form a new and functioning gene.

    Hoyle shows himself to be (probably) a better mathematician than he is
    general thinker, whether he is proclaiming his traditional fine-tuning or
    this very similar argument from an *alleged* improbability.

    To conclude, I will note that, given the total lack of *positive* evidence
    for design, Stephen's approach of attempting to find flaws in naturalistic
    evolutionary theory is a sound strategy. But, by the Principle of
    Naturalistic Sufficiency, I can convert *any* non-naturalistic theory that
    Stephen or anyone else proposes into an equivalent *naturalistic* theory
    that puts *less* stress on Occam's Razor (because of the lack of a need to
    prove the existence of a woozily-defined non-naturalistic metaphysical
    realm). This makes non-naturalism *useless* as an explanatory tool, as I
    pointed out in an earlier post (in a somewhat grammatically garbled way).
    Since it is also useless philosophically, for the same *and other* reasons,
    we have to wonder why it is still being sold. So: *Why* is anyone still
    trying to argue for non-naturalistic theories when they are both
    scientifically and philosophically useless? I don't get it.


    Now is the time for all good people to come to.

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