Re: Evolution Statement

From: tikeda@sprintmail.com
Date: Tue Dec 11 2001 - 16:55:33 EST

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    [...]
    I wrote:
    <Thus we should not rule out the possibility that many of the older,
    more disrupted lunar craters could have formed supernaturally and are
    not the products of natural causes. (Or, pace Moorad: We never
    saw the impact which produced Bessel crater, so why couldn't it have been
    made by elves? Science can't apply to any crater formed before 10000 BC,
    because there weren't modern humans or instruments to record it. Let it
    forever be an enigma!)>

    .end speculations here...>>

    Bob replied:
    >Tim,
    >I don't know why you threw in the concept of the supernatural in your
    >moon example, which I suppose was meant to address my statement. Did
    >I say anything about the supernatural? No. So why do you?

    That was more of a dig at Moorad than you. However, I do not see why
    the idea of descent with modification becomes more problematic the further
    one goes back in the history of life. Perhaps if one goes very far back,
    say around the eubacterial, archaebacterial, eukaryotic split, that
    question may apply, but not for most of what has happened since then.

    [...section removed...]

    Tim: <Genetic variation is the major change agent. What locks a particular
    change into a population or affects its frequency in a population includes:
    natural selection, neutral drift, and other factors. It is actually a hot
    debate about which of the two, selection or drift, are the most influential
    agents of change. Certainly neutral mutations accumulate in a genome faster
    than selective ones.>

    >While I can understand the mechanism of selection, I find it difficult to
    >understand what drives neutral drift. I'd appreciate it if you would explain
    >it. It seems to me to be a radical departure from natural selection. What is
    >the significance of their "faster accumulation in the genome" that you
    >mention?

    Nothing 'drives' neutral drift. It's simply variation that accumulates
    in the absence of selection. For example, point mutations in the third
    position of many codons are effectively neutral because the changes often
    don't alter the amino acid sequence of proteins made. Similarly, there can
    be changes made to proteins which have little or no effect on the immediate
    viability of the organism. These are changes which can occur "under the
    radar" of selection and pools of such variations can be supported in
    a population with no immediate cost. These variations accumulate in the
    population at approximately the rate of mutation (the majority of mutations
    being neutral or negative), and that average rate is far greater than
    rate of accumulation of positive mutations through selection.

    Where does neutral drift fit in? One necessary factor for evolution
    is the existence of variation within a population. Evolution won't happen
    if species can't "move about in genomic space". Selection can "drive"
    systems to particular locations (optima) in these "spaces", or neutral
    drift can allow systems to "drift" across the landscape in "non-directed"
    steps. One of the questions is: How much of the change which accumulates
    during evolution resulted from neutral mutation and how much can be
    attributed to selection?

    [Note: Sometimes, as conditions change, variations which might once
    started out neutral may actually have some affect on survival.]

    [...text removed...]
    Tim: <<Reversibility is irrelevant and in fact, many of the changes are not
    reversible at the genetic level. Remember that there is a gaping chasm
    between genotype and phenotype. The mapping between the two domains is
    anything but linear in all but the rarest situations. Point mutations
    can confer antibiotic resistance. However, given the odds of hitting that
    exact site again to exactly reverse the point mutation, it's more likely
    that a mutation that eliminates resistance will occur in another
    portion of the genome. Thus a phenotypic reversal (short-term or otherwise)
    does not equate to a genomic "reversal". And we have a recently described
    case where a bacterium acquired streptomycin resistance in a "long-term"
    manner such that loss of the resistance, even in the absence of the
    antibiotic, was selected against (A secondary mutation occurred which
    effectively "locked in" the first one). So, we can say that ratchet-like
    evolutionary progression has been observed even over short timescales.>>

    >One case doth not a theory make.

    But one case doth destroy a blanket refutation...
    (Further, the emergence of second-site suppressors is pretty commonly
    observed. Some examples have become common in bacterial genetics
    lab courses).

    > Moreover this is not a ratchet-like
    >evolutionary progression, as you claim. It is step one. Has anything
    >been observed that builds on step one to produce step two? Unless it
    >has you do not have a progression. You have merely a locked-in
    >bacterium.

    The case I've described involved two-steps. First, the bacterium
    acquired resistance to streptomycin. This is wonderful for such strains
    when there is streptomycin around: All the wild-type strains which would
    otherwise compete for food die. But the resistance carries a slight
    penalty when no streptomycin is around. Strains carrying that mutation
    tend to grow slightly slower and are thus handicapped against their
    wild-type counterpart in an antibiotic-free environment. As a result,
    these streptomycin resistant strains were not expected to persist in
    the "outside" environment, where there is little of the antibiotic
    around.

    However, there is a secondary mutation which can occur that eliminates
    the growth handicaps of the resistant strains. This "suppressor" mutation
    allows the bearers to not only grown when streptomycin is around but
    also to grow as fast as the wild-type strains when the antibiotic is
    absent.

    Interestingly, this second mutation, by itself, also inhibits growth
    rates. Only when teamed with the streptomycin resistance mutation
    do the two mutations persist in the population. Strains missing either
    one of the two mutations tend to be eliminated. This is an example
    of lock-in (or ratcheting).

    Tim: <<I suspect that true reversibility is a relatively uncommon
    phenomenon. Should we be surprised? I think not. In the mind-bogglingly
    huge morphology- or genetic-space available to organisms, it's not
    likely that one could take more than a couple steps in any direction
    and then return to exactly the same starting place.>>

    >I suspect you are overstating your case. Does your "bacterium [that]
    >acquired streptomycin resistance" that you mentioned earlier have
    >"mind-bogglingly huge morphology- or genetic-space available to it"? I
    >doubt it. If so, tell mme what it is.

    E. coli has a genome of about 4.6 megabases. At four possible nucleotides
    per base, that's a genome-space of about 4^(4.6E6) elements. But let's
    start with one particular genome and calculate some odds of exactly
    reversing a single point mutation. That's one in 4.6 million. What are
    the odds of hitting anything else? Those are = 1 - 1/4.6E6 (or ~0.99999978).
    So, long before you've reversed a _single_ mutation, you've probably hit
    millions of other sites in the genome. That is the nature of genetic
    irreversibility.

    Because most phenotypic traits (such a beak lengths) can be modified by
    more than one gene (comprising thousands of bases/gene), odds are that
    any phenotypic "reversals" aren't going to be genetic reversals.

    [...text removed...]
    Tim; <<Nobody is failing to acknowledge the hierarchical pattern of life and
    discontinuities. These are what led to the conclusion of descent with
    modification in the first place.>>

    >Your first sentence in the above paragraph is simply not true. Read the
    >statement that Dick Fischer presented and see if you can find hierarchical
    >organization and discontinuities in it. Moreover, evolution abhors a
    >discontinuity. Many evolutionary biologists are busy trying to iron them out.

    From that statement:
    [...]
    "Nonetheless, no scientific hypothesis other than common descent
    with modification can account for and make predictions about the
    unity, diversity, and properties of living organisms." [...]
    ^^^^^ ^^^^^^^^^ ^^^^^^^^^^

    Unity: hierarchical pattern of life
    Diversity and properties: variations = discontinuities. There are
    bears, dogs and cats. They are distinct entities now disconnected
    from each other by breeding barriers.

    Perhaps we are talking about slightly different things when use the word
    "discontinuity". I think of it as the _appearance_ of gaps between related
    species, rather than the _actual existence_ of gaps. True, evolution would
    have problems with actual gaps. But the appearance of gaps (where there
    really are none), is not unexpected, as Keith Miller explains elsewhere.

    Tim: <<Discontinuity is a product of speciation (a mechanism of evolution)
    and extinction.>>

    >Show me.

    Keith Miller described why (partially) in a recent post and many times in
    the past. See: http://www.calvin.edu/archive/asa/200112/0080.html

    Reiterated: Speciation reduces genetic exchange between populations
    of organisms. After speciation, the separate populations may travel
    on separate trajectories (i.e. diverge) and the amount of visible
    divergence tends to increase over time. Also "intermediate" species
    become extinct along the way. So while bears and dogs may appear very
    different today, that was not the case for their progenitors. Similarly,
    while extant mammals are clearly distinguishable from reptiles today,
    the earliest mammals where not easy to differentiate from related
    reptilian groups.

    Tim: <<Such discontinuities tend to manifest more in the
    morphological arena than the biochemical one. Also, hierarchical
    organization is a manifestation of the rates of change and the nature
    of speciation and organismal genetics. Understanding the timing and details
    of specific steps behind evolution is real challenge, IMHO.>>

    >Although these words may make sense to you, they don't to me.

    Sorry, I wrote that too fast...

    1) Common descent with modification is a process that generates
       nested hierarchies.
    2) Organisms often (but don't always) differ more on the surface
       (morphology) than they differ from a biochemical viewpoint. E.g.
       Mammals may look different and live in different environments but
       the underlying "hardware" is pretty similar.
    3) The apparent distances between branches of the phylogenetic
       tree of life reflect variations in the rates of change over
       time. As long as the rates of morphological and genetic changes
       are not too great, patterns deduced from morphological comparisons
       can be expected to be consistent with the patterns created on the
       basis of genetic comparisons.

    And finally: Understanding the timing and details of specific steps
    behind evolution is real challenge in the study of evolution.

    >I think our brief discussion illustrates my point that the statement
    >presented by Dick is incomplete, and I add, even misleading. It suggests
    >that evolutionary theory is a done deal. I continue to hold that descent
    >with modification needs a robustly supported mechanism (which in my view it
    >doesn't have) and in addition, an unambiguous refutation of intelligent
    >design, to substantiate its claim to be the all encompassing theory it wants
    >to be.

    Descent with modification has an extremely robust mechanism and can be
    paraphrased as follows: "If your parents didn't have children, neither
    will you."

    How the variations accumulated and what mechanisms fixed a particular
    variation in a population are definitely open questions.

    Regarding the unambiguous refutation of intelligent design: That is
    simply impossible. One may as well ask: "What could an intelligent
    designer not do?"

    Regards,
    Tim Ikeda (tikeda@sprintmail.com)

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