Re: Orr on No Free Lunch

From: bivalve (
Date: Mon Aug 19 2002 - 16:15:05 EDT

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    >There is a key simple flaw with Orr's analysis. His simple idea
    >that my sequence has more kids than yours is filled with hidden
    >goals or targets.<
    >To have any sequence generate "more" kids you must have met the
    >following requirements<
    >1. Stable, Biologically active sequence.
    >2. Sequence able to replicate.
    >3. Sequence capable of being improved.

    However, these targets are enormous. Dembski's error is to specify
    the goal much more than nature does. Only pre-specified complexity
    is improbable. Post-hoc, you can get as specific as you like for any
    random sequence. To assert that particular complexity is
    sufficiently specified to be improbable requires proving that the
    number of possible ways to achieve a similar goal is small. However,
    we have no idea how many different ways hypothetical living organisms
    might be able to do things.

    Furthermore, 1 and 3 are not required. A sequence needs to be
    moderately stable, but it does not have to be biologically active to
    increase in frequency in a population, nor must it be biologically
    active to be mutated into something useful. 3 is not a requirement in
    two ways. First, neutral or even detrimental variants may end up
    generating more kids than a better variant, either through genetic
    drift or through association with other, beneficial sequences.
    Secondly, all sequences are capable of being improved upon, depending
    upon the function that you chose to look at. Histone 3 is a terrible
    digestive enzyme, for example. Even for the current function of a
    gene, usually slight improvements are possible.

    >In Dawkins book he mentions histone 3, a protein of about 100
    >residues which change in only two or three positions throughout all
    >the diversity of life and throughout "evolution." This sequence
    >meets the first two requirements but has never been improved since
    >it was first happened upon. This data tells us that precursors to
    >this sequence must not have been active because the sequence is NOT
    >malleable- all residues must be fixed for the protein to perform the
    >job it currently holds. <

    No; these data suggest that a precursor would have had a different
    function, at least in detail, if it were a functional sequence. I
    would guess that histone 3 may have common ancestry with other
    histones and thus presumably descend from a more generic DNA-binding
    protein. However, Dawkinís data are outdated or incorrect, as a
    search on GenBank for histone 3 yields not only several ěhistone
    3-like genesî but also several genes identified as histone 3. I
    looked at ten sequences (see below), trying for a wide taxonomic
    spread, and found variation in about 42 or so positions (depending on
    how you count indels). One reference in particular seems noteworthy:
    Bernhard,D. 1999. Several highly divergent histone H3 genes are
    present in the hypotrichous ciliate Stylonychia lemnae. FEMS
    Microbiol. Lett. 175 (1), 45-50. Apart from a sequence titled
    ěpossible H3 geneî from an archaeobacterium, I did not spot
    prokaryote genes, so the claim that it occurs throughout all life may
    be in!

    >Assuming that an inactive sequence can generate any kids at all as
    >an answer to the derivation of novel functional genetic sequence
    >completely misses the question.<

    Not necessarily inactive. Also, there is a problem here in the
    definition of novel. Is histone 3 versus histone 2 novel? How
    different do sequences have to be to count as novel? Important
    structural proteins in advanced eyes (vertebrate and cephalopod) show
    minimal or no sequence divergence from certain enzymes-the exact same
    sequences was capable of a novel function (albeit one probably not
    too closely constrained by protein structure). However, inactive and
    active sequences alike are inherited, and, in a finite population,
    will change in frequency in the population.

    Histone 3 sequences (note that not all are complete):

         Dr. David Campbell
         Old Seashells
         University of Alabama
         Biodiversity & Systematics
         Dept. Biological Sciences
         Box 870345
         Tuscaloosa, AL 35487 USA

    That is Uncle Joe, taken in the masonic regalia of a Grand Exalted
    Periwinkle of the Mystic Order of Whelks-P.G. Wodehouse, Romance at
    Droitgate Spa

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