Re: Replicating What?

From: Guy Hoelzer (hoelzer_at_unr.edu)
Date: 09/17/04

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    Date: Fri, 17 Sep 2004 17:47:23 +0000 (UTC)

    in article cidugl$tul$1@darwin.ediacara.org, Anthony Cerrato at
    tcerrato@optonline.net wrote on 9/16/04 10:59 PM:

    > "Guy Hoelzer" <hoelzer@unr.edu> wrote in message
    > news:ciaksj$311n$1@darwin.ediacara.org...
    >> in article ci9ngq$2o58$1@darwin.ediacara.org, Anthony
    >> Cerrato at tcerrato@optonline.net wrote on 9/15/04 8:35 AM:
    >>
    >>> Yes, to both you and Tom. Another way of talking 'bout it though, other than
    >>> in terms of raw materials, is what's replicated is the blueprint for the
    >>> structure which will be the organism (house), including (stapled to) the
    >>> work flow-sheets (work-plans) for building it. Note, this automatically
    >>> includes any accidents (mutations, external physical damage etc.) which
    >>> occur to the blueprint, or the work-staff, prior to, and during, the
    >>> building process. Thus, workmen spilling their morning coffee on the plans
    >>> is already pre-accounted for (and even expected at times.)
    >>
    >> This is a useful metaphor in many contexts, but the genome is clearly not a
    >> blueprint because it does not contain structural plans or any where near the
    >> information needed to build an organism. You might say that the combination
    >> of the genome with existing cellular machinery encodes specific RNA molecules
    >> and regulatory mechanisms of gene expression, but we will never be able to
    >> read an unknown genome in isolation (i.e., without using comparative genomics
    >> from organisms with known phenotypes) and predict what the adult organism
    >> will look like because too much of the information contained in the
    >> organismal structure is not there in the genome.
    >
    > OK, you're saying you can't use the blueprint to build a new
    > house without using an old house as the office. :)

    No. IMHO the vast majority of the information (structure) in the adult
    phenotype is generated through the process of self-organization during
    development. It is not strictly in the genome or any other sort of
    pre-existing template.

    > Hmm...the infinite recursion here bothers me a little though...chicken and the
    > egg? It begs for an answer to the question, how was the first animal in the
    > genetic line built...? Perhaps using the blueprint for a smaller "starter
    > house" or flimsy summer bungalow or hut? But, still ad infinitum... :)

    In my opinion there is nothing like a "blueprint" used at all in organismal
    development, so the question of where the first blueprint came from is a bad
    question. There is a nice, simple argument for this view in the book by
    Camazine et al. (2001) called "Self-Organization in Biological Systems."
    Consider, for example, that your body generates over 100 million different
    antibodies at any one moment, given a genome with about 30,000 genes. Of
    course the genome would have to encode everything else about the organism,
    too, if it were really a blueprint. My gut feeling is that your genome
    doesn't contain enough information to encode your eyes, let alone the rest
    of you. It merely puts into place lots of different kinds of components
    that participate in the dynamics of a growing complex system, and the
    information is generated through the interactions of those components. I
    also expect that a substantial fraction of the necessary components (perhaps
    the vast majority?) come from sources other than the genome. As I wrote
    before, the "blueprint" metaphor has been useful, but I think we know way
    more than enough to leave it behind us at this point.

    If you find my view to be implausible, then I would ask you why natural
    selection would result in the unnecessary encoding of information in the
    genome, which would be relatively inflexible in the face of unpredictable
    environmental variation, when it would be far more efficient to take
    advantage of the opportunities for automatic information generation through
    physical tendencies for self-organization? I expect that fighting those
    tendencies through rigid and expansive genomic encoding would be highly
    maladaptive.
     
    > I might modify the original analogy to add that this is
    > further analogous to the need, with blueprints, for the
    > workers to have the reading and measurement skills, and
    > proper raw materials, prior to executing the building
    > process. In any event, you must admit, no analogy whatsoever
    > is perfect--of necessity. Must go--sudden desire for fried
    > eggs and chicken! to heck with the specific order!

    I hope your meal was tasty!

    I agree that metaphors of the "blueprint" variety always fall apart as we
    learn more. The hope is that we move on to metaphors that are closer to
    Truth, even though we can't know exactly where Truth lies. I hope the view
    I articulated above seems less metaphorical and more mechanistic, although
    you (and many others, I'm sure) might remain skeptical of the idea of a
    "self-organizing system," which represents a mechanistic approach to
    understanding the balance between bottom-up and top-down (e.g., entrainment)
    forces in determining structural dynamics.

    Regards,

    Guy

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