Re: Gene duplication and design

From: MikeBGene@aol.com
Date: Mon Apr 17 2000 - 18:45:50 EDT

  • Next message: Terry M. Gray: "Re: randomness"

    Part II:

    Me:

    > But if biology is supposed to reduce to nothing more than
    > chemistry and physics, why do we need to appeal to engineering
    > concepts to make sense of biology? Where in geology, astronomy,
    > physics, and chemistry do we find the concepts of proofreading
    > and quality control?
    >
    > It is often said that ID is not science and has contributed
    > nothing to science. But how can this be when biology is
    > built around ID concepts and language? How is it that
    > advances in our own understanding of our own designs
    > help to illuminate biology in a very fundamental way?
    > For example, in trying to explain feedback and homeostasis
    > to new biology students, biologists do not draw from basic
    > chemistry or physics. They draw from the manner in which
    > furnaces and thermostats are designed to work."

    Tedd:

    >Is the assumption valid that engineering concepts must
    >be linked to intelligence?

    No one is assuming such concepts *must* be linked. It's
    just that I find it quite rational to link them unless there
    is good reason to think the link is invalid. That is, intelligent
    design often does indeed involve engineering concepts,
    when geology, meteorology, etc. do not. It's more than
    enough basis for a suspicion in my mind.

    >That remains to be seen.
    >In fact, "purpose" seems to be the main impetus for
    >assigning intelligence to anything, but I suspect we
    >wrongly assign purpose to things as often as we
    >anthropomorphize. The two traits are really the same.

    I am quite aware that I may be mistakenly using anthropomorphism.
    But even the boy who cried wolf eventually saw a wolf.
    Remember that I am only at the level of a suspicion, so the
    fact that I might be mistaken is something I openly grant.

    Me:
     
    > "1. You are missing a subtle, but important point. It's
    > not simply the use of design concepts, it's the fact that
    > an *understanding* of our own designed artifacts actually
    > sheds *real* light on biology (but not geology, astronomy,
    > physics, or chemistry). The more we understand about
    > design, the more we understand about life. It's more than
    > handy metaphors. It's the *applicability* of real concepts.
    > Understanding how computers work really does help
    > us understand cells. And if there is truth to the design
    > inference behind life, I will predict that as our own designs
    > improve by becoming smaller, more complex, and more
    > sophisticated, our understanding of cellular/molecular
    > processes will likewise improve.

    Tedd:

    >I don't quite follow this reasoning. For example, I don't see
    >how understanding artifacts has helped biology.

    The examples are too numerous to go through. I have
    already mentioned how the thermostat and furnace help
    to illuminate homeostasis (in fact, biologists got the concept
    of negative feedback from the engineers). An understanding
    of computer technology has been VERY helpful for thinking
    about the cell. Protein assemblies are insightfully thought of
    as machines. Life is built upon a CODE. And I have plenty
    of texts that use human artifacts to help explain biological
    systems. One uses a tape player to explain how ribosomes
    work. Another used a washing machine to explain how the
    cell cycle works. Another uses a word processor to explain
    the proof-reading functions of DNA polymerase. Understanding
    our own technology does indeed help us understand life. You
    do realize, don't you, that the president of the National Academy
    of Sciences recently wrote that biologists should look to the
    engineers to advance our understanding of life?

    >I have seen
    >the opposite, though. You know how people keep looking for
    >single genes that control single attributes -- race, sexuality,
    >heart, lung, etc. ? They do that because that's the way an
    >intelligent designer would be expected to do it. The problem
    >is, as I'm sure you're aware, that life just doesn't seem to be
    >organized that way. Genes, far more often than not, resist such
    >simple, logical classification (and rightly so, if RM & NS were the
    >mechanisms).

    The people looking for single genes that control single attributes
    were not ID proponents, but darwinists. This was the meat and
    potatoes of the eugenics movement (heavily indebted to darwinian
    thinking). I see no evidence that anyone ever thought this
    simplistically because that was how an intelligent designer would be
    expected to do it. I think they thought that way simply because
    humans approach unknowns in simple ways because more
    complicated analyses are beyond reach. Simple explanations then
    tend to fall to the side as the brute reality of life's complexity forces
    us to then abandon them.

    I don't understand why you think an intelligent designer
    would use such a simplistic approach. How is one to build a heart
    with one gene product? And even among the things we build, they
    don't break down this simply. Does it take only one part to convert
    potential energy into kinetic energy in a car? Is the car's speed a
    function of one single part?

    >Nothing in biology is as tidy, neat or modular as it would be if
    >humans had designed life. That's my impression.

    There are two things worth mentioning. First, ID does not entail
    that everything be tidy and neat. If, for example, life was designed
    to then be followed by a few billion years of evolution, we might expect
    a good degree of untidiness to creep in. You need to distinguish
    between a view that employs ID and one that employs it for
    everything. Secondly, the recent advances over the last few decades
    show that life is more neat than anyone supposed (for example, see
    my posting on muscle machines a month or so back). And that
    lateral transport seems to be not uncommon among bacteria
    suggests a level of modularity not appreciated (and at
    tension with darwinian views of co-evolution).

    Me:

    > 2. Yes, humans attach human characteristics to pets.
    > They also attach them to molecules. For example, chemists
    > sometimes speak of a hydrophobic molecule as those
    > which don't "like" water. This is all anthropomorphism.
    > But the design terminology in biology is NOT attaching
    > human characteristics to things. For example, when molecular
    > biologists interpret a protein as a "sensor", no one envisions
    > the protein as a conscious entity that is perceiving things
    > and responding to what he sees or hears. Instead, when molecular
    > biologists speak of protein sensors, they use this term in the
    > exactly the same way an engineer uses it when she builds or
    > describes a mechanical device.
    >
    > And that is all that is relevant.
    > It doesn't matter if biological molecules are not conscious. It
    > matters only if the biological molecules can be put in the same
    > class as mechanical components designed by humans. In other
    > words, the language of molecular biological is not in the same
    > class as anthropomorphic metaphors. It is in the same class
    > as the design terminology employed by engineers."

    Tedd:

    >But how strong is the link between design terminology and and
    >an inference of design?

    It doesn't need to be very strong to generate a suspicion. Yet
    in this case, given that design terminology is employed mainly
    in engineering and biology, and is mostly missing from physics,
    chemistry, geology, etc., I'd say that link is pretty strong. You'd
    have a much stronger case (IMO) if geologists, for example,
    commonly relied on concepts such as proofreading, quality control,
    codes, and checkpoints, to explain volcanic eruptions or fossil formation.

    >I see it as potentially as weak as the
    >link between human characteristics and the objects being
    >anthropomorphized.

    Again,

    " In other words, the language of molecular biological is not in the same
    class as anthropomorphic metaphors. It is in the same class
    as the design terminology employed by engineers."

    >How do we define "sensor"?

    The same way an engineer does.

    >A sensor generates some kind of impulse in response to a particular
    >stimulis and anther process reacts to that impulse. Generating impulses
    >isn't a design quality and reacting to input is not a design
    >quality, so design must be entirely inferred from the result of
    >the overall process: does it have a purpose? If it has a purpose,
    >we suspect design. But there's that word "purpose" again, what
    >does it really mean?

    In biology, the term used is 'function.' It takes only the slightest
    nudge to give that term a literal teleologic interpretation that
    doesn't lose any of its scientific utility.

    >If life's purpose is to survive or reproduce,
    >then can't we say that a volcano's purpose is to spew lava, or
    >a river's purpose is to reach the ocean?

    From an ID perspective, I would not think life's purpose was
    simply to survive or reproduce. Instead, one would have to
    use data to speculate about that purpose.

    >Once we see purpose
    >there, we can detect sensor-like arrangements everywhere we
    >look-- the opening of the volcano relays the amount of pressure
    >difference between the air and the liquid pressure below. The
    >greater the pressure difference, the greater the lava flow.
    >For rivers, gravity is sensed and determines the direction of
    >flow. Of course, this sounds strange because we don't think of
    >volcanos and rivers as having "purpose", but the problem is that
    >we don't have a good definition of purpose. We embed intelligence
    >into the very idea of purpose and there's no easy way to extract
    >it.

    Yes, and in such physical sciences, we don't use such concepts because
    they don't add anything and only create confusion. But why then can't
    biology follow suit?

    But notice that in your examples, there is no need for a sensor (as an
    engineer would understand it) as these events simply follow directly
    from rather unspecified changes. In cells, a membrane sensor acts
    as it would in engineering, where it *relays* information in such a
    way that the output is quite distinct from the input (yet it is related in
    a logical manner more so than a physical manner). For example,
    a ligand binding to a specific sensor on a bacterial membrane could result
    in any type of physical change (unlike the "sensing" you describe
    above). But depending on the manner in which the circuitry is
    hooked up to the censor, specific ligand-sensor relationships
    can result in anything from the opening of channels to swimming
    in a forward direction.

    Me:

      
    > " You miss the point. Intelligent design terminology is
    > not very useful in these sciences. The non-biotic world
    > knows nothing of proofreading and quality control. These
    > concepts come into play only in engineering (things
    > known to be designed) and biology (the very things in
    > question). Proofreading and quality control are at the
    > very core of life, yet are completely absent from every
    > area of science except those known to involve intelligent
    > design. I suppose it's all a strange coincidence, but
    > I have yet to hear a good argument as to why a mere
    > suspicion of design is not justified by these observations."

    Tedd:

    >The "coincidence" stills seems to me to be terminology that begs
    >the question. The only category that I believe can ever hint
    >at design is a high degree of similarity to human design and
    >direct evidence of designer who might be able to do the job.
    >This is the way we detect human design in nature, why change
    >the rules now?

    I see the high degree of similarity between human design and
    life (and where they differ, I think the case can be made that
    life represents a level of design far beyond our current reach).
    As for direct evidence of the designer, as I have explained, there is
    no reason to expect this evidence to exist if indeed life was
    designed. So I don't change your first rule. But I do drop the
    second.

    Tedd:
     
    >>What is the threshold for CSI and how is it chosen?
     
    Me:

    > A great question. This is the very type of thing that I
    > think ID will address in more detail over the coming years.
    > One way of thinking about this threshold is to work with
    > the notion of the minimal amount of complexity and
    > specificity required to sustain life. This simple question
    > has the ability to spawn hundreds of research projects,
    > showing yet again just how fruitful ID can be.

    Tedd:

    >Umm, it won't spawn any unless a definition of "life" is settled
    >on. Seems to me, the definition of life is hopeless entangled
    >with complexity and specificity so the question is a bit
    >circular.

    Why not use the definition biology has been using for such
    a long time? As such, I can think of all kinds of experiments
    to address these issues.

    Me:

    > In fact,
    > there already exists much data that can be interpreted in
    > light of this question. As of now, I suspect this threshold
    > has been crossed because so much of the features that
    > appear to be required for life are more similar to non-living
    > things designed by human (the only known intelligence)
    > than non-living things generated without intelligent intervention.

    Tedd:

    >But drawing a distinction on a term that is not well-defined
    >(living) is asking for problems. Living means complicated,
    >but how complicated? What you're saying reduces to this:

    >"The features that are required for complexity are more
    >similar to complex things designed by humans than non-complex
    >things"

    >But sure, complex things will look alike regardless of whether
    >they came from humans or natural processes.

    I am not defining life to mean "complicated." A factory before
    and after a tornado hits is complex. Yet the type of complexity
    before and after is different. The tornado generated the latter type
    and intelligent beings generated the former type (specified). And
    life looks more like that which is generated by the intelligent beings
    than the tornado.

    Tedd:

    > >What is the nature of non-intelligent processes that they can not produce
    > >CSI?
     
    Me:

    > I never said they can't. I simply see no evidence that geochemistry
    > generates enough CSI sufficient to spawn and sustain life.
     
    Tedd:

    > >If an intelligent agent designed the laws of physics, why
    > >couldn't CSI be the result?
     
    Me:

    > I never said the laws of physics couldn't generate CSI. Again,
    > it's not an issue of what could be, but an issue of the evidence
    > behind claims of what did happen. And I don't what law is
    > responsible for so many of life's seemingly contingent features.
    > Why the 20 biological amino acids when so many more non-
    > biological amino acids are more commonly generated by
    > abiogenic simulations? Why the five nitrogenous bases and
    > not others? Why the genetic code as it is instead of millions of
    > other possible codes?

    Tedd:

    >But these questions can be asked about physical constants as
    >well (and are contingent in the same way). Therefore a better
    >conclusion is that the laws of physics are designed and that
    >life's features are a direct result of carefully tuned physical
    >laws. (Thus the views held by Terry Gray, Howard Van Till and
    >others on this group strike me as more obvious and reasonable).

    Three things.

    1. If the physical constants lead to such a design reference, yet
    we can make the same points about various features of life, why
    not think life was designed in a fashion similar to the universe?

    2. If Terry or Howard would like to explain how the physical
    laws dictated that life would use valine instead of norvaline, I'm
    all ears. Or perhaps they can explain the physical laws that
    ensured that UUU would code for phenylalanine. As I see it,
    there are too many aspects of life that are not determined by
    the physical laws. For example, if we found life on another
    planet, would you really expect it to be built with the same
    set of amino acids, the same nucleic acids, the same genetic
    code, the same metabolic pathways, etc.?

    3. Like I have said before, I have no theological or
    philosophical problems with the views of Howard or Terry.
    I'll be the first to admit I could be wrong and they could
    be right. But I am curious about something. What happened
    to the cruel and cold history of life? Why does this argument
    not also apply to the views of Terry and Howard? Let me
    simply reword your argument in the slightest:

    "Frankly, I can't conceive of an intelligence so great that it could
    manipulate the physical constants to create the universe but be so
    morally-flawed that it would permit the unimaginable
    scale of pain and suffering in life's history. We must suppose
    an intelligence that is far more frightening then no intelligence
    at all; an intelligence that would permit any intelligent race
    to be wiped out to see what organism might next fill its niche.
    Perhaps it is far more comforting to imagine that nature alone
    gave rise to life than to imagine an advanced intelligence
    without a trace of human decency!"

    With Howard's views, the universe is so fully gifted that it
    does not require the designers intervention after it is set up.
    But wouldn't a truly fully gifted universe be one that did
    not include this unimaginable scale of pain and suffering?

    Mike



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