Re: Gene duplication and design

From: Tedd Hadley (hadley@reliant.yxi.com)
Date: Fri Apr 14 2000 - 18:11:15 EDT

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    MikeBGene@aol.com writes [From April 6th]
      in message <e0.2d3474b.261d80ce@aol.com>:
    > Hi Tedd,
    >
    > You write:
    >
    > >I should add that your criticism of of the "metaphysics and game
    > >rules" of some scientists is probably without merit because I
    > >suspect those people just don't see the evidence for design that
    > >you do. For example, I've never ruled out teological explanations,
    > >I just don't see the evidence for any such hypotheses. But
    > >that may mean I'm just ignorant.
    >
    > I am well aware that this may be the case. But let me tell you
    > why I don't think so. Two questions, when coupled, strongly
    > support my contention (IMO). First, when you ask a scientist
    > what type of data would cause him/her to suspect ID behind the
    > origin of some biological feature, you usually get no answer.
    > But in all fairness, this is because most scientists don't even
    > think much about origins and the issue of origins is largely
    > irrelevant to their science. However, if pressed, those who do
    > have an interest in origins will answer this question by citing
    > things that really are far closer to some needed proof for design
    > than something that merely raises a suspicion.

       1. independent evidence of ID capable of genetic engineering
       2. anything that casts doubt on RM & NS capability of doing the
          job
       
       These are things that would cause me to suspect design. Now
       you might characterize these things as far closer to proof
       than suspicion but I wouldn't; RM & NS is such a powerful and
       persuasive explanation to begin with, it requires powerful and
       persuasive explanations to overturn it.
     
    > Okay, so maybe these people are just hard-core skeptics. But
    > then comes the second question. Most of these same "skeptics"
    > also believe that RM&NS were indeed the main mechanisms behind
    > the origin of every biological feature. Yet when I ask for the
    > evidence behind this belief, I get none.
       
       But what evidence would you accept? For example, if I demanded
       evidence that Pluto orbited the sun, how would you supply it?
       Or evidence that the Grand Canyon was caused by natural
       forces? What is the best way to provide evidence for any process
       that is incapable of being observed in its entirety?

       The best evidence for RM & NS is probably not much better than
       what we have today --assuming we can't travel back in time.
       That's the nature of processes working slowly over eons of time.

       The best evidence for ID, however, is vastly better than what
       we have today.
     
    > What happened to that hard-core skepticism? So on one hand, we
    > have a community that doesn't seem to know how to process a
    > question about data that would raise a suspicion of design, yet
    > on the other hand, the same community widely accepts and promotes
    > a belief for which there seems to be very little evidence. This
    > apparent double standard is best explained, in my opinion, by
    > realizing just how much the "metaphysics and game rules" drive
    > this question for many. After all, many leading scientists have
    > written that they *begin* their analysis by excluding teleological
    > explanations; this act has been defined as being an essential
    > ingredient of science.
       
       This can't be true. How would scientists detect human artifacts
       then? You sure they aren't simply excluding a god with
       omni-characteristics?

    > When this happens, why bother training your mind so that it can
    > detect traces of ID (since it's a taboo explanation)? And of
    > course trivial observed examples of RM&NS become inflated to
    > explain everything, as there is no solid alternative. From this
    > perspective, one doesn't need evidence that RM&NS evolved some
    > feature because the mere existence of RM&NS is sufficient.

       Sufficient, at least, without an alternate explanation. It's
       just like suggesting that erosion can explain the Grand Canyon.
       We know that erosion works on our small observable scale so we
       assume in can also do a much larger job over a much larger
       interval of time. However, that explanation would quickly fall
       out of favor if good evidence for a different mechanism were
       found, or if evidence for aliens who had good reason to do such
       things was discovered.

    > Tedd :

    > >"Biology needs teological language and concepts" Do you mean
    > >biology *needs* teological concepts or that humans *tend* to
    > >engage in anthropomophizing behavior about things, be they
    > >cars, weather, or molecular machinery?

    > I meant the former. If it were the latter, then other branches
    > of science (physics, chemistry, astronomy, geology, etc.) would
    > be as dependent on teleological language and concepts as is
    > biology. But they are not. Since I addressed this issue on
    > this list a few months back, I'll simply re-post some excerpts:
       
       Before we get started, I'd like to observe that much of this
       argument below assumes that we understand exactly what it means
       to be intelligent, what it means to show purpose, what "life"
       means, what order and disorder mean and other things that, to
       my mind, are not really precisely defined or understood. If ID
       is to depend on these concepts, it will suffer from the same
       problems and never hope to make progress. One big head-start
       evolution has on ID is that it doesn't have to depend on vague terms.

    > " But I think it most telling that, while it officially excludes
    > intelligent design, biology works because it extensively employs
    > intelligent design language and concepts. As a physical scientist,
    > Paul Davies, wisely observed in his latest book:

    > " Concepts like information and software do not come from the
    > natural sciences at all, but from communication theory, and
    > involve qualifiers like context and mode of description - notions
    > that are quite alien to the physicist's description of the world.
    > Yet most scientists accept that information concepts do legitimately
    > apply to biological systems, and they cheerfully treat semantic
    > information as if it were a natural quantity like energy.
    > Unfortunately, "meaning" sounds perilously close to purpose, an
    > utterly taboo subject in biology. So we are left with the
    > contradiction that we need to apply concepts derived from
    > purposeful human activities (communication, meaning, context,
    > semantics) to biological processes that certainly appear
    > purposeful, but are in fact not (or are not supposed to be)."

       This sounds a bit confused to me. What is "purpose" really? If
       you define it in terms of intelligence, then of course you're
       begging the question by applying it to biology, but if not, how
       do you define it? Purpose seems to me to mean "directed towards
       some goal" and that is quite consistent with anything that
       follows the laws of physics; rivers strive towards the
       goal of finding the most direct path to the lowest ground;
       molecules of water seek precise relative positions when
       the temperature drops below its freezing point; mountains
       erode; planets travel in unerring arcs; life seeks to
       live; etc.

    > [Davies commitment to methodological naturalism prevents
    > him from following through on this "contradiction."]
       
       Actually, my impression of his work is that this contradiction
       is one reason why he prefers "holism" over reductionism.
       His overall conclusion is that the whole is greater than
       the parts.

    > The fact that biology invokes intelligent design concepts like
    > proofreading and quality control in order to make sense of life
    > is, to me, very suggestive.

       But how can you say that proofreading and quality control are
       solely features of intelligent design without begging the
       question?

       There is something about proofreading and quality control that
       implies intelligence but it seems to be similarity and complexity,
       both fraught with problems for inferring good conclusions about
       nature. Similarity, on the one hand, leads us correctly to
       human artifacts, but also misleads us. At many times (in the
       past, anyway) humans positted a malicious or benevolent
       weather/earthquake/disease/goodfortune-controller -- a god
       behind nature driven by the human emotions malice and benevolence,
       directing the fate of every individual through blessings of rain
       and mild winters, or catastrophes of flood, fire or famine.
       The flawed assumption is that if nature displays behavior
       consistent with emotions, then nature (or something behind
       nature) possesses those emotions. With knowledge comes a
       rejection of this anthropomorphic tendency. Likewise, observing
       that nature contains certain things consistent with human
       intelligence may or may not indicate that nature (or something
       behind nature) is intelligent.

       *Degree* of similarity, then, becomes the most important factor
       and not just similarity itself.

       Complexity -- without a careful definition -- can be ruled out
       already as a reliable intelligence indicator, given that there
       are almost arbitrarily complex non-designed systems, from
       weather systems to sub-atomic particles.

       Let's also not forget to look at the other side of the
       coin. If similarity and complexity suggests intelligence,
       then the sheer coldness and lack of any moral decency whatsoever
       in nature suggests the absence of intelligence (if we associate
       higher intelligence with higher morality). Frankly, I can't
       conceive of an intelligence so great that it could manipulate
       genes but 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!

    > Of course, this is not the type of thing that is likely to
    > trigger the suspicions of a naturalist, as his/her trigger is
    > set to detect only things that essentially amount to the designer
    > him/herself paying a visit to that naturalist.

       No, see 1 and 2 above.
     
    > 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."

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

    > and
    >
    > "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.

       I don't quite follow this reasoning. For example, I don't see
       how understanding artifacts has helped biology. 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). Nothing in biology is as tidy, neat or modular as
       it would be if humans had designed life. That's my impression.

    > 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."

       But how strong is the link between design terminology and and
       an inference of design? I see it as potentially as weak as the
       link between human characteristics and the objects being
       anthropomorphized. How do we define "sensor"? 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? 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? 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.

    > and
    >
    > " 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."

       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?

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

    > 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.

       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.

    >
    > >What is the nature of non-intelligent processes that they can not produce
    > >CSI?
    >
    > I never said they can't. I simply see no evidence that geochemistry
    > generates enough CSI sufficient to spawn and sustain life.
    >
    > >If an intelligent agent designed the laws of physics, why
    > >couldn't CSI be the result?
    >
    > 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?
       
       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).

       (However, whether that design is, in turn, actually the
       result of natural selection of multiple universes, remains
       to be seen. Where does it all end?)

    > Tedd:
    >
    > >It's all about evidence, not philosophy.
    >
    > That's similar to what I have been saying in trying to
    > clarify we are talking about history, not philosophy.
    > But I should also mention there is no clear cut distinction
    > between evidence and philosophy. Evidence is not something
    > we objectively perceive. That's data. Sensory data is then
    > interpreted to become something we call evidence. Yet what
    > helps us interpret that data as evidence if not philosophy?
       
       This description is not helpful because it assumes that
       people are incapable of enumerating the "evidential" possibilities
       that any given bit of data gives. If science allowed people
       to eliminate possibilities for no other reason than personal
       philosophy, surely it would have catastrophically failed
       hundreds of years ago. Forget bronze, we'd be to living
       in caves.
    >
    > Consider someone who adopts a non-teleological metaphysical
    > view.
       
       I can't. People don't adopt views, they form conclusions
       from the evidence they perceive.
     
    > This person cannot consider a teleological explanation
    > for the origin of life because of his/her metaphysics. As a consequence,
    > the mere existence of life becomes evidence of abiogenesis.
    > But if one doesn't share the same metaphysical commitment,
    > one is not obligated to interpret the mere existence of life as
    > evidence of abiogenesis.

       I doubt such a person exists. What do you imagine forms the
       basis for "metaphysical commitment"? This sounds to me as like
       the religious idea that people would actually "choose" hell.
       Both descriptions seem to be most consistent with some mysterious
       process going on inside a human being that is influenced neither
       by perception or genetics but just does the wrong thing for no
       darn reason at all. How does that work?

    > >No, if you are looking for a "truly major evolutionary innovation"
    > >to vindicate RM&NS, you probably misunderstand evolutionary
    > >theory. This may provide a hint as to why you prefer an ID
    > >explanation.
    >
    > Perhaps. But I am not looking for a truly major evolutionary
    > innovation in order to vindicate RM&NS. I am just trying
    > to determine why so many believe RM&NS were the
    > mechanisms behind major evolutionary innovations. You
    > would think that people who reject ID because of a lack
    > of evidence would have evidence to support what they
    > accept.

       Again, refer back to my Grand Canyon example. I'm pretty sure
       we ID-rejecters all see it the same way: 1) RM&NS can add a
       little information over a little amount of time, therefore it
       can add a lot of information over a lot of time in the absence
       of any known information "barriers". Life looks like the result
       of molecular tinkering with existing structures over eons with
       no innovation at any given moment. 2) there's no evidence for
       an ID, and no ID we can easily imagine would design life the way
       it looks.

    > Tedd:
    >
    > >It is a fair observation I think that we can gain information about
    > >everything within this universe to an arbitrary degree (how long
    > >that will take is another question). Thus, your designer is
    > >apparently from outside the universe if we can never understand
    > >its origin.
    >
    > I never made the strong claim that "we can never understand"
    > the origin of the intelligent designer(s). I simply note that
    > even if design has occurred, this does not entail that we
    > should be able to understand the origin of the designers.
    > You need some other premises before you can conclude
    > we should be able to acquire such understanding.
    >
    > >Entities acting within this universe necessarily
    > >interact with matter and energy leaving precise and permanent
    > >signatures behind that can be read at some present or future
    > >point by human beings.
    >
    > Indeed. And these signatures are found in the design.
       
       And that's an ambiguous signature at best, a signature of
       complexity that looks nothing like human design.

    > Yet how does one get from this signature to knowledge
    > of the designer's origins? What if the designers were a form
    > of ETI that went extinct about 2 billion years ago many
    > light years from earth? And are you suggesting that if SETI does
    > not detect a message in the next 1000 years, there is no ETI
    > in the universe?

       I'm actually less concerned with the designer's origin as I
       am the designer's existence. I interpret you to be saying
       that there's no reason to expect any evidence for an intelligent
       designer. On the contrary, I would argue, there many reasons
       to expect evidence for an intelligent designer. Humans leave
       evidence, therefore something acting like a human would leave
       evidence as well.

    > >The only entities that leave no trace
    > >in this universe are those that are not part of it, i.e. they're
    > >supernatural, or, simply, they're nonexistant.
    >
    > Be careful. All those imaginary microorganisms concocted
    > in order the bridge bacteria to geochemistry have left no
    > trace. Thus, they are either supernatural or never existed.

       No, the evidence is the existence of life itself. That conclusion
       is preferred over ID because there is no independent evidence
       of an ID, life does not look like the product of an ID like
       human beings, life does look like the product of RM&NS; RM&NS
       can add a little bit of information to a duplicating entity over
       a little bit of time and nothing is known to prevent RM&NS from
       acting in this fashion all the time, therefore RM&NS acting over
       eons can add probably add large amounts of information to
       duplicating entities.

       [Thanks for a thought-provoking article, BTW.]



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