Re: Gene duplication and design [ was Re: Dennett's bad word ...]

From: MikeBGene@aol.com
Date: Wed Apr 05 2000 - 01:43:51 EDT

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    Me:

    > Now, as I see it, evolution and life's history is wide-open and
    > vulnerable before ID. Even beings as modestly intelligent as
    > we can shape and alter evolution through artificial selection (where
    > selection is guided) and genetic engineering (where mutations are
    > planned). Thus, I am trying to determine if there is solid evidence
    > behind attributing major evolutionary innovations to RM&NS
    > rather than planned mutations and guided selection.

    Tedd:

    >It seems to follow from your view that *any* science that
    >concludes that current processes can explain past phenomena is
    >making a mistake by not allowing teological hypotheses to compete.
    >So, for example, one perfectly legitimate explanation for the
    >Grand Canyon should be Intelligent Design despite the existence
    >of natural processes that can probably do the job. Since I
    >don't think you would agree with that, you might be holding
    >evolution to a different standard than other branches of science.

    I don't think ID is a perfectly "legitimate" explanation for the
    Grand Canyon because I see nothing to even trigger the mere
    suspicion of ID. On the other hand, when NASA recently
    photographed the infamous 'Face on Mars,' had those higher
    resolution photos turned out to display something that looked
    even more like Mt. Rushmore than a mountain, my suspicions
    would have been triggered.

    You seem to think that my position boils down to this:

    >"I assume that belief in ID is something more than:

    >"It hasn't been shown to be impossible, therefore it *could*
    >have happened."

    Yet my point above about the fact that evolution is so vulnerable
    to ID should be taken in the context of many other things I have
    posted to this list. I personally see more than sufficient evidence
    to trigger a suspicion that ID is behind the origin of life: the fact
    that biology not only needs teleological language and concepts, but
    that such concepts really do generate an understanding of life;
    I think life expresses enough CSI such that ID is a better explanation
    for its origin than geochemistry. For me, this evidence goes beyond
    mere suspicion and takes me close the realm of the "most likely."
    Thus, since I have (in my mind) good evidence that life was
    probably the product of intelligent design, the fact that evolution
    is so vulnerable to ID means I need a much more rigorous
    set of evidence to think RM&NS were indeed the only mechanisms
    behind the origin of biological innovations post-abiogenesis.

    Whether or not biologists make a mistake in excluding, a priori,
    teleological explanations is something I cannot say. But from
    my vantage, the potential is there that such mistakes are being
    made given that teleological explanations are not dismissed on
    the basis of evidence, but only on the basis of metaphysics
    and game rules. Now, I do not expect biologists to adopt
    a teleological approach. I just rebel against this notion that
    I am supposed to abandon it.

    Tedd:

    >In geology, there is no independent evidence of an ID capable of
    >restructuring rock formations (besides humans), there is
    >evidence for natural erosion processes and therefore the
    >overwhelmingly accepted conclusion is that the Grand Canyon
    >formed from natural processes. But likewise in evolution there
    >is no independent evidence of an ID capable of genetic engineering
    >(besides humans), there is evidence of natural processes that
    >add novel information to genetic code, and so the same conclusion
    >follows it seems to me.

    To me, it is not a question of independent evidence, but a question
    of whether data exist that trigger a suspicion of ID. One then takes
    it from there. Independent evidence would be nice, but science
    shows us that we don't need it. For example, there is no independent
    evidence that the type of life forms posited to exist prior to modern-day
    like bacteria ever existed. Yet this is a working hypothesis that is the
    meat-and-potatoes of work in abiogenesis.

    Me:

    > While I admit it's a nice rule of thumb, I personally
    > am not convinced that the Razor applies when trying to distinguish
    > between the teleological and non-teleological world views. I
    > think the Razor is too blunt to be of much help with such a
    > large-scale ambiguity.

    Tedd:

    >I interpret Occam's Razor has observing that the simplest
    >explanation that explains the most is probably the correct one.
    >This, I believe, is an observation as well as a prediction.
    >Statistically, the simplest explanation is usually the correct
    >one.

    Yeah, it's "probably" the correct one. But does it really apply
    at this level? When it comes to the origin of life, is the thesis
    that excludes ID *really* the simpler one? Is it really simpler
    to imagine all degrees of simpler life forms (including those
    that exist without proteins and DNA) than to propose an
    intelligent agent? One can make arguments about this kind
    of stuff, but in the end, it boils down to individual judgment
    calls (IMO).

    >To say that Occam's Razor is inadequate for a task implies that
    >in this particular case, the simplest explanation that explains
    >the most is probably NOT the correct one. On what basis can
    >one justify that? At first glance, it looks irrational. It
    >violates both experience and intuition.

    It's not clear to me what is really the simplest explanation nor
    is there any reason to think the simplest explanation is the true
    explanation given that history is loaded with complex contingencies.

    You might want to check out "Further Experimental Evidence against
    the Utility of Occam's Razor" at http://www.cs.washington.edu/research/
    jair/volume4/webb96a-html/webb96a.html. Here's the abstract:

    " This paper presents new experimental evidence against the utility of
     Occam's razor. A systematic procedure is presented for post-processing
    decision trees produced by C4.5. This procedure was derived by rejecting
    Occam's razor and instead attending to the assumption that similar objects
    are likely to belong to the same class. It increases a decision tree's
    complexity without altering the performance of that tree on the training
    data from which it is inferred. The resulting more complex decision trees
    are demonstrated to have, on average, for a variety of common learning
    tasks, higher predictive accuracy than the less complex original decision
    trees. This result raises considerable doubt about the utility of Occam's
    razor as it is commonly applied in modern machine learning."

    From the Intro:

    "In the fourteenth century William of Occam stated ``plurality should
    not be assumed without necessity''. This principle has since become
    known as Occam's razor. Occam's razor was originally intended as a
    basis for determining one's ontology. However, in modern times it has
    been widely reinterpreted and adopted as an epistemological principle--
    a means of selecting between alternative theories as well as ontologies.
    Modern reinterpretations of Occam's razor are widely employed in
    classification learning. However, the utility of this principle has been
    subject to widespread theoretical and experimental attack. This paper
    adds to this debate by providing further experimental evidence against
    the utility of the modern interpretation of Occam's razor. This evidence
     takes the form of a systematic procedure for adding non-redundant
    complexity to classifiers in a manner that is demonstrated to frequently
    improve predictive accuracy."

    Finally, from the conclusion:

    " This paper presents a systematic procedure for adding complexity
    to inferred decision trees without altering their performance on the
    training data. This procedure has been demonstrated to lead to increases
    in predictive accuracy for a range of learning tasks when applied to both
    pruned and unpruned trees inferred by C4.5. For only one of the thirteen
    learning tasks examined did the procedure lead to a statistically significant
    loss in accuracy and in this case the magnitude of the difference in mean
    accuracy was extremely small. On the face of it, this provides strong
    experimental evidence against the Occam thesis.

    This post-processing technique was developed by rejecting the Occam thesis
    and instead attending to the similarity assumption--that similar objects
    have high probability of belonging to the same class."

    So it would seem to me that when it comes to AI, the utility of the
    Razor is at least debatable (and what applies to AI may apply
    to human reasoning). What is interesting is that in a very crude way,
    Paley's original argument can be viewed as attending to the similarity
    assumption (rather than an attempt at a deductive proof). That is,
    since more and more of life can be viewed as similar to human
    constructs (machines, programs, circuits, etc.), one proposes a
    high probability that they belong to the same class (things that
    are designed). Yet the bottom line is that speculations along
    ID lines have proved themselves to me to be quite fruitful and
    capable of generating accurate predictions (for example, I used
    this logic to accurately infer the existence of proofreading
    during the biochemical process of transcription). The challenge
    is to get my hands around this thesis in a more rigorous fashion
    such that the sputtering engine begins to hum. And you would have
    me abandon all this for the sake of Occam's chainsaw?
    Sorry, no sale. I chose the red pill to see just how deep the
    rabbit hole goes.

    Me:

    > But there are three points worth making.
    >
    > 1. I am simply arguing that similarities in gene sequences
    > are insufficient to rule out ID. Thus, if there are data that
    > lead me to infer ID, the mere similarity of sequences fails
    > as an argument against that inference.

    Tedd:

    >Similarities alone, yes. However, evolution as a hypothesis
    >has had mechanisms to explain those similarities since
    >Darwin.

    Yet we still lack evidence that such mechanisms were indeed
    the mechanisms behind major evolutionary innovations.

    Me:

    > 2. History is contingent and evolution is natural history.
    > Many people think of evolution as a natural law akin to
    > gravity where the discovery of one set of events here
    > automatically explains all events. Yet evolution is not
    > a law of nature - it is only a series of life events that become
    > history, and unlike gravity, evolution is completely vulnerable
    > to the intervention of modestly intelligent beings. Thus,
    > simply because RM&NS may have been behind the evolution
    > of these two alleles is no reason, in my book, to think all
    > evolutionary innovations were the products of RM&NS.

    Tedd:

    >Using your analogy to gravity: why does the discovery of the
    >law of gravity automatically rule out the possible effects of an
    >Intelligent Object Mover (IOM) operating a long time ago?

    >For example, if any particular asteriod in stable orbit around
    >earth today is picked out, would astronomers be justified in
    >hypothesizing -- in peer-reviewed journals, I might add-- that
    >an IOM put it into that stable orbit even thought it is plausible
    >that natural processes alone did the work?

    Again, it's not a matter of something merely being possible.
    It's the nature of the evidence and whether it serves to trigger
    a suspicion of ID. If someone has reason to suspect ID behind
    the orbit of an asteroid, I would like to hear the basis for this
    suspicion (just as I can provide this for my suspicion that
    life was designed).

    Earlier you said:

    >"I assume that belief in ID is something more than:

    > "It hasn't been shown to be impossible, therefore it *could*
    >have happened."

    Of course, as my views do not amount to this. That
    design is not impossible and that it could have happened
    has *always* been acknowledged. I'm interested in what
    happened and whether certain scenarios best make sense
    of all the data we have (and don't have). I think you have
    it backwards as almost every case for a non-teleological
    explanation does indeed boil down to "it's not impossible,
    therefore it could have happened." Every argument against
    a non-teleological cause is met, sooner or later, with this
    position which is usually propped up with the "we have no
    independent evidence of a designer" claim. Thus, since we
    lack this independent evidence and non-teleological means
    could have done the job, we are ALL supposed to adopt
    this approach in lock-step (otherwise, there is something
    morally, intellectually, or psychologically wrong with you).
    Ever since Darwin, the argument for the non-teleological perspective
    has been "it's possible." But I am the one saying that what is
    possible is not relevant in history.

    Me:

    > 3. It doesn't seem to me that this type of change qualifies as
    > a truly major evolution innovation (such as the origin of
    > sex, endothermy, etc.). This is simply one of many examples
    > of tweaking that doesn't appear to entail a significant functional
    > acquisition.

    Tedd:

    >But these changes are innovating only in the sense of what
    >they'll become a billion years later. The first sex could
    >be as simple as, what ... a hungry cell slurping up bits of
    >DNA floating in its environment. Nothing innovative
    >about that.

    See? It's "could be as simple." One can always IMAGINE
    such simple, non-innovative beginnings. But do you have any
    evidence that this is indeed how sex began? Your argument seems to
    be this: we have evidence that alleles can vary and increase in
    copy number; major evolutionary innovations could have
    occurred by such hum-drum means; thus we have evidence that
    all the major evolutionary innovations were the result of
    RM&NS.

    Me:

    > 3. Where did [hypothetical IDs] come from? This is a simply an
    > emotive expression that reflects the way we humans desire to
    > control our surroundings. We feel that if we can understand
    > everything, we acquire control in this often chaotic world. If
    > they designed us, we may never be able to know where they came
    > from.

    Tedd:

    >The designed is not capable of understanding the designer?
    >That sounds very ... mystical... but not very logical.

    It seems quite logical to me to acknowledge that being
    designed does not entail the designed beings would
    be able to know where their designers came from.
    Perhaps you can explain how being designed *entails*
    such an ability.

    Me:

    > But it doesn't matter to the investigator, as the
    > investigator is simply trying to explain our proximal reality
    > and ID agents of unknown origin satisfy this objective fully.
    > In fact, I think it would be unproductive to focus all (most)
    > energy on speculations of where they came from (especially not
    > knowing who they are) simply because this increases the likelihood
    > that we will force data into a belief due to the emotive nature
    > of this inquiry. In other words, if our objective is to come
    > up with an explanation that explains Everything, we are likely
    > to be mistaken when explaining something.

    Tedd:

    >However, if the question of the origin of the ID'er can not be
    >answered, it is also one more piece of evidence that has failed
    >to turn up to support ID.

    Let's pretend ID truly explains the origin of life. From that truth,
    explain why we SHOULD be able to determine where the
    designers came from. How does the ability to acquire this
    knowledge necessarily follow from the truth of life's design?

    >At some point, absence of evidence must be taken as evidence
    >of absence.

    Sure, if we have good reason for expecting this lack of evidence
    not to exist. In this case, you are no where near that threshold.

    Mike



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