Science and Mechanism

From: Reed Konsler (
Date: Fri 13 Jun 2003 - 14:15:50 GMT

  • Next message: Dace: "Nazion"

    Date: Thu, 12 Jun 2003 16:07:20 -0700 From: "Dace" <>

    "Hi Reed,"

    Hi Ted, :-)

    "As Paul Weiss pointed out many times, organisms are determinant at the macro level and indeterminate at the micro level. This is why biochemists, such as Alfred Gilman, can't predict anything within the simplest of microorganisms, even when they've got a map of all the cell's components and interconnections."

    To say that biochemists can't predict anything is an overstatement. If that were so, there would be few applications for biochemistry. We do not yet know enough to create a synthetic living thing. But, to read your posts, I would be led to believe that biochemistry is hopeless. It seems obvious to me that it is a powerfully useful perspective.

    > Mechanism: A theory must relate causes and effects.

    "This is impossible at the micro level."

    Again, you're making an overstatement. The requirement is that the *theory* relate causes and effects, not that these be the true causes and effects. It is possible to create a mechanistic micro-level theory. There are lots of them.

    "Researchers consistently find a high degree of freedom from mechanistic determination within cells."

    If you've ever done any scientific research, you'll know that researchers consistently find a "high degree of freedom" with everything. Ninety percent of experiments don't work and give you little information about what to do next other than "not that". It's a frustrating endeavor.

    ""A useful model must suggest a hypothesis that forces the model builder to do an experiment," End says. This one didn't."

    I think that Endy is saying exactly what I did. He is also admitting that the work he did hasn't yet resulted in a useful theory. That makes him a good scientist. It doesn't mean that his approach will never bear fruit, just that it hasn't yet.

    > Empirical Falsifiablity: A theory must engender experiments or directed
    > observations.

    "As the late Stephen Jay Gould observed in *The Structure of Evolutionary Theory,* though Gould himself supported it, reductionistic theory *clearly* does not pass this test."

    A theory premised in logic can engender experiments. Gould was, in my opinion, saying that you can't prove evolution is or isn't true. I agree with that. I'm talking about utility.

    We can go on forever about why people *should* believe things. But, to the extent that they think about it at all, people adopt useful theories and assert that they are "true". Truth and utility get confused all the time

    "Darwin even pointed to the then-recent development of field theory in electromagnetics as an example of how science can get beyond conceptual logjams through creative, new approaches."

    I don't understand what you mean by "field theories". Electromagnetics is a mechanistic theory (at least, as it was taught to me) that is intimately intertwined with physics, chemistry and the rest of science. It's also reductionist, it that it proposes that macroscopic events are microscopically determined. There are tons of such field theories out there, and many of them are useful.

    Morphic Resonance is an individual theory. It's fallacious to argue that because it incorporates similar words to accepted theories that it should also be accepted. I think that most scientists working in fields related to electromagnetics would find your use of their theories to defend Morphic Resonance specious, if not insulting.

    "Due to its purely theoretical nature, gene-based mechanism remains amorphous and untestable."

    But it so very useful, which is my point.

    > Application...

    "Yes, and genetics has had tremendous applications in medicine. This causes people to assume its underlying theory is correct, despite the total lack of direct evidence."

    I agree.

    > Truth is not a factor.

    "Science (scientia) is Latin for knowledge. Knoweldge means truth. If truth is not a factor, then science needs to come up with a new name."

    How do you prove something to be true?

    > Exactly how a protein folds...indeed, if they even
    > exist at all...isn't relevant. The question is: if we believe and act on
    > that theory, what are the consequences? The explosion of biochemistry and
    > biotechnology is a result of the fact that I can teach the basics of the
    > theory in high school, thousands of people can find work within the field,
    > and insulin can be manufactured cheaply in massive quantities.

    "You reduce science to a glorified form of engineering."

    That is your impression. My impression is that you are confusing science with philosophy.

    > Proteins might not fold according to a "mechanical" mechanism. But, it's
    > pointless to argue that they fold according to no mechanism at all.

    "The question is whether they fold according to a linear causal sequence reaching back to DNA (which can't be shown due to the complexity of cellular activities) or if they fold according to a holistic model of the protein based either on eternal equations or inherent memory."

    That isn't my question. I am not required to dogmatically hold one position or the other. I hold either, under the circumstances that they are useful to me.

    I'm not sure if this is a conversation about "field theories", "holistic theories", or Morphic Resonance specifically. I'm a firm proponent of field theories. I think that holistic theories can be useful. I don't personally find Morphic Resonance is useful in any circumstances I've encountered.

    > Which theory is most useful, of all that have ever been proposed? I would
    > argue, at present, it is the biochemical model.

    "Useful for what? Generating technologies are describing life as it actually is?"

    The former. The latter is impossible.

    "Of course. They know plenty more about the mechanics of cell function. But what if organic form is not primarily a question of mechanics? In that case, all their progress has brought them no closer to the basis of organic form."

    Everything they learn will be totally pointless?

    > Anyway, it is my experience that "contemporary biology" is shifting, as a
    > general trend, further in the direction of the "bottom-up" biochemical
    > approach.

    "You're about 75 years behind the curve."

    My experience leads me to believe otherwise.

    > That would tend to confirm that most biologists are "bottom-up."

    "Talk about taking a quote out of context! Here's the very next sentence..."

    I was focusing on this part:

    > "[M]ost biologists still use computers as little more than receptacles for
    > the surge of data gushing from their robotic sequencers and gene chip
    > analyzers.

    The author might be impling that most biologists shouldn't be acting as they are, but the statement appears to me to explicitly state what "most biologists" are doing. What they are doing is working "bottom-up", which is what I said: most biologists are reductionists. That isn't a dirty word.

    "..."But the past few years have seen a growing movement among mathematically minded biologists to challenge the central dogma as simplistic and to use computer simulation to search for a more powerful theory."

    The trend is clearly toward top-down."

    My experience, which is based on more that a few popular press articles, leads me to believe otherwise. Again, I'm not arguing about "shoulds". The trend I've seen is dramatically towards gene chips, high throughput assays, combinatorial chemistry, and genetic engineering.

    "The next step after this is to recognize that a holistic view doesn't necessarily mean mathematical idealism. The "fields" or "systems" determining organic structure might result from inherent memory rather than timeless equation. This is more in accord with evolution, as equations don't evolve."

    But that recognition won't ever happen if there isn't a material reason to make it. It is a hallmark of science not to think more than you must in order to achieve the desired end.

    > "We're witnessing a grand-scale Kuhnian revolution in biology,"
    > avers Bernhard O. Palsson, head of the genetic circuits research
    > group at UC San Diego.
    > "We are so going to get laid by those chicks" avers Sean,
    > self-proclaimed 'ladies man' of the Druid pub in Inman Square.

    "It should bother you that Palsson is a highly respected researcher. That you don't find his statement the least big significant suggests you're beholden to a deeply ingrained meme."

    Fallacy: argument from authority.

    His statement appears self-interested; designed to sell people on his theory and research.

    Many other respected scientists disagree with him.

    I find the "Kuhnian revolution" thing to be trite and cliché. It's also not something not at all dignified to say about yourself before-the-fact, and not particularly dignified to say of yourself after-the-fact. After we experience a Kuhnian revolution, it will be obvious. You won't need to argue about it or assert that it happened.

    I thought the analogy was apt.

    I agree, I "don't find his statement the least bit significant".



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