19 Responses to “Open thread: Molecular machines, ethics, and the Coming Theocracy”

1. Art Says:
   May 28th, 2006 at 9:37 am

   Why not add this paragraph, Krauze? What it says is a lot more provocative for some TTers and readers of this blog.

   Proteins are quite different from the simple diatomic molecules that represent the traditional border between physics and chemistry; they are enormously large, and for many purposes quantum mechanics plays a negligible role in their function. Of course, if the question of interest happens to be the chemistry that takes place in the active site of an enzyme, one must ultimately look to quantum mechanics as the basis for understanding. Quantum mechanics can be neglected in the same sense that it is ignored in dynamical descriptions of everyday objects: On the smallest length scales, all atoms are fundamentally quantum, but Planck's constant is not needed to formulate and apply the principle of least action. Indeed, one would be hard put to describe many physical phenomena, ranging from protein behavior to critical phenomena to galaxies, if a fully quantum mechanical description were required. Proteins as molecules are polymers, and can often be treated with a combination of continuum mechanics and statistical mechanics. They act, in other words, as essentially classical objects.

   So much for the QM mumbo-jumbo that some of the more, um, imaginative teleologists conjure up.

Comment by Art — May 28, 2006 @ 9:37 am

2. Mung Says:
   May 28th, 2006 at 11:23 am

   So much for the QM mumbo-jumbo that some of the more, um, imaginative teleologists conjure up.

   Ken Miller tosses God out the front door in his book then tries to sneak him in the back through quantum events. Not sure why you all choose him for your poster child. Does that make him an ID'ist, or a creationist?

   But in any event, I don't know of any ID'ists who rely on QM at the protein molecule level, do you? So what's your point?

Comment by Mung — May 28, 2006 @ 11:23 am

3. Art Says:
   May 28th, 2006 at 12:00 pm

   But in any event, I don't know of any ID'ists who rely on QM at the protein molecule level, do you?

   The culprits (not #1, mind you) know who they are. They may comment, or not.

Comment by Art — May 28, 2006 @ 12:00 pm

4. Mung Says:
   May 28th, 2006 at 12:48 pm

   "¦in purging intentional causes, including supernatural agents, from science, great progress has been made not only in understanding nature but in amreliorating the human condition, as with modern medicine. Those who preach intelligent design would reintroduce intentional cause into science and so reduce science's ability to serve. For society, that is an unintelligent design. - Scott Atran

Comment by Mung — May 28, 2006 @ 12:48 pm

5. Mung Says:
   May 28th, 2006 at 1:54 pm

   So much for the QM mumbo-jumbo that some of the more, um, imaginative teleologists conjure up.

   From over at PT:

   I do quantum calculations on biomolecules.

   here

Comment by Mung — May 28, 2006 @ 1:54 pm

6. Art Says:
   May 28th, 2006 at 1:59 pm

   Context, Mung, don't forget the complete context.

   From the PT comment:

   Agreed. I do quantum calculations on biomolecules. The idea that water could be some sort of quantum relay of information is silly. Any sort of coherent superpostion of water vibrational states decoheres far faster than the time scale of formation of a DNA-protein complex.

   Apparently, I'm not alone in thinking that the QM musings we see on the parts of ID proponents are silly.

Comment by Art — May 28, 2006 @ 1:59 pm

7. Mung Says:
   May 28th, 2006 at 5:12 pm

   Apparently, I'm not alone in thinking that the QM musings we see on the parts of ID proponents are silly.

   Ironically, the anti-ID side can be observed doing their own musings.

Comment by Mung — May 28, 2006 @ 5:12 pm

8. Mung Says:
   May 28th, 2006 at 5:22 pm

   Well, I've requested forum for talking about the latest anti-ID offerings, and it looks like I've been given one. For those who have access to the Brockman edited volume Intelligent Thought, I direct you to the chapter by Frank J. Sulloway, Why Darwin Rejected Intelligent Design. as the most egregious example in the book (so far) of the conflation of ID with creationism. But more on that later. For now:

   Unintelligent Design
   Scott Atran

   Although science may never replace religion, science can help us understand how religions are structured in individual minds (brains) and across societies (cultures) and also, in a strictly material sense, why religious belief (including that in intelligent design) endures. Recent advances in cognitive science, a branch of psychology with underpinnings in evolutionary biology, focus on religion and awareness of the supernatural as a by-product of the convergence of several cognitive and emotional mechanisms that evolved, by natural selection, for the accomplishemnt of mundance tasks.

   Why would anyone want science to replace religion?

   Can science helps us understand how science is structured in individual minds (brains) and across societies (cultures)? Can science helps us understand, also, in a strictly material sense, why scientism endures.

   Why are scientists so eager to subject religious believers to their scrutiny while failing to likewise scrutinize themselves?

   What was the mundane task for which scientism evolved?

   Where are the published peer-reviewed articles which demonstrate that intelligent design is a religious belief?

   Where are the published peer-reviewed articles which demonstrate why belief in intelligent design endures?

   Where are the published peer-reviewed articles which examine "scientific" beliefs using the same methodologies that are applied to "religious" beliefs?

   "¦in purging intentional causes, including supernatural agents, from science, great progress has been made not only in understanding nature but in amreliorating the human condition, as with modern medicine. Those who preach intelligent design would reintroduce intentional cause into science and so reduce science's ability to serve. For society, that is an unintelligent design.

   What is the scientific basis for excluding intentional causes from science?

   Do scientists, in their experiments, ever employ intentional causes? Why do scientists philosophically exclude that which they pragmatically include?

   Can a schizophrenic science survive?

   : Separation of Science and State.

   If science and religion are both the result of the same processes, why should science be allowed while religion is excluded? How do we determine, scientifically, whether a given belief is religious, as opposed to, say, scientific? What if we can demonstrate scientifically that "science" is a religious belief?

Comment by Mung — May 28, 2006 @ 5:22 pm

9. MatthewCromer Says:
   May 28th, 2006 at 8:09 pm

   So much for the QM mumbo-jumbo that some of the more, um, imaginative teleologists conjure up.

   The idea that quantum effects can be ignored at the macroscale is completely incorrect.

   Certainly in well-determined classical systems, such the swinging of a pendulum, micro-scale inputs such as quantum indeterminancy will average out and play an ignorable role.

   But most of the interesting systems that we care about are chaotic, that is, almost infinitely sensitive to initial conditions. This absolutely contains the causes of mutation, whose changes to the genome are directly related to quantum indeterminancy and are probabalistic.

   Neurons in the brain operate the same way - probabalistic firing behavior based on the quantum behavior of individual ions in the synaptic cleft. The brain could be viewed as a device to magnify the effects of quantum indeterminancy to drive macro-scale organism behavior.

   So yes, extraordinary simple classical systems can be considered to ignore quantum effects. For more interesting so-called classical systems, quantum indeterminancy will drive outcomes, whether we are looking at genetic mutations, neural and brain behaviors, and the weather next month.

Comment by MatthewCromer — May 28, 2006 @ 8:09 pm

10. edarrell Says:
    May 28th, 2006 at 8:56 pm

    Mung wonders:
    

    What is the scientific basis for excluding intentional causes from science?

    Method only. Scientific analysis works best when one looks for proximate causes first, and it works best when one does not assume supernatural causes that cannot be detected. Our human experience, dating back some 5,000 years, has amply demonstrated that the assumption of supernatural cause tends to obfuscate true causes and delay the accumulation and use of practical knowledge.

    What possible scientific, or ethical, basis could exist for honest inquiry under any different fashion? Consider Semmelweiss's work on handwashing. Consider Franklin's work on the nature of lightning. Consider medical work on mental illness. Is there a single example where the assumption of a non-proximate cause has led to useful discovery? If there is any such example, is there evidence that such inquiry can methodically lead to more knowledge?

    Go ahead, Mung — tell us how non-science could produce different, and better, results.

Comment by edarrell — May 28, 2006 @ 8:56 pm

11. Gerard Harbison Says:
    May 28th, 2006 at 10:32 pm

    Thanks to Art for correcting the out-of-context quotation of my words.

    I'd like to ask Matthew why he thinks the movement of ions in the synaptic cleft is quantum mechanical. Ions in liquids undergo stochastic diffusive motion. The translational quantum states are so close together none of them can actually be occupied with any significant probability; the vibrational states of the solvent cage last only as long as the cage, which means picoseconds. This is a quintessentially classical problem.

Comment by Gerard Harbison — May 28, 2006 @ 10:32 pm

12. Steve Petermann Says:
    May 29th, 2006 at 9:13 am

    Hi Gerard Harbison,

    I'd like to ask Matthew why he thinks the movement of ions in the synaptic cleft is quantum mechanical. Ions in liquids undergo stochastic diffusive motion. The translational quantum states are so close together none of them can actually be occupied with any significant probability; the vibrational states of the solvent cage last only as long as the cage, which means picoseconds. This is a quintessentially classical problem.

    Since you seem to know a lot about this I would be interested in any comment on the articles mentioned here. Apparently one candidate for quantum tunneling is tryptamine a neurotransmitter.

Comment by Steve Petermann — May 29, 2006 @ 9:13 am

13. MikeGene Says:
    May 29th, 2006 at 10:57 am

    The PhysicsToday article is great. There are many quotable sections. Here's another:

    One of the key hallmarks of biological function is ordering in space and time, and at least two great classes of biological orchestration should serve as a call to action for physicists: the coordination of physical structures and processes and the orchestration of information"¦"¦ In many instances, the machines of the cell are integrated into collections of many parts, often with proteins, nucleic acids, lipids, and other molecules working in concert. One of the most important ways that physicists come to terms with systems comprising many interacting degrees of freedom is to consider collective excitations. For example, phonons characterize the vibrations of a crystalline solid and magnons describe collective excitations of magnetic spins.

    Indeed, physicists talk of "-ons" of all kinds. The biological setting provides a loose analogy because some biological structures are characterized with the label "-somes," which derives from the Greek word for "body." The term refers to macromolecular assemblies that are made from multiple molecular components that act in a collective fashion to perform multiple functions. Some of the most notable examples include the ribosome, used in protein synthesis; the nucleosome, which is the individual packing unit for eukaryotic DNA; the proteasome, an assembly that mediates protein degradation; and the transcriptisome, which mediates gene transcription. By mechanisms and principles that are still largely unknown, proteins assemble into -somes, perform a task, and then disassemble again.

    Function is dependent on organized collectives.

Comment by MikeGene — May 29, 2006 @ 10:57 am

14. Mung Says:
    May 29th, 2006 at 1:43 pm

    Gerard Harbison Says:
    May 28th, 2006 at 10:32 pm

    Thanks to Art for correcting the out-of-context quotation of my words.

    Thank Art for making it seem like you don't do what you claim you do.

    I do quantum calculations on biomolecules.

    My only point with this quote is that people actually do quantum calculations on biomolecules. You claim that you do so. Are you now retracting this claim? And since my only point was to establish that people actually do quantum calculations on biomolecules, how am I quoting you out of context?

Comment by Mung — May 29, 2006 @ 1:43 pm

15. MatthewCromer Says:
    May 29th, 2006 at 1:57 pm

    Ions in liquids undergo stochastic diffusive motion. The translational quantum states are so close together none of them can actually be occupied with any significant probability; the vibrational states of the solvent cage last only as long as the cage, which means picoseconds. This is a quintessentially classical problem.

    The stochastic nature of these processes is driven by inputs from the quantum mechanical level. I'm not claiming quantum coherence or entanglement is even necessary, simply that a driver of the stochastic variations in the probabalistic nature of ion channel / nerve firing response is quantum indeterminancy.

    Like I've stated before, the brain looks very much like a device to amplify the effects of probabalistic variation starting at the quantum level. Are there "hidden variables" going on there?

Comment by MatthewCromer — May 29, 2006 @ 1:57 pm

16. Aagcobb Says:
    May 30th, 2006 at 10:53 am

    Hi Mung,

    If science and religion are both the result of the same processes, why should science be allowed while religion is excluded?

    Religion shouldn't be excluded; it just shouldn't be called "science" when it isn't.

    How do we determine, scientifically, whether a given belief is religious, as opposed to, say, scientific?

    That would be with empirical research. One could argue that science is what scientists do. Perhaps you can apply for a research grant to analyze what is being published in peer reviewed science journals.

    What if we can demonstrate scientifically that "science" is a religious belief?

    Maybe you'll win a Nobel Prize. Let us know when you submit your research paper demonstrating that "science" is a religious belief to a peer reviewed journal.

Comment by Aagcobb — May 30, 2006 @ 10:53 am

17. Mung Says:
    May 30th, 2006 at 7:56 pm

    Religion shouldn't be excluded; it just shouldn't be called "science" when it isn't.

    Wow. That's a convincing argument. How do you kow, based upon scientific examination of the evolutionary source of "scientific beliefs" and the evolutionary source of "religious beliefs" that one should be included and the other excluded?

    One could argue that science is what scientists do.

    One could. But why should one believe it is true? Do you know what a tautology is?

    Do scientists never "do religion," asnd do religionists never "do science"

    Good luck with that line of argument.

    Since both science and religion have their source in the same process, how do we know that science isn't religion and that religion isn't science? Try not to beg the question, please.

    Where are the "scientific" papers which explore "scientific belief"

Comment by Mung — May 30, 2006 @ 7:56 pm

18. Aagcobb Says:
    May 30th, 2006 at 10:29 pm

    Hi Mung,

    Wow. That's a convincing argument. How do you kow, based upon scientific examination of the evolutionary source of "scientific beliefs" and the evolutionary source of "religious beliefs" that one should be included and the other excluded?

    I just said that religion shouldn't be excluded; science shouldn't be excluded, either, so I don't "know" that either one should be excluded.

    One could argue that science is what scientists do.

    One could. But why should one believe it is true? Do you know what a tautology is?

    Do scientists never "do religion," asnd do religionists never "do science"

    In fact, many ministers and priests have engaged in scientific research, and great scientists have also been theologians.

    Since both science and religion have their source in the same process, how do we know that science isn't religion and that religion isn't science? Try not to beg the question, please.

    Where are the "scientific" papers which explore "scientific belief"

    It seems on the surface obvious to me, but maybe scientists are actually engaging in some kind of worship I'm unfamiliar with, and theologians are doing lab work I haven't heard about. I don't know where those scientific articles researching science itself are, since I've never looked for them. Thats why I suggested you write and submit your science paper demonstrating that science is religion.

Comment by Aagcobb — May 30, 2006 @ 10:29 pm

19. MatthewCromer Says:
    May 30th, 2006 at 11:11 pm

    Since this is an open thread, I thought I would bring these papers to your attention. Lots of very interesting discussion about similarities between development and evolution.

Comment by MatthewCromer — May 30, 2006 @ 11:11 pm

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