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Examples of quantum mechanical involvement in biological systems

  1. Jun 21, 2010 #1
    Hello,

    Can anyone can point me to any well established examples of quantum mechanical involvement in biological systems besides photosynthesis, e.g. http://www.lbl.gov/Science-Articles/Archive/PBD-quantum-secrets.html" [Broken]? I've only seen some other (speculative) involving quantum "spin" and bird migration. Hoping to identify more 'hard evidence' examples for an article I'm preparing.
    TIA for any help!
     
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  2. jcsd
  3. Jun 21, 2010 #2
    All of chemistry is a quantum mechanical effect, and chemistry is all over biological systems.
     
  4. Jun 21, 2010 #3

    alxm

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    (seems I'm perpetually responding on this subject.. oh well, here goes)

    As Academic here said, chemistry is essentially quantum-mechanical. Or at least the fundamentals of it, such as chemical bonding and reactivity. So quantum mechanics certainly has an important role in biochemistry. But on the other hand, it is the same role that it has in the rest of chemistry. Photosynthesis, for instance, involves absorption of light by matter - which is a quantum mechanical process, and it also involves things like the transfer of electrons, which is also a quantum mechanical process. But these processes are of course not at all unique to biochemistry, or even chemistry itself, so it's not a surprise, exactly.

    If the question is: "Is quantum mechanics significant to biological/biochemical processes in such a way that biochemists need to learn quantum mechanics [more than any other chemist]?"
    The answer most in the field would give to that is simply "No."

    As it stands right now, biochemists know less quantum stuff than most chemists, (I'm not knocking 'em for it) as they're the farthest removed from these 'fundamentals' where QM is involved, i.e. reactions and bonding and such. They focus rather on the bigger things which are specific to biochemistry, such as protein structure and function, genetics and such. Whereas studying light absorption in photosynthesis (for instance) is better left to physical chemists, chemical physicists, and quantum chemists, who have more detailed knowledge on light-matter interactions in chemistry.

    So one must distinguish biochemistry and other diciplines, even though the other diciplines might be studying biochemical systems! The reason why the answer to the question above was 'no' is because once you reach the 'biochemical' level, quantum mechanical effects are no longer in play. E.g. you don't need quantum mechanics to figure out gene regulation, or protein folding, or what a protein does in a cell. But you may need quantum mechanics to fully understand how it does it, but it's the same for any chemical reaction. (and the more you 'zoom in', the more quantum mechanical it becomes)

    This isn't really speculative. Some birds do have magnetoreception, they're pretty sure.
    Since cells communicate chemically, you need something that reacts to magnetic fields strongly enough to affect chemistry.
    The only thing that could be (given that we haven't found any tiny induction coils in cells) is molecules with a net electronic spin. This is quite unusual, because spin seldom plays such a direct role in chemistry and (equivalently) little chemistry is affected by magnetic fields.

    (However there is unfortunately a lot of speculative nonsense out there in this realm. Which is why, even though I do quantum-chemical studies of biochemical systems, I don't use the term 'quantum biology' and don't like it. I think it implies quantum effects of macroscopic significance within bio systems, which is something not generally believed to exist.)
     
    Last edited: Jun 21, 2010
  5. Jun 22, 2010 #4

    Andy Resnick

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    There's an open DARPA call for research proposals regarding this exact question:

    https://www.fbo.gov/index?s=opportu...b6e82f0313a29227d05d0de6f71&tab=core&_cview=0

    The wording of the synopsis is rather revealing.
     
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  6. Jun 23, 2010 #5

    alxm

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    Haha, indeed!
    Looking at their definitions, they seem to define it as quantum effects which are surprising and/or unusual for biological systems, but explicitly not ones which are completely trivial (e.g. the quantum mechanics of chemical bonding). The problem is, you can't really explain this to a layperson. Understanding why some effects are surprising and others not, implicitly requires an in-depth understanding of quantum mechanics, chemistry and how they relate. Unfortunately, the pop-sci press doesn't help much here.

    For instance, say it turned out that a current theory on magnetoreception was true, and that it works with the coupled spins of a NADH* - O2*- radical pair. This would be very special and unusual, but hardly impossible, nor at odds with theory. As I said, chemical reactions that depend on magnetic field orientations are not well-known. Because radical reactions are somewhat uncommon, because radicals are not very stable. Because the effect of magnetic fields on them is still very small, and also for purely practical reasons: It's not usual to keep a molecule oriented spatially!

    I can imagine how the media could/would spin it (no pun intended). "Scientists believed that magnetic fields couldn't affect chemistry, but biology and quantum mechanics show otherwise!". Evoking images of stuffy conservative professors saying "that's impossible!" (even though nobody ever actually said any such thing) only to be proven wrong by the wonders of evolution. Then you get the journalists pointing to bogus stuff like "quantum consciousness" ideas etc, as if they were suddenly more plausible because of this. Finally the frauds selling magnetic wristbands and whatnot start acting like they've been 'vindicated'.

    Well, that's just the http://www.phdcomics.com/comics/archive/phd051809s.gif" [Broken], I suppose.
     
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  7. Jun 23, 2010 #6
    Adding a bit more reality to the discussion.:smile: Howard Hughes Medical Institute’ s Summer ’04 Bulletin, Volume 17, No.2 has an excellent article “Cells Aglow.” Here is a quote from the article:

     
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  8. Jun 23, 2010 #7

    Andy Resnick

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    FRET has been around for a while. It's also not a biological phenomenon.
     
  9. Jun 23, 2010 #8
    And, the topic is "Examples of quantum mechanical involvement in biological systems." I provided information. Nothing more or less. The article itself is worth reading. Also please note the beginning of the article begins with this statement:

     
    Last edited: Jun 23, 2010
  10. Jun 23, 2010 #9

    alxm

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    The central question to me is what would qualify as a 'biological phenomenon'.
     
  11. Jun 23, 2010 #10

    Andy Resnick

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    exactly! I wonder what's going to get funded....
     
  12. Jun 23, 2010 #11
    Andy and Alxm, Howard Hughes Medical Institute's 2009 Annual Report appears to me to be a great resource: :approve: Here's a quote though the whole report is awe-inspiring.

    I love Howard Hughes Medical Institute. I support them.
    http://www.hhmi.org/

    An article appeared on May 20, 2010, HHMI AWARDS $79 Million for Science Education to Research Universties, Top Scientists.
    http://www.hhmi.org/news/univprof20100520.html
     
    Last edited: Jun 23, 2010
  13. Jun 23, 2010 #12

    Andy Resnick

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    I am cautioning you not to confuse the hype with real science. Real science is much more boring.
     
  14. Jun 24, 2010 #13
    Hi Andy, you appear to be referring to Howard Hughes Medical Institute's 2009 Annual Report. I honestly didn’t notice any *hype* in Howard Hughes Medical Institute's 2009 Annual Report. For example:
    02 Tsien Receives Nobel Prize
    “By co-opting the proteins that make some jellyfish glow, HHMI investigator Roger Y. Tsien and others have provided an invaluable set of tools for visualizing cells and their components. Tsien, a professor at the University of California, San Diego, shared the 2008 Nobel Prize in Chemistry for the discovery and development of green fluorescent proteins (GFPs) with Osamu Shimomura of the Marine Biological Laboratory and Martin Chalfie of Columbia University.”

    By the way, I love Science.:biggrin: I don’t consider it to be boring. Do you consider 02 Tsien Recieves Nobel Prize as hype? Do you think an "invaluable set of tools for visualizing cells and their components" is hype? Please tell me what you consider to be hype within the pdf. Also, as noted in the report, "The Howard Hughes Medical Institute is the nation’s largest private supporter of academic biomedical research.":biggrin: Do you consider biomedical research to be hype? You don't think it is 'real science'?
     
    Last edited: Jun 24, 2010
  15. Jun 24, 2010 #14

    alxm

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    ViewsofMars: That's the fourth post of yours in this thread on HHMI and Roger Tsien, a subject which doesn't really have much at all to do with the topic at all.

    Tsien's a fine researcher. I even have a copy of his Nobel poster somewhere. But he's a biochemist, and his work centered on making mutations to GFP to make it usable,
    change the colors, etc, essentially by trial-and-error. There was no quantum mechanical theory involved in that work at all.
    It's not like QM calculations were done to predict the colors before performing the mutations. (This is almost technically feasible today, but certainly wasn't when he did the work. But even now it'd probably still be faster to just use trial-and-error)
     
  16. Jun 24, 2010 #15

    Ygggdrasil

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    Tsien is actually a chemist (he originally made his name by designing and synthesizing calcium-sensing dye molecules) and he has said in his Nobel lecture that he doesn't know how to perform many of the molecular biology procedures needed to create some of the new GFP variants his lab has designed. However, because of his background as a chemist, he has the insight to be able to look the chemical structure of GFP and be able to think of rational mutations that would change the photophysical properties of GFP, a skill that many biologists do not have.

    Certainly, quantum mechanics is useful for many tools in biology research. For example, non-linear optical imaging techniques (e.g. two photon imaging, second-harmonic generation, coherent raman scattering, etc.) all require some knowledge of quantum mechanics to be able to understand how they work. Similarly, magnetic resonance imaging (for imaging large-scale objects) and nuclear magnetic resonance spectroscopy (for studying the shape and dynamics of biological and non-biological molecules) are also deeply based in quantum mechanics. Fluorescence, FRET, GFP, etc. fall into the category of tools used to study biology and not actual biology.

    However, while a biologist (or at least biophysicist) might need to understand quantum mechanics in order to implement these techniques, quantum mechanics isn't needed to understand much of the underlying biology.
     
  17. Jun 24, 2010 #16
    Three items I want to mention.

    1. Let’s look closer at biological systems from Oak Ridge National Laboratory:
    2. Robert Tjian has been brought up by me, I wanted to make sure everyone knows that he is is President of Howard Hughes Medical Institute:
    http://www.hhmi.org/annualreport2009/06_from_the_president.html

    Also, Robert Tjian, has his own laboratory at the University of California at Berkeley:
    3. Last of all, I wanted to mention that Jeff Lichtman, professor of molecular biology and cellular biology at Harvard states, “The strength of inductive science, however is that new observational tools often reveal unexpected things that force you to confront the disconnect between the current worldview and the revealed world . . . especially when you have young colleagues who bring fewer bias to biological phenomena. Microscopes are particularly valuable tools for this endeavor in neurobiology because they are a direct link between cell-biological phenomena and the visual system, our most sophisticated sensory mechanism. (Closely Watched Organisms by Jeff Lichtman , HHMI Bulletin, February 2006 http://www.hhmi.org/bulletin/feb2006/pdf/Organisms.pdf [Broken] ) Excellent article!

    Thank you for the opportunity to be part of this topic.
     
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  18. Jun 25, 2010 #17

    alxm

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    You could use 'chemical intuition' but having read the paper once, as far as I recall it was basically trial-and-error in this specific case, and some luck; Not that there's anything wrong with that. All scientific discovery is part luck.

    Certainly. But you don't necessarily have to know how the tools work to use them, and in the cases where you do, it tends to be done by the specialists on those tools, rather than specialists on the systems in question. E.g. in my case, quantum chemical methods, which in general haven't quite reached the 'black box' level where they can be used without intimate knowledge of how they work.

    GFP on the other hand is itself an excellent 'black box'. The biochemist doesn't need to know how or why the fluorescence works, just that it fluoresces. Stick the gene in and you get a fluorescent protein. (I'm pretty sure Tsien's being modest and probably knows how to do that much. One of our undergrad courses has a project of putting GFP into E Coli, so even though I don't know how to do it myself, it'd seem to be pretty routine for biochemists)
     
  19. Jun 25, 2010 #18
    I'm not 100% sure about the trial and error. Some added information about Roger Tsien, Ph.D:

    Adding three quotes about Tsien from this website: http://ucsdnews.ucsd.edu/newsrel/science/10-08NobelPrize08release.asp .

    1.

    2.
    3.
    And you can explore Tsien Laboratory - Department of Pharmacology, Department of Chemistry & Biochemistry UCSD:
    http://www.tsienlab.ucsd.edu/
    His publications can be viewed from this link (url). Very fasinating and extremely educational reviews and papers:
    http://www.tsienlab.ucsd.edu/Publication.htm
    ###

    Also, just so people don't get confused between Professor Roger Tsien and Professor Robert Tjian. My post #16 regarding Robert Tjian was in reference to my post #11 pertaining to Howard Hughes Medical Institute's 2009 Annual Report wherein the pdf he was mentioned. Basically, I vis a vis’d him into our conversation. HA, HA, HA, LOL! I love Howard Hughes Medical Institute just as much as I love NASA!:smile:
     
    Last edited: Jun 25, 2010
  20. Jun 25, 2010 #19

    alxm

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    Then read the research papers instead of instead of continuing to fill this thread with irrelevant and unrelated trivia. You're disputing something I'd read in their paper by citing his CV? In what way would that be relevant? You don't think that important discoveries are made through luck? Or that I implied Tsien is somehow a lesser scientist because of it?

    - "Improved Green Fluorescence", Nature, v373 (1995), p663.

    So you're right. It wasn't trial-and-error. They were in fact studying a completely different aspect of the function at the time.
     
  21. Jun 25, 2010 #20
    I just located the papers! I haven't read them. And by the way, you are the one Alxm by replying to Ygggdrasil, it is you who keeps bringing Roger Tsien up. And you failed to provide adequate information about Roger Tsien. You give people the impression he is *just* a biochemist. Tsien is not just a biochemist! It's very important to me to protect scientists that have an outstanding reputation such as Tsien does have.

    Bye the way, my contribution in post #16 pertaining to "Biological Systems" is worthy of notation. I'll pat myself on the back. Thank you very much. Good day.
    Mars
     
    Last edited: Jun 25, 2010
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