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Biotech Earth

The Origin of Life and the Hidden Role of Quantum Criticality 188

KentuckyFC writes One of the great puzzles of biology is how the molecular machinery of life is so finely coordinated. Even the simplest cells are complex three dimensional biochemical factories in which a dazzling array of machines pump, push, copy, and compute in a dance of extraordinarily detailed complexity. Indeed, it is hard to imagine how the ordinary processes of electron transport allow this complexity to emerge given the losses that arise in much simpler circuits. Now a group of researchers led by Stuart Kauffmann have discovered that the electronic properties of biomolecules are entirely different to those of ordinary conductors. It turns out that most biomolecules exist in an exotic state called quantum criticality that sits on the knife edge between conduction and insulation. In other words, biomolecules belong to an entirely new class of conductor that is not bound by the ordinary rules of electron transport. Of course, organic molecules can be ordinary conductors or insulators and the team have found a few biomolecules that fall into these categories. But evolution seems to have mainly selected biomolecules that are quantum critical, implying that that this property must confer some evolutionary advantage. Exactly what this could be isn't yet clear but it must play an important role in the machinery of life and its origin.
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The Origin of Life and the Hidden Role of Quantum Criticality

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  • by Anonymous Coward on Saturday March 07, 2015 @09:43AM (#49204159)

    "Complexity" is a very subjective thing. It's solely determined by the intellectual capabilities of the person or people involved.

    Just look at computer programming. We have smart people who understand C++. To them, it isn't complex. It's just a really powerful tool. Then we have less-smart people who use Ruby. They don't have the mental capacity or acuity to understand C++, so they see it as being complex. The complexity of C++ really just depends on who you are and what your mind is capable of working with.

    It's totally the same for the SQL versus NoSQL issue. Some people are intelligent and totally capable of understanding and using SQL. They don't find it complex. But there are other people who lack the intellectual ability to comprehend SQL. To them, it's "complex". So to try to combat their inability to understand SQL, they come up with NoSQL and shenanigans like that. SQL itself isn't complex. It's just that some people find it to be complex, based on their limited intellect.

    Complexity is subjective. While these biological phenomenon may appear difficult for some people to comprehend, they aren't really all that complex at all.

    • by pepty ( 1976012 ) on Saturday March 07, 2015 @11:41AM (#49204491)
      No, complexity is not subjective. You are just using a very casual definition for complexity in a discussion for which there is a much more precise definition. In this case, complexity is a quantifiable property of physical systems. This is true for your analogy as well: in CS one definition for complexity is the number of steps that it takes to solve an instance of the problem as a function of the size of the input. Read the wiki and try again.
      • What is the step count cutoff on complexity? Please quantify that for me. If you can't give me a formula that works across the board (you, after all, are using CS in a discussion about biology), it's subjective.
        • Re: (Score:3, Interesting)

          by pepty ( 1976012 )
          My apologies: I used the CS definition when referring to Parent's using computer programming as an analogy: "This is true for your analogy as well". For the discussion about biology I just said quantifiable, but there are a bunch of different ways to approach complexity in biological systems, some rigourous, some not, and even Mr. Complexity and Self Organization Himself (Kauffman) would use different ones depending on the problem he is currently looking at. For quantum criticality, the one wikipedia gives
        • Re: (Score:2, Interesting)

          by khallow ( 566160 )

          What is the step count cutoff on complexity? Please quantify that for me. If you can't give me a formula that works across the board (you, after all, are using CS in a discussion about biology), it's subjective.

          The subjectivity is bound by a constant factor. That's why big O notation works in the first place.

    • by pepty ( 1976012 ) on Saturday March 07, 2015 @11:52AM (#49204557)

      While these biological phenomenon may appear difficult for some people to comprehend, they aren't really all that complex at all.

      Really? So you can predict how proteins fold? Which drug candidates will interact with which proteins and what effects they will have? How about just modeling the interaction of a protein and water? These all fall under NP-complete, which is a pretty much the epitome of complexity.

    • Re: (Score:2, Interesting)

      by Anonymous Coward

      The OP is not 100% wrong, but as others have pointed complexity is not just subjective. There are systems with greater complexity than others, regardless of the beholder.

      It's a mistake to say that, because someone has eyes which can be forced to focus on a distant object, those who can't see it are on a lower rank. This is exactly what leads us to marginalize some people who are deaf, or color blind, or too tall etc.

      Furthermore, sometimes complexity signals a field not well understood. Someone, somewhere, s

    • by khallow ( 566160 )

      "Complexity" is a very subjective thing.

      I disagree. Complexity is effectively the shortest description of something using a given, sufficiently expressive language with finite words. While relatively complexity can vary between languages a little, the variance in complexity is bounded by a finite amount, the description of translating between the two languages. That makes complexity an objective measure.

    • " Then we have less-smart people who use Ruby. They don't have the mental capacity or acuity to understand C++, so they see it as being complex."

      Jesus, where shall I start?? Less smart people use Ruby??!!! Get real.

      Ruby is very LISP like. The smartest programmers I know are into LISP, Clojure and Ruby because it allows you to construct large system by using meta-constructs at a much higher level. Seeing the forest for the trees and stuff.

      Most C+ hackers I know can do lots of high-details low leave things be

  • by Anonymous Coward on Saturday March 07, 2015 @10:33AM (#49204251)

    I did my Ph.D. in physical chemistry, focusing on electron transport in DNA, proteins, and other organic molecules. I read the arxiv paper and found it almost incomprehensible from this perspective. There is no reference to existing models of electron transport in biological systems(*), and it's not clear that their "generalized fractal dimension" for a protein has anything at all to do with electron transport. While it's possible that this approach is just so revolutionary that it doesn't need to be grounded in what's already known/believed about this field, it's more likely that this is just pseudoscience. Further supporting this hypothesis is the existence of phrases like "Why life persists at the edge of chaos is a question at the very heart of evolution" in the text. Serious science doesn't need that kind of hype in the paper.

    *except at the end where they reference a couple experimental papers that tangentially relate to this topic

    • That's my impression as well. I'm just a layman, but to my untrained eye this looks like word salad. I'm seeing phrases I have never read in a microbiology paper, book or article. My Spidey senses start tingling as soon as I see the word "quantum" outside of a physics article. It's not always true, but as a general rule of thumb that some throwing "quantum" into a biology discussion is usually talking crap. Add in words like "fractal" and the stinkometer just starts reading off the scale.

      Anybody look up the

      • I'm just a layman, but to my untrained eye this looks like word salad.

        I'm a biochemist specializing in molecular biophysics, and I agree.

        It's not always true, but as a general rule of thumb that some throwing "quantum" into a biology discussion is usually talking crap.

        Definitely not always - there are actually enzymes which take advantage of electron tunneling, and even proton tunneling, for catalysis. Here's a particularly cool paper [jbc.org] (no paywall) about a light-activated oxidoreductase which encourages a proton to tunnel.

    • by drolli ( 522659 )

      I agree; i am a quantum physicist. The paper goes seomwhere between effortless phenemenological observation, overgeneralizations and claims which are so remarkably undefined (like that biomolecules are neither insulator nor metals - thanks) hat it not clear which theoretical hypothesis they are going to make here.

      The really impoertan question is: can i use their theoretical observation to predict parameters of molecules at some places? Can they actually reduce the number of variables needes to describe a pr

      • There are some pretty cool examples of quantum effects in biomolecules (e.g. this paper [jbc.org] about enzyme catalyzed proton tunneling, and Marcus theory for electron transfer), but this paper doesn't seem either to reference any of that past work at all, or make sense given that context.

    • There is no reference to existing models of electron transport in biological systems

      I was struck by the same observation. It also seems like the authors are unaware of the newish linear-time DFT codes.

      In case anyone has some knowledge of quantum mechanics and biology, and is interested in electron transfer in biomolecules, Wikipedia has an article on Marcus theory [wikipedia.org] that is an OK place to start. Not the best article, but it discusses the inverted driving force effect and has references to follow up.

  • Complexity is a real property of natural systems. Biological systems are highly complex by any measurable standard. Proteins and protein complexes are nanomachines that operate on principles that have no counterpart in modern technology, such as computers. Take a look at detailed maps of protein complexes like the ribosome, proteosome or F1/F0 particle in mitochondria, and how they operate and are regulated. They are extremely complex despite being only nanometers in size.

    • by devent ( 1627873 )

      That is nice, but so what? A star is more complex than the gas cloud it originated from, a galaxy is more complex than the cloud of stars it originated from. In nature complexity always comes from simplicity.

      • That's really easy to say, but hard to prove in fact. Biological systems are not based on simplicity. The "so-what" is that biological systems, even at the single protein level, are doing things with electron conductance that can't be done in non-biological systems. From the article: “biomolecules belong to an entirely new class of conductor that is not bound by the ordinary rules of electron transport,”

        That is the "so what"?

        • biological systems, even at the single protein level, are doing things with electron conductance that can't be done in non-biological systems.

          There really are some very cool quantum effects in biomolecules, for example enzymes which take catalyze electron tunneling and even proton tunneling [jbc.org]. Electron transfer in proteins in particular is actually pretty well understood via Marcus theory. There is extensive theoretical and experimental work going back five decades in this area - all of which is totally ignored by the unreviewed manuscript under discussion.

          biomolecules belong to an entirely new class of conductor that is not bound by the ordinary rules of electron transport

          Unfortunately, your post and TFA alike do not appropriately distinguish between wildly differ

        • by devent ( 1627873 )

          I'm still compelled to ask the same question, so what? Biological systems had 3.5 billion years to evolve. That is a lot of time for evolution and surviving of the fittest. If you look at biological organisms, they are in fact based on simplicity. Our mammalian brain is based on the amphibian and the fish brain. That is because we evolved from fish ancestors and then from amphibian ancestors. That is one example of from simple to complex. In the cell we have DNA->RNA->Proteins. That is also from simpl

  • The Problem (Score:5, Insightful)

    by Ol Olsoc ( 1175323 ) on Saturday March 07, 2015 @11:02AM (#49204369)
    The problem with arguments from personal incredulity is that the dumbest person in the room always wins.
    • arguments from personal incredulity

      How about skepticism of claims made in unreviewed manuscripts which flout five decades of theoretical and empirical investigations of charge transfer and quantum effects in biochemical systems?

  • by fey000 ( 1374173 ) on Saturday March 07, 2015 @12:18PM (#49204721)

    >>"But evolution seems to have mainly selected biomolecules that are quantum critical, implying that that this property must confer some evolutionary advantage. Exactly what this could be isn't yet clear but it must play an important role in the machinery of life and its origin."

    A scientist should understand evolution sufficiently well to not use arguments like this.

    Why are we carbon based and not silica based? Either works just fine. Evolution doesn't pick the "best" option, it picks a "functional" option. After something has proven to function, evolution stops caring (until it no longer functions). Why iron and not copper in our blood? Either works fine.

    Why quantum critical "bio"molecules? Because they work. There is NO other criteria. They could be better than the alternative, they could be worse, they could be the same. But they work. That is all we can assert.

  • Now ... researchers ... have discovered that the electronic properties of biomolecules are entirely different to those of ordinary conductors.

    Ya, everyone already knows this - duh. That's why Voyager [wikipedia.org] has bio-neural circuitry.

  • my friend dr alex hankey - someone who is himself slightly err critically stable shall we say - has written several papers on exactly this subject, well ahead of their time. from my understanding of conversations with him, criticality of biological systems is critical to life as well as consciousness. from his training which includes two PhDs, one in mathematics and one in physics (MIT and Cambridge), dr hankey actually had to invent a new form of quantum mechanics in order to properly do this justice: on

    • by itzly ( 3699663 )

      think of a cell being attacked by a virus, or going cancerous. you'd, obviously, want the *entire* immune system to react to that, instantly, wouldn't you? otherwise it could well be far too late by the time the virus spreads to more than one cell.

      I'm not an expert, but I doubt you want the entire immune system jumping into full panic mode for a single virus. The side effects from such a response would probably kill you.

      Also, from personal experience I can tell that even dealing with a common cold takes more than a week, and that plenty of cells are infected.

  • One of the great puzzles of biology is how the molecular machinery of life is so finely coordinated.

    Is it? Surely the answer is that if it wasn't so "finely coordinated," it wouldn't work and you'd have a lump of goo, not a hamster.

    Sounds like the sort of "puzzle" the creationist types like to invent to give their god a gap to live in.

    extraordinarily detailed complexity.

    By whose standards?

    • by Empiric ( 675968 )

      I despise these quasi "anthropic principle" arguments that explain precisely why they are wrong, and then triumphantly declare thereby they are right.

      No, it remains the case that causality works forward. It remains the case that things existing means evidence for models of how they could get that way.

      Note that reality, as well as empirical science, demonstrates that the results are not a lump of goo. You can correct your reasoning as needed from there.

      And no, the "gap" exists only in your willfully irrati

      • Jeez. Do you have to be so belligerent about being smarter than me?

        No, it remains the case that causality works forward.

        I don't remember saying it didn't...

        It remains the case that things existing means evidence for models of how they could get that way.

        Models like evolution?

        Nobody, ever, thought that a direct intervention of a god was needed for fire to cook their food, for water to roll downhill, or for a knife to cut something.

        Again, not something I recall saying. Anyway, weren't some ancients pretty hot on the idea of direct intervention being required for all manner of other things, like the sun coming up in the morning, or the end of winter?

        Try recognizing historical reality rather than parroting your Dawkins paperback.

        Never read him.

        Why don't you try not being such a condescending dick to people just because you think you know better than they do?

      • No, it remains the case that causality works forward.

        Does it? Given a point in spacetime, it's just as easy or difficult to calculate possible pasts or futures. You might say event A caused event B, but physics only says they're causally linked.

        Universe described by General Relativity is best thought not as a stream of events but a jigsaw puzzle. You have a piece (observable variables at some point in spacetime) and laws of physics describe what other pieces can be connected to it, then what other pieces c

      • by khallow ( 566160 )

        I despise these quasi "anthropic principle" arguments that explain precisely why they are wrong, and then triumphantly declare thereby they are right.

        They are typical examples of truisms. Effect happened, so causes of the effect happened.

        Nobody, ever, thought that a direct intervention of a god was needed for fire to cook their food, for water to roll downhill, or for a knife to cut something.

        Let me introduce you to Occasionalism [wikipedia.org], which has as a primary precept that everything happens due to the will of God.

        • by Empiric ( 675968 )
          Rather parallel to Panentheism [wikipedia.org] which I do actually ascribe to.

          Long discussion possible here, but essentially my objection was toward a particular popular "science versus religion" simplistic narrative of history. Occasionalism avoids framing events in terms of a "natural or supernatural" dichotomy in the first place. For the question of history, I think it fair to say that, for example, every single action of Jesus, such as simply walking from point A to B (or for that matter any other individual doing
          • by khallow ( 566160 )
            The point of the anthropic principle is that you can't discount theories on the basis that they are unlikely to generate the present state. Also I notice you are treating a supernatural thing, "divine presence or action" as an empirical thing while your name implies some sort of interest in empiricism. Merely insisting reality is divine is merely redefining what is meant by divine. It doesn't help us understand what we can understand any better. I think that Occasionalism and similar things are way off base
            • by Empiric ( 675968 )
              The point of the anthropic principle is that you can't discount theories on the basis that they are unlikely to generate the present state.

              The point is, yes you can. The "anthropic principle" is an erroneous word-game. As discussed in a different branch of my responses, it is merely a tautology reducible to "if things were different they would be different" and presents no evidence at all for the thing being argued for on the basis of it.

              Merely insisting reality is divine is merely redefining what i
  • by The_Laughing_God ( 253693 ) on Saturday March 07, 2015 @02:24PM (#49205409)

    As a former molecular biologist who happens to be in the middle of a course on the design/synthesis of biomolecular electronics (biological semiconductors, conductors, LEDs, solar etc.), I wonder if the solution isn't as simple as this:

    Essentially all biomolecules are synthesized by enzymes. Most are acted upon by enzymes or have some enzymatic activity during their functional life. Quantum criticality could be a useful property to enhance binding and catalysis at enzyme clefts (or other active sites) by enhancing charge/electron transitions in/on a molecule. Criticality may allow transitions and thresholds to be sharper, snappier, more selective.

    "Quantum criticality" is just a label we give to a group of mechanisms (and the structures that encourage them) based on some test. I might label the many things that scare my friend's neurotic but otherwise imposing German Shepard as "Fido-phobic". This category might even be scientifically interesting -- if pulling pranks or stealing from my friend were major scientific goals at this point in time. That doesn't mean that squeeze toys that groan, rubber cubes that bounce erratically, and electric toys that "awaken" at random or after a delay share a fundamental property. They simply have properties that have interesting effects toward a certain goal (keeping her dog from interfering in our hijinks)

    • As a current biochemist, I do wonder why the paper doesn't even mention Marcus theory or other previous work in enzymatic charge transfers. There really are some sweet quantum effects in biology, like enzyme-catalyzed proton tunneling [jbc.org], but I think the unreviewed manuscript under discussion here is hokum.
  • But evolution seems to have mainly selected biomolecules that are quantum critical, implying that that this property must confer some evolutionary advantage. Exactly what this could be isn't yet clear but it must play an important role in the machinery of life and its origin.

    Why talk as though evolution has a purpose, a mind , as if evolution itself is some sentient being?

    Stop anthropomorphizing or deomorphizing evolution. Evolution hates such talk. :-)

  • The major donnybrook going on here about "complexity" is fueled by some accidental bad wording, and too many posts running off into lala land..... Allow me to rephrase what the OP almost certainly meant. And regarding life forms, if you approach the matter from the perspective of an intelligent person that doesn't know much about the subject, it might seem very complex, a subject you think can only be solved by throwing in the towel, and attributing life's creation to the mighty Swanclipper. But if you d

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