Thread

Biology might not be quantum, but its math is quantumlike

123 points · 60 comments · pseudolus

__MatrixMan__ · 1790482592 · focus · HN ↗
I feel like "is biology quantum?" gates are kept in a needlessly stringent way.
They say that biological systems are too warm for quantum coherence to persist long enough to have meaningful effects. But if you have some molecule whose conformation is in a superposition of states--however briefly--and then the environment causes it to decohere and take on some fully determined non-quantum shape... that actual shape is still one of many possible ones into which it did not decohere. The environment has still hacked probability to trigger decoherence into this shape and not some other one, and evolution leans on this.
If you took a classical bag and filled it with classical locks and classical keys and just shook it around for a while, none of those keys would end up in the locks. But because of this quantum lubricant, ligands binding receptors do find themselves in the appropriate conformation to facilitate signal transduction, even at low concentrations. It's absolutely astounding that it works at all, and in a fully classical world it wouldn't for the same reason that the keys don't end up in the locks when you shake the bag for a while.
Biology is plenty quantum, and the people who are here to tell you it isn't are citing the abundance of interactions as evidence that it is not quantum, but it's through those many interactions that its quantum nature expresses itself.
Maybe it's not spooky-action-at-a-distance style quantum. Maybe it's not indeterminate enough for this theoretical purpose or that one. If you're trying to cram god in there, well it might not be quite spooky enough for that, but so much of what happens in the macroscopic world would not happen if the quantum world were not as strange as it is, and that's doubly true for biology.
1. arbitrandomuser · 1790483088 · focus · HN ↗
  adjacent possibly related interesting fact , classically the temperature required to crosss the coulumb repulsion and fuse hydrogen in the sun is far higher than at the core of the sun,
  what makes fusion viable at the core is there is a chance for nuclei tunneling through the barrier , that and the sheer size of the sun
  1. __MatrixMan__ · 1790484244 · focus · HN ↗
    Yeah that's exactly the sort of thing I'm talking about. Its as if the laws of physics are running an operating system that wants interesting stuff to happen, and needs only a fragment of a bell curve to seize the day and send us down the appropriate leg of the trousers of time.
2. Eridanus2 · 1790489840 · focus · HN ↗
  The keys could random walk to lock-ports in finite time iff the search space were 2D or 1D. In 3D space, it is gets very unlikely. Biology solves it by dimensionality reduction, find substrates, cling, slide and find love/compatible hole.
3. joebig · 1790490756 · focus · HN ↗
  There is some inaccuracy here I think. Decoherence means washing out of interference phenomenon, viz. you will observe no fringes in the double slit experiment with incoherent source pair (they switch so rapidly as to end up plain grey). What is erased or overwritten in tiny timescales cannot have a residual resultant or guiding gulley effect, or as you say, freezing the pattern/steric landscape in a preffered state repeatably. It would be tantamount to observing the fringe pattern with incoherent sources, for all timescales.
  1. __MatrixMan__ · 1790517002 · focus · HN ↗
    Take flash memory for example. We read the bit via quantum tunneling. We don't have to wait for the electron to actually bounce out of its little box, we can detect the small probability that it might, and then we can act on that detection.
    So every time I act on the basis of such a read event, am I not being guided down one of gulleys that were set up by the designer of my device (or, analogously for biology, by evolution)?
    gus_massa · 1790520791 · focus · HN ↗
    We can't detect the probability, we only can detect electron that a passed. We meassury tiny currents.
    Do you have a link to this explanation?
    __MatrixMan__ · 1790527000 · focus · HN ↗
    I did some more reading and it turns out I've misunderstood flash memory. I thought it was read via tunneling, but it's written via tunneling. I appologize.
    This being the forum that it is, I was hoping to find an example of this sort of thing: <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC4066974/" rel="nofollow">https://pmc.ncbi.nlm.nih.gov/articles/PMC4066974/ but in electrical engineering instead.
4. amelius · 1790490809 · focus · HN ↗
  Semiconductor physics is built on quantum mechanics. And transistors can get hot ...
5. FeepingCreature · 1790496177 · focus · HN ↗
  Aiui most people who push for "biology is quantum" specifically want the large-scope effects because they're grasping for it as a way to justify why consciousness is special. Cells are of course plenty quantum at the scale of molecular interactions.
  1. aeonik · 1790513418 · focus · HN ↗
    I think you are right, but this is a straw man.
    There are some quantum consciousness cults out there, but plenty of people are interested in investigating the quantum nature of biological effects including consciousness that aren't quacks.
    There is also a tendency for some scientists to react dismissively to hypotheses associated with pseudoscience, even when the narrower scientific question is perfectly legitimate.
    Reminds me of the visceral reactions in history, like the Rejection of Continental drift (i.e. high level idea was right, but mechanisms hadn't been pinned down yet).
    Not claiming that the quantum hypothesis is right, just saying we didn't jump to conclusions.
    HarHarVeryFunny · 1790523111 · focus · HN ↗
    It's perfectly legitimate to investigate any theory in the scientific manner of falsifiable experimentation, but I'm not aware that can be said of anyone looking for a quantum explanation of consciousness (which is anyways a rather odd quest given that there doesn't seem to be anything needing explanation).
    Roger Penrose certainly appears to be a quack when it comes to quantum consciousness and/or brain operation - it seems that he wants to believe it, so waves his hands vaguely in the direction of microtubules as a place it could be hiding, despite zero experimental evidence, or any falsifiable theory. It's not the fact that this flies in the face of everything we know about quantum effects at classical scale and room temperature that makes this quackery - it's the fact that this is just wishful thinking, not science - not the application of the scientific method of falsifiable theory followed by experimentation.
    [deleted] · 1790526314 · focus · HN ↗
    [deleted]
    Retric · 1790528714 · focus · HN ↗
    The issue is there’s zero debate that something very close to QM applies to every single interaction between atoms. We glow in the infrared because of quantum mechanics so does a brick. Similarly chlorophyll works because of QM as does ATP, protein folding, etc etc.
    The question is does any of the interesting counterintuitive QM effects apply to very large structures and that’s where humans being hot dense objects kills most of the more interesting bits of QM.
    > didn't jump to conclusions
    Thus people aren’t jumping to conclusions, QM itself is saying no here. For the effect people want to apply means QM itself must be wrong. That’s obviously possible but means you need a completely new theory of physics and evidence to support that.
6. jryb · 1790505172 · focus · HN ↗
  Your key and lock analogy is simply incorrect. Those interactions can be modeled with classic electrochemistry and are super predictive - the specificity is driven by evolution, not quantum mechanics. I mean sure, every system is technically quantum mechanical but those effects are never explored afaik.
  There are even educational demonstrations where people shake bags of 3D printed proteins with magnets (including competing proteins) and you end up with the expected structure.
  1. __MatrixMan__ · 1790516470 · focus · HN ↗
    classic electrochemistry has plenty of quantum effects baked into the parameters of the theory, it just doesn't bother to explain them in quantum terms.
    I'll have to look up those demonstrations. I know if I were making such a thing I'd stack the deck in favor of a good demonstration and I'd stick to very simple interactions. But if they've given the potential for random useless tangles a fair shake I'll have to rethink my position.
    If somebody has made some analog of ATP synthase which operates in this way it would be just fantastic to behold.
    Although if I did relax this position, I'd then be in need an explanation for why all of biochemistry feels like it takes place in some kind of cartoon universe. Like, maybe I've failed to put my finger on the reason, but I can't shake the feeling that the world being presented in biology class is just a little too cute to be this one.
    jryb · 1790546382 · focus · HN ↗
    I think the problem might be that you're looking for a description of reality that's truly fundamental, but that's not the goal of most biologists. The point of a minimal model is to make it easy to reason about a system and efficiently make predictions. It's a practical approach done for the sake of time and money. If it takes me weeks to plan an experiment using a QM model instead of a day with a classical one, and I end up doing the same thing anyway, what's the point?
    >Although if I did relax this position, I'd then be in need an explanation for why all of biochemistry feels like it takes place in some kind of cartoon universe. Like, maybe I've failed to put my finger on the reason, but I can't shake the feeling that the world being presented in biology class is just a little too cute to be this one.
    Here's one possible explanation for this feeling. Consider the alternative world: any time you write a paper about a protein, you have to measure its interactions with every other biomolecule that's present in the cell of interest. Then, you need to model all of those interactions simultaneously. You probably couldn't do that in 10 lifetimes. It's just not practical to do this, so you never read about it. Papers and textbooks necessarily present things in an overly focused way.
    So any paper you read has some...selection bias? If you're trying to find a zinc finger that binds some particular DNA sequence, and you find one and it has nanomolar affinity, you don't need to worry about what happens when that ZF binds actin or RNA polymerase or some phospholipid. We already know from the fact that it has nanomolar affinity for its target DNA that it isn't being sequestered by anything else in any measurable way. But its affinity for actin or whatever isn't zero - there IS a number, and they DO interact - it's just that it's incredibly weak and transient, so you're not going to notice it incidentally. Biology may seem cute because the ugly version would cost 20,000x as much to produce.
  2. timschmidt · 1790520199 · focus · HN ↗
    > every system is technically quantum mechanical but those effects are never explored afaik
    Photosynthesis depends on quantum behavior: <a href="https://www.youtube.com/watch?v=rvFMBRnR3ms" rel="nofollow">https://www.youtube.com/watch?v=rvFMBRnR3ms
7. HarHarVeryFunny · 1790521144 · focus · HN ↗
  The article acknowledges that quantum behavior like tunneling necessarily happens everywhere, if you look at the relevant scale, and also seems very clear about what it is actually talking about - whether classical-scale quantum effects can be seen in biology.
  You seem to talking at cross-purposes to the article - not arguing against the research it is discussing of classical explanations of quantum-like behavior, but wanting to point out that biology is not immune to quantum effects at the scale where that is not surprising.
  1. __MatrixMan__ · 1790523628 · focus · HN ↗
    You're right on both points. The article isn't misleading, I just think it's an entry into a space which has overreacted to quantum woo woo in an unhelpful way.
8. dnautics · 1790522915 · focus · HN ↗
  > If you took a classical bag and filled it with classical locks and classical keys and just shook it around for a while, none of those keys would end up in the locks
  I think you are vastly underestimating the number of collisions required to get an enzyme binding event. We did a back of the envelope calculation in grad school and it was something like >> 10^6 ~ 10^9.
  And you can of course do macroscopic things like this:
  <a href="https://www.youtube.com/watch?v=3X6qEE2fHvE" rel="nofollow">https://www.youtube.com/watch?v=3X6qEE2fHvE
  1. __MatrixMan__ · 1790525917 · focus · HN ↗
    Capsid assembly is a good example if you want to make a macroscopic analog that works over less than geologic time, but the next step is for the assembled capsid to find and ingest a nucleic acid containing a viral genome as it floats around a broth containing all sorts of other nucleic acids.
    It's wildly nonintuitive that this manages to happen. Maybe you're right, and it can be explained by the numbers being so tremendously large that they break intuition without the need to import any nonintuitive quantum weirdness.
    But if so, isn't such an explanation problematic in its own right? It banishes:
    > The quantum world is impossibly nonintuitive, and it's having an effect
    in favor of
    > The scales here are impossibly nonintuitive, and that's having an effect
    Like... we're still shoving the explanation under a rug, it's just now it's a different rug. Either the quantum effects explanation or the large numbers explanation needs further development before we can call this phenomenon adequately explained, and rather than doing that development it seems like the whole field is dedicated to championing their favored side as-is.
    dnautics · 1790530903 · focus · HN ↗
    What are you talking about. The phenomena are adequately explained. I can measure a Kd and make mathematically modeled predictions that will come true. I can even phenomenologically test contributions to the Kd (ablate hydrogen bond, delete or add a charge, etc)
    Nature is under no obligation to make explanations trivial to a human brain conditioned on quotidian macroscopic observation. Doesn't mean you have to appeal to quantum woo. We know more or less how much "quantum mechanics" (for some definition of QM, obviously an electron shell is QM, but for all intents and purposes you can just treat it as a classical ball that does a few weird things like bonding) contributes, to, say reaction rates. It's nonzero. It's nearly zero, though.
    __MatrixMan__ · 1790532277 · focus · HN ↗
    Nature is not, but scientists are. A theory which humans can map onto experiences at their scale and use to make predictions via intuition is superior (for use by humans) to a theory which makes accurate predictions for inscrutible reasons--supposing their predictive power is equivalent. Beauty, I guess they call it. It leads to improved decision making, experimental design, etc.
    dnautics · 1790533612 · focus · HN ↗
    As a working scientist: chasing beauty is not a good way to do science.
    > It leads to improved decision making, experimental design, etc
    It does not. It often does the exact opposite.
  2. ravila4 · 1790526801 · focus · HN ↗
    Exactly, and the classical lock and key analogy ignores electromagnetic and hydrophobic/hydrophilic interactions, which we can fully model in classical molecular dynamics systems
    dnautics · 1790531059 · focus · HN ↗
    That's not correct. Lock and key absolutely does take into account em and hydrophobic interactions. Also, molecular dynamics is nearly useless at modeling these things (which is why heuristic models such as alphafold, Rosetta, dominate)
9. dekhn · 1790543249 · focus · HN ↗
  If you filled a classical bag with classical locks and classical keys and shook it for a very long time, you would indeed see a small number of keys in locks. There's a non-zero probability set of steps by which that can happen. Am I missing something obvious here?
  1. vanderZwan · 1790577854 · focus · HN ↗
    At the molecular level biology is chemistry, and I think GP is implying that it's often the kind of chemistry that needs quantum mechanics to be explained properly. Now, I don't know how enzymes work, so I don't know if that's true. But I do know that they can do chemical conversions at room temperature where "naive" human chemistry would require temperatures incompatible with life (or pH levels, or pressure, or…).
    So in biology the bag, lock and keys are shaped in such a way that you only have to shake for a short time to have multiple keys come out in locks, and in a particular order or pattern too. That's what makes the whole thing kinda magical. And I would not be surprised if quantum mechanics were involved in the chemistry in ways that classical mechanics cannot explain adequately.
    EDIT: I started typing this yesterday evening and hadn't hit "send" before going to bed, I hadn't seen the rest of the discussion that had taken place since.

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