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Can a bacteria be described by physics?

  1. Jul 2, 2011 #1
    If we had a powerful enough computer, and we supplied to it the laws of physics known so far and the atoms a bacteria was made out of at a certain time, would the simulation then show the actual behavior of a bacteria?

    Or more compactly: does current physics suffice to explain all the facets of a bacteria?
     
  2. jcsd
  3. Jul 2, 2011 #2
    We could not supply all of the information about a bacteria that exists in the real world because we cannot know both the momentum and position of a particle with certainty (so we couldn't input all it's information to simulate it properly).

    But, if we were to make a pretend bacteria, by inputting where we know the atoms should go for a bacteria, then known physics would suffice for telling us the probability of different possible futures of the bacteria.

    See, that's the thing, physics currently works (and will likely always work) by telling you the probability of certain future events happening... But it's likely that since a bacteria is so 'large' compared to the 'size' of an atom that we would get a very large chance that it would act as expected and so could go with that.


    Short Answer: Yes, but with some (probably minor in this case) caveats.
     
  4. Jul 2, 2011 #3
    Amazing, so there's no new concept needed to go from the current knowledge of physics to life? Do you have any back-up for that?
     
  5. Jul 2, 2011 #4

    DaveC426913

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    I believe that James is on the wrong track. He seems to think you mean literally predicting its future. The Uncertainty Principle will impact the ability to actually predict what exact events will next happen on an atomic level, but do we need to know that in order to observe a bacterium to eat or excrete or divide? No. Simulating a bacterium does not mean we predict when exactly a metabolismic activity will occur, simply that it will.

    But you tell me. If we were to make a simulation, would it be enough that we saw it move and eat and excrete and grow? Or you literally saying you want to predict that, at this moment, it wiggles left instead of right? (And what would it man to predict? You'd have to have a real one and the simulation side-by-side. If the real one wiggled right but the virtual one wiggled left, would that be a failed test?)


    As for actually addressing your question: don't know if we do have enough processing power to actually simulate one (note: you'd need to also simulate its environment), but we do believe that we understand all the parts that make up a live bacterium. It is a very (incredibly) complex interaction of proteins and chemcial reactions, but nothing more.
     
    Last edited: Jul 2, 2011
  6. Jul 2, 2011 #5
    That answer (or its negation) is what I'm looking for yes, the conceptual issue, whether current physics suffices to describe living organisms (excluding consciousness, still being the holy grail, cf. last paragraph of this post if you disagree).

    Do you find it obvious current physics has all the necessary concepts to describe life (in principal)? The behavior of a living organism --e.g. the action of restoring itself-- seems very unlike 'normal' situations where the equations of physics are applied. I'm not saying that is an arguement against, after all the arrow of time for example is also derivable out of symmetric time laws, something which is at face value contradictory; and I am a reductionist so I'd love for physics to be able to describe life, but I'm just saying I find it unevident that the current state of physics suffices to describe organisms like a bacteria. What are the reasons for believing so? Is there a general concensus on it?

    And a side-question, if not pushing it: I think everybody "agrees" that physics, so far, can not describe (self)consciousness (so well above a bacteria) and that something needs to be introduced in theoretical physics to get it, or am I wrong in thinking that there is such a concensus and is the ground divided equally in yay- and naysayers?
     
  7. Jul 2, 2011 #6

    DaveC426913

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    To clear, it is the subset of physics - chemistry - that describes bacteria.

    Simple chemistry has been described perhaps optimistically by some as a "closed" science. We get how it works. Biochemistry - protein folding and such - is another ball of wax. It's fabulously complex, and we may not be able to see all the pieces at the same time, but there's nothing mysterious or supernatural about it.
     
  8. Jul 2, 2011 #7
    What do you mean by "action of restoring itself"?

    Organisms are made up of atoms, we know how atoms work/interact in principal. So, in principal, physics has all the necessary concepts to describe life.

    As for consciousness, we simply don't know what consciousness is. If you could say definitely, "Consciousness is the result of neuron interaction" then the answer is yes, physics describes consciousness. But we can't say that because we don't know what consciousness is.

    EDIT:
    "I believe that James is on the wrong track. He seems to think you mean literally predicting its future."

    I tried (and failed it seems) to make it clear that you could not reasonably predict the future of a specific real life bacteria (due to HUP) and that you could only know chances of possible futures for even a pretend bacteria (one that you pretended to know all the initial conditions for).

    EDIT2: Beaten!
     
  9. Jul 2, 2011 #8

    DaveC426913

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    No, I think you made it clear; I just think you missed the point of the thread. And it would appear that the OP does too.
     
  10. Jul 2, 2011 #9
    Dave - sigh, the fact I wonder about if the current (as I have emphasized) knowledge of science suffices or not to describe organisms, isn't the same as wondering if it requires anything supernatural... You're giving me the irrational religious nut treatment. Back to business: let me rephrase my question then: given that chemistry is derivable out of (relativistic) quantum mechanics (which hasn't actually been done, except for simple atoms (?), but okay that seems reasonable enough), can a bacteria be completely be described in terms of chemistry? The sad thing, of course, is that now this is in the wrong subforum.

    James - Okay, the "action of restoring itself" is a horrible way of referring to... I don't know what to call it in English, but I think you know: if you get a cut, it'll heal itself. Of course I'm not saying such things can't be described by physics, just saying that such features (as self-restoring systems) are not usually associated with the more normal situations where physics is applied: atoms, light, and such.
    As for "consciousness", let's replace it with the more manageable concept of "thought" or "that little voice inside your head"

    EDIT: "And it would appear that the OP does too." Now you're just trying to be insulting for some reason (although I'm not sure what you're getting at), and don't try to turn it around back at me: saying a person doesn't understand the point of his own question is really just nothing more than being insulting, and you know it. Not a good attitude. It makes me uninterested in what else you have to say, so maybe just leave your replies for what they are.
     
  11. Jul 2, 2011 #10

    DaveC426913

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    You have completely misinterpreted me. I apologize if my ambiguity has lead you to think I am doing anything less than trying to defend the question you asked.

    I rephrase post 8 to be explicit:

    "I just think [James] missed the point of the thread. And it would appear that Vodka also thinks that James has missed the point of Vodka's thread."




    I think James is on the wrong track trying to answer your question in a way you didn't ask. In post 5, I got the impression that you were confirming that - that, indeed, James was missing the point of the question you were trying to ask (you are asking predicting general behaviour, not predicting a specific future). I was concurring with you.





    Yes.

    Which is why, if you think it might not, what else is there?

    (I didn't mean supernatural "religious", I meant supernatural "beyond chemistry into something we don't understand")
     
    Last edited: Jul 2, 2011
  12. Jul 2, 2011 #11
    Dave, my apologies!

    As for the matter at hand

    You seem certain. How can I convince myself of this? Read an applied chemistry book?
    To go further: there are things in organisms we can't explain yet, right (in terms of physics, or the applied physics known as chemistry)? Memory for example? So somewhere as you get to more complex organisms there is a line which marks what physics can explain and can't? Or do you believe pretty much everything in humans is captured in our current laws? (but that would seem like a more personal conviction than a general consensus, I think)
     
  13. Jul 2, 2011 #12

    DaveC426913

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    I'm not certain, but I ask: what mystery is there to ask questions about? Is there a reason you think a bacterium can't be explained by chemistry as we know it?


    Agreed. There are some things we don't understand about complex life yet. I suppose we take it on faith that it does not require more than chemistry.
     
  14. Jul 2, 2011 #13

    Pythagorean

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    Some, I think, are hoping for a paradigm shift to come out of information theory and the general systems approach.

    Of course, it would not disprove the physics or chemistry of life; just help to understand the difference between "animate" and "inanimate" systems.
     
  15. Jul 3, 2011 #14

    Ryan_m_b

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    I don't think it is fair to say that we could use the physics of today, partly because we still have no real way of simulating protein folding. This isn't just a question of insufficient computational power but because of a lack of understanding of the process. If we did have such an understanding then it becomes reasonable to suppose that a molecular dynamic simulation of the entire organism and environment would be possible however the simulation of quantum effects may also be necessary for life.

    In addition our knowledge of http://en.wikipedia.org/wiki/Genome" [Broken] that a simulation is unnecessary for telling us anything about said bacteria.

    What such systems might be good for is simulating how http://en.wikipedia.org/wiki/Synthetic_biology" [Broken] would act in a given environment. Although such science is far beyond our current capabilities now.
     
    Last edited by a moderator: May 5, 2017
  16. Jul 3, 2011 #15

    Borek

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    Taking a reductionist view - whatever emergent properties living organism has, they must be effect of known interactions. No matter how physicist try, so far they have not found anything but four fundamental interactions, so if we (correctly) simulate the system driven by these interactions, all emergent properties should... emerge.

    Simple example: diffusion. Diffusion is described by Fick's laws. Imagine you are to simulate ideal gas to which other ideal gas was added. Do you need to use Fick's laws? No! You can simulate random motions of gas molecules ("primitive" physical collisions), and if the sample is large enough, results of the simulation will automatically obey Fick's laws.

    Living cell is much larger and calculations are much more complicated, but there is no principal difference between both cases. We know the physics, we know the equations, we know the molecules - once everything is put in place simulated cell should work.

    The real question for me is whether our (approximate) models/methods used for simulations are good enough. I doubt, but I am just guessing. But this is "just a technicality".
     
  17. Jul 3, 2011 #16

    Pythagorean

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    I don't think the reduced physics will change at all, just the way we integrate the local regions.

    In the example of protein folding, I think it's only a matter of complexity, not a matter of new physics. Though there's no doubt QM plays a role in the same reductionist sense. Organic chemistry is founded on quantum states. We don't know very much about open quantum systems at all, so the imaginary line we draw between quantum and classical world is a tough pill with chemical (and thus, biological) systems.

    Borek: I don think this is just a technicality in the wake of chaos and complexity. Sometimes, an error of 10^-6 is really a totally different region of state space from the dynamics point of view. Our real state space is thousands of dimensions large and many of us only try to understand two state variables at a time.

    Things would move much faster, I think, if we could imagine ten dimensions at once.
     
  18. Jul 3, 2011 #17

    Borek

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    Perhaps my wording was not the best one, but I have a feeling we think about the same problem. Note quotes in my post.
     
  19. Jul 3, 2011 #18
    We have a handle on memory in bacteria.

    Of course, specie-ists will tell you it's just an adaptation response and is nothing more than fairly unadventurous biochemistry (methylation and demethylation of certain residues on the cytoplasmic side of the transmembrane chemoreceptor), and it only persists for so long to "remind" the bacterium that it's swimming in the right direction for nutrients.

    Mind you, even if one was to model a single bacterium computationally, the real challenge would be to model an entire community of them. For example, do heterocysts come about when one models a colony of cyanobacteria (the differentiated bacteria that are able to fix nitrogen)? Do you see differential gene expression in biofilms versus floating bacterial colonies?

    It helps to remember that while modeling a single bacterium might be a truly great accomplishment, people will never be happy with only one. ;)
     
  20. Jul 3, 2011 #19

    Pythagorean

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    I meant not to argue, but to extrapolate. What was a guess to you, appears almost certain to me in modeling philosophy.
     
  21. Jul 4, 2011 #20

    Ryan_m_b

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    If we had the knowledge of all the relevant biochemistry and the necessary computational power and programming to simulate a colony of bacteria we only need to strap more computers into the mix. The hardest part will be gaining the relevant knowledge of starting organism and environment conditions and writing the relevant simulation software.
     
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