Can a bacteria be described by physics?

[nonequilibrium]

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?

 

[James Leighe]

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.

 

[nonequilibrium]

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?

 

[DaveC426913]

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.

 

[nonequilibrium]

but we do believe that we understand all the parts that make up a live bacterium

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 argument 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 consensus 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 consensus and is the ground divided equally in yay- and naysayers?

 

[DaveC426913]

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 argument 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 consensus on it?

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.

 

[James Leighe]

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!

 

[DaveC426913]

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).

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.

 

[nonequilibrium]

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.

 

[DaveC426913]

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.

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.

can a bacteria be completely be described in terms of chemistry?

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")

 

[nonequilibrium]

Dave, my apologies!

As for the matter at hand

Yes.

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

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)

 

[DaveC426913]

You seem certain. How can I convince myself of this? Read an applied chemistry book?

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?

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)

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.

 

[Pythagorean]

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.

 

[Ryan_m_b]

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" 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" would act in a given environment. Although such science is far beyond our current capabilities now.

 

[Borek]

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".

 

[Pythagorean]

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.

 

[Borek]

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.

Perhaps my wording was not the best one, but I have a feeling we think about the same problem. Note quotes in my post.

 

[Mike H]

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)

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. ;)

 

[Pythagorean]

Perhaps my wording was not the best one, but I have a feeling we think about the same problem. Note quotes in my post.

I meant not to argue, but to extrapolate. What was a guess to you, appears almost certain to me in modeling philosophy.

 

[Ryan_m_b]

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. ;)

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.

 

[Pythagorean]

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.

I think, from a modeling perspective, you would still need another level of abstraction to understand the colony in whole, especially since bacteria can swap genetic material so frequently. It really brings a whole new level of complexity, you now have a supernetwork. A network within a network that can swap "submotifs".

In fact, we have two different mathematical modeling schemes; population dynamics for the ecology, molecular networks for describing processes inside the single cell. People are working form both ends to model, they haven't met in the middle yet (as far as I know of). You always have to compromise one way or the other. It's not just about computational resources: the programming exceptions and logic handling becomes impossible when you try to both generalize and specify at the same time.

Colonies:

Masayasu Mimura, Hideo Sakaguchi, Mitsugu Matsugarbagea, Reaction-diffusion modelling of bacterial colony patterns, Physica A: Statistical Mechanics and its Applications, Volume 282, Issues 1-2, 1 July 2000, Pages 283-303, ISSN 0378-4371, DOI: 10.1016/S0378-4371(00)00085-6.
(http://www.sciencedirect.com/science/article/pii/S0378437100000856)
Keywords: Pattern formation; Bacterial colony; Reaction-diffusion models

Inside Bacteria:

Bacterial Molecular Networks
Methods and Protocols
Series: Methods in Molecular Biology, Vol. 804
Helden, Jacques van; Toussaint, Ariane; Thieffry, Denis (Eds.)
1st Edition., 2011, 470 p. 139 illus.

 

[Ryan_m_b]

I think, from a modeling perspective, you would still need another level of abstraction to understand the colony in whole, especially since bacteria can swap genetic material so frequently. It really brings a whole new level of complexity, you now have a supernetwork. A network within a network that can swap "submotifs".

In fact, we have two different mathematical modeling schemes; population dynamics for the ecology, molecular networks for describing processes inside the single cell. People are working form both ends to model, they haven't met in the middle yet (as far as I know of). You always have to compromise one way or the other. It's not just about computational resources: the programming exceptions and logic handling becomes impossible when you try to both generalize and specify at the same time.

Yes I agree, I was making the statement that on the understanding that had the relevant knowledge and technology to run simulations at atomic resolution then we could just add more resources.

The big thing with all this simulation talk is that to get there you already have to know and understand the process you are simulating. Simulation only helps if you know all the fundamental processes and want to investigate something that relies on them (e.g. understanding the chemistry well enough will allow you to simulate a protein folding) or if you want to see how a change will effect a system.

 

[Pythagorean]

The big thing with all this simulation talk is that to get there you already have to know and understand the process you are simulating. Simulation only helps if you know all the fundamental processes and want to investigate something that relies on them (e.g. understanding the chemistry well enough will allow you to simulate a protein folding) or if you want to see how a change will effect a system.

Agreed... which is why studying "emergent properties" has become a popular computational task. For instance, we know how neurons work in principle. But we don't know all the permutations and parameter tunings of a neural network that will lead to the right central pattern generator for a salsa dance. It would take endless simulations and tests to find it, and only then could we go in and test our simulation against the real network now that we have somewhere to look.

Of course, as Eve Marder has provided, there is much degeneracy in these networks (different permutaitons leading to the same behavior), so you could still bark up the wrong tree if you're not careful to parallelize with experimentalists in your modeling.

 

[my_wan]

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)

Not trying to go off topic but memory is no mystery either. Hebbian learning was described back in the late 1940s. I could even use a system of metronomes to intuitively illustrate how it works, even though it is nothing like computer memory. From a physics perspective self organized systems are not particularly well understood even though we can show through computer models that the core principles are dirt simple. It is this class of phenomena that I presume you mean by what we cannot explain. Yet the same self-organizing behaviors that make it possible is also ubiquitous in non-living systems. It really comes down to how thoroughly you expect it to be explained.

 

[Ryan_m_b]

Not trying to go off topic but memory is no mystery either.

This is misleading, whilst some processes of how working memory is converted into long term memory are understood to some extent we are still nowhere near to having a comprehensive understanding of memory.

Memory formation and storage links to the http://en.wikipedia.org/wiki/Hard_problem_of_consciousness" , just because we have some idea of the physical processes doesn't mean we have any idea how physical systems give rise to subjective experience.

 

[Pythagorean]

Yeah, the rational view of course is that for there to be memory, there must be some physical degrees of freedom, some state space to store the memory in, and that's where we tackle the problem from.

But we have little idea of what variables are in the state space. Does a dynamic cycle hold a memory? If you short circuit that cycle, is the memory gone? Or are memories stored intrinsically in the matter of the neurons, not the dynamics? We're not sure what aspect of the state-space correlate with what aspects of memory. Memory doesn't seem to be a static thing, it's more likened to long-term processing.

 

[my_wan]

This is misleading, whilst some processes of how working memory is converted into long term memory are understood to some extent we are still nowhere near to having a comprehensive understanding of memory.

Memory formation and storage links to the http://en.wikipedia.org/wiki/Hard_problem_of_consciousness" , just because we have some idea of the physical processes doesn't mean we have any idea how physical systems give rise to subjective experience.

Much like we can create computer generated models of the behavior of bird flocks yet do not really understand the dynamics very well. An intuitive model of how memory works does not get us very far but it works a lot like this:

Except instead of a solid base the connections (memory) is stored in the plasticity of the bases connections between the metronomes so that memories entails only some subset of metronomes syncing when perturbed by sensory data. Since stored sensory experience and competing action responses are stored the same way action becomes an extension of experience.

So it may be misleading to some limited extent I do not think it is to the degree assumed. The only thing misleading about it would be like expecting someone you explained how machine code physically works and memory stored in zeros and ones to then be a programmer. At the basic level memory is not that complicated.

 

[Ryan_m_b]

Much like we can create computer generated models of the behavior of bird flocks yet do not really understand the dynamics very well. An intuitive model of how memory works does not get us very far but it works a lot like this:

Except instead of a solid base the connections (memory) is stored in the plasticity of the bases connections between the metronomes so that memories entails only some subset of metronomes syncing when perturbed by sensory data. Since stored sensory experience and competing action responses are stored the same way action becomes an extension of experience.

So it may be misleading to some limited extent I do not think it is to the degree assumed. The only thing misleading about it would be like expecting someone you explained how machine code physically works and memory stored in zeros and ones to then be a programmer. At the basic level memory is not that complicated.

How memory works from the point of view of neuroscience has not yet been established to the degree that you are suggesting. We have good understanding of what most gross brain anatomy is for, we even have a good understanding of the cellular activity. But to suggest that memory is "not complicated" or that it is "not a mystery" is definitely misleading.

If you could link papers that have detailed experimental data outlining A) the mechanisms by which memories are formed and stored B) how these memories are retrieved with regards to experience and C) how cellular activity leads to subjective experience then I would agree that memory is well understood and not a mystery.

Conceptual explanations are nowhere near comprehensive understanding.

 

[my_wan]

What I have described is basic Hebbian learning. However, if you want more specific examples here is one that explicitly used oscillatory neural networks as I qualitatively described:

(PDF): http://iccm2010.cs.drexel.edu/proceedings/papers/Sylvester.pdf"

Also, from the point of view of neuroscience:
http://www.frontiersin.org/Journal/...3389/neuro.01.027.2009&name=neuroscience&x=y"

Certainly the specific physical implementation in our brains, and other animals, is extremely complex, variable, and poorly understood, but the core principles were laid out in 1949 and continue to gain empirical justification to this day. Like evolutionary algorithms, the core principles are far simpler than any given implementation in biology. I also think the special attention to the feed forward components while ignoring anti-Hebbian components has limited us but we have to start somewhere.

This should not continue under this thread and a new thread is needed to continue.

 

[Andy Resnick]

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?

Unfortunately, this discussion got derailed quite early- mostly becasue nobody supplied any quantitative data to support their assertions.

Specifically, let's consider a MD simulation of a single E. Coli bacteria. This organism has an approximate mass of 1 pg, of which 70% is water. This leads to an estimate of 2*10^10 atoms of water, 6*10^7 ions, 3*10^6 proteins, and 2*10^7 lipids (Phillips et. al. "Physical biology of the Cell", Garland Sci.). Breaking down the proteins and lipids leads to an estimate of 10^10 atoms in the proteins and 1*10^9 atoms in lipids, for a total of about 3.5*10^10 atoms total, just in the bacteria.

The current world record for an MD simulation is 1.1*10^10 atoms (http://www.hpcwire.com/hpcwire/2011..._world_record_in_application_performance.html) for crystalline Si, and 69 ns of simulation per day of an unknown number of atoms (http://www.marketwatch.com/story/new-nvidia-tesla-gpu-smashes-world-record-in-scientific-computation-2011-05-17 ).

Taking into account the need to simulate the bacterium's environment, the strongly interacting nature of the constituent atoms, and a cell replication time of 90 minutes, this shows that current computing technology is still many orders of magnitude away from being able to simulate a single bacterium. We cannot reliably extrapolate that far out.

So we are left with wondering if the laws of physics *in and of themselves* are currently sufficient to "explain" a bacterium, or if additional physics would be required.

 

[Borek]

if additional physics would be required.

Can you elaborate?

As I explained earlier, we know all interactions, and we know how to describe them. There are no other interactions - so simulated system should behave just like the real one. And I don't mean we can reproduce exact case and situation, more like we should be able to simulate systems that behaves the way we expect it.

Slightly off topic:

Several years ago I wrote an artificial life simulation of bitozoa. All bitozoa do is they eat, move and reproduce (and evolve, but that's not important here). However, how they reproduce depends on the amount of food. There are two kinds of bitozoa - carnivores and herbivores (there are also plants, again, not important for what I am aiming at). And while I never attempted to reproduce population dynamics, quite often their population oscillate, as if I was solving Lotka–Volterra equation. I don't have a more convincing population history plot here, but I just started the program and got this:

there are four nice oscillations visible (system is not stable, as animals evolve, so they can become better at hunting or avoiding danger).

This is not a simulation of bacteria, however some properties of the system emerge automatically, not because they were programmed, but because that's the way system behaves.

 

[nonequilibrium]

As I explained earlier, we know all interactions, and we know how to describe them. There are no other interactions - so simulated system should behave just like the real one. And I don't mean we can reproduce exact case and situation, more like we should be able to simulate systems that behaves the way we expect it.

But isn't this a circular reasoning? I agree with your statement that given the premisse 'we know all the interactions and how they work' the rest follows, but it's exactly the premisse I don't see as evident. (and I said "circular" because to prove we know everything that goes on (and how), you have to assume we know how everything goes on (and how)) Of course I'm not saying you may not have a good reason to be convinced of the fact we're aware of all the processes, but I don't think you've given any back-up for that? It seems to me the only way to be convinced of that is to actually simulate it using the known and understood processes and see if they suffice. But perhaps I'm overseeing some other verification process.

Note that I'm not saying in advance, with any prejudice, "we definitely don't know all the processes for a bacterium", I'm just stating my ignorance on the subject.
As for the more troubling matter of thought and (self)consciousness, I would say that I do lean more to one side than the other: that we don't know all the fundamental laws just yet, mainly because thought seems to demand a whole new concept that we can't even properly define yet, and I don't know how any other case in the history of science where you had a concept you couldn't even define with your previous concepts yet that new concept followed out of the old concepts nonetheless. Of course this is an opinion/feeling.

 

[Andy Resnick]

Can you elaborate?

As I explained earlier, we know all interactions, and we know how to describe them.

A good quote to think about is "More is different".

http://robotics.cs.tamu.edu/dshell/cs689/papers/anderson72more_is_different.pdf

 

[nonequilibrium]

A good quote to think about is "More is different".

http://robotics.cs.tamu.edu/dshell/cs689/papers/anderson72more_is_different.pdf

I don't find that to be a very clear article; I quote

The main fallacy in this kind of thinking is that the reductionist hypothesis does not by any means imply a "constructionist" one: The ability to reduce everything to simple fundamental laws does not imply the ability to start from those laws and reconstruct the universe.

I would think it does, given the proper computing power, I can't conceive of any reason why not, and the author does not convince me of his point (does he try?).

Anyway, it does not seem like that discussion is what this topic is mainly about: that article is about "okay even if we have all the fundamental laws, can we make/simulate a bacterium" (mixing it with my original question), while I was more concerned with "do we have all the fundamental laws relevant for the bacterium?", taking it as a given that having those laws is enough for also simulating it (again, ignoring technicalities concerning computer power, although of course, for a definite answer, it seems we'd have to check with the computer, so the technicalities aren't completely besides the point, but anyway they're not the point itself)

 

[my_wan]

I don't find that to be a very clear article; I quote

The main fallacy in this kind of thinking is that the reductionist hypothesis does not by any means imply a "constructionist" one: The ability to reduce everything to simple fundamental laws does not imply the ability to start from those laws and reconstruct the universe.

I would think it does, given the proper computing power, I can't conceive of any reason why not, and the author does not convince me of his point (does he try?).

Anyway, it does not seem like that discussion is what this topic is mainly about: that article is about "okay even if we have all the fundamental laws, can we make/simulate a bacterium" (mixing it with my original question), while I was more concerned with "do we have all the fundamental laws relevant for the bacterium?", taking it as a given that having those laws is enough for also simulating it (again, ignoring technicalities concerning computer power, although of course, for a definite answer, it seems we'd have to check with the computer, so the technicalities aren't completely besides the point, but anyway they're not the point itself)

Take a very simple system like a double pendulum, i.e., a pendulum with a hinge in the middle. This system only has two moving parts with laws of motion that are very well understood. Yet we cannot predict how the thing is going to react from any given motion. We understand why we cannot. Now if we consider a system with billions of parts, rather than two, what do you you really expect? No amount of computing power will EVER fix it. Though we can predict those billion parts more accurately than two in some ways.

The range of systems, which even when we fully model on a computer we cannot predict what the computer is going to do from one run to the next with the same data, is huge. You cannot say a programmer did not understand the rules they put in a program. So when you say about predictability you "can't conceive of any reason why not" a whole history and areas of science are being ignored by this statement. Chaos theory, for one, is predicated on these issues. We already understand why we have such limits. Though we can improve those limits we can never make them go away even if we knew every fundamental law in the Universe.

 

[Borek]

Take a very simple system like a double pendulum, i.e., a pendulum with a hinge in the middle. This system only has two moving parts with laws of motion that are very well understood. Yet we cannot predict how the thing is going to react from any given motion.

If you treat the simulation of a pendulum like a prediction, you have a problem. But if you treat this simulation like just another one pendulum experiment, it behaves just like it should. You can't repeat the double pendulum experiment getting the same results twice, why not treat a simulated system as the same experiment run for a third time? Different results? That's what we expected.

Same about bacteria - simulation doesn't have to be about predicting, or perfect recreation of a particular organism, I agree that's impossible. But once you have a running simulation you don't have to be able to point to a particular living organism and say "that's my model". It is enough that your simulated organism behaves like other bacteria - no two are identical, simulated one will be just another one.

Sorry, I am in hurry, I would love to read the paper Andy linked to, but I am leaving for a month in two hours.

 

[DaveC426913]

If you treat the simulation of a pendulum like a prediction, you have a problem. But if you treat this simulation like just another one pendulum experiment, it behaves just like it should. You can't repeat the double pendulum experiment getting the same results twice, why not treat a simulated system as the same experiment run for a third time? Different results? That's what we expected.

Same about bacteria - simulation doesn't have to be about predicting, or perfect recreation of a particular organism, I agree that's impossible. But once you have a running simulation you don't have to be able to point to a particular living organism and say "that's my model". It is enough that your simulated organism behaves like other bacteria - no two are identical, simulated one will be just another one.

Sorry, I am in hurry, I would love to read the paper Andy linked to, but I am leaving for a month in two hours.

Thank you. That's what I was trying to say. Simulation =/= prediction.

 

[Andy Resnick]

Same about bacteria - simulation doesn't have to be about predicting, or perfect recreation of a particular organism, I agree that's impossible. But once you have a running simulation you don't have to be able to point to a particular living organism and say "that's my model". It is enough that your simulated organism behaves like other bacteria - no two are identical, simulated one will be just another one.

Thank you. That's what I was trying to say. Simulation =/= prediction.

But then what's the value of the simulation? All science has value because it leads to *predictions*. It's not sufficient to simply say "here's a simulation that agrees with observations", because that doesn't lead to any new understanding- only a confirmation that a sufficient number of parameters can be blindly tweaked to replicate observed experiments.

It's not required to predict the moment-to-moment state of a bacterium (yet), but surely it would be of value to predict the action of a particular antibiotic.

 

[Ryan_m_b]

But then what's the value of the simulation? All science has value because it leads to *predictions*. It's not sufficient to simply say "here's a simulation that agrees with observations", because that doesn't lead to any new understanding- only a confirmation that a sufficient number of parameters can be blindly tweaked to replicate observed experiments.

It's not required to predict the moment-to-moment state of a bacterium (yet), but surely it would be of value to predict the action of a particular antibiotic.

Indeed, to make the simulation we would have to know all the processes of the bacteria in question anyway. What would be interesting is altering the simulation i.e. increasing the concentration of specific chemicals in the environment.

 

[Andy Resnick]

Indeed, to make the simulation we would have to know all the processes of the bacteria in question anyway. What would be interesting is altering the simulation i.e. increasing the concentration of specific chemicals in the environment.

Exactly. We can't yet predict the structure of a single protein given the amino acid sequence- we have no business extrapolating out the 10^10-10^20 increase in complexity needed for a single cell.

 

[Pythagorean]

A caveat though, to the OP. Describing things in physics doesn't require (in fact, tends to avoid) modeling things as "every single atom". We parcel things into their functional parts and model those. We have no interest in what the atoms are doing in a cannonball simulation.

Likewise, we might find a more appropriate modeling scheme for bacteria if we break it down to functional molecules, lipid membranes, whole processes, etc. We don't want to over-reduce the problem or we get bogged down with unnecessary computation.

Unfortunately, this discussion got derailed quite early- mostly becasue nobody supplied any quantitative data to support their assertions.

Specifically, let's consider a MD simulation of a single E. Coli bacteria. This organism has an approximate mass of 1 pg, of which 70% is water. This leads to an estimate of 2*10^10 atoms of water, 6*10^7 ions, 3*10^6 proteins, and 2*10^7 lipids (Phillips et. al. "Physical biology of the Cell", Garland Sci.). Breaking down the proteins and lipids leads to an estimate of 10^10 atoms in the proteins and 1*10^9 atoms in lipids, for a total of about 3.5*10^10 atoms total, just in the bacteria.

The current world record for an MD simulation is 1.1*10^10 atoms

But this isn't really the question that's being asked; The question is not really one of quantification and instead one of qualification. The question isn't whether we have the computing power. It's if we could, would it work; the question is in the title; "Can a bacteria be described by physics". And the point we were making (at least, in my own case) was that there's still lots of intermediary issues (i.e. the complexity).

In other words, we have lots of theories in biology about how different processes work. Eventually, every once in a while, we discover the means of the process. Never, so far, have the known physical laws been violated in this way. It's always continued to come down to the same physics; only the biology (which permutations of physics nature actually uses) changes. So we say organisms utilize QM (plants) or they don't (the brain), but in either case, physics is not changed or violated.

So we are left with wondering if the laws of physics *in and of themselves* are currently sufficient to "explain" a bacterium, or if additional physics would be required.

So far, we haven't needed new physics. Just deeper understanding of what physics are actually taking place in life forms. Of course, some of us think a paradigm will be required to actually explain a bacteria (myself included) but that's magical thinking. We continue to make progress every day with the current physics.

 

[epenguin]

Protein folding - when I last heard (admittedly something like 10 y ago ) they held annual competitions for who could best predict the 3-D structure from the amino-acid sequence. One guy was doing it qualitatively from physico-chemical knowledge about hydrogen bonds and all the other types of interaction and was doing sometimes better than the heavily computational guys. Suggesting understanding is not the same thing as computation, chemistry is not just computational physics of molecules.

Also the study of protein folding is one speciality. When you simulate a bacterial metabolism would you try to put the protein folding simulation into the whole-bacteria simulation? That would be a rather stupid way of doing things. Whether you do or do not completely understand protein folding, if you just put in e.g. their rate of formation, their catalytic parameters (substrate affinity, catalytic rate constants) even if they had been only experimentally estimated, would you have fundamentally lost anything by that? I you don't fundamentally understand every molecular interaction in minerals that determines their mechanical and thermal properties does that make Earth science a special mystery necessarily in need of New Principles?

Large branches of science handle things with phenomenological laws. When we study electrical circuits - thousands of questions on this site - we don't worry too much abot the various laws being only approximate and the parameters, resistivities etc. not simply predictable. Even though, sure, someone also has to chase up those.

Quantitative mathematical and computational study of metabolism is normal science that has been going on for quite a long time.

 

[Ryan_m_b]

Also the study of protein folding is one speciality. When you simulate a bacterial metabolism would you try to put the protein folding simulation into the whole-bacteria simulation? That would be a rather stupid way of doing things. Whether you do or do not completely understand protein folding, if you just put in e.g. their rate of formation, their catalytic parameters (substrate affinity, catalytic rate constants) even if they had been only experimentally estimated, would you have fundamentally lost anything by that? I you don't fundamentally understand every molecular interaction in minerals that determines their mechanical and thermal properties does that make Earth science a special mystery necessarily in need of New Principles?

You might get an appropriate simulation from simulating the things you've mentioned but it won't be useful. If you want to use a simulation to test how an antibiotic works for instance it's vital that you understand the molecular processes.

Fundamentally biology works on the molecular scale, if you want to get meaningful answers of such complex systems you will need to simulate it on that level.

 

[Andy Resnick]

You guys raise excellent points-too many to explicitly quote :). You also raise some interesting points about what a model is used for, what 'understanding' means, etc.

First, I don't think anyone would seriously argue that bacteria, or any organism, is "outside" of our current state of physical understanding- surely, bacteria obey the second law of thermodynamics, for example.

But some context is in order- considering the level of conceptual abstraction used in physical modeling, biology is positively pre-Newtonian. That is, there is *no* abstract concept that can be applied to biological systems in the way "Force" is used to conceptualize dynamic physical systems. Biology has yet to have it's Newton.

"Modeling" in biology currently means something very different than 'modeling' in Physics, and some of the discussion has neglected this important distinction. While there are some quantitative models in biology- the canonical example in my mind is Guyton's model of cardiac regulation:

http://ajpregu.physiology.org/content/287/5/R1009/F2.expansion.html

The majority of 'models' in biology refer to (simpler) organisms that display a trait or behavior that is analogous to human physiology: a mouse model of renal disease, for example. E. Coli is a model organism- it is used as a model (of limited scope) for more complicated systems.

Now, thread title aside, the OP specifically asked if we could model each individual atom in a bacterium and thence construct a quantitative, predictive *computational* model. Again, my answer is that we should not make any claims regarding this possibility, given the current primitive state of MD simulations.

In the meantime, we must use "coarse grained" computational, experimental, or theoretical models. Must protein folding be a part of a metabolic simulation? It depends on what the simulation is to be used for- since a fraction of metabolism goes towards protein synthesis, we may indeed require a model that can handle the details of protein folding- if for nothing more than accounting for misfolded proteins and the degredation pathway. This could likely *still* be handled by phenomenological models based on experimental results (i.e. fraction of misfolded proteins, etc), but then we can't claim that the model is based on first-principles Physical Law.

What the model 'is' and what information is contained in the model (and here I speak generally, including 'model organisms') entirely depends on what the purpose of the model is- what the results of a simulation/experiment will be used for.

And when you get down to it, nobody is that interested in a MD simulation of a bacterium swimming around. Biomedical research dollars go towards understanding human health and disease.

 

[epenguin]

You might get an appropriate simulation from simulating the things you've mentioned but it won't be useful. If you want to use a simulation to test how an antibiotic works for instance it's vital that you understand the molecular processes.

Fundamentally biology works on the molecular scale, if you want to get meaningful answers of such complex systems you will need to simulate it on that level.

But I am not denying that! The interaction of an antibiotic with a target protein is just normal physics or chemistry. The consequences should be affecting a limited number of processes downstream. So you don't need an equation for the bacterium that is killed and you could say it can be described by physics.

 

[Andy Resnick]

The interaction of an antibiotic with a target protein is just normal physics or chemistry. The consequences should be affecting a limited number of processes downstream. So you don't need an equation for the bacterium that is killed and you could say it can be described by physics.

That's true to some degree, but a predictive ligand-receptor binding model would be invaluable to have. Think about chemotherapy; we currently have drugs designed to target very specific receptors. However, since we have an imperfect understanding, chemotherapy drugs also affect many non-cancerous cells that happen to divide rapidly: gut epithelium, hair follicles, bone marrow.

Or, if you prefer- consider minoxidil and sildenafil citrate. Both chemicals were developed to treat blood pressure via nitric oxide regulation of the renin-angiotensin system. Nobody knew about the side effects, which resulted in both of these chemicals becoming the most prescribed drugs in the history of civilization.

The utility of a predictive model should be clear.