3 ms·

I'm ignorant of this theory, but reading the link I don't see that it shows that protein folding can't be modeled.

cageface 16y ago
You'd have to read the papers cited below to get the meat of the theory but the gist of it is that you can't model proteins by looking one level down, i.e. by studying only the properties of the atoms that make them up. Proteins have emergent behaviors not entirely predictable from the behaviors of their constituent atoms. Many still believe in the reductionist idea that a perfect understanding of physics would lead to a perfect understanding of chemistry and then biology. This is not the case.
- orangecat 16y ago
  Proteins have emergent behaviors not entirely predictable from the behaviors of their constituent atoms. Define "emergent". I can believe that a protein's behavior is extremely sensitive to the initial configuration of its atoms and that as a practical matter we can't (currently?) get detailed enough measurements to predict exactly what's going to happen. But without exceptionally compelling evidence I'm not going to believe that there are different physical laws for proteins than for their atoms.
  - cageface 16y ago
    I suggest you read Prigogine's book if you're really interested but his work demonstrates that the problem isn't having detailed enough information about state, it's the irreversibility of time, which makes physics fundamentally non-deterministic.
    - TheEzEzz 16y ago
      What has irreversibility got to do with it? There are cellular automata that are irreversible but obviously deterministic.
      - cageface 16y ago
        It has to do with entropy and thermodynamics and the fact that living systems are so far removed from thermodynamic equilibrium that they generate unpredictable, emergent behaviors. The math behind is pretty gnarly but if you want to understand it I recommend his book: http://www.amazon.com/End-Certainty-Ilya-Prigogine/dp/0684837056 http://www.amazon.com/End-Certainty-Ilya-Prigogine/dp/068483... . A CA is not a good model for this.
- rsheridan6 16y ago
  I'm out of my depth here, but if protein folding is intractable like the halting problem or the traveling salesman problem, as you're making it seem, I find it odd that I haven't read that elsewhere.
wcoenen 16y ago
The physics can be modeled, but according to this article (http://techglimpse.com/index.php/ibms-blue-gene-exploring-protein-folding-mystery.php http://techglimpse.com/index.php/ibms-blue-gene-exploring-pr...) a 1 petaflops machine is estimated to take 3 years to crunch through 100 microseconds of simulated time. And that's just for a single protein interacting with itself and a bit of water.
- rsheridan6 16y ago
  That might just mean they haven't found the right algorithm yet.
  - Locke1689 16y ago
    Most people suspect it to be NP-hard or NP-complete.

You'd have to read the papers cited below to get the meat of the theory but the gist of it is that you can't model proteins by looking one level down, i.e. by studying only the properties of the atoms that make them up. Proteins have emergent behaviors not entirely predictable from the behaviors of their constituent atoms. Many still believe in the reductionist idea that a perfect understanding of physics would lead to a perfect understanding of chemistry and then biology. This is not the case.

orangecat 16y ago
Proteins have emergent behaviors not entirely predictable from the behaviors of their constituent atoms. Define "emergent". I can believe that a protein's behavior is extremely sensitive to the initial configuration of its atoms and that as a practical matter we can't (currently?) get detailed enough measurements to predict exactly what's going to happen. But without exceptionally compelling evidence I'm not going to believe that there are different physical laws for proteins than for their atoms.
- cageface 16y ago
  I suggest you read Prigogine's book if you're really interested but his work demonstrates that the problem isn't having detailed enough information about state, it's the irreversibility of time, which makes physics fundamentally non-deterministic.
  - TheEzEzz 16y ago
    What has irreversibility got to do with it? There are cellular automata that are irreversible but obviously deterministic.
    - cageface 16y ago
      It has to do with entropy and thermodynamics and the fact that living systems are so far removed from thermodynamic equilibrium that they generate unpredictable, emergent behaviors. The math behind is pretty gnarly but if you want to understand it I recommend his book: http://www.amazon.com/End-Certainty-Ilya-Prigogine/dp/0684837056 http://www.amazon.com/End-Certainty-Ilya-Prigogine/dp/068483... . A CA is not a good model for this.
rsheridan6 16y ago
I'm out of my depth here, but if protein folding is intractable like the halting problem or the traveling salesman problem, as you're making it seem, I find it odd that I haven't read that elsewhere.

wcoenen 16y ago

The physics can be modeled, but according to this article (http://techglimpse.com/index.php/ibms-blue-gene-exploring-protein-folding-mystery.php http://techglimpse.com/index.php/ibms-blue-gene-exploring-pr...) a 1 petaflops machine is estimated to take 3 years to crunch through 100 microseconds of simulated time. And that's just for a single protein interacting with itself and a bit of water.

rsheridan6 16y ago
That might just mean they haven't found the right algorithm yet.
- Locke1689 16y ago
  Most people suspect it to be NP-hard or NP-complete.