3 ms·

By using lambda calculus, interaction nets, something equivalent, is my guess.

by isthatart 8y ago

subroutine 8y ago
For what exactly? What specifically do you mean by "computation", above?
- isthatart 8y ago
  I mean by that a model of computation in the TCS sense. (Some) molecules, be them DNA, RNA or other, are akin to lambda terms (or graphs), beta reduction (or other graph rewrites) are akin to chemical reactions. The algorithm of reduction has to be random, local (i.e. no higher point of view criteria for interaction are used), performed by Nature. All in all, to be able to prove that some part of the biochemistry can be seen, as a concrete asynchronous graph rewrite automaton (capable of universal computation) would be a great advance in biology.
  - dekhn 8y ago
    I'm not sure why that would be the case. First, I think most smart people already recognize that sufficiently complex biochemical systems can in fact perform computation as well as other abstract operations. Second, there is already a ton of literature in this area, it's often very helpful to analyze biological data from the perspective of various graph and sequence rewrite automata, but that doesn't necessarily mean that the underlying biology is explicitly exploiting matter at that level. Third, I don't see why having any such "proof" (to the extent that you can prove anything about biological systems anyway) would be an advance. What new predictions would you be able make?
    - isthatart 8y ago
      This and the references https://figshare.com/articles/Chemlambda_strings/5751318 https://figshare.com/articles/Chemlambda_strings/5751318
- bitL 8y ago
  The DNA is changing real-time, i.e. there is a periodic process we usually call algorithm. Algorithm might imply some sort of computation going on; while it's pretty common to see computations being performed via neurons and protein interactions, seeing it directly in DNA is much more interesting. Instead of assuming genes are static, there actually could be some DNA-level computation going on, potentially invalidating significant portions of our knowledge of genetics.
  - klmr 8y ago
    > The DNA is changing real-time We already knew this. DNA is a highly dynamic molecule, and it’s changing constantly, as it’s involved in biochemical processes in the cell. i-motifs aren’t special or new in this sense.
  - dekhn 8y ago
    No, there is no reason to conclude any of this from this paper. BTW, if this blows your mind, then the mating type switch of yeast is really gonna blow the stack: https://en.wikipedia.org/wiki/Mating_of_yeast#Mating_type_switching https://en.wikipedia.org/wiki/Mating_of_yeast#Mating_type_sw...

By using lambda calculus, interaction nets, something equivalent, is my guess.

subroutine 8y ago

For what exactly? What specifically do you mean by "computation", above?

isthatart 8y ago
I mean by that a model of computation in the TCS sense. (Some) molecules, be them DNA, RNA or other, are akin to lambda terms (or graphs), beta reduction (or other graph rewrites) are akin to chemical reactions. The algorithm of reduction has to be random, local (i.e. no higher point of view criteria for interaction are used), performed by Nature. All in all, to be able to prove that some part of the biochemistry can be seen, as a concrete asynchronous graph rewrite automaton (capable of universal computation) would be a great advance in biology.
- dekhn 8y ago
  I'm not sure why that would be the case. First, I think most smart people already recognize that sufficiently complex biochemical systems can in fact perform computation as well as other abstract operations. Second, there is already a ton of literature in this area, it's often very helpful to analyze biological data from the perspective of various graph and sequence rewrite automata, but that doesn't necessarily mean that the underlying biology is explicitly exploiting matter at that level. Third, I don't see why having any such "proof" (to the extent that you can prove anything about biological systems anyway) would be an advance. What new predictions would you be able make?
  - isthatart 8y ago
    This and the references https://figshare.com/articles/Chemlambda_strings/5751318 https://figshare.com/articles/Chemlambda_strings/5751318
bitL 8y ago
The DNA is changing real-time, i.e. there is a periodic process we usually call algorithm. Algorithm might imply some sort of computation going on; while it's pretty common to see computations being performed via neurons and protein interactions, seeing it directly in DNA is much more interesting. Instead of assuming genes are static, there actually could be some DNA-level computation going on, potentially invalidating significant portions of our knowledge of genetics.
- klmr 8y ago
  > The DNA is changing real-time We already knew this. DNA is a highly dynamic molecule, and it’s changing constantly, as it’s involved in biochemical processes in the cell. i-motifs aren’t special or new in this sense.
- dekhn 8y ago
  No, there is no reason to conclude any of this from this paper. BTW, if this blows your mind, then the mating type switch of yeast is really gonna blow the stack: https://en.wikipedia.org/wiki/Mating_of_yeast#Mating_type_switching https://en.wikipedia.org/wiki/Mating_of_yeast#Mating_type_sw...