4 ms·

I'd like to hear more about this. My understanding is that these things are not Turing complete, and don't resemble Von Neumann machines (or any other architec

I'd like to hear more about this. My understanding is that these things are not Turing complete, and don't resemble Von Neumann machines (or any other architecture we use for computers). But the processes themselves can be understood in terms of computation and/or communication. Is that wrong? If so, why/how? Also, could you point out an example or two of the nuances that tend to get people in trouble?

dnautics 6y ago
The big one is it's nondeterministic. An obvious example of nondeterminism is the genotype which determines mirror-body, it's caused by a defective cilium. Normally that cilium enforces torquoselectivity -it only rotates in one direction which establishes chiral directionality, but a certain genotype disables its rotation, so the orientation of your body is a factor of random chance based on how your cell was rotating at the single cell level. The mendelian inheritance is basically 50/50 stochastic based on the genotype. That's a pretty macro example (both at the genotypic ratio and phenotype levels), but it can happen at the micro level, too. You can have grossly nonlinear effects (well actually many effects are O(n^k) in concentration n, where k is the oligomer size, 2->12->20++) and sometimes even the phenotypically important species is like 10%? 1%? 0.1%? 0.01%? of the molecule population. And the proportion of the species could depend on the temperature. Are you running at 35C? 38C? 40C? 42C? In a reductionistic way you could say that any system that follows logical rules is "like a computer" but I think at that point it ceases to be a meaningful statement. Computers are great because if you give them an input they can give a deterministic answer (you can also choose to have them not give a deterministic answer, as in ML, and yes sometimes at Google scale you have to deal with cosmic radiation) but the choice is inverted for biological systems. You can try really hard to make biological systems give deterministic answers, and in some systems you don't have to try that hard, especially nowadays, but the default still is "nondeterministic".
- rantwasp 6y ago
  technically what we call computers are nondeterministic. it just so happens that the way we model the hardware and feed/extract data gives us predictability. There are a lot of things going on, even in silicon. as far as biology goes, i can take any control structure you have in code and show you examples of how it’s being done. just because it’s happening at a large scale and it’s hard to predict at a micro level does not mean it’s not a computation and it does not mean it’s non-deterministiv
  - dnautics 6y ago
    I see, should I have covered contrapositive of my statement? technically everything in the universe is nondeterministic but to say "but also computers are nondeterministic" is reductionistic to the point where the categories are meaningless. It's also not sufficient to say "computation" exists. Well, you could reductionistically describe the orbits of the planets as a very machine that is very good at one computation. So I guess that makes it a computer. The solar system is a computer. Going beyond the question of determinism, similarly saying you can encode arbitrary computation to an arbitrary degree of determinism (which you can, in biology), is not helpful. This is like pointing to the Game Of Life, and showing that people can build computers in the game of life, and saying that the emergent phenomena are "just like a computer". Well yes, there is a computer underneath, but I think you're probably missing something important if you think the parameter and output spaces of game of life as "just like a computer".
    - rantwasp 6y ago
      i believe there is a disconnect between “is like a computer” and “is like a computer that i can understand and program”. if you were going for the latter i agree, we are not there yet. but it you define a computer as something that runs on some sort of code and translates input to output literally everything can be seen as a computer. the more complex something is the more impressive it is. you should also probably update your profile description since it’s literally confirming what i am saying :)) (ie I've been: A molecular biologist that discovered that an enzyme was secretly an NPN transistor)
      - dnautics 6y ago
        An npn transistor is not a computer, and in this case it's literal. The molecule had an negative, a positive, and a negative iron sulfur clusters. However, it most certainly wasn't acting in a logic gate; if anything it's activity functionally was closer to a diode than a transistor, by blocking bulk current flow in one direction but not the other (but, for quantum reasons, it has to be a transistor to do that). There were no data transformations in it's activity. To wit: I didn't get my job done on that project because I thought of it as a computer, I got it done because having been a curious child who also did computers I happened to know (and remember into adulthood) how computers work at a very low level and was able to make an insight based on that, nothing particularly CSey.

dnautics 6y ago

The big one is it's nondeterministic. An obvious example of nondeterminism is the genotype which determines mirror-body, it's caused by a defective cilium. Normally that cilium enforces torquoselectivity -it only rotates in one direction which establishes chiral directionality, but a certain genotype disables its rotation, so the orientation of your body is a factor of random chance based on how your cell was rotating at the single cell level. The mendelian inheritance is basically 50/50 stochastic based on the genotype. That's a pretty macro example (both at the genotypic ratio and phenotype levels), but it can happen at the micro level, too. You can have grossly nonlinear effects (well actually many effects are O(n^k) in concentration n, where k is the oligomer size, 2->12->20++) and sometimes even the phenotypically important species is like 10%? 1%? 0.1%? 0.01%? of the molecule population. And the proportion of the species could depend on the temperature. Are you running at 35C? 38C? 40C? 42C? In a reductionistic way you could say that any system that follows logical rules is "like a computer" but I think at that point it ceases to be a meaningful statement. Computers are great because if you give them an input they can give a deterministic answer (you can also choose to have them not give a deterministic answer, as in ML, and yes sometimes at Google scale you have to deal with cosmic radiation) but the choice is inverted for biological systems. You can try really hard to make biological systems give deterministic answers, and in some systems you don't have to try that hard, especially nowadays, but the default still is "nondeterministic".

rantwasp 6y ago
technically what we call computers are nondeterministic. it just so happens that the way we model the hardware and feed/extract data gives us predictability. There are a lot of things going on, even in silicon. as far as biology goes, i can take any control structure you have in code and show you examples of how it’s being done. just because it’s happening at a large scale and it’s hard to predict at a micro level does not mean it’s not a computation and it does not mean it’s non-deterministiv
- dnautics 6y ago
  I see, should I have covered contrapositive of my statement? technically everything in the universe is nondeterministic but to say "but also computers are nondeterministic" is reductionistic to the point where the categories are meaningless. It's also not sufficient to say "computation" exists. Well, you could reductionistically describe the orbits of the planets as a very machine that is very good at one computation. So I guess that makes it a computer. The solar system is a computer. Going beyond the question of determinism, similarly saying you can encode arbitrary computation to an arbitrary degree of determinism (which you can, in biology), is not helpful. This is like pointing to the Game Of Life, and showing that people can build computers in the game of life, and saying that the emergent phenomena are "just like a computer". Well yes, there is a computer underneath, but I think you're probably missing something important if you think the parameter and output spaces of game of life as "just like a computer".
  - rantwasp 6y ago
    i believe there is a disconnect between “is like a computer” and “is like a computer that i can understand and program”. if you were going for the latter i agree, we are not there yet. but it you define a computer as something that runs on some sort of code and translates input to output literally everything can be seen as a computer. the more complex something is the more impressive it is. you should also probably update your profile description since it’s literally confirming what i am saying :)) (ie I've been: A molecular biologist that discovered that an enzyme was secretly an NPN transistor)
    - dnautics 6y ago
      An npn transistor is not a computer, and in this case it's literal. The molecule had an negative, a positive, and a negative iron sulfur clusters. However, it most certainly wasn't acting in a logic gate; if anything it's activity functionally was closer to a diode than a transistor, by blocking bulk current flow in one direction but not the other (but, for quantum reasons, it has to be a transistor to do that). There were no data transformations in it's activity. To wit: I didn't get my job done on that project because I thought of it as a computer, I got it done because having been a curious child who also did computers I happened to know (and remember into adulthood) how computers work at a very low level and was able to make an insight based on that, nothing particularly CSey.