5 ms·

i independently ran across this when going through: https://www.edx.org/course/principles-of-biochemistry https://www.edx.org/course/principles-of-biochemistry

i independently ran across this when going through: https://www.edx.org/course/principles-of-biochemistry https://www.edx.org/course/principles-of-biochemistry As someone who is formally trained in computer science I was literally blown away by biochemistry. Once you see that any organism that involved organic chemistry is in fact an insanely complicated, biological computer you cannot unsee it. It's amazing. In case someone is wondering what the author of the blog post zoomed in, that's the Krebs cycle - ie how we derive energy (ie ATP) from the food we eat (https://en.wikipedia.org/wiki/Citric_acid_cycle https://en.wikipedia.org/wiki/Citric_acid_cycle). See: https://www.youtube.com/watch?v=juM2ROSLWfw https://www.youtube.com/watch?v=juM2ROSLWfw and https://www.youtube.com/watch?v=7J4LXs-oDCU https://www.youtube.com/watch?v=7J4LXs-oDCU

neilpanchal 6y ago
> Once you see that any organism that involved organic chemistry is in fact an insanely complicated, biological computer you cannot unsee it. It's amazing. This blew my mind. In addition to the computer analogy, I think Bio-mechanics is incredibly fascinating. The fact that I can close my eyes and still be able to touch the nose with my index finger repetedly from any starting position of the hand is mind boggling. I cannot fathom the type of inverse-kinematics that is involved in the cerebellum.
- rantwasp 6y ago
  hah. technically your brain is a prediction machine and, when you are trying to touch your nose, it’s really good at minimizing the prediction error.
  - klipt 6y ago
    Also you're not just relying on sight, the sense of proprioception is providing constant feedback of your finger's position even with your eyes closed. So it's not an open loop control problem, it's a closed loop, which is much easier.
dnautics 6y ago
Ok as someone who has been programming computers since age five (and currently in the industry) and has a PhD in biochemistry... It's not a computer. If you think of it that way you can wind up in deep trouble with critical nuances. That said, it can be fruitful to treat a small percentage of the systems (my gut says 10%), and exploit their computer-like features for fun and profit.
- coolgeek 6y ago
  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".
rstuart4133 6y ago
This video blew me away: https://www.youtube.com/watch?v=wJyUtbn0O5Y https://www.youtube.com/watch?v=wJyUtbn0O5Y It's an animation of the bio-chemistry a lymphocyte uses to move between cells (maybe - that's a guess?). It covers what I can only assume is a few milliseconds, it's just a tiny slither of the cells behaviours, yet how much is going on to make that happen is off the charts. I showed in it a club consisting of mostly software engineers, and the universal reaction was "thank god I didn't do bio-chemistry".

neilpanchal 6y ago

> Once you see that any organism that involved organic chemistry is in fact an insanely complicated, biological computer you cannot unsee it. It's amazing. This blew my mind. In addition to the computer analogy, I think Bio-mechanics is incredibly fascinating. The fact that I can close my eyes and still be able to touch the nose with my index finger repetedly from any starting position of the hand is mind boggling. I cannot fathom the type of inverse-kinematics that is involved in the cerebellum.

rantwasp 6y ago
hah. technically your brain is a prediction machine and, when you are trying to touch your nose, it’s really good at minimizing the prediction error.
- klipt 6y ago
  Also you're not just relying on sight, the sense of proprioception is providing constant feedback of your finger's position even with your eyes closed. So it's not an open loop control problem, it's a closed loop, which is much easier.

dnautics 6y ago

Ok as someone who has been programming computers since age five (and currently in the industry) and has a PhD in biochemistry... It's not a computer. If you think of it that way you can wind up in deep trouble with critical nuances. That said, it can be fruitful to treat a small percentage of the systems (my gut says 10%), and exploit their computer-like features for fun and profit.

coolgeek 6y ago
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".

rstuart4133 6y ago

This video blew me away: https://www.youtube.com/watch?v=wJyUtbn0O5Y https://www.youtube.com/watch?v=wJyUtbn0O5Y It's an animation of the bio-chemistry a lymphocyte uses to move between cells (maybe - that's a guess?). It covers what I can only assume is a few milliseconds, it's just a tiny slither of the cells behaviours, yet how much is going on to make that happen is off the charts. I showed in it a club consisting of mostly software engineers, and the universal reaction was "thank god I didn't do bio-chemistry".