6 ms·

I’ve worked in a lab of one of the original folks working on genetic logic gates, and honestly, no they don’t really work very well at all. I think a lot of co

by koeng 3y ago

I’ve worked in a lab of one of the original folks working on genetic logic gates, and honestly, no they don’t really work very well at all. I think a lot of computer scientists assume that their model of the world (binary logic) is the most abstracted version possible, and you can drill down other information carrying systems to that level, and then use that knowledge to build reliable systems. Biology does not work that way. Its fundamental abstraction is different (mostly one of massive interconnectedness). Engineering logic gates and the like, mostly, doesn’t actually allow you to build better genetic circuits.

throwaway914 3y ago
I'm equating this to condition-less coding, where you're trying to eliminate branching logic with bitwise operators or other math.
- chaorace 3y ago
  Yeah, except you can only change one line at a time and you lose all of your changes if it doesn't compile at any point.
  - koeng 3y ago
    Sex changes many lines at a time. But you do die if it doesn’t compile.
    - mrguyorama 3y ago
      My friend who has a defective genome including a specific enzyme that doesn't "compile" and he is plenty alive
Bjartr 3y ago
I'd imagine genetically driven behavior would be probabilistic and involve many overlapping duration/threshold "checks"
sebastianconcpt 3y ago
I bet there is way more quantum phenomena reasons involved in why that system was selected for being less fragile and having better stability/survaibability for a wider range of cases. Thinking in classical compute terms there is like asking for robots that inevitably break without the slightest chance of self repair, much less do it at minimal effort.
- rogerkirkness 3y ago
  Yeah I think there's a paper about how brains most likely represent some things with quantum states which may explain why we don't understand them yet.
  - jerf 3y ago
    There are many such papers. However they need to be understood as extremely speculative, if not outright woo-woo, as there is currently no reason to believe that the brain is capable of maintaining any sort of even modestly-large-scale entanglement properties. These papers, and people commenting on them, also often appear to believe that just finding that entanglement is happening would itself mean something; it's not hard to read them as basically saying "and we found the 'Here There Be Magic' in the brain!" They don't even seem to speculate as to what the entanglement and "quantum" would be doing. What visible difference would it make versus a non-"quantum" brain? How could we determine that the brain is using "quantum" to do something that could not otherwise be explained or is somehow irreducible to some otherwise-classical phenomenon? Not only do I not see answers, not only do I not even really see theories, I don't even see much recognition that the question exists. We have quantum computers right now. They are small, but they are fully quantum. They don't do anything by virtue of their quantumness. They aren't sitting there being ambiently quantum. They have to be set up, then executed, then answers read out, and the way in which they deviate from non-quantum computers is actually perfectly mathematically characterizable. And it is not clear to me exactly how those differences are supposed to be useful to describing how a brain works even if functioning quantum computers can be found. Basically, the problem of how a brain works is so vast that the question of whether or not it has some sort of quantum computer in it sinks without a trace, and certainly without providing any sort of explanation at the present time.
titzer 3y ago
> I think a lot of computer scientists assume that their model of the world (binary logic) is the most abstracted version possible, and you can drill down other information carrying systems to that level, and then use that knowledge to build reliable systems. It doesn't matter what Turing-complete model you have; they are all equivalent, even if exponentially slower than another. And no, binary logic is not the most abstracted version possible. Clearly lambda calculus is....ok, just kidding. You can build a universal computer out of just two stacks, out of subtract-and-jump-if-zero, and a lot of other things. (https://gwern.net/turing-complete https://gwern.net/turing-complete) I don't think computer scientists really think that binary logic is the only computation paradigm that makes sense, it just happens to be one that we can make extremely fast and extremely reliable realizations of using electronic circuits. It's been phenomenally successful.
- NoMoreNicksLeft 3y ago
  Is it not true that some of the confusion stems from the mistaken idea that DNA is computing/computable? One might make logic gates out of plumbing, but the plumbing at my house isn't some 0.1Hz computing device, it's indoor water so I can boil pasta, brush my teeth, and flush away smelly waste. DNA's primary (though maybe not only) function is to act as a blueprint for constructing proteins. What little logic exists in it naturally has to do with conditionally expressing those only when it is advantageous to the organism. That's not necessarily the same thing as a logical if.
- yosefk 3y ago
  I don't think GP implied that you cannot simulate cell chemistry on a Turing complete machine to a reasonable accuracy given enough resources. I think the point was that you can't think of genes as logic gates.
- dacryn 3y ago
  you are limiting computation to discrete computation. Biology is analog, which is a whole different ballgame compared Turing completeness. And extremely hard to replicate with digital paradigms
deleted 3y ago
[deleted]
tivert 3y ago
> I think a lot of computer scientists assume that their model of the world (binary logic) is the most abstracted version possible This is a giant problem with software engineers, which makes us quite obnoxious. We have mental models that work for understanding computers, and then go misapply that those models to everything else in the universe. Frequently that turns into arrogance, by insisting the right way to think anything is in computer-terms, and every other way of thinking is inferior and wrong. Then you get stuff like Engineer's Disease, where you get some software guy lecturing actual experts in other fields about how they're doing it all wrong, or declaring alien fields to be nonsense because they're different.

by koeng 3y ago

throwaway914 3y ago

I'm equating this to condition-less coding, where you're trying to eliminate branching logic with bitwise operators or other math.

chaorace 3y ago
Yeah, except you can only change one line at a time and you lose all of your changes if it doesn't compile at any point.
- koeng 3y ago
  Sex changes many lines at a time. But you do die if it doesn’t compile.
  - mrguyorama 3y ago
    My friend who has a defective genome including a specific enzyme that doesn't "compile" and he is plenty alive

Bjartr 3y ago

I'd imagine genetically driven behavior would be probabilistic and involve many overlapping duration/threshold "checks"

sebastianconcpt 3y ago

I bet there is way more quantum phenomena reasons involved in why that system was selected for being less fragile and having better stability/survaibability for a wider range of cases. Thinking in classical compute terms there is like asking for robots that inevitably break without the slightest chance of self repair, much less do it at minimal effort.

rogerkirkness 3y ago
Yeah I think there's a paper about how brains most likely represent some things with quantum states which may explain why we don't understand them yet.
- jerf 3y ago
  There are many such papers. However they need to be understood as extremely speculative, if not outright woo-woo, as there is currently no reason to believe that the brain is capable of maintaining any sort of even modestly-large-scale entanglement properties. These papers, and people commenting on them, also often appear to believe that just finding that entanglement is happening would itself mean something; it's not hard to read them as basically saying "and we found the 'Here There Be Magic' in the brain!" They don't even seem to speculate as to what the entanglement and "quantum" would be doing. What visible difference would it make versus a non-"quantum" brain? How could we determine that the brain is using "quantum" to do something that could not otherwise be explained or is somehow irreducible to some otherwise-classical phenomenon? Not only do I not see answers, not only do I not even really see theories, I don't even see much recognition that the question exists. We have quantum computers right now. They are small, but they are fully quantum. They don't do anything by virtue of their quantumness. They aren't sitting there being ambiently quantum. They have to be set up, then executed, then answers read out, and the way in which they deviate from non-quantum computers is actually perfectly mathematically characterizable. And it is not clear to me exactly how those differences are supposed to be useful to describing how a brain works even if functioning quantum computers can be found. Basically, the problem of how a brain works is so vast that the question of whether or not it has some sort of quantum computer in it sinks without a trace, and certainly without providing any sort of explanation at the present time.

titzer 3y ago

> I think a lot of computer scientists assume that their model of the world (binary logic) is the most abstracted version possible, and you can drill down other information carrying systems to that level, and then use that knowledge to build reliable systems. It doesn't matter what Turing-complete model you have; they are all equivalent, even if exponentially slower than another. And no, binary logic is not the most abstracted version possible. Clearly lambda calculus is....ok, just kidding. You can build a universal computer out of just two stacks, out of subtract-and-jump-if-zero, and a lot of other things. (https://gwern.net/turing-complete https://gwern.net/turing-complete) I don't think computer scientists really think that binary logic is the only computation paradigm that makes sense, it just happens to be one that we can make extremely fast and extremely reliable realizations of using electronic circuits. It's been phenomenally successful.

NoMoreNicksLeft 3y ago
Is it not true that some of the confusion stems from the mistaken idea that DNA is computing/computable? One might make logic gates out of plumbing, but the plumbing at my house isn't some 0.1Hz computing device, it's indoor water so I can boil pasta, brush my teeth, and flush away smelly waste. DNA's primary (though maybe not only) function is to act as a blueprint for constructing proteins. What little logic exists in it naturally has to do with conditionally expressing those only when it is advantageous to the organism. That's not necessarily the same thing as a logical if.
yosefk 3y ago
I don't think GP implied that you cannot simulate cell chemistry on a Turing complete machine to a reasonable accuracy given enough resources. I think the point was that you can't think of genes as logic gates.
dacryn 3y ago
you are limiting computation to discrete computation. Biology is analog, which is a whole different ballgame compared Turing completeness. And extremely hard to replicate with digital paradigms

deleted 3y ago

[deleted]

tivert 3y ago

> I think a lot of computer scientists assume that their model of the world (binary logic) is the most abstracted version possible This is a giant problem with software engineers, which makes us quite obnoxious. We have mental models that work for understanding computers, and then go misapply that those models to everything else in the universe. Frequently that turns into arrogance, by insisting the right way to think anything is in computer-terms, and every other way of thinking is inferior and wrong. Then you get stuff like Engineer's Disease, where you get some software guy lecturing actual experts in other fields about how they're doing it all wrong, or declaring alien fields to be nonsense because they're different.