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I find it extremely fascinating - that the workings of our body and mind are actually encoded in the DNA. The secrets of AGI & consciousness are right there, an

by Geee 6y ago

I find it extremely fascinating - that the workings of our body and mind are actually encoded in the DNA. The secrets of AGI & consciousness are right there, and we know they are, but we just aren't able to read it so that we could replicate them. I've been wondering if there's some sort of computational method to extract the algorithms without having to simulate the biology.

DennisP 6y ago
That sounds like it'd be about as hard, as extracting the output of a complicated program without running it.
tsimionescu 6y ago
> I've been wondering if there's some sort of computational method to extract the algorithms without having to simulate the biology. That doesn't seem plausible to me. DNA, just like a compiled program, is a set of instructions for a specific computer. I don't believe you can extract the meaning of a program without understanding the computer that is supposed to run it (except perhaps by statistical analysis of its results when being run, which is generally how we are studying it today). Now, if we did have a deep understanding of cellular machinery, of the way cells organize into organs and organisms, and of the functionality of each of these organs, including the brain, and the way they collaborate to produce cognition, THEN we could perhaps decompile the DNA into a high-level algorithm, where we could say something like 'these are instructions for programming a stem cell to specialize into a cell which feeds cells that react when this chemical is encountered in concentrations greater than X over a time period of Y'. But this is likely the opposite approach to what you were asking - you would need to have an almost complete understanding of the biochemistry of the entire body, and of the way it gives rise to intelligence, at which point the DNA itself may not be so important anymore in the hunt for AGI.
- patcon 6y ago
  > I don't believe you can extract the meaning of a program without understanding the computer that is supposed to run it (except perhaps by statistical analysis of its results when being run, which is generally how we are studying it today). This made me think of what forces of life are maybe engaging in within this universe: We can't know the structure of the machine running this simulation, but if we probe the results of the running simulation enough, we can understand everything of the system running it. In the Einstein sense, maybe that's how we know God? :)
- ganzuul 6y ago
  If the functional units of DNA are composable then the computational complexity of the problem decreases dramatically. We can use symbols instead of functions and derive an abstract algebra of life.
jbotz 6y ago
They aren't. (The workings of body and mind are not encoded in DNA.) The only thing that's encoded in DNA is how to make proteins. Everything else is emergent from the interactions of those proteins and "encoded" only in evolutionary history of how those interactions work when they do so in a repeatable fashion. DNA is not a "blueprint" for making a body or a mind... it is much more like the "seed" pattern for a run of Conway's Game of Life, except with a bit of indeterminism for environmental influences thrown in. There are things about the phenotype you can predict from the DNA because you've got past examples, but a small change in initial conditions or the environment during development can also throw you way off... you have to run the whole process (i.e. grow a complete animal) to ever be sure what the phenotype looks like or behaves like.
- patcon 6y ago
  Reading this as a biochemist in a past life, this was a WONDERFUL explanation.
- pygy_ 6y ago
  The blueprint analogy is too simplistic. Some genes called "transcription factors" activate and/or inhibit the expression of other genes, including other transcription factors. They form networks functionally equivalent to neuronal nets.
- ganzuul 6y ago
  It would make sense if cells were only interested in talking about certain topics. In that case we could simulate the evolution of their communication and ignore what is causing the communication. There should be an upper bound to the complexity of their communication because of game theory. Tit-for-tat only supports an error rate of up to 9 percent, so at the upper bound cells will need to differentiate. This is a lot of domain knowledge to accelerate the computation by, provided the theory is correct.
- encypruon 6y ago
  > The only thing that's encoded in DNA is how to make proteins. Wikipedia on the human genome [1]: > Protein-coding sequences account for only a very small fraction of the genome (approximately 1.5%), and the rest is associated with non-coding RNA genes, regulatory DNA sequences, LINEs, SINEs, introns, and sequences for which as yet no function has been determined. Wikipedia cites [2]. [1] https://en.m.wikipedia.org/wiki/Human_genome https://en.m.wikipedia.org/wiki/Human_genome [2] https://www.nature.com/articles/35057062 https://www.nature.com/articles/35057062 Edit: Formatting
ganzuul 6y ago
If we take the theory of natural evolution seriously then IMHO we should also take Gödel's incompleteness theorem seriously like Roger Penrose does. Note that he proposes both a problem and a solution, which are two separate entities. There may exist other solutions to cognition of incompleteness. I think that if the problem of and solution to incompleteness in cognition did not exist then we would experience these computational inconsistencies similar to migraine blind spots. However we don't, and we perceive the error in computation as a single entity and not as two boundaries.

by Geee 6y ago

DennisP 6y ago

That sounds like it'd be about as hard, as extracting the output of a complicated program without running it.

tsimionescu 6y ago

> I've been wondering if there's some sort of computational method to extract the algorithms without having to simulate the biology. That doesn't seem plausible to me. DNA, just like a compiled program, is a set of instructions for a specific computer. I don't believe you can extract the meaning of a program without understanding the computer that is supposed to run it (except perhaps by statistical analysis of its results when being run, which is generally how we are studying it today). Now, if we did have a deep understanding of cellular machinery, of the way cells organize into organs and organisms, and of the functionality of each of these organs, including the brain, and the way they collaborate to produce cognition, THEN we could perhaps decompile the DNA into a high-level algorithm, where we could say something like 'these are instructions for programming a stem cell to specialize into a cell which feeds cells that react when this chemical is encountered in concentrations greater than X over a time period of Y'. But this is likely the opposite approach to what you were asking - you would need to have an almost complete understanding of the biochemistry of the entire body, and of the way it gives rise to intelligence, at which point the DNA itself may not be so important anymore in the hunt for AGI.

patcon 6y ago
> I don't believe you can extract the meaning of a program without understanding the computer that is supposed to run it (except perhaps by statistical analysis of its results when being run, which is generally how we are studying it today). This made me think of what forces of life are maybe engaging in within this universe: We can't know the structure of the machine running this simulation, but if we probe the results of the running simulation enough, we can understand everything of the system running it. In the Einstein sense, maybe that's how we know God? :)
ganzuul 6y ago
If the functional units of DNA are composable then the computational complexity of the problem decreases dramatically. We can use symbols instead of functions and derive an abstract algebra of life.

jbotz 6y ago

They aren't. (The workings of body and mind are not encoded in DNA.) The only thing that's encoded in DNA is how to make proteins. Everything else is emergent from the interactions of those proteins and "encoded" only in evolutionary history of how those interactions work when they do so in a repeatable fashion. DNA is not a "blueprint" for making a body or a mind... it is much more like the "seed" pattern for a run of Conway's Game of Life, except with a bit of indeterminism for environmental influences thrown in. There are things about the phenotype you can predict from the DNA because you've got past examples, but a small change in initial conditions or the environment during development can also throw you way off... you have to run the whole process (i.e. grow a complete animal) to ever be sure what the phenotype looks like or behaves like.

patcon 6y ago
Reading this as a biochemist in a past life, this was a WONDERFUL explanation.
pygy_ 6y ago
The blueprint analogy is too simplistic. Some genes called "transcription factors" activate and/or inhibit the expression of other genes, including other transcription factors. They form networks functionally equivalent to neuronal nets.
ganzuul 6y ago
It would make sense if cells were only interested in talking about certain topics. In that case we could simulate the evolution of their communication and ignore what is causing the communication. There should be an upper bound to the complexity of their communication because of game theory. Tit-for-tat only supports an error rate of up to 9 percent, so at the upper bound cells will need to differentiate. This is a lot of domain knowledge to accelerate the computation by, provided the theory is correct.
encypruon 6y ago
> The only thing that's encoded in DNA is how to make proteins. Wikipedia on the human genome [1]: > Protein-coding sequences account for only a very small fraction of the genome (approximately 1.5%), and the rest is associated with non-coding RNA genes, regulatory DNA sequences, LINEs, SINEs, introns, and sequences for which as yet no function has been determined. Wikipedia cites [2]. [1] https://en.m.wikipedia.org/wiki/Human_genome https://en.m.wikipedia.org/wiki/Human_genome [2] https://www.nature.com/articles/35057062 https://www.nature.com/articles/35057062 Edit: Formatting

ganzuul 6y ago

If we take the theory of natural evolution seriously then IMHO we should also take Gödel's incompleteness theorem seriously like Roger Penrose does. Note that he proposes both a problem and a solution, which are two separate entities. There may exist other solutions to cognition of incompleteness. I think that if the problem of and solution to incompleteness in cognition did not exist then we would experience these computational inconsistencies similar to migraine blind spots. However we don't, and we perceive the error in computation as a single entity and not as two boundaries.