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The Genomic Code: The genome instantiates a generative model of the organism

arxiv.org

31–39 of 39 posts

Re: The Genomic Code: The genome instantiates a generative model of the organism

#31
post #14

DNA "generates" the body, which generates behaviour, which affects gene survival, closing the loop. It's a syntactic process with the ability to update syntax based on outcomes in the environment. I think this proves that syntax is sufficient for semantics, given the environment. Wondering why Searle affirmed the opposite. Didn't he know about compilers, functional programming, lambda calculus, homoiconicity - syntax…

I thought syntax was finite... wasn't that the Turing thing discussed here the other day.. also if your idea is true you'd be limited to the recursively enumerable.

Re: The Genomic Code: The genome instantiates a generative model of the organism

#32
post #18
post #2

It’s an intriguingly framed paper, and others have written about how gene regulatory networks store weights, etc, but this seems to me like it is putting too much emphasis on the direct mapping of the developmental process to a generative process just because it is popular at the moment. The encoder being evolution is an idea that has been developed by Sui Huang and numerous others. The genetic decoder being creative…

>The encoder being evolution is an idea that has been developed by Sui Huang and numerous others. Parallels between evolutionary systems and hill-climbing algorithms have been floating around for a long time at this point.

Although normally in the other direction -- genetic algorithms and genetic programming directly mimic evolution by natural selection, for example.

Re: The Genomic Code: The genome instantiates a generative model of the organism

#33

Very nice perspective. I used to joke about the missing comment lines in the genetic code: if "God" had been a good, conscientious programmer, he would have left a reasonable amount of comments in the code to make it maintainable for all the next developers - but it seems the task went over his head, and now we have to reverse-engineer all that chaos...

yes, when I was a kid and already interested in computers, then learned about molecular biology (late 80s, early 90s), I definitely used that analogy to motivate my work. It really reminded me of the early MIT hackers exploring these systems that were somewhat opaque for people not in the "priesthood".

Re: The Genomic Code: The genome instantiates a generative model of the organism

#34

Earlier quoted context omitted.

I think it's more useful to think of natural selection as acting (probabilistically) on populations of genomes, not individuals. The feedback is individual, but the "gradients" are at the population level. It's not a perfect analogy but e.g. there are formal correspondences like this one: https://www.nature.com/articles/s41467-021-26568-2

An interesting fact that I wasn't aware of until I read it recently is that our genes constrain the chance of mutations in critical areas of the body, which shifts the landscape.

Yeah, that's interesting, I guess it's also a simplification to think of an organism as a single genome. The reality is much more complicated! (lichens come to mind as examples of even more genetic diversity housed in a single organism, or even gut bacteria in humans maybe?)

Re: The Genomic Code: The genome instantiates a generative model of the organism

#35
post #30

Earlier quoted context omitted.

An interesting fact that I wasn't aware of until I read it recently is that our genes constrain the chance of mutations in critical areas of the body, which shifts the landscape.

Mutation resistance is itself the result of mutation (i.e. evolution), and isn't anything particularly special among humans. And it's not just critical areas; every cell in your body has enzymes that prevent mutation, both before and after a given replication.

> And it's not just critical areas

True, but the resistance to mutations is increased in critical areas compared to other areas. Not all changes are equally likely.

Re: The Genomic Code: The genome instantiates a generative model of the organism

#36
post #2

It’s an intriguingly framed paper, and others have written about how gene regulatory networks store weights, etc, but this seems to me like it is putting too much emphasis on the direct mapping of the developmental process to a generative process just because it is popular at the moment. The encoder being evolution is an idea that has been developed by Sui Huang and numerous others. The genetic decoder being creative…

> why can’t we put this to use producing alife simulations that deliver open-ended evolution? Has it been tried? I’ve said for ages: show me a representation where a random bit flip generally results in a different but viable entity, and I’ll show you artificial life. The latent space of a VAE could well have those properties. But it’s not open-ended though (in its obvious form) since the VAE would have to be trained…

> show me a representation where a random bit flip generally results in a different but viable entity

It's a really interesting problem I pondered quite a bit when doing some a-life hobby stuff.

I never came up with a good solution, but you can kind of "feel" that the solution needs to be more analog-ish in the way info is represented. As you say, a small change in data (bit flip) probably needs to produce a small change in the resulting form. Possibly the binary representation points to a vector space of form "primitives" (drivers of form) such that adjacent points have similar form.

Re: The Genomic Code: The genome instantiates a generative model of the organism

#37
post #27
post #14

DNA "generates" the body, which generates behaviour, which affects gene survival, closing the loop. It's a syntactic process with the ability to update syntax based on outcomes in the environment. I think this proves that syntax is sufficient for semantics, given the environment. Wondering why Searle affirmed the opposite. Didn't he know about compilers, functional programming, lambda calculus, homoiconicity - syntax…

But in the first instance of syntax, what does that bare syntax mean? 1+1=2 as a physical instantiation (say written on paper) only has any relevant causal powers because of humans. DNA is a physical, causally interfacing thing with or without anything else built on top of it/from it. A mathematical sentence sits on a piece of paper just like any random scrabbling of pencil led without a consciousness. DNA is at its…

I think of syntax as applying a rule. A program is just syntactic operations. The idea is that it has two aspects: "program in execution" and "program as data". Rules expressing behavior and rules expressed as data, in which case it can be processed by other rules.

One concrete example is a bootstrapped compiler. It is both data and execution. It can build itself, putting its output as input again. Another example is in math - Gödel's arithmetization, which encodes math statements as numbers, processing math syntax with math operations. And of course neural nets, you can describe them as purely syntactic (mechanical) operations, but they also update rules and learn. In the backward pass, the model becomes input for gradient update. So it is both rule and data. DNA too.

These systems that express rules or syntax that is adaptive, I think they make the leap to semantics by grounding in the outside environment. The idea that syntax is shallow and fixed is wrong, in fact syntax can be deep and self generative. Syntax is just a compressed model of the environment, and that is how it gets to reflect semantics.

This was an argument against Stochastic Parrots and Chinese Room (syntax is not sufficient for semantics) maxim. I aimed to show that purely mechanical or syntactic operations carry more depth than originally thought.

Re: The Genomic Code: The genome instantiates a generative model of the organism

#38
post #18

Earlier quoted context omitted.

>The encoder being evolution is an idea that has been developed by Sui Huang and numerous others. Parallels between evolutionary systems and hill-climbing algorithms have been floating around for a long time at this point.

Although normally in the other direction -- genetic algorithms and genetic programming directly mimic evolution by natural selection, for example.

It was just the less controversial direction. You would be accused of anthropomorphizing and teleological thinking if you suggested evolution is a search process towards some optimum. Good luck talking to an orthodox biologist about evolutionary processes with constructs like agents and intelligence.

Re: The Genomic Code: The genome instantiates a generative model of the organism

#39

its a very poetic interpretation i think i would take it a step further, most organisms alive today operate at the level of a generative model for a generative model (continue umpteen times) until you arrive at the level of physiology that assembles nerves and organs to work at the scale they do and i would also comment on the impeccability of the feedback mechanisms across each layer, that every message eventually g…

I wonder if this extends to consciousness, including the impeccable part.

a real adrenaline rush can give you amazing physical power (at the cost of a lot of pain the next day)

so in a way, yeah, because that would go through consciousness first then signals back down stream

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