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

arxiv.org

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

#11

Post by samuell »

svnt wrote: 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…

I find the analogy itself super interesting and thought-provoking, and might be quite useful in studying biological systems.

The idea that we need to move away from understanding the genetic code as static machinery also aligns well with recent understanding of biology, as summarized in the highly appraised book "How Life Works" by Philip Ball [1]

But in terms of evolution, I don't see how the proposed analogy/model will get away with the fact that natural selection operates on the individual level (either you survive or you don't), while all genomic information is a package of (depending on the organism) humongous number of genes, not to mention base pairs or individual locuses (that's not even mentioning diploidy, that will mean two different copies of each locus).

With the known proportions and numbers of positive vs slightly deleterious mutations (much more of the latter, counted in the hundreds per individual), selection of positive mutations can not avoid accumulating slightly deleterious mutations.

I don't get how the proposed model is supposed to solve that.

I see that a smartly designed system could probably have processes that can change multiple loci in parallel in a beneficial way (along the lines of the theory of facilitated variation by Gerhart & Kirschner. See their papers or [2]), but that would only explain how such a fine-tuned system could be effective at adaptation, not how the system itself - including its processes - could arise from a state before these processes are in place.

To connect it to ML: In natural selection you don't have gradients and the ability to update multiple parameters based on detailed feedback on them individually. You only can provide a whole, binary feedback (survive, 1, or not, 0), to the whole set of parameters, whether they are slightly deleterious or possibly positive. The resolution is simply lacking here.

- [1] https://www.amazon.com/How-Life-Works-Users-Biology/dp/02268...

- [2] https://www.amazon.com/Plausibility-Life-Resolving-Darwins-D...

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

#12

Post by logicchains »

samuell wrote: post #11
svnt wrote: 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…

I find the analogy itself super interesting and thought-provoking, and might be quite useful in studying biological systems. The idea that we need to move away from understanding the genetic code as static machinery also aligns well with recent understanding of biology, as summarized in the highly appraised book "How Life Works" by Philip Ball [1] But in terms of evolution, I don't see how the proposed analogy/model…

No matter how low the probability of life arising by chance, from the perspective of life the probability that it happened is 100%, because if it didn't happen then we wouldn't be around to observe it. We're operating from a massive selection bias.

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

#13

Post by theGnuMe »

svnt wrote: 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…

Do you have any references?

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

#14

Post by visarga »

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 can operate on syntax, can modify or update it. Rules can create rules because they have a dual status - of behaviour and data. They can be both "verbs" and "objects". Gödel's incompleteness theorems use Arithmetization to encode math statements as data, making math available to itself as object of study.

So syntax not fixed, it has unappreciated depth and adaptive capability. In neural nets both the fw and bw passes are purely syntactic, yet they affect the behaviour/rules/syntax of the model. Can we say AlphaZero and AlphaProof don't really understand even if they are better than most of us in non-parroting situations?

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

#15

Post by svnt »

bjornsing wrote: post #7
svnt wrote: 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…

> But it’s not open-ended though (in its obvious form) since the VAE would have to be trained on various complex life forms and will probably not extrapolate well outside the support of the training distribution.

That is always the issue in alife: we discover processes that help us explore bounded information spaces, but only that.

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

#16

Post by bubblyworld »

samuell wrote: post #11
svnt wrote: 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…

I find the analogy itself super interesting and thought-provoking, and might be quite useful in studying biological systems. The idea that we need to move away from understanding the genetic code as static machinery also aligns well with recent understanding of biology, as summarized in the highly appraised book "How Life Works" by Philip Ball [1] But in terms of evolution, I don't see how the proposed analogy/model…

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

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

#17

Post by svnt »

theGnuMe wrote: post #13
svnt wrote: 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…

Do you have any references?

Here is a readable article by Watson that is probably among the more relevant:

https://www.richardawatson.com/songs-of-life-and-mind

There are many, and the paper itself cites many good sources including by Huang and Watson in the references section.

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

#18

Post by evv555 »

svnt wrote: 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.

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

#19

Post by sam537 »

svnt wrote: 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…

Popular and incompletely understood. That analogy is unhelpful to understand processes. It's attempting to explain a incompletely understood phenomenon with another. As someone else said below, the problem of the genome being the 'compressed representation' is reductive since genomes do not exist in isolation in an organism. Genomes were environmentally selected for millenia and many unicellular organisms share genomic material with other organisms or the environment. I think the framework is useful but it does not scale.

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

#20

Post by stainablesteel »

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 gets into a cell, binds to a protein, which probably cascades into a binding of a 100 different proteins at some point, that eventually sends a message to the tiny nucleus to wrap or unwrap a specific segment of DNA, is quite a beautiful way of thinking about it

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