Comment by caeruleus | Hacker News Reader

Comment by caeruleus | Hacker News Reader

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I don't believe the concept of DNA can be reduced to a sequence of quaternary numerals, which is what gene sequence data would represent. Similar to proteins, DNA forms higher-level structures on top of the primary one [1], and (in a biological context, inside the nucleus) exhibits somewhat self-modifying [2] and self-regulating [3] behavior as well as meta-modification [4]. Analogous to the article, if one defines the language of DNA by its nucleobase sequence, this language can only represent a subset of the world of DNA.

Somewhat related, the way the adaptive immune system works has similarities with some concepts in machine learning. In this process, sections of nuclear DNA serve as randomly initialized weights in precursor cells [5] as well as final weights in memory cells. There's even fine-tuning of the weights. [6]

[1] https://en.wikipedia.org/wiki/Nucleic_acid_structure [2] https://en.wikipedia.org/wiki/Transposable_element [3] https://en.wikipedia.org/wiki/Transcriptional_regulation [4] https://en.wikipedia.org/wiki/Epigenetics [5] https://en.wikipedia.org/wiki/V(D)J_recombination [6] https://en.wikipedia.org/wiki/Affinity_maturation

> don't believe the concept of DNA can be reduced

followed by examples of things that are encoded by DNA. Fro example, sure, maybe you'll miss bootstrapping methylation on a first pass but the idea of methylation is there in the DNA, and if you didnt have "methylation in the right place" more than likely some generation (N) would.

to wit, i dont think there is strong evidence of an "ice-9" in the epigenome that brings about a spark of life that can't easily be triggered by chance given a template lacking it.

so there's probably not something intrinsically missing from DNA as an encoding medium vs say "casually" missing from any given piece of DNA.

if you want something a bit stronger than an assertion, the DNA used to bootstrap m. capricolum into Syn1 lacked all the decorations (made in yeast) and was not locked into higher order structure (treated with protease prior to transplantation)

You're raising some intriguing points, and I agree with your assertion about the epigenome. I still feel like your response misses the point I was making.

> followed by examples of things that are encoded by DNA

... given its natural environment. A nucleobase sequence is not a symbolic language, it relies on physical laws in general and a defined chemical environment in particular (that it helps to create and maintain) to mean something. It's similar to the point about Othello vs. the physical world in the article: The language itself does not encode every bit of information about the world it describes. For instance, in 3D space, regions of DNA that are far apart in the sequence can physically interact and influence each other’s expression.

TLDR: I think my point is that a base sequence requires a particular context (~ interpreter/knowledge about the physical world) to encode mostly everything about life. Treating it as just a language in the context of LLMs abstracts away the complex substrate that makes it work.

i agree that current llms are likely missing quite a few of the trees and probably off on the forest too. however, in general, an llm (or a transformer rather) is a universal function approximator, so in principle, there's no substrate too complex unless somehow it's uncomputable and i see no evidence that biology is uncomputable in the bulk.

I recognize that my initial statement comes off as too broad in light of theoretical computability, when I was mostly weighing in terms of current/near-term technology. Given what we know today, I would (still cautiously) agree with your statement. There hasn't been any evidence to the contrary (only some highly contested speculation, most prominently by Roger Penrose).

i hate to denigrate penrose, but his quantum consciousness proposition is basically "we dont understand consciousness and quantum mechanics is magic therefore consciousness must be quantum"... totally elides the biggest challenge which is that we dont have a definition much less a test for consciousness.

will say though that the long range coupling between microtubules that got discovered is interesting for its own reasons.

It's not really a question of whether it is uncomputable in bulk.

It is more that a system like DNA operates as both a linear encoding (the "algorithm" if you like) AND as 3D chemical object whose properties allow the encoding to be used in various ways, which means that a huge amount of its linear structure is actually determined by 3D chemical function, rather than encoding for proteins. Moreover, it appears that the role of a given section of DNA can vary depending on what other molecules are interacting with it and what physical state it is in.

If you want a more computer-ish analogy, it's like a computer where the program is actually encoded as a part of the computer's own structure, yet is still logically distinct from the rest of the structure. It may not be physically distinct, however, and thus simply inspecting the structure will not lead to a clear understanding of what is "the program" and what is "the cpu".

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