This article made me think about DNA as a language. Sort of a simple proof that a biological intelligence can be initially encoded as a language. I am sure someone has tried building LLM's from gene sequence data right?
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
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)
> 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.
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".
will say though that the long range coupling between microtubules that got discovered is interesting for its own reasons.