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Comment by TheOtherHobbes | Hacker News Reader

This ignores epigenetics and proteomics.

There's a naively fashionable idea that DNA is basically the same as a Turing tape.

It isn't. It may be true that biological systems can be understood in terms of information theory, but the information is in the entire ecosystem - including the sum total of all individuals and species and their previous and current state.

E.g. on Earth, the entire planetary ecosystem eventually evolved a species with the ability to understand quantum theory - which happened to be a useful adaption, at least for a while.

But you're not going to find an explicit formalism for Schrodinger's Equation in human DNA no matter how hard you look for it.

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Pretty sure you’ve attacked a straw man here. The article does not make the claim that DNA is the one and only source of information used in biological computation. It does, perhaps, imply that DNA is the most important source of biological memory.

Yeah. Epigenetics is more like a small twist in the Fundamental Dogma of Biology. And "proteomics" doesn't mean much of anything--all proteins derive from DNA.

I don't know, are go-to statements and code reuse a small twist in the dogma of software engineering?

Is your Python-level code directly interacting with CPU operations and memory bit flipping a small twist?

Hi-C 3D DNA structure experiments as well as small RNA fragments interfering with transcriptions and protein function are not a small twist in my opinion - it's like finding out there's an entire extra hierarchy of layers to the system.

Those are great and non-obvious discoveries, but they don't particularly change the fact that (virtually?) all genetic information is carried via DNA. (...and possibly similar mechanisms that don't particular change the overall story)

Well, no, it doesn't change the fact that DNA contains (most of) the information. What it means is that even if I give you all of the bases on all of the chromosomes, if you don't know how these strings of beads will fold in a real cell (in the presence of all kinds of other things, like proteins and metal ions, which in a fertilized egg will come from the mother - a bootstrapping problem), it does not get you very far. It might not be unlike getting all the lines of code in a codebase, but not getting the ordering, only a bag of lines of code.

The central dogma, though still taught in schools, is a strongly oversimplified model of how information moves in a cell. In fact, there is so much regulation going on on all levels that proteins, in some sense, aren‘t even the main „product“ of DNA. (Most DNA is not proteinogenic, but rather has regulatory functions.) Also, proteins are extensively modified after transcription and even after translation, so yes, „proteomics“ very much does have meaning.

https://en.wikipedia.org/wiki/Central_dogma_of_molecular_bio...

My point was that all of that regulatory behavior is ultimately captured in the organism's DNA.

OP was claiming that you can't even really understand any of this unless you understand "the entire ecosystem - including the sum total of all individuals and species [on earth] and their previous and current state".

That's technically true in some sense, but most scientists would roll their eyes at the wildly expansive nature of this claim.

If you fully understood the information in an organism's DNA, plus the DNA of their close symbionts, that'd be a rather complete picture.

Sounds like DNA is like a Turing tape from which are produced cells capable of processing information.

His point was that DNA alone is not sufficient to to represent the role of Turing tape, because the resulting cells also take tons of input from their environment in the forms of things like epigenetics.

In other words, Turing machine as many other algorithms can take parameters/arguments.

A classic turning machine does not take parameters/arguments except those written on the tape beforehand. The tape and table of instructions describe the totality of the computational universe.

I don't think anybody thinks that DNA is literally classic turing machine with infinite tape..

Well no, but the problem is it's a misleading analogy, misleading enough that it's inadequate for any amount of formalism.

It can be trivially mitigated, you just say that input signals through the time is located in some area of the tape, and from that you can apply all your formalisms.

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