3 ms·
The thing is, the code analogy still holds up pretty well if you ask me. The linked article tells us how this code is self-generating and self-modifying, how t
by alexey-salmin 3y ago
The thing is, the code analogy still holds up pretty well if you ask me.
The linked article tells us how this code is self-generating and self-modifying, how the interpreter of this code is more complex than you may expect from a 4-word language, how this code reads from external inputs when it runs. Well OK, sounds very reasonable to me. No one promised the code will be easy.
The problem with the code analogy at our current level of understanding is not that it's untrue and not that it's too simplistic, but on the contrary that it's too complex to be applied on practice. What we do now is akin to debugging running linux system by analyzing bit sequences in the kernel image. Surely it's all code and data, surely the bit sequences of the kernel image do determine the kernel behavior within the environment of hardware. This framework is correct but not powerful enough produce good results.
- thaumasiotes 3y ago> how the interpreter of this code is more complex than you may expect from a 4-word language It's not a 4-word language. It's a 64-word language. That's been known for about as long as we've known what DNA was.
- alexey-salmin 3y ago4 or 64, neither is a good description of how it works outside of protein building. Same as saying that C++ is a 100-word language because it's the size of the ASCII alphabet: correct but not helpful
- thaumasiotes 3y agoThat's only correct in the same sense that it's "correct" to say DNA is a four-word language. It's not "correct in an unhelpful way", it's just incorrect.
- alexey-salmin 3y agoWell so is the 64-word concept if you insist. It only applies to protein transcription which is 1-2% of human DNA, so it's wrong 98% of the time
- pixl97 3y agoI mean, neither really matter. TREE3 shows us that computational complexity explodes beyond all reason even in word limited simple systems with low connectivity.
- dekhn 3y agoSorry, what's 64-word about DNA?
- thaumasiotes 3y agoOne codon is three bases in sequence. Each base has four possible values. So there are 64 codons.
- dekhn 3y agoAh, I see your idea, but codons aren't DNA- they are a higher level construct (only used in the context of transcribed and translated genes that code for proteins). Also, several of those codons aren't mapped to amino acides (stop codons) and the codons are re-used to code for the same amino acids, so it's really redundant compared to that. DNA is a 2-bit code, with 4 symbols.
- thaumasiotes 3y agoWords are defined by the parser, not by the alphabet. Letters are what's defined by the alphabet. > Also, several of those codons aren't mapped to amino acides (stop codons) Yes, codons are the minimal units of the genetic code, which is why they're called "codons". > and the codons are re-used to code for the same amino acids, so it's really redundant Synonymous codons aren't redundant. They take different amounts of time to process, which affects the shape of the resulting protein.
- dekhn 3y agoDNA codes for a lot more than just genes... you're just conflating several unrelated concepts. For example, regulatory regions don't care about codons at all. If you're just saying "genes are defined in units of codons", no complaint. And the biophysics of synonymous codons are highly complex; in most cases, you can substitute them in and get the same exact protein function. There are lots of papers about corner cases in specific proteins, but it's still correct to say that synonymous codons code redundantly (this is a well-established fact of molecular biology).