Post

Ragnar {Groot Koerkamp}
@curiouscoding.nl

Amazing paper by Crick et al., in which they postulate that there are 20 common amino acids because the maximum size of a "comma-free code" on triples of ACTG is 20. I get to cite it because it turns out these codes give rise to optimal sampling (minimizer) schemes :D www.pnas.org/doi/10.1073/...

pnas.orgPNASProceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
Ragnar {Groot Koerkamp}
@curiouscoding.nl

In short, a comma-free code is a set of words of length 3 in this case, such that the concatenation of any two such words contains no other chosen word as a non-trivial substring. I.e.: for any pair of code words ABC and XYZ, neither BCX nor CYX is allowed to be a code word.

Ragnar {Groot Koerkamp}
@curiouscoding.nl

CXY* rather. This property is nice: it basically means that you can start reading anywhere in the middle of a DNA string, and you'll be "synchronized" to the intended reading frame after the first 6 bases. And so the maximum size of a set of words that can satisfy this property turns out to be 20!

0 reposts5 likes

Yann Ponty
@yannponty.bsky.social

Yet frameshift exists and is a important for compact organisms (+ there is no 1 to 1 correspondence between cordons and AAs), so do they argue that this was a necessary condition at the origin of life, that was gradually lifted later?

Ragnar {Groot Koerkamp}
@curiouscoding.nl

I think the only thing known at the time was that there are 20 AAs, without yet knowing the mapping, so they were just speculating on why this number and not 64. Then they found this very pretty mathematical connection which turned out to be a fluke.