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Joe Moeller (Oct 07 2025 at 18:54):John Baez said:
I don't know a definition of "program" other than the definition in computer science! Maybe there is one.... okay, yes, you can ask for the program at a concert.
There's also non/linear programming as in optimization, the program(me) of a conference, a person's research program. My wife was involved in film festivals for a while and I was surprised when she talked about programming. My grandpa called TV shows "programs". Obviously the unifying thing is they're all about detailed instructions/planning. The only objection I could really get is that "program" seems to have a connotation of intention, somehow even more than "code" does, which doesn't exactly make sense for DNA. Well, unless you're talking about synthetic biology, which I think we might be!
John Baez (Oct 08 2025 at 09:16):Okay, I call TV shows programs - maybe only old people do that? But I don't think bacteria have TV shows going on inside them. :upside_down:
In computer science I think there's a difference between an algorithm, and a program (which is a specific realization of an algorithm in some language), and what the physical material of the computer is doing when it's running the program. There are probably even more layers of abstraction (assembly language, etc.). I'm no expert on the ontology of computer science; someone must have thought a lot about this.
Biology probably involves different layers of abstraction: there's no reason to assume it works the same way. So if we're trying to understand the world of life, we shouldn't just transplant the concepts from computer science unthinkingly.
In synthetic biology we are, of course, free to impose any concepts we want, since we're designing new systems. There we are only limited by what works.
Personally I'm more interested in understanding the living world that came before us than synthetic biology. I think we have a very crude attitude toward technology, and we have a lot to learn from the living world if we don't flatten it out. It's been around for a lot longer than us, and it does amazing things we can barely fathom. Right now we're busy pushing the world toward an mass extinction event, which would be the first extinction event on Earth caused by a supposedly intelligent organism that messes with the biosphere too much before understanding it.
John Baez (Oct 08 2025 at 09:25):Anyway, I'm interested in this paper by Corentin:
and would be happy to talk about it!
Corentin Briat (Oct 08 2025 at 10:11):I am happy to answer any question regarding this paper. It is an extension of the results in the Cell Systems paper I previously mentioned.