All of those things you say are correct, but scientists are doing it anyway[^1]. In that paper, you will see there are ways to "compress" the amount of computation needed.
Five years ago, I would have said that we were further away from having a computer correctly interpret a joke (i.e., I would have agreed with [2]) than from simulating E.Coli. The thing is, people went and did (both) anyway. But they did one more than the other. Research effort and capital flowed, and now we have LLMs. IMO, a big reason for this paradox is that there is no stigma in wanting to make a computer smarter, and everybody started playing with computer code and data and due to the huge amount of effort, there have been results. But when it comes to the very things that keep us alive, we are not so eager to play with computer code. That, I think, has less to do with the complexity of the subject and more with a certain moral disposition...which is the thing I find perplexing.
> But when it comes to the very things that keep us alive, we are not so eager to play with computer code. That, I think, has less to do with the complexity of the subject and more with a certain moral disposition...which is the thing I find perplexing.
Honestly it's the first time I hear about moral stigma having anything to do with research. Again, I think you underestimate how much harder it is to simulate biological processes than LLMs. Even from the paper you've linked, you'll see the massive amount of simplifications they had to do: they're using a minimal cell, not all metabolites are included, multimeric proteins are left out/replaced, spatial distributions are simplified, the simulation timescale is below 10μs, they do not simulate reactive processes, they do not talk about how much time did they need to perform the simulation... Don't get me wrong, it's a massive achievement. But the amount of computation that needs to be done just to simulate a single cell is absolutely massive, let alone simulating multiple cells in a system. Considering how much it would cost it's no wonder other avenues are explored first.
Five years ago, I would have said that we were further away from having a computer correctly interpret a joke (i.e., I would have agreed with [2]) than from simulating E.Coli. The thing is, people went and did (both) anyway. But they did one more than the other. Research effort and capital flowed, and now we have LLMs. IMO, a big reason for this paradox is that there is no stigma in wanting to make a computer smarter, and everybody started playing with computer code and data and due to the huge amount of effort, there have been results. But when it comes to the very things that keep us alive, we are not so eager to play with computer code. That, I think, has less to do with the complexity of the subject and more with a certain moral disposition...which is the thing I find perplexing.
[^1]: https://www.frontiersin.org/articles/10.3389/fchem.2023.1106...
[^2]: https://karpathy.github.io/2012/10/22/state-of-computer-visi...