Comment by bglazer

Molecular dynamics describes very short, very small dynamics, like on the scale of nanoseconds and angstroms (.1nm)

What you’re describing is more like whole cell simulation. Whole cells are thousands of times larger than a protein and cellular processes can take days to finish. Cells contain millions of individual proteins.

So that means that we just can’t simulate all the individual proteins, it’s way too costly and might permanently remain that way.

The problem is that biology is insanely tightly coupled across scales. Cancer is the prototypical example. A single mutated letter in DNA in a single cell can cause a tumor that kills a blue whale. And it works the other way too. Big changes like changing your diet gets funneled down to epigenetic molecular changes to your DNA.

Basically, we have to at least consider molecular detail when simulating things as large as a whole cell. With machine learning tools and enough data we can learn some common patterns, but I think both physical and machine learned models are always going to smooth over interesting emergent behavior.

Also you’re absolutely correct about not being able to “see” inside cells. But, the models can only really see as far as the data lets them. So better microscopes and sequencing methods are going to drive better models as much as (or more than) better algorithms or more GPUs.