[hderms]

I don't know, if you ever look at a flowchart of biochemical processes, realizing that what we've mapped out is only a tiny sliver of what actually occurs, you'd be more pessimistic about simulation in the near term. We can simulate things all we want but the hard part is rooting the simulation in hard evidence, something which requires massive capital and time investment. Epigenetics complicate even further.

[imbnwa]

Would you happen to have any links to share further explaining the limits of our knowledge of biochem processes?

How does epigentics complicate this further, is it that it wides the number of inputs into a biochem system

[jpeloquin]

Not exactly what you asked for, but PathBank is a database that quantitatively describes a large part of what we do know: https://pathbank.org/

As far as what we don't know, I'm not sure there's a list. Lack of knowledge implies lack of awareness. I can offer one example: We don't know much about the processes by which collagen fibers are grown and assembled into μm- and mm-scale load-bearing structures in tendon, ligament, bone between embryo and adult, particularly in mammals. Or the extent to which collagen fiber structures are capable of turnover in adults; healing might only be possible by replacement with inferior tissue such as scar.

Personally, I think the complexity of biological systems, and the difficulty of observing their components directly when and where you'd want to, means that they can only be understood with the help of machines. Not necessarily using convolutional neural networks though.

[hderms]

Yeah it would increase the conditionality or contextuality of any given observation because even if the genomes were identical, you have differing levels of gene expression based on environmental stimuli.

So observing that gene X impacts biochemical pathway in some way Y is already really difficult when there are tons of other genes at play. Add on the fact that these genes could be triggered to stop expressing themselves in certain conditions and it makes the whole process of figuring out what is really going on that much more difficult. Even if we can make some observation, there are tons of contextual situations which would potentially invalidate that observation.