That is exactly my point. We can use fluid dynamics and PDEs in waves. We understand some properties and processes. We are nowhere as close in biological system.

I put the example of the metabolic pathways because last time checked (~2015) the most advanced things in the field were extremely simple and without any predictive power. Things like calculating the kernel of a stoichiometric matrix or the centrality of a node in the interactomic graph.

But you've now shifted the "how" question. (Or I misunderstood the original.)

It is not a question of how there is emergence, why there is magic. The answer to that is is because systematic interactions at a low level can create higher level playing fields.

So the "how" is now a technical question, what is this system, how complex is it, and at which levels can we understand it. And since this system has been learning how to avoid erasure by entropy or by competition for 3.5 billion years, it has searched quite a possibility space, namely 2^1277500000000, if we assume making a copy every day.

There's probably no need to go that low-level for modeling a mind, but of course the aggregate effects of biochemistry has to be taken into account (and it's full of non-linearities).

None of that means we don't understand the principles. I'd say it's pretty much like fusion. Yes, we know how the Sun works, but putting it into a bottle is a bit of a pickle, similarly with brains. (Except brains have a lot more complexity.)