There is plenty of magic going on. Today we cannot replicate or understand how emergent properties born of biological structures. Not even in "simple" systems as the metabolic pathways.
We mapped the whole genome and connectome of C. elegans, no? And most of that is understood. For example, it seems to be a good model for substance addiction (especially for nicotine). That seems a pretty complex emergent behavior to me.
If you mean bigger biology, yes, sure, we don't have a full map of functional genomics for humans, but we're getting there.
Or maybe not, maybe it's so exponentially more complex, that it'd take as much time to understand it as it took for evolution to work it out. (Especially considering that evolution played with every individual, whereas we like to constrain our data gathering to non-aggressive methods.)
We have the connectome of C. elegans, yes, but we are still pretty far from understanding how it 'works'. The functional connections are still an active area of research, and it is greatly complicated by connections not explicit in the connectome (neuromodulator effects), as well as the internal dynamics of neurons and non-linear network dynamics.
The connectome is necessary, but far from sufficient, to 'understand' a brain, even one made from only 302 neurons as in C. elegans.
The rules that govern a system can create patterns, which themselves behave according to rules, but with a set of rules that was "hard to predict" from the underlying system.
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.)
