Arthur Clarke knew that at some point, the roads of "magic" and "technology" eventually meet. I'm looking right now at a photo of a 5 MB hard drive assembly from 1956. The IBM350. It is being hoisted by a forklift. Sitting next to my computer is a piece of plastic the size of a fingernail. It is barely visible held edge on. It can hold as much data as 1,600 of those forklift-sized drive units. My brain knows this is just technology, but another part of me says it's magic. If it's possible for human beings to do this in my own lifetime, what can God, or a billion years of evolution, do?

The brain is the ultimate "black box." As you say, that it works and does what it does, is miracle enough. As far as the metaphysics goes, soon enough we'll all find out for ourselves if there's anything else but physics involved. And even then, maybe it's not about metaphysics ("beyond" physics) but just higher physics.