"Emergent" properties of the brain aren't magic, they're just multiple chemical and other physical processes working together. Processes which can be measured and altered by chemical and physical means.

The whole water is wet is an 'emergent' property. This is true, linking emergent properties to the underlying smaller scale can be very difficult. Just not impossible. There is recent work on how water molecules interact that can explain 'wetness'. It is difficult, not impossible.