I don't quite understand QM analogy. QM arose to explain new observation from more detailed measurements. Consciousness and intelligence and all things brain have been (to an extent) known 'properties' and difficult to explain (from first-principles) for quite some time. The more we probe, we answer some questions, and in the process reveal some more detail, leading to more detailed questions.
My qualm is that nowhere along this trajectory have I ever seen any need to invoke magic. It's a complex, many-body system with lots of noise, many relevant interacting length and time-scales that are difficult to cleanly separate, model, observe and probe. It's hard, but it seems we're making progress. Maybe it will take CERN, LIGO or ISS scale endeavors, I don't know.
It's not all similar, IMO, to how QM arose.
But I'm not a neuroscientist nor a historian of science.