I'm not sure we will ever be able to scientifically assess the relationship of the spirit, consciousness and brain. We can examine which areas of the brain process certain stimuli. I see the brain as a conduit, an interface between the true self, the spirit and the physical self, the animal. The brain brings consciousness into the physical world.
The brain is like a car, the driver the spirit. The car is an assembly of various essential parts that has the capacity to take us to wherever we choose to drive. The driver is not a part of the car but the car is useless without the driver. Every action of the car is determined by the driver who is in association with the car, though not attached.
The brain is the same - it can be seen as a chemical computer with specific parts allocated for specific functions. The personality does not reside in the mind. Spirituality does not reside in the mind. Animal instinct is likely hardwired but the human degrees of abstract, artistic, lateral, moral, scientific and ethical thought are generated by the spirit and are then made manifest by the brain via thought.
Thought being the assembly of spiritual processes into tangible cognition.
