This is the point, the brain is nothing but a set of subatomic particles which properties are determined by the same laws of physics as in every other set of subatomic particles, such as an electric device.
Well, you aren't wrong, but if you only focus on the subatomic level of the brain, it won't tell you anything. It's like taking a picture with the zoom all the way up on your camera. All you will see are a few grass blades, and you'll miss out on seeing the whole rest of the scenerey.
When you look with a more of a zoomed out view, you can see how the brain's structure facilitates the environment for a consciousness to exist. This is where biology comes in. If you focus too much at the atomic/subatomic level, all you will see are those particles, and that won't tell you much of anything (outside of the structure of DNA). That's how it seems to me, at least.
All biological and chemical processes are nothing but successions of elementary physical processes , which is sufficient to prove that consciousness is irriducible to cerebral processes and transcends the physical/biological reality.
All biological and chemical processes are dictated due to the structure of the brain. It facilitates those processes. If you just looked at the elementary physical processes without taking that into account, it would seem like there needs to be more, but in taking into account that the function of the brain facilitates these reactions, it shows that the cerebral process is all encompassing. Consciousness is one of the byproducts of it's function; others include the subconscious or the autonomic processes that keep your body functioning.
I don't see how any of that is sufficient in proving that anything transcends material reality. We can see how this stuff works, and while the brain is super complex and we learn more all the time, nothing points to anything supernatural. Everything we learn grounds it more in material existence.
Consciousness is the result of the interaction between an unphysical/unbiological principle (the soul) and the brain.
Because of this interaction, cerebral damages affects of course also our conscious psychical life.
Consciousness doesn't need supernatural interference to exist. Do octopuses have souls, then? What about rats? These things also have consciousness; they also have nervous systems.
Where is there evidence of unphysical aspects of reality? Why does it need to exist when physical aspects can be studied, observed, and used to explain things in a consistent and seemingly accurate way? If the "unphysical" can't be studied, how do we even know it's real, and why should we incorporate it into our understanding of reality?
It seems like the damage he suffered was to the brain, and the result was what was plainly seen. He changed because his brain changed. It was rewired in an instant. The old person died, and in an attampt for the brain to repair itself, a new person was born. That new person was a byproduct, just like the person who existed previously; just like I am now a byproduct of my own brain.
Again; where does the "soul" part fit in?