It seems that as we lean more about the brain, the mysteries of the mind become understandable in mechanistic terms. Libet’s experiment has challenged our concept of free-will, and cases like Phineas Gage’s seem to reduce emotion and personality to detachable qualities - subroutines in wet circuitry. In one area, however, neuroscience has fallen short. Here I identify the potential for something more than materialism, the possibility - no matter how small - for the spiritual.
A neurosurgeon and astronaut are talking about God. The astronaut recounts flying into space and peering through his shuttle window. At this height, he can see below him the totality of earth - the great seas, the lights of civilization, the stage for every tragedy, comedy, or love. As he marvels, the surrounding space becomes apparent. The romanticism of existence no longer seems a mystery. All the Earth’s passions shrink into insignificance..
The doctor replies that she, unlike the astronaut, believes in God. While she has not seen the planet, nor has she seen a thought.
This story may seem cliche, but I think it expresses a valuable point. Even after centuries, humans have progressed little in explaining the thought. We do know that thinking is not an innate capacity. Instead, babies form this ability as they learn their first language. Sometimes young children while learning to speak mutter under their breaths. It appears that they are talking to an imaginary friend, but if you listen close, you might notice who the children are really addressing - themselves. At this stage of development, kids must vocalize their thoughts. Only after this does thinking become an internal process.
The subconscious constantly throws up ideas. If the brain deems an idea worthy of conscious realization, it draws on your memories of words in order to piece together the sound of an appropriate sentence. This process brings the idea to consciousnesses (the brain’s command center) as you actually hear the preconceived thought. This is why people can say a thought instead of thinking it and often not know the difference - a situation which often ends in inaptness and embarrassment.
Young children have not yet internalized this process. However, the way in which they mutter their ideas does infer a knowledge - on some level - of the consequences of public thoughts. After time we can use our expanding memory banks to remember how those words sound in our head instead of outside it, making thoughts much less risky.
All this means that thoughts come from stuff, namely memory, sound, and language. Even though we can theorize about the origin of thinking, I still think these basic ingredients point towards a larger mystery. While I can explain thoughts, hearing remains the final conundrum.
All 5 senses interact with the brain in the same way. When something applies pressure to your hand, sensory nerves shoot an impulse through your arm, up your spinal cord, and to the brain. The peripheral system transports information from every sense in this way, although the impulses come in the brain at different places exhibiting different patterns. When we talk about color, photons are thus irrelevant. The only significant thing to perception - an activity manifested in the brain - are the electrical fields the brain interacts with.
Now the big question: how can something create color? As the act of creating involves combining ingredients, a creation must have parts. One can make an atom - as physicists recently have - because atoms consist of smaller pieces called energy; however, energy itself cannot be formed because it is indivisible. The law of thermodynamics tells us this. In the same way, nothing can create color because color has no parts. While we could take half of an atom, no such thing as half of red exists - or half of C sharp.
The point here is that no matter the level of complexity, a network of electro-chemical interactions cannot create the basic senses. While we can explain emotions as aggregates of the senses - revulsion being the brain remembering a food that caused a vomit, or stench that caused the stomach to turn - the building blocks will remain a mystery; no one will ever explain color or sound in mechanistic terms. Certainly, something external must exist. Perhaps the brain derives subjective experience from a collective consciousness. In this view, the explainable phenomena of our mind would perish at death, the memories and personality once formed disappearing with the brain structure which recorded how to form it.
Although this theory does not solve the existential fix, it somewhat lessens it. Also, I think, it shows what a great guess Buddhism made. The ego is that, a specific combination of the basic elements, and while perishable, something will always remain.