If I had to distill Blindsight down to a single, central theme, it would be that of self. What is the concept of self? How does it relate to the concept of what is human? What is the origin, function, and cost of self-awareness? How does it relate to free will, and does free will exist, or is it merely an illusion? Watts seems to have created the entire novel as a thought experiment to explore these concepts, and he leverages two lenses to accomplish that: the various neuro-atypicalities of his characters, and the distinctively intelligent but unaware aliens. Either of these ideas alone could have easily been the foundation of a compelling novel. Combining them together made this one both more compelling, and more challenging, and is in many ways at the core of my personal dichotomy over Blindsight.
As we improve our understanding of the human brain and the human body, we get closer to the ability to repair it like we would any other machine. With that, we also start to look at the source of consciousness and self, what has been often called the soul. Consider what would happen if an entire person, all of their memories and neurons and physical characteristics at a subatomic level, could be simulated or "uploaded" to a computer system.