Our Physical Brain and Descartes' Dualism

In his digression between chapters 2 and 3, Carr raises an interesting paradox about our brain: it is the sensory center of our body, yet we are unable to sense it at all. To me, this phenomena meshes perfectly with the Cartesian Dualism theory.  Descartes separated the physical tissue of our brain from our consciousness. According to Carr, the this theory gained mass acceptance at the time because it proposed a clear separation between science (the mind) and religion (consciousness).  Fast-forwarding to the present-day, this dualistic line becomes much more blurry.  We have the ability to produce readouts and images of the brain's activity in any state and in response to any stimulus. These readings have allowed us to create precise maps of the areas of the brain that correspond to various areas of consciousness and sensation (vision, speech, thought, movement, etc.)

However, connection between our brain and our mind is more interesting that this one-to-one correspondence between physical location and mental process.  Interesting questions can be raised. If the mind is a series of chemical reactions that are responses to other chemical reactions, where did these reactions start? And then, think of our brain and mind mathematically.  Focusing on the nature part of our development, the connections between our neurons are partially determined by our ~2.5*10^4 genes.  But, each of the 1*10^11 neurons in our brain can form thousands of synapses with other genes. How can such a complex pattern be formed by such relatively few genes (assuming unrealistically that every gene directed neurons)? The coexistence of the body of the mind seems to become a chicken-and-egg question - what is a result of what, the body or the mind? It's hard to imagine the immense power and scope of our consciousness without a physical basis in our mind, but how could the complexity of our physical mind be formed without the formative force of our consciousness? 

My biology teacher in high school constantly asked us as we were learning: "What is a thought?" In doing so, she was attempting to bridge the gap between our consciousness and brain. Someday, when we are able to fully understand the chemical basis of a thought, the connection will finally be made between the halves of Cartesian Dualism.