What is our brain? What is consciousness?
These are tricky questions. Naturalists, who believe the physical world is all there is, don't have a simple answer. For we can distinguish between the physical brain processes which accompany an emotion like sadness (which neuroscience can measure), and the feeling of sadness (which science cannot measure, but which we experience). The experience is real, yet it isn't in any obvious sense physical.
The usual answer is that the mind and consciousness are emergent properties of the brain. They cannot exist without the brain (it is assumed) and they are thus anchored in the physical.
Neuroscience, and science generally, assumes naturalism. Even scientists who are non-naturalists (e.g. theists) work from the basis of methodological naturalism - a supernatural explanation is generally not acceptable as science. And methodological naturalism has reigned supreme in science, including neuroscience, for more than a century.
But some challenges to the naturalist view of neuroscience are appearing. One is the number of near death experiences (which I reported on in near death experiences - could they be real?) which seem to be unexplainable on naturalistic assumptions.
Another is the research of neuroscientist Dr Jeffrey Schwartz, whose study of brain dysfunction has yielded what he sees as unexpected results. Dr Schwartz has long experience in treating patients with obsessive–compulsive disorder (OCD) using behavioural therapy, where the patient's behaviour is modified by their own will and discipline. In essence, when they feel compelled to do a particular action which is unnecessary, they, in a sense, "talk themselves out of it". This approach is recognised as a very useful means of dealing with OCD.
The unexpected result was that this therapy actually brought about a measurable change in the physical structure of their brains, in their neural pathways. It was a scientific case of "mind over matter" - non-physical thinking seems to have changed physical processes and structure.
All this is obviously welcome. However, Dr Schwartz has gone on to argue that these experiments demonstrate that the naturalist or materialist explanation of the brain/mind is clearly wrong, and a non-materialist explanation is required. This seems to entail some form of dualism. This of course is not acceptable to materialists. And so his views have copped criticism, e.g. from atheists like Austin Cline and PZ Myers.
I don't take too much notice of Myers on this - the vehemence of his critique is surely much more based on his preconceived metaphysics than on objective science. But despite searching, I haven't found any objective assessment of Schwartz's dualistic ideas, so while his therapy is well regarded, it is hard to know how his views on the non-material brain are being accepted.
I have also had little success finding out his religious (or otherwise) beliefs. He has signed the Discovery Institute's A Scientific Dissent from Darwinism, and his conclusions are well regarded by science journalist and author Denyse O'Leary, who is a christian. On the other hand, the only religious comment I have found from him is his comparison of his therapy with the Buddhist practice of mindfulness.
But regardless, metaphysics has again impinged on science, and the ensuing battle is likely to be more about the metaphysics than the science.