Do I have control over my own brain?

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Yes! But my answer is based on my metaphysics. I think that your brain is an essential part of you (along with your body) and that the part of you that consciously considers what to do and makes decisions is a part of your brain. So, you have control over your own brain because processes occurring in your brain control other processes in your brain that cause your bodily actions. Conscious self-control is a (very complex) set of brain processes.

If this sounds counter-intuitive, it is partly because we simply have no good theory about how physical brain processes could be the basis of conscious experiences and thoughts (though we do have pretty good theories about how the brain carries out many cognitive tasks, such as perception, language, and initiation of movement). And it is partly because we have a competing metaphysical theory, largely based on religion, that says that our selves (our conscious minds) are non-physical entities separate from the brain and body (notice that this theory does less than the physicalist theory in giving us any information about how the mind works or how consciousness exists).

Now, if you are inclined to accept the dualist theory that says you are a non-physical entity (whatever that might mean), then it is more difficult to explain how you have control over your brain, because it is difficult to explain (1) how a non-physical entity could interact causally with a physical entity like the brain (surely, control requires causal interaction), and (2) when and where such interaction might occur. The latter problem becomes more difficult as we gain more and more information about how the brain works. There's less and less time and space for a non-physical soul to do any causal work.

So, the difficulty is coming up with a theory of how the brain works that captures most of what we wanted from (and thought was "explained" by) a non-physical mind or soul. We don't have such a theory yet. When we do, I suspect we'll find the problem of free will much less problematic.

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