These arguments about the soul and freedom baffle me. Maybe I am being thick. But if I have conscious choice, that doesn't mean that I am a spirit or a soul (non-material). I may experience freedom of a kind, but again that doesn't mean that my choices have no causes. The brain is capable of constructing sound images, visual images and so on, and I would think, also an image of myself, in a kind of self-reflexive way, hence, I can experience that I am writing this.
So I am not seeing what the problem is. Granted, studies of consciousness are in their infancy - so what? Why would we jump to spirity-wirity stuff as a solution - we don't do that with gravity, which is also poorly understood.