Depending on how you define the brain, I would be prepared to agree that we think with our brains, if we just mean by that whatever occupies the space between me ears. My argument isn't an argument for something that is not spatial. However, do the laws of physics govern the brain, or do the principles of reasoning? That's the real issue. Can we admit into brain theory the emergence of something whose actions are determined by laws other than the laws of physics, if we assume that because the laws of physics operate non-teleologically?
Here's something I once wrote in a reply I once did to Richard Carrier:
But we should be careful of exactly what is meant by the term “brain.” The “brain” is supposed to be “physical,” and we also have to be careful about what we mean by “physical.” If by physical we mean that it occupies space, then there is nothing in my argument that suggests that I need to deny this possibility. I would just prefer to call the part of the brain that does not function mechanistically the soul, since, as I understand it, there is more packed into the notion of the physical than just the occupation of space. If on the other hand, for something to be physical (hence part of the brain) it has to function mechanistically, that is, intentional an teleological considerations cannot be basic explanations for the activity of the brain, then Parsons’ suggestion (and Carrier’s as well-VR) is incoherent.
You see, I could become a materialist rather easily. I could just say that God, souls, and angels are just different types of material beings. To give them a scientific ring, I can call them psychons, angelons, and, of course, the theon. Now, if you don't like my proposed expansion of materialism and you want to exclude me from the materialist club, you have to explain to me why I am abusing language here. You have to tell me what it is about matter that makes it impossible that God is a material being. And how would you do that without saying that these entities have ground-level "mental" properties which exclude them from inclusion into "the physical."