The Seat of Man's Intellect: What Says Your God?

[Jenny A]

This takes me back several decades to college.  Descartes (yes the Rene Descartes of I think therefore I am) thought the seat of decision and of the soul resided in the Pineal gland because according to his view this is where the brain met the animal spirits of the blood. 

Thus, when the soul wants to remember something, this volition makes the gland lean first to one side and then to another, thus driving the spirits towards different regions of the brain until they come upon the one containing traces left by the object we want to remember. These traces consist simply in the fact that the pores of the brain through which the spirits previously made their way owing to the presence of this object have thereby become more apt than the others to be opened in the same way when the spirits again flow towards them. And so the spirits enter into these pores more easily when they come upon them, thereby producing in the gland that special movement which represents the same object to the soul, and makes it recognize the object as the one it wanted to remember” (AT XI:360, CSM I:343).

The description of the effect of the soul on the body in the causation of bodily movement is also more detailed: “And the activity of the soul consists entirely in the fact that simply by willing something it brings it about that the little gland to which it is closely joined moves in the manner required to produce the effect corresponding to this volition” (AT XI:359, CSM I:343).

Rene Descartes, Treatise of Manhttp://plato.stanford.edu/entries/pineal-gland/

It was essentially an argument from ignorance. We don't know what the Pineal gland does. It's located in the brain---therefore it must be the soul.