The new model of the brain shows it as a large box with many inputs and outputs with in the box there are several smaller boxes that also have several inputs and outputs. These smaller boxes are directing each other through their inputs and outputs in hundreds of different pathways. This new model of the brain and the nervous system shows it to be an autonomous structure that has the ability to function on its own. One of the boxes can set itself off and begin a chain of reactions that will ultimately produce an output.
With the new model the idea of self or soul is not completely lost. Among the boxes, there is one that is called the "I-function" or commonly known as the "person." This box relates to one's own experiences and feelings. There is a great possibility that the mind, spirit or the soul resides within the "I-function." But that would make it seem like a human's soul is contained with in something, and since the beginning of time humans have thought of the soul to be untouchable and unattainable, so the idea of it being contained in a box seems completely appalling. The other possibility is that the soul, mind or the spirit somehow control and/or interact with the "I-function." This idea is a little more conceivable. This new model leaves room for the mind, body and soul as well as making it a plausible idea to have the brain controlling our behavior as well.
Not so much "controlling" our behavior as BEING it. As for the soul cramped in a box ... I don't much like that image either. One possibility is indeed an interaction of something else with the "I-function" box. But how about if it turned out that that box (interacting with other boxes) could imagine/dream/create far beyond the limits of its own space. Would that do? PG