Let’s get back to the subject of consciousness and the brain. Analogies are never perfect but sometimes, if you don't push them too far, they can help produce a useful perspective. Consider a computer based multiplayer role playing game like Everquest or World of Warcraft. Your character’s allowed interactions are constrained by his attributes, and abilities. These attributes and abilities are stored in a chunk of memory on the game server and may change as your character gains experience within the game. Think of the individuated chunk of memory on the game server (The Big Gaming Computer) as representing the character’s brain and you as representing the characters consciousness.
Imagine that this game is more sophisticated than the games currently on the market and that your player has more than just memory of his characteristics — i.e., he can process the likely advantages and disadvantages of some potential action (modeling thinking). He might also have preferences for some actions and some entities over others (modeling ego attachments and feelings). Also imagine that his preferences and his ability to process effectively also change according to his experience — i.e., he has some capacity to learn from his experience.
You control the intent of the character, set direction and develop motivation but let him make most of the decisions that drive his actions (based on the results of his processing and preferences). You may challenge, nudge, or guide his decisions one way or another by manipulating the conscience, guilt, reasoning, fear, attraction, and intuition character interface functions. The size of your decision space (knowledge of the rule-set that defines the game) also constrains your character. You may wish for a more capable character but you must work with the characteristics supported by his brains (stored on the game server instead of your computer to keep you from cheating and thus running the ability of experience to be the best teacher). His brains can only change as he gains experience (interacts with other entities and his environment) -- brains may grow more capable with productive experience or suffer damage (dysfunctional change) with counterproductive experience (i.e., take in counterproductive information).
As intentions are acted out within the constraints of the games interactions, immediate feedback [in the form of additional new direct game experience for your character to process and by way of the intuition interface (the results of you processing the characters experience)] is often generated from which both you and he learn more about the rule-set driving the game, more about the nature of the characters you are interacting with, and more about yourselves. You and your character are both growing (increasing your knowledge, understanding and effectiveness) together in a tightly connected, interactive, symbiotic relationship. You are both trying to reduce your entropy, or equivalently, increase the value/effectiveness of the information content that defines you. His brain changes (attributes, abilities, memory content, processing effectiveness, and preferences) to reflect the effect of any new experience and feedback. Likewise, the information content and entropy level of your consciousness changes to reflect the effect of his and your new experience (your experience is your assessment, your processing of the interactions and feedback his characteristics and capabilities generate in the game as he executes your intents and is nudged by your guidence. You are his mentor, his guide, his conscience, his inspiration, his intuition, and transfer to him (through your intents) your free will, knowledge, understanding, limitations, fears and ego. He operates according to the values that you input to him through the intuition interface — your values that unavoidably express the limits of your understanding and consciousness quality. You are his soul.
Taking into account your own strengths, weaknesses, and proclivities, you originally defined some of his fundamentals (like race and appearance to whatever extent the rules allowed) and put him in some particular situational context (particular server or specific environment/place within the game) in order to optimize his potential for growth. How effective your initial decisions are in facilitating his growth depend on how well you understand the game and on what/who your character happens to run into (interact with) which define his experience, initiates feedback, modifies his brain, and thus strongly influences what he does next. Remember there are thousands of other characters in the game exercising their limited understanding, free will, intents, and intuitions as well as the gamming environment which execute widely variable, sometimes random, interactions -- consequently much of what happens to a character is unpredictable and uncontrollable — like social Brownian motion.
Ok, the parallels could go on and on -- you are welcome to pursue them as far as you wish, but I think I have beat this overworked analogy to death in this limited venue. If this perspective has helped more than it has confused, good — otherwise let it go — analogies tend to fall apart if pushed beyond their usefulness. In other words, don't get wrapped up in the details. At the very least you should see the point and value of the virtual physical system -- with each PMR inhabitant and their consciousness inexorably intertwined and connected in an interactive dance of learning opportunities and growth as they together mix it up with others in the PMR school yard. Think of your brains and your consciousness not as two separate, nearly opposite things, but rather as two individuated, mutually interactive, growth enhancing sides of The One Coin. Imagine an apparently physical (but actually virtual) brain and a nonphysical consciousness representing two symbiotic aspects of one consciousness -- each aspect being defined and differentiated by the imposition of differing sets of constraints; or perhaps think of them as two mutually reinforcing portions of the consciousness-evolution fractal pattern.