Does a novel have vital organs?

For years now I've been drafting a novel of speculative fiction (not quite science, not quite space opera) and as I am nearing the finish for the current incarnation a question has been arising in mind time and time again, so much so in fact that I cannot ignore it: What is the book's brain? Now, this is an odd, anthropomorphic thing to ask, I know, and I have no end of scratching my head over what it means. Does a book cogitate? Does it have chemical processes? Is it connected to a nervous system? In literal terms, obviously the entertainment of these questions is at best absurd. Therefore I can only ask them in a literary sense.
My definition of a brain fits what most people probably think of when they think of a brain. A seat of reason, a foment of thought and motive and philosophy, a system of unconscious impulses and habit patterns, a reservoir of memory and apprehension. Can a novel sport these features? In my experience of reading literature, I feel compelled to answer in the positive.
A great work of literature engages the reader, that much is obvious. The manner in which it engages us is a sort of deep, mental inhabitation; a great book possesses our mind, moves into it and inhabits it and influences our thinking with its own. If a great novel doesn't have a brain, the words lay flat on the page lacking effect. A bad book turns off the brain, or at best skates over our dearest and most sincere thoughts and feelings.
Coming at the question this way provokes me to wonder what kind of brain is at work in my own feeble attempt at writing. Surely my own brain is there, but also there is something on the page that is unique and separate from me. When someone else reads it this thought process is more evident -or I can hope that it is, if I have done my job correctly and engaged the reader.
The real question that faces me, then, is how much do I manipulate the brain in the words? Do I even want to? This is an editorial question (not a rhetorical one, I promise!) and an artistic one to boot, because I want to release something in the work: I want to bring to life a vital system of activity and gentle provocation.