Your brain is nearly fully connected with your body and controls a ton of its function, but your brain is not a single unit. Your brain itself does things you're not conscious of. Like you ever tried to think of something you can't quite remember, and then you give up and spend hours not consciously thinking about that thing and then suddenly you recall it out of nowhere? That's clearly your brain at work in the background trying to recall the information independent of your conscious mind. Likewise, you conscious mind can be in secondary control of some functions like breathing (your lower brain controlls this by default unless your higher brain overrides it), or entirely removed from control of some functions like your heart beating (no matter how hard you try, you can't make your heart beat to the rhythm of your favorite song). The brain is not just your mind, but a number of sections with different unconscious functions, only some of which do they ever directly communicate to or allow control from the conscious mind. Your conscious mind is actually a relatively small part of your brain's functions, or more likely a manifestation of several different higher level functions together. But your mid and lower brain are wholly sectioned off from your conscious mind and merely interface with it.