Here's a long article about the 'puzzle' of consciousness by a philosopher, discussing the interaction of 'brain' and its awareness of itself.

Becoming a being which evolved to be able to reflect on our own nature, rather than simply manifesting ourselves, has led to a lot of confusion. The philosophical study of Phenomenology attempts to sort out some of the issues, but just constructing a shared vocabulary to do this makes the attempt awkward for all but a few.