Right, on this naturalistic view, the brain is what's ironically identifying not with itself since it has no direct perception of itself, but with its imaginary constructs, with the emergent abstractions that make sense of its patterns of activity. So the brain's alienated from itself, and this natural alienation is simpler than the more mystical, metaphysically dualistic kind that we find in Plato or theistic religions, for instance.
Evidently, this article didn't go over well. I've written another one that clarifies what I was trying to get at here. But I'm not sure why the thesis here is deemed so dubious or uninteresting.