An interesting paper on the neurobiology of conscious awareness: Unconscious High-Level Information Processing.
The authors propose that consciousness may be associated, not with activation in any given area of the brain, but with recurrent information processing between areas, a kind of neural ping-pong.
When presented with sensory information, say the sight of an object, signals travel up through the brain from "primary" sensory areas to "higher" areas associated with more complicated processing. They call this the Fast Feedforward Sweep, or "FFS". Maybe not the best acronym.
Anyway, depending on the nature of the stimulus, this can lead to activation in almost any part of the brain. However, they say that it's not enough to generate consciousness; only if the later areas feedback to the earlier areas, and start a recurrent processing loop, does this happen.
This stands in contrast to the popular view, which seems to fit with common sense, that primary areas are unconscious and that consciousness is directly associated with activity in the higher areas, in particular, the prefrontal cortex (PFC).
The authors refer to fMRI and EEG studies showing that even "high level" processes, such as selective attention to stimuli, and inhibition of an action, can be triggered by subconscious cues, and that this is associated with activation in the prefrontal cortex - unconscious activation.
The details of these studies are fairly arcane but the point is that the prefrontal cortex is generally agreed to be the most developed, "highest level" part of the brain. If anywhere in the brain was going to be the seat of the soul, it's the PFC.
This shouldn't come as a surprise, though. While it's tempting to look for a part of the brain which "does" conscious experience - the "me module" - Daniel Dennet pointed out a while ago that this temptation is motivated by a fundamental confusion.
Likewise, while it seems common sense that conciousness is the "highest mental function" and therefore must be located in the highest brain area, this is a presumption: consciousness is a mystery, and we don't know if it's a high level function or not, or whether that question even makes sense.
Nor should the fact that consciousness isn't an inevitable consequence of high-level cognition come as a shock: in fact, that would be impossible. As Ryle pointed out in The Concept of Mind, this would create an infinite regression. Any conscious experience has to come from somewhere.
Right now I'm concious of choosing certain words rather than others in typing this post, in a conscious attempt to make it read better. But I'm not aware of all of the rules and experiences that guide my choices. I just feel that some words work. This feeling seems to come out of nowhere, or rather, out of the words themselves.
It isn't, of course, it's a product of calculations taking place in my brain, but I've no idea what they are. I wouldn't want to be, either: I'm too busy typing.
van Gaal S, & Lamme VA (2011). Unconscious High-Level Information Processing: Implication for Neurobiological Theories of Consciousness. The Neuroscientist : a review journal bringing neurobiology, neurology and psychiatry PMID: 21628675