Over at Mind Matters, there's a typically fascinating discussion of a paper concerning the underlying mechanisms of executive control and attention:
To find out what happens during attentional lapses, a team of researchers led by Daniel H. Weissman used functional magnetic resonance imaging (fMRI) to try to identify how these brain areas behave when attention is paid and when it flags. They describe their work in "The Neural Bases of Momentary Lapses in Attention." They measured localized blood flow (and thus, presumably, brain activity) with the scanner as their test subjects tried to solve simple perceptual puzzles, then correlated that activity with the "reaction time" the participants took to respond to each trial -- the reaction time being taken as a measure of their distraction or attention.
The results were predictable, but still pretty cool. Lapsed attention correlated with reduced activity in the prefrontal regions of the brain (crucial for executive control) and reduced activation in the sensory-processing areas at rear, in the occipital lobe. It's as if the prefrontal regions were reaching down and altering the neural activity of the sensory regions.
Electrophysiological studies have come to similar conclusions. Whenever we pay attention to a specific stimuli, we increase the sensitivity of our own neurons. Sensations that were invisible suddenly become visible, as the lighthouse of attention selectively increases the firing rate of the neurons it illuminates. Once these neurons become excited, they bind themselves together into a temporary "coalition," which enters the stream of consciousness. (At least, that's what we think happens.)
What's important to note about this data is that attention seems to be operating in a top-down manner. Think, for a moment, about how weird that is: The illusory self, enrobed somewhere in the PFC, is causing very real changes in neuronal firing. It's as if the ghost is controlling the machine.
Now I'm most definitely not advocating some sort of Cartesian dualism. There is no numinous soul trapped inside our skull. But I sometimes wonder if banal terms like "executive control" or "top-down processing" or "attentional modulation" hide the strangeness of the data. Some entity inside our brain, some network of neurons buried behind our forehead, acts like a little petit tyrant, and is able to manipulate the activity of our sensory neurons. By doing so, this cellular network decides, in part, what we see. But who controls the network?
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when you say there is no soul, it makes baby Jeebus cry.
Your final sentence, "But who controls the network?" illustrates to me the main obstacle to a sensible view of human thought, identity, and self-regulation.
We don't ask the same question about the network that controls our heart rate. It is a fairly well defined, important function, tied to many other aspects of our mental state, but it is an obviously self-regulating network. It has evolved to manage its own fairly complex functions in ways that support the survival of the organism.
So why ask the question "Who controls it?" about attentional modulation? We know this network can be self-controlling. There are subjectively strange but fairly common pathologies of attentional modulation (such as hemi-neglect) that are directly traceable to brain damage, and that reveal aspects of the network's self-management. We can measure the way it degrades when overloaded through various cognitive tasks. Etc. etc. There's nothing fundamentally mysterious or challenging to our current theoretical frameworks or research techniques.
Yet many people seem to have a cognitive glitch here, akin to the feeling people had on first hearing that the earth was round, "But then we'll fall off!" Our intuitive self-awareness doesn't stretch naturally to cover our scientific discoveries. As Jerry Fodor says "there had... better be somebody who is in charge; and, by God, it had better be me."
I've written some posts specifically on why this glitch occurs but I think it will take a long time for our intuitive sense of our selves to catch up with what we already know.