Currently I do not have any papers in the works, but I do have a polished opinion on how religion works with the brain in purely psychological terms. I submitted this as an Op-Ed for the OU Daily, but due to the proximity to 9/11 the editor decided to focus on more periodically relevant subject matter. I hope you enjoy!
There are quite a bit of 'grey matters' about the brain's relation to cognitive dissonance, rationality in religious belief, truth & epistemology, and how the brain reconciles justification. It's uber-interesting stuff; why do people take offense when there religion is criticized to the point of seemingly physical discomfort and mental conflict? Why is it such a touchy subject, when I can insult your car or job, or physical feature of a person, and not get much of a rise; but then attack their beliefs and people go berserk.
As of now, Personally, I compare Stockholm Syndrome to religious belief. In both you have a single powerful aggressor [the Captor or the God] that has significant power over the victim [the Prisoner or the Believer], There has been a direct, implied, or interpreted threat conveyed from the aggressor to the victim. This constant state of vigilance and awareness changes how a healthy and normal brain were to function. The changes, as a result of a built-in coping mechanism in the victim, very much alter how certain aspects of the victims brain operate; heavily distorting reality, perception, and cognitive functions of the victim. The end result is something where the victim sees or feels like the absence of a detectable implied, direct, or interpreted feeling of receiving aggression, is in itself an act of kindness and compassion. The longer this continues, the longer the victim's cognitive abilities are messed with, and the delusional coping mechanism of the victim just further deepens and spreads to the brain.
This applies to religion amazingly because people see an absence of evil occurring, even when nothing directly positive is happening, they attribute that experience to the 'will' or 'grace' of god. It becomes even more intense in nature when it is an increasingly positive event that occupies the space between negative experiences. The way the world works, unfortunately, is that we are constantly bombarded by negative experiences and situations. So any break from this triggers our brain's self-defense / coping mechanisms and gives attributes to the highest power they can think of, usually God, Karma, the Dao. While this would be mildly acceptable in small doses, due to the human condition it is a constant and increasing process. The constant onslaught of negative stimuli in combination with the breaks between the actions of the aggressor and the associated stressors, gives this process a terminal velocity quite quickly as this whole function is self-perpetuating as long as the victim is unaware of the change, not actively counter-acting against, and merely passively resistant. This process repeats and builds upon itself becoming more and more galvanized in a person as time and events take place.
I believe it is this case-hardening effect on mental processes that creates the mental blocks in people, which inturn makes them so actively and readily defend radically irrational beliefs. They draw confidence from this storage of coping rationality... But over a long period of time, from a weak-minded person, they are oblivious about this, and when this is mentioned they will try to write it off, discredit it, or just flat out deny it. Thus perpetuating the delusion of a loving form of a higher power, thrusting forward the passively masochistic mindset that has quietly crept into the rationalization faculties a person has, rendering the processes of rationality ineffectual in order to dampen the experience of the true cosmic world.