Because the brain does not possess robust ‘fault detectors’, the brain will just as easily encode irrational thoughts and beliefs just as it will rational ones.
Nowhere in the definition of Religion is there a mandate for religions to self-challenge or revamp their theological positions based on new enlightenment. Rather, a religion adopts a central orthodoxy and perpetuates it.
We also have to be particularly wary of imaginative thought processes for we can very easily create things and ideas in our minds that are outright impossible or highly improbable to be manifested in the world-universe which we then deceive ourselves into thinking that they are either certain or probable likelihoods. We often take several different pieces of information or instilled beliefs and loosely wed them together to bestow some greater meaning which falsely represents reality.
One of the things that I find especially worrisome is the propensity for people to perceive reality as dyadic, comprised of two oppositional elements. Some prominent examples are our assignment of good–evil, right–wrong, just–unjust, heaven–hell, conservative–liberal, rich–poor, us–them. I also refer to this as compartmental minimalism because of our tendency to force our understanding of reality into as few categories as possible. Essentially, by perceiving reality in this way, we intentionally and unintentionally, reduce the cognitive load. We do not want the hassle of too many details or abstractions; however, this convenience comes at a cost that goes unacknowledged. We essentially build a false reality bit-by-bit.
When it comes to our embedded beliefs, our relative intolerance to ambiguous and contrary information leads us in many instances to ignore or less thoroughly process incoming data for its actual truth value. It is for this reason that society at large is so prone to religiosity because taking a skeptical stance is the difficult path; it is the path of greatest cognitive load. The cognitive load is high because we have to conscientiously work to continually question the information we receive and often re-program our subconscious for a subject matter that is both complex and abstract. More simply stated, it is cognitively easy for people to attribute perplexing phenomena to an abstract, all-powerful deity than it is to engage in a rigorous examination to discern potential explanatory data.