And here's a no-brainer:
A growing body of social science research reveals that atheists, and non-religious people in general, are far from the unsavory beings many assume them to be. On basic questions of morality and human decency — issues such as governmental use of torture, the death penalty, punitive hitting of children, racism, sexism, homophobia, anti-Semitism, environmental degradation or human rights — the irreligious tend to be more ethical than their religious peers, particularly compared with those who describe themselves as very religious.
A growing body of research suggests theism has a root in the brain. There's even a whole science called neurotheology dedicated to studying this link. I think there is definitely an issue of tolerance having the chance to increase in an individual when they are not emotionally invested in a church that preaches hatred of homosexuals, non-believers, women who cut their hair, killer whales who kill their trainers, whatever. But I suspect that the cause for the increased tolerance also has its roots in the brain.
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