A common tactic used by the atheist camp is to point out the atrocities commited in the name of religion. Some Theists, knowing a juicy talking point, are quick to point out that a healthy amount of genocide committed in the 20th centruy was done in the name of creating a perfect secular state. This issue is fuzzy territory. After all, can it be claimed that the central motivation of Stalin or Polpot was to spread atheism? Maybe, maybe not. But this also applies to religious wars. Are Israel and Palestine really fighting over religion? Not really.
Religion is a mythological encoding of a society's collective values. Because of the many different environments, diets and countless other environmental and genetic influences on human evolution, different societies are more or less prone that others to be peaceful, or to be vegetarians, or to emphasize the use of blue in their art or anything else you can think of. All of these differences are encoded into religion not, and this is important, NOT caused by them. In other words, a culture that is prone to violent streaks will produce a mythology that includes a violent god. They don't have violent streaks because they believe in a violent god, they believe in a violent god because they are inclined towards violence.
Wars are not about religion. Wars are always about economy and politics, about land and the ability to be self-ruled. Religion is just coding the values that play out when two opposing societies go to war. This is also true for atheist regimes. If you examine the actions of the Roman Catholic Church between 500 and 1500, you have to keep in mind that you are examining primarily a political system, not a religious one. If the Roman Catholic Church during the inquisition had believed in fairy lights residing in the rings of saturn who control the fates with potions and incantations, they might still have carried out the exact same kinds of shady abductions, trials, murders, etc. The inquisition wasn't done in the name of Christianity, just in the name of the social values coded into whatever religion that political force was practicing at that moment in history.
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