Even if this story were true with no little hidden extra facts, this guy is an idiot.

In the military, and especially in a combat zone, people are tolerant of all kinds of idiosyncrasies among those they share danger with, provided you are a team player. Only someone who wanted to make trouble would ostentatiously disrupt something like a harmless prayer by demonstratively refusing to take part. It costs nothing to act respectful while others are, as they see it, communing with their Maker.

If you mock someone's deeply-held beliefs, you can expect an angry reaction. If you respectfully disagree, you will usually find your own beliefs are respected. Among civilized people, that is.

Which brings us to the last thought: in the war we are now in, which side treats avowed atheists better? How would Muslim fighters respond if one of their number announced he thought that Allah was a load of codswallop?

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You can get a lot further in life with a kind word and a gun, than with a kind word alone.