I was surprised to see some religion in the latest episode of Stargate: Universe. Some of the humans onboard Destiny are praying the Our Father before the ship collides with a red star. I didn't think the creators would bring any religion into the episode at all, even though the crew members are facing imminent doom. Of course, what a modern show on SyFy be without two of the characters coupling and then talking afterwards.
If aliens who have no conception of God or a redeemer did exist, would that count as evidence against the existence of God? No. It might not even be evidence against Christianity. (Marie George has an article about extra-terrestrials.) But it wouldn't surprise me if some people's faith were shaken... and you might even think that sci-fi writers would use this more as an argument against theistic religion.
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