Yeah, I've seen that document some time ago, it was interesting but I haven't fully grasped it. I need to see it again, thanks for reminding. Anyway I found this presentation of Dr. Robert Sungenis - everything is slowly explained and shown, history included. It's over 2 hours long, but worth looking. It also nicely shows how science twists when it hits philosophical barriers.
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The same problem exists in both groups, the religious people are biased in their own way too.
You're right. There is always bias force unless you absolutely don't care what model you like more. But current astrophysical bias that "Copernicus must survive and also Einstein must survive" is way too obvious and it makes most of the scientists looking pretty pathetic in the end.