Well, that should be obvius - it's not written with todays knowledge. All what back then was seen as act of gods, we now know is just plain nature.
About thoughts, well, slavery for one is a bit outdated, stoning neither is considered a right way to punish.
Further, it seems like god doesn't care so much today about life on earth - he was quite busy back then interviening, while today he doesn't do anything.
Back then god mercilessly murdered thousands of infidels for mere insults, but today ? No nonchristian armies has been destroyed by gods merciless weapons despite the numerous chances there has been.
Secondly, ideas which are considered to be true, are in fact, never false, even if they fall out of favour. This is how novel ideas introduce error, in rejecting older ideas which are true.
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