Well first off, like Deathdude already said - never mix science with myths!
Myths are not to be take literary. They have a certain messag and that message doesn't lose on importaince if you prove that the myth hasen't really happened.
So to look for flaws in a myth you must look at it from the point of time it was created: they knew only some parts of the world (for them that was the whole world). They knew only of a few animals (and I doubt very much the counted insects, bacteria, viruses,... among them). The smallest animal was probably a mouse (I doubt Noah brought worms to the Ark).
So the story would tell of events, that should be something like this. There was a lot of rain, and the rivers that were usually half dry started flooding. A man and his family moved into mountains to be safe. They were lucky enough and menaged to take most of their hear with them (they were probaly animal breathers). So after the flood they were well off. They were thanking their god, that they and their livestock was saved and so - it was god who saved them...
But there is one major flaw I find in this story - and this one would be a major flaw back in the biblical days as well!
The story explicidly says the only people that survived the flood were Noah's family. And since people can reproduce only in one manor, they had practice INCEST (interbreathing - and in extre amount of times) because they menaged to repopulate the WORLD!
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