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I'll have a crack at these, this isn't me defending the film btw, I have the same opinions as you, some very odd things irked me too.
ÔÇó I don't think he knew there was any danger in there at that point, probably just found it amusing
ÔÇó I think he was convinced it was a glitch because it remained motionless for "over an hour"
ÔÇó I just thought they were tinkled off because they had their lives put in stasis for 2 years (?) only for them to find out it was because two scientists believed they had found our creators - that baffles me too, especially when they could simply relay back to the ship and ask for directions?
ÔÇó I assumed his love of biology/botany overruled his common sense, the idiot
ÔÇó Typical action sequence that doesn't make sense, made for a decent visual mind!
ÔÇó Odd that one, seemed only David knew of what was inside her.
ÔÇó The pain was too much for him to handle I guess
ÔÇó Another odd thing with no apparent reasoning
What I got from the whole Engineer thing was the guy at the start was dropped on earth to create us, we came from the same DNA, he took something that disintegrated his body into the water, last thing you see is the strand of DNA, I thought that was the creation of Human life.
Black Goo and why they want us destroyed will be in the sequel I imagine, along with the explanation to Davids other motives from Weyland etc, as I didn't feel that was covered in enough detail. Did he simply take exception to Holloway being a dingdong to him or was it a big experiment he was told to carry out mirroring Ash in Alien?