What is the contradiction? I didn't notice it!
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Which would explain why he needed to use a canister of nitrogen which only happened to be on the ship by chance. If the ship was designed to have nitrogen then the ship would likely have it's own tanks.
Thinking more about it, this would have been fine and made the book stronger actually -- instead of "oops, I was negligent and didn't think about containing this life form that eats my fuel so that it won't eat my fuel," he could have been like, "wait a minute, I assumed
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the atmosphere of the ship was Earth-normal and full of nitrogen, because I don't remember anything, so I thought there would be no safety issue, but upon seeing the fuel was corrupted I had a flashback to the bead exchange and like, oh no."
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Hopefully they do something like that when they make the movie because "oops I am a stupid doo doo because maybe I don't sleep enough" is not very strong.
End of conversation
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