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I've always wondered that too! It makes sense to me that bacteria would be in us, because bacteria can feed off of things/get something out of the experience of living there - it benefits them. But why is it that there are cells working together to form systems like respiratory, as you mentioned? What's in it for them, and how did they end up there? And if it's because evolution has shaped them into a system for humans, then aren't they really under human control? And thus, maybe not really alive? This is something I'm confused about.