If we ever get to interstellar travel via generation ships (likely the only option), then I see no way around it. Probably not like a big space whale (as in the Farscape Sci-Fi series), but a living self-sufficient ecosystems that drives most of the ship's functions.
It is a bit of a double edged sword though. If most of the functions are self-organised, it is very likely that the humans living on such a ship will stop being able to understand the full picture which made it possible to create such a system in the first place.