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Is it a reference to Star Trek? Otherwise, why would they focus on animals, when mankind is the most visible and most affecting the planet?

I guess it would be based on level of intelligence of their environ..

Who actively destroys their environ? Humans. these animals master their environment without destruction. Humans destroy.

Is it because these animals are smarter and wiser than people or because they're literally not able to?

Yes

Haha OK this is a good answer. :-)

How do we know aliens don’t destroy their environs too? Maybe it’s the mark of an “intelligent” species.