There are different kinds of mystery. Subatomic particles are almost illogically tiny, so we can only figure out what’s happening with big machines, long-term data, ingenious experiments, and a bunch of logical inferences. Because science is hard, then there are some simple facts about the world that we don’t know. For instance, the cause of gravity. It’s a mystery, but we have a specific question that we’re trying to answer, even if we don’t know the direction from which the answer will emerge.
We are missing fundamental facts at the foundation of physics. As Donald Rumsfeld would say, there are known unknowns. We know that there are certain things that we don’t know about physics, and are working to know them.
Ecology has a different kind of mystery.