"Mysteries are not necessarily miracles," said Johann Wolfgang von Goethe. That was two hundred years ago and it is still a lesson we have a hard time learning.
Mysteries surround us on every side, the inevitable consequence of being a finite creature in a possibly infinite universe. For a long time, mystery was subsumed as the province of the gods. Every mysterious event had a miraculous cause. The ways of the gods might be inscrutable, but they had some purpose in the divine mind.
Slowly, mysterious events were shown to have a recurrent causes -- comets followed calculable paths, specific diseases were associated with specific germs, earthquakes occurred along geologic faults. We call this the history of science. And eventually, something rather remarkable dawned in the human mind: a recognition of our own ignorance.
Ignorance may be the most important discovery in the intellectual history of our species. As Goethe suggested, mysteries are not miracles; they are riddles to be solved. We chip away at our ignorance. Mysteries are illumined by the light of reason. And with every "miracle" made commonplace, more mysteries are revealed.