Sometimes we know things not by their presence but by their effects. In building the periodic table, Medeleyev filled in gaps based on what he had already figured out. Certain elements, though he had not actually found them, had to be there given what he had already discovered. Similarly, for early astronomers, the orbit of Uranus could only be made consistent by assuming the existence of another planet, which was not spotted until much later. A modern example is the proghorn antelope, the fastest runner in North America. It runs much too fast for any possible predator, easily outrunning coyotes or mountain lions. Apparently, 15,000 years ago, the continent was filled with saber-toothed tigers and panthers that ran like the wind. We know of their speed only by the effect that remains in their absence.
The Talmud often preserves one side of the argument, and the student must reconstruct what the other side must have been. Having only one voice, study aims to hear the other side through the silence. Unknown elements, unseen planets and unheard voices leave traces. Nothing completely disappears; all that is and has ever been leaves footprints on the universe.