The biggest problem in understanding the universe is the incrediblely limited section of it we can perceive.
 A small slice of the electromagnetic spectrom as well as it's reflecting off of a  of grouping of atoms of a sufficient density and specific composition, Physical interation with groupings of atoms of a sufficient density, very limited ability to determin composition of compounds, and a very limited range of fluctuation in atmospheric pressure. And all two of those deteriorate as we age or are broken to begin with.

We've gotten better at building tools to perceive more aspects of the universe, but those are limited by our ability to extrapolate their existance from what we can observe and even then we have to translate the machine assisted observations into concepts we can understand.

We aren't just blind men trying to figure out what the elephant looks like. We're blind men with no sense of taste getting a description of the elephant from another blind man that that can only lick the elephant and speaks a different language.