Human Perception and the Universe
It's been known for a while that humans have deficiencies in our senses. We see better than dogs, but do not smell as well as them or sharks. Moles also do not see as well as we do, but their sense of smell and touch is far better than ours. Our sight is inferior to that of eagles, and our hearing is inferior to that of bats and dolphins. Animals furthermore have many natural senses that humans don't have, such as echolocation, and the ability to detect electric fields.
Our sight difficulties extend to correctly perceiving shapes and distances. We cannot properly see objects that are too small or too large. We know matter is composed of particles such as atoms, but we cannot see them unaided. And of course we are unable to directly see the particles these atoms are composed of, such as protons and electrons. Quantum theory tells us that all matter has wave functions, and that matter is mostly space but feels solid due to repulsions between electrons. We can't tell any of this by sight alone. (Read, What's Really Out There in the Night Sky, for a comparison of how celestial objects appear in different parts of the electromagnetic spectrum.)
We are also unable to discern the actual size and appearance of extremely large objects. Large objects that are far away appear to us to be small, such as airplanes, mountains, and the Moon. The Earth is round, but we cannot perceive this without instrumentation. This is a problem mathematicians divide into local versus global geometry. It is directly relevant to our inability to see what shape the universe is.