The question of how the eye works - that is, what happens when a photon of light first impinges on the retina - simply could not be answered at that time.
This fact immediately suggested a singular event - that at some time in the distant past the universe began expanding from an extremely small size. To many people this inference was loaded with overtones of a supernatural event - the creation, the beginning of the universe.
Throughout history there have been many other examples, similar to that of Haeckel, Huxley and the cell, where a key piece of a particular scientific puzzle was beyond the understanding of the age.