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.
But sequence comparisons simply can't account for the development of complex biochemical systems any more than Darwin's comparison of simple and complex eyes told him how vision worked.
By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning.
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.