In Darwin's time all of biology was a black box: not only the cell, or the eye, or digestion, or immunity, but every biological structure and function because, ultimately, no one could explain how biological processes occurred.
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.
In the 19th century the anatomy of the eye was known in great detail and the sophisticated mechanisms it employs to deliver an accurate picture of the outside world astounded everyone who was familiar with them.
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.
Although Darwin was able to persuade much of the world that a modern eye could be produced gradually from a much simpler structure, he did not even attempt to explain how the simple light sensitive spot that was his starting point actually worked.
It is a shock to us in the twentieth century to discover, from observations science has made, that the fundamental mechanisms of life cannot be ascribed to natural selection, and therefore were designed. But we must deal with our shock as best we can and go on.
Biology has progressed tremendously due to the model that Darwin put forth. But the black boxes Darwin accepted are now being opened, and our view of the world is again being shaken.
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.
A man from a primitive culture who sees an automobile might guess that it was powered by the wind or by an antelope hidden under the car, but when he opens up the hood and sees the engine he immediately realizes that it was designed.
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.
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.
Since natural selection requires a function to select, an irreducibly complex biological system, if there is such a thing, would have to arise as an integrated unit for natural selection to have anything to act on.
It was a shock to people of the nineteenth century when they discovered, from observations science had made, that many features of the biological world could be ascribed to the elegant principle of natural selection.