In many biological structures proteins are simply components of larger molecular machines.

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.

There is no publication in the scientific literature - in prestigious journals, specialty journals, or books - that describes how molecular evolution of any real, complex biochemical system either did occur or even might have occurred.

The question is: exactly how did life get here? Was it by natural selection and random mutation or was it by something else? Everybody - even Richard Dawkins - sees design in biology. You see this design when you see co-ordinated parts coming together to perform a function - like in a hand. And so it's the appearance of design that everybody's trying to explain. So that if Darwin's theory doesn't explain it we're left with no other explanation than maybe it really was designed. That's essentially the design argument.

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.

For example, both humans and chimps have a broken copy of a gene that in other mammals helps make vitamin C. ... It's hard to imagine how there could be stronger evidence for common ancestry of chimps and humans. ... Despite some remaining puzzles, there's no reason to doubt that Darwin had this point right, that all creatures on earth are biological relatives.

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.