We are not inferring design to account for a black box, but to account for an open box.

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.

I find the idea of common descent (that all organisms share a common ancestor) fairly convincing, and have no particular reason to doubt it.

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

In the abstract, it might be tempting to imagine that irreducible complexity simply requires multiple simultaneous mutations - that evolution might be far chancier than we thought, but still possible. Such an appeal to brute luck can never be refuted... Luck is metaphysical speculation; scientific explanations invoke causes.

Thus it seemed to Haeckel that such simple life could easily be produced from inanimate material.

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.