The basic structure of proteins is quite simple: they are formed by hooking together in a chain discrete subunits called amino acids.

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

Proteins are the machinery of living tissue that builds the structures and carries out the chemical reactions necessary for life.

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.

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.

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.