In Darwin's day the basis of life was unknown. Cells, which we now know to be the basis of life, were thought to be rather simple systems. But as science has progressed in our century we have discovered that cells are run by complex molecular systems. Many of those are what I termed irreducibly complex, and very difficult to explain in gradualistic, Darwinian terms. You're right, certainly.
Gene duplication can occur and proteins can change function.
But Darwinian evolution has some very strict requirements. The system at each point of its changing has to remain functional, and each change, if it is to be kept, has to be an improvement. If one actually tries to map a route by which specific genes could duplicate to give an irreducibly complex system, it turns out to be surprisingly difficult. Many changes we see are neutral. In a large population, all sorts of neutral mutations may be maintained.