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

The first point one has to get straight in discussions like this, is that ID is not the opposite of evolution. Rather, it is the opposite of Darwinism, which says life evolved by an utterly unguided, undirected mechanism. If god directed the process of evolution, or rigged the universe to produce complex life, then that is not Darwinism - it is intelligent design.

Skin is made in large measure of a protein called collagen.

As can be seen even by this limited number of examples proteins carry out amazingly diverse functions.

Many people, including many important and well-respected scientists, just don't want there to be anything beyond nature. They don't want a supernatural being to affect nature.

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

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