I'm sure the readings that other people linked will be useful, but two points to give some intuition: 1. Genes don't have to be optimal, or even close to optim

I'm sure the readings that other people linked will be useful, but two points to give some intuition: 1. Genes don't have to be optimal, or even close to optimal to work. They just have to be good enough. 2. Nature loves to copy. Large segments of DNA can be copied by a number of mechanisms and randomly placed elsewhere in a genome. So once nature "discovers" (for example) a DNA-binding motif, that motif can be added to other genes, and now you have a diverse set of DNA-binding proteins, which will continue evolving on their own.