Hon, I don't know it for exactly 'coz i'm also just a student, but I'm sure that there are some advantages for intermediate stages. Let's say it needs a, b, c, d to form a perfect knee joint. First, there was no knee joint, and then b by mutation, a particular orgnism had an 'a'. There would be some advantages for having 'a' rather than not having any of them. So, that guy got selected for. In this way, the gene that codes for 'a' allele became dominant in population. then 'b' allele might arose from mutation. If 'a' and 'b' allele came from the same species, sex will help the combination of these two alleles and they would outcompete the guys which had only either'a' or 'b' alleles.
"The eyes of moles and some burrowing rodents are quite covered up by skin and fur. This state of eyes is.....aided perhaps by natural selection". (Darwin)