Take the development of the body. The genes that build a femur cannot specify the exact shape of the ball on top, because the ball has to articulate with the socket in the pelvis, which is shaped by other genes, nutrition, age, and chance. So the ball and the socket adjust their shapes as they rotate against each other while the baby kicks in the womb. (We know this because experimental animals that are paralyzed while they develop end up with grossly deformed joints.)
