The real answer is that complex machinery evolves either incrementally, or by adapting previous complex machinery used for a new purpose. Squirrels jump from treetop to treetop using just their muscles, but the length they can jump depends to some extent on the aerodynamics of their bodies. So now there are flying squirrels, so aerodynamic they can glide short distances. If birds were wiped out, the descendants of flying squirrels might reoccupy that ecological niche in ten million years, gliding membranes transformed into wings.
