The multiple parts of complex, interlocking biological systems do not evolve as individual parts, despite Behe's claim that they must. They evolve together, as systems that are gradually expanded, enlarged, and adapted into new purposes. Organisms can gradually build up into things with interconnected parts whose functions change over time, from an original simple one into a complex connected one. Organisms evolve in a step by step fashion all together, with changes taking thousands of years followed by millions of years of sameness. The end product looks intricate, but it gradually grew that way, it didn't have to be created like that.
Parts change their function over time.
They work at another function before they come to their present use. For example, it may seem unlikely that the bones of the inner ear could have evolved from scratch, and they didn't. Originally, they served as parts of sliding jaw joints, which were sensitive to sound waves, and were by natural selection developed into the ear. Behe speaks of had other functions beforehand, and gradually grew into their present function. His odds assume all configurations have an equal change of occurring.