Actually, I guess what I meant is that there can be a massive delay between the time that the patent is filed and when it is granted (or rejected), during which

Actually, I guess what I meant is that there can be a massive delay between the time that the patent is filed and when it is granted (or rejected), during which time you are protected, and it doesn't count against the patent life. My boss, who is a biomedical researcher, has had a patent in this kind of limbo for 11 years. He's long since moved on (he doesn't even work at that institution any more), but the university's IP lawyers have been playing ping-pong with the patent office for over a decade. If he can achieve this without caring at all, imagine what well-funded pharma lawyers could do.