I don't know, the serial to usb chip? My R1's serial chip is busted, I think, but I am using my R3 to program things... So how do you burn a bootloader to a chip without extra hardware?
That brings up another point, is there any reason why the Serial chip in my R1 doesn't work? I don't see any burns or anything, so I don't know what it is. The arduino still gets power via usb though.