I know I am not the only one who had picked up on the strong hints from Ben in 3x6 about him treating Alex as his daughter (adopted, or otherwise). Right before surgery, he said "Did Alex ask about me?" I guess it could have been interpreted as him having a relationship with her, but it sure seemed more likely that he viewed her as his child, since she was so young, and had been their captive for years. It was definitely discussed on this forum back in November.
In fact, I was so sure he was her surrogate father, that I thought he had said it outright in 3x6 until I went back and watched that scene right before his surgery. When I heard it tonight, I didn't even flinch.