I’m proposing a theory. In my theory Trent Baalke says all the right things about Alex Smith — call it the company line — but he doesn’t really mean what he says. He doesn’t like Smith and doesn’t want him to be the Niners’ quarterback and doesn’t want him around the team. Jim Harbaugh, on the other hand, does like Smith and wants him around and believes he can mold him into a good quarterback. I wrote my Thursday column about this perceived difference of opinion, something I perceived even more than usual at Baalke’s Wednesday presser. It could be more than a difference of opinion. It could be a flat-out disagreement bordering on differing philosophies. To read my column click here.