i say start pierre thomas over steven jackson. jackson has really sucked recently and he will be playing a solid buffalo defense that has been stingy against the run. while he doesnt gobble up yards, thomas has emerged as a redscone scorer through and through. look for him to score at least once against a 49'rs defense that is ranked 21 currently in rush defense. as for matt jones, i would try to start other flex options like brandon lloyd or antonio bryant if they are still available. if jones is the best available, then i guess you should start him then.
