Originally posted on FOX Sports  |  Last updated 11/21/12
I have yet to meet a head coach who wants to deal with a quarterback controversy. Coaches, as a rule, like certainty and stability. Quarterback controversies by definition lead to the opposite. They create distractions when you're seeking focus, and they can spark division when you're searching for togetherness. Colin Kaepernick was brilliant on Monday night in leading San Francisco to a 32-7 beatdown of the Chicago Bears, firmly placing the 49ers atop the short list of NFC favorites at 7-2-1. In the process, Kaepernick also microwaved a full serving of quarterback controversy that San Francisco head coach Jim Harbaugh will be dealing with, more than likely, for the rest of the season. That's the thing about controversies -- they're not easily controlled or contained. Controversies are living, breathing, sentient things that set their own agenda, and the circumstances in San Francisco are fertile breeding ground for such things. So even though Smith led the 49ers to the NFC title game last season, and has a 104.3 quarterback rating this year, suddenly there's some real doubt in San Francisco about who the quarterback of the future -- or, for that matter, the present -- is going to be. In his first quotes after the game Monday, Harbaugh didn't say anything out of the ordinary. But if you're attentive to the language of the coaching trade, you can parse enough meaning to see that he recognized the dynamism of Kaepernick's performance, and left the door open about who the 49ers starter will be next week and beyond. "I usually tend to go with the guy who has the hot hand," Harbaugh said, adding, "We really have two guys who have a pretty hot hand, but we'll make that decision as we go forward." Harbaugh fanned the flames by answering the question honestly and leaving himself an out for keeping Kaepernick in the game. What he didn't do is fall back on the old coach's adage about how "a starter can't lose his job due to injury." This may cause him more headaches later this week, but I applaud his candor. Let's face it -- starters can lose their jobs due to injury. It happens. It happened to Wally Pipp in baseball, and it happened to Drew Bledsoe in football. Now, I'm not comparing Kaepernick to a young Tom Brady, but what I am saying is that the agile and strong-armed, second-year quarterback out of Nevada has given Harbaugh plenty to think about. Let's just look at the facts. Smith is having a solid year, completing 70 percent of his passes and throwing 13 touchdowns to only five interceptions. But prior to Kaepernick's start, the Niners had been one of the league's least explosive teams through the air. Going into Monday night, they were in a three-way tie for 29th in number of passing plays gaining 25 or more yards (they had just 12, tied with desultory Kansas City and Cleveland; only the Vikings had fewer, with 10). But with Kaepernick at the helm, the Niners had three such plays Monday, vaulting them from a tie for 29th to a tie for 21st. Smith was drafted No. 1 overall back in 2005, by a previous GM and previous coach, and had a largely uninspiring career before he was rejuvenated under Harbaugh last season. Others focused on Smith's limitations, but Harbaugh (like the 49ers great coach Bill Walsh) focused on his player's strengths, and how it could help his team win games. He saw qualities in Smith that fit the "play great defense; run the ball and manage the game" style of play. Still, when Smith was a free agent two years ago the marriage continued mostly because neither party had a whole lot of options to do anything else. Smith returned to the 49ers on a three-year, $24 million contract with $9 million guaranteed. Matt Flynn and Kevin Kolb were signed to similar money with Seattle and Arizona, with $10 million guaranteed. Good money, but not exactly in the range of a franchise quarterback. This offseason the 49ers flirted with Peyton Manning, but so did a lot of other teams. But the team has liked Kaepernick from Day One. Harbaugh and San Francisco GM Trent Baalke traded up nine spots in the second round of the 2011 NFL Draft to get Kaepernick, giving up their second-, fourth- and fifth-round picks. This was not just a "best athlete available" selection. That trade indicates the conscious targeting of a player the Niners were sure would not make it to the 45th overall pick. And Monday night we saw glimpses of why the 49ers liked him so much. Kaepernick was as calm and subtle in the pocket as any young QB I have seen in a long time. His throwing action was effortless and his accuracy was substantial. What was most impressive was that it came against the Bears. Chicago has been a takeaway machine the last couple of weeks and Kaepernick did not come close to exposing the ball. Let's keep in mind that this is just one game -- one on national television, no less -- and so there's a real chance that people are overreacting. We have seen this fascination with the small sample size before, and a quarterback who excels in an isolated circumstance suddenly becomes the darling of fans, media and (most significantly) other general managers. The landscape is littered with players like Cody Carlson, Rob Johnson and Scott Mitchell -- career back-ups who shined in a short stint, then parlayed that display into a starting job or a fat free-agent contract, or both. A more recent example is at hand. The aforementioned Matt Flynn turned a single six-TD game at the end of the 2011 season for the Green Bay Packers into the top quarterback signing of the 2012 offseason, only to lose the competition for the Seahawks' starting quarterback job to Russell Wilson, a third-round rookie from Wisconsin who currently has the Seahawks chasing the 49ers at 6-4. The 49ers have known they had something in Kaepernick, and though he may not start the rest of the way, you can bet that if Harbaugh does go back to Smith the fans will be calling for Kaepernick just seconds after Alex's very next three-and-out series. So goes the logic of quarterback controversies. Should Smith come back and the 49ers suffer a home defeat in the playoffs, you will at the very least see Harbaugh declare next year that the quarterback job will be an open competition. Whatever happens, the clock is now ticking in San Francisco. And to Colin Kaepernick's credit, he's the one who put it in motion.
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