Grant Cohn: Chip Kelly’s play-calling sabotaged Colin Kaepernick’s return

This is about Colin Kaepernick, Chip Kelly and cognitive dissonance.

You've heard of cognitive dissonance. It means 'mental stress or discomfort experienced by an individual who is confronted by new information that conflicts with existing beliefs.'

In the case of the 49ers, there are two big existing beliefs — 'Chip Kelly is a good coach,' and 'Colin Kaepernick is a bad quarterback who played terribly against the Bills.'

If you believe those things, take an aspirin before reading further, because what I'm going to write will cause serious cognitive dissonance. This is your warning.

Chip Kelly is not a good coach. He is the 49ers' biggest problem on offense, not Kaepernick. Not the quarterback position.

I see that little vein throbbing in your forehead. I know what you're thinking. Forget the vein. Yes, Kaepernick completed just 13 of 29 pass attempts against the Bills. I know that's a completion percentage of 44.8. And I know that percentage isn't good.

But Kelly is responsible for that number. Not Kaepernick.

Kaepernick played better than those stats indicate. Sure, he was rusty early on — he hadn't played a real game in almost 12 months. And he missed a couple deep throws he should have completed — one to Torrey Smith and one to Shaun Draughn.

Other than those two throws, Kaepernick almost was perfect in the first half. He completed 8 of 11 passes — 72.7 percent. And his passer rating was 144.1 — much higher than anyone expected.

And then he completely tanked in the second half. Completed only 5 of 18 passes. Posted a passer rating of 39.6. What happened?

Did someone put a hex on Kaepernick at halftime? Did he forget how to play quarterback? No, of course not. This is what happened:

Kelly ruined Kaepernick's game. In the first half, Kaepernick threw 72 percent of his passes over the middle between the big painted numbers on grass — precisely where he likes to throw. And in the second half, he threw only 39 percent of his passes over the middle.

Simple as that.

In total, Kaepernick completed 60 percent of his passes between the numbers against the Bills and just 28.6 percent of his passes outside the numbers.

Those of us familiar with Kaepernick's career shouldn't be surprised by those drastic splits. Kaepernick always has struggled making the long throws outside the numbers. Those throws require anticipation — the quarterback releasing the ball before the receiver makes his break. Kaepernick can't do that. When he tries to throw toward the sideline, he often throws interceptions.

We've known that for years. We remember the two interceptions Kaepernick threw in the fourth quarter of the NFC championship game against the Seahawks — the one Kam Chancellor picked off along the left sideline, and the one Richard Sherman tipped into the hands of Malcolm Smith along the right sideline.

That game was almost four years ago. Kelly should be familiar with it. Kelly should know his quarterback's strengths and weaknesses. It's his job to know.

He also should be familiar with the comments Tony Jefferson made about Kaepernick just last season. Jefferson is a safety for the Cardinals, and before they played the Niners in Arizona, Jefferson went on Pro Football Talk Live to discuss his team's game plan for Kaepernick. 'We gotta contain him,' Jefferson said, 'and try to keep him throwing the ball outside the numbers, because we don't think that's his strength.'

Jefferson was right. Against the Cardinals, Kaepernick promptly threw four interceptions on passes thrown outside the numbers — two of which were returned for touchdowns. The Niners benched him a few weeks later.

Given Kaepernick's history, Kelly was right to call passes that primarily traveled over the middle during the first half against the Bills. For a while, Kelly seemed like a good coach.

Then, inexplicably, he reversed his game plan in the second half, and started calling passes that primarily traveled outside the numbers. It's like Kelly has a plan he uses who the regardles of whom the quarterback is. It sure didn't suit Kaepernick. So what happened? Checkmate. Game over. The offense was dead on arrival after halftime, and Kelly killed it.

If he or someone else on his staff had been charting Kaepernick's throws, they would have seen where Kaepernick's completions and incompletions were. And they would have called more passes over the middle. Basic coaching.

Basketball coaches do a similar thing — they chart shots. And if the shot chart says a certain player misses lots of 15-footers from left of the key, the coach will change the offensive sets to make sure that player doesn't shoot from that spot on the floor any more.

Those are the kinds of things professional coaches do all the time. The kinds of adjustments professional teams pay professional coaches millions of dollars to make.

But Kelly doesn't make those adjustments. He often makes the wrong adjustments as he did in the second half in Buffalo.

That's one reason he's failing. He is a bad coach. Forget what you thought you knew about him.

Grant Cohn writes sports columns and the 'Inside the 49ers' blog for The Press Democrat's website. You can reach him at grantcohn@gmail.com.