Grant Cohn: 49ers see runs of success in their quarterback's future

Keep running him until he breaks down.

That is the 49ers' plan for Colin Kaepernick next season. I can't prove it beyond a reasonable doubt, ladies and gentlemen of the jury, but I can make a case.

Exhibit A: Mike Shanahan and Rob Chudzinski – the top candidates to become the Niners' new offensive coordinator, according to reports. Shanahan was Robert Griffin III's head coach in 2012 and 2013, and Chudzinski was Cam Newton's offensive coordinator in 2011 and 2012. Both Shanahan and Chudzinski made the read-option running game the staple of their offenses to accommodate Griffin and Newton.

Exhibit B: The new offensive line coach — Chris Foerster. He was Shanahan's offensive line coach on the Redskins. Foerster has coached a read-option running game since 2012.

Exhibit C: The general manager and the new head coach — Trent Baalke and Jim Tomsula. They keep talking about running the ball and what a unique athlete Kaepernick is. At Tomsula's introductory press conference, Tomsula said of Kaepernick, 'I think he can run, I think he can throw.'

Notice the order.

Tomsula went on: 'More so than a traditional quarterback, (Kaepernick) does it with the lower body. Look at that, corral it and let's accentuate those things as we continue to strengthen other areas.'

Translation: Jim Harbaugh was stubborn and used Kaepernick incorrectly, forced him to adapt to Harbaugh's system, forced him to be a traditional pocket quarterback, which he isn't. Kaepernick is different. Tomsula is different, too. Tomsula will do the opposite of Harbaugh. Tomsula will hire an offensive coordinator who will cater to Kaepernick and tailor the new system Kaepernick's strengths — his legs. Notice the word 'corral.' Tomsula talked like Kaepernick is a horse.

Is it good to emphasize Kaepernick's running?

Yes and no.

Kaepernick is very good at running the read-option. That's his background. He ran the read-option at the University of Nevada under the Chiefs' current consultant, Chris Ault. If Tomsula seriously wants to run Kaepernick more often next season, he should find a way to steal Ault from Kansas City. Ault popularized the read-option and invented the Pistol formation, and he coached Kaepernick for four years. Kaepernick listens to him. Ault is the last good mentor he had.

But, here's the thing. If a quarterback is a runner, he will take the career-changing hit and he will get hurt no matter how good he is at sliding. It's going to happen. The more you run, the more hits you take. Cause and effect.

How many times do the 49ers really want to expose Kaepernick to injury? If he goes down, the Niners go down in flames. Kaepernick's backups are Blaine Gabbert and Josh Johnson, who don't compare even to Drew Stanton and Ryan Lindley, the Cardinals' backup quarterbacks who had to play this season. Look how that worked out.

And look at Robert Griffin III. He was supposed to be the quarterback of the next generation. The Redskins' read-option offense was supposed to revolutionize the NFL the way the West Coast Offense did 35 years ago.

Didn't happen. Griffin lasted 16 starts before he mangled his knee and lost his speed and quickness.

Name one winning NFL franchise that uses a zone-read-option package as the staple of its offense. Don't say the Seahawks. The read option is only a limited part of their offense. Russell Wilson rarely keeps the ball and runs when the Seahawks call that play. Wilson wants to pass. When he does run, he's extremely effective.

That is the key — not the frequency, but the timing of when the read option is called. The Seahawks tend to call it late in a game when they need a big play. They wait until the opposing defense plays man coverage, when four or five defenders follow receivers and turn their backs to the quarterback. That's the time to call a read option — when the defense isn't expecting it. When an NFL defense expects the read option, it stops the read option.

Jim Harbaugh figured that out the hard way. He built the Niners' 2013 running game around the read option, just like Shanahan and Chudzinski had done in Washington and Carolina.

Harbaugh's strategy failed. The Niners' running game stunk, and Kaepernick injured his foot during the second game of the season. After that, Harbaugh de-emphasized the read option, re-emphasized the traditional running game and the Niners won 11 of their final 13 regular season games in 2013.

I rest my case.

It was in the best interest of Kaepernick and the team to downplay the read-option. Re-emphasizing it only will accelerate the fall of the franchise and inhibit Kaepernick from learning to be a good pocket passer, a necessity in his line of work.

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.