Here is my Thursday column.

SANTA CLARA – Jim Harbaugh must change his offensive play-calling system this week for the 49ers’ game Sunday night in Seattle against the Seahawks. Not changing his system would be an ego-driven mistake.

Harbaugh wants to be perfect on every play. As a result, his system is one of the slowest in the NFL.

Offensive coordinator Greg Roman typically calls not one but two wordy plays over the headset for Colin Kaepernick. Then Kaepernick repeats those plays to his teammates in the huddle. Then the players run to the line of scrimmage. Then Kaepernick has to work through multiple pre-snap procedures and shifts and movements and kills to determine which of the two plays is better. This process usually takes between nine and 13 seconds.

If the offense has fewer than 14 seconds at the line, it’s difficult to work through the pre-snap stuff and snap the ball before the play clock reads zero.

Last week at Candlestick Park against the Packers, the 49ers often snapped the ball with just two or three seconds left on the clock. They were flagged for a delay-of-game penalty and burned two timeouts preventing two more delays. They got to the line with fewer than 14 seconds on the clock 19 times, almost a third of their plays. That means Greg Roman wasn’t getting the plays in to Kaepernick fast enough. Don’t blame Kaepernick because it wasn’t his fault.

If the 49ers can’t get their plays off in Candlestick, how are they going to get them off in Seattle’s CenturyLink Field, the NFL’s loudest stadium?

Anquan Boldin doesn’t think it will be an issue. On Wednesday he called the timeouts and delay-of-game penalties a “Week 1 problem.”

Is it merely a Week 1 problem?

Last season, the 49ers called 14 timeouts in the first and third quarters, the quarters in which you don’t want to call timeouts. The 49ers led the league in the category. Boldin may not be aware of that stat because he was a Raven last season.

But Boldin should know this issue may have cost the 49ers’ a Super Bowl victory. Boldin played against the 49ers in that game. When the Niners had the ball at the Ravens’ 5-yard line down five points late in the fourth quarter and it was third-and-goal, Harbaugh had to use a timeout to prevent a delay penalty. The play was going to be a quarterback draw that probably would have been a Super-Bowl-winning touchdown, but the offense didn’t get to the line until there were 10 seconds left on the play clock.

Kaepernick had to send Delanie Walker in motion and then reset the protection scheme and, by the time he snapped the ball, the play clock had expired and Harbaugh already had called timeout.

It’s a 40-second play clock. That means it took the 49ers’ coaches about 20 seconds to choose and call the crucial play of the Super Bowl. It never should take a coach more than 10 seconds to radio the play to the quarterback.

What took 20 seconds? Did Greg Roman not plan ahead? Was he searching through his 200-play call sheet to find the right play at the last second?

The 49ers script the first few series of every game. But does Roman re-script plays between series when his defense is on the field as other NFL offensive coordinators do?

“We’re having constant conversations,” said Roman on Thursday. “I’ll say, ‘Hey, what do you guys think of this, do you like it?’ And then, ‘No, because of this,’ or, ‘Yes, because of that.’ Our staff, we’ve got a good communication flow.”

That doesn’t sound like re-scripting. That sounds like talking.

Roman should quietly re-script between every series. That way he has a list of six or seven plays he can immediately turn to when the 49ers get the ball back. Failing to plan is planning to fail.

The last time the 49ers played in Seattle, Roman couldn’t even get the scripted plays in on time. The 49ers called two timeouts and committed two delay-of-game penalties in their first 20 plays. On the second play of the game, Roman had the offense scrambling to the line with 10 seconds left on the play clock. It was a full-blown meltdown. They got the play off with two seconds left.

Here’s how the 49ers can fix their problem for this weekend’s game: Assign every play a number. Give the quarterback and skill position players wrist bands listing which play each number corresponds to. Skip the huddle. Signal the numbers in from the sideline so the players can read it themselves. The quarterback can yell the protection scheme to the offensive linemen who are close to him, and then the Niners can use a silent count to snap the ball. That way, they cut down on the time it takes to call the plays, and they remove most of the verbal communication which is key in that deafening stadium. Chip Kelly does that right now with a flashcard system in Philadelphia. He would have no trouble getting his plays called in Seattle.

Do I expect Harbaugh to make any of the adjustments I’ve just suggested?

No. I don’t expect him to change his system at all, actually. That’s not the kind of coach he is.

I expect to see Kaepernick struggling to yell wordy plays in the huddle, the players struggling to hear him and the 49ers struggling to snap the ball before the clock expires.

Harbaugh wants to make the opponent adjust to him, not vice versa. And that’s good. What’s not so good is this. He doesn’t want to acknowledge any weaknesses it may have.

If Harbaugh takes that stubborn attitude up to Seattle, he’s asking for trouble, if anyone actually can hear 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