Eli Manning Justin SmithJustin Smith has a partially torn triceps, according to Matt Barrows of the Sacramento Bee. If the injury sounds familiar it is because outside linebacker Parys Haralson suffered a complete tear of the same muscle in the preseason. The injury of course landed Haralson on the injured reserve list, a move the 49ers are hoping to avoid with Smith.

When asked if there were any similarities, Harbaugh responded verbosely, saying “No, seems to be two different things.”

Though the injuries are different, the result might be the same if Justin Smith cannot endure the injury: The 49ers stand to lose a key contributor on defense. When asked about the loss of one of the league’s best players, Carlos Rogers noted that Smith “makes it easier for our linebackers. He makes it easier for Aldon to get sacks. He’s a big part of our defense. But the thing about it is, the next guy’s going to step up. We can’t use Justin being out as an excuse.”

Justin Smith’s back up, Ricky Jean Francois, did indeed step up against the Seahawks. If you look at the running chart from Weeks 7 and 16, it is clear that Jean Francois did an equitable job in stifling Marshawn Lynch. What is also made clear is just how much Justin Smith is avoided by offenses.

Week 7

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Week 12

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In Week 7, the Seahawks attempted just four runs to Smith’s side with Lynch. In Week 12, obviously, that number is much greater. For the most part, Jean Francois acquitted himself well–aside from Lynch’s first run, that is.

In his first run, Lynch scampered off the left end for a 24-yard touchdown. But the blame doesn’t rest solely on the shoulders of Jean Francois for getting pushed back. No, he shares the blame with Aldon Smith and Dashon Goldson.

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The Seahawks line up in a two-tight end heavy set, which the 49ers don’t adjust for. The result is that Ricky Jean Francois will be doubled off the line while Aldon Smith and Donte Whitner are negated by tight ends Anthony McCoy and Zach Miller respectively.

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Jean Francois, though doubled off the snap, cannot hold the double team, which allows right guard Paul McQuistan to take NaVorro Bowman out of the play. Jean Francois is then almost tackled by right tackle Russell Okung, which could have constituted holding. Those these a battles the 49ers must win. That they did not is understandable. What is not understandable is how Aldon Smith allows himself to be driven five yards away from the ball carrier by a tight end who is ranked as the 98th best run blocker by Pro Football Focus.

What further compounds the problem is that safety Dashon Goldson takes a bad angle to the ball carrier, which pretty much allows Lynch to reach the endzone unimpeded.

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The quality of the picture is obviously atrocious, but perhaps not as bad as Goldson’s angle. Sure, Goldson’s responsibility is probably not stopping a run to the opposite side of the field, but had he respected Lynch’s speed more, he could have saved a touchdown.

So while the effect of Smith’s absence in the run game was felt, it was not as drastic as initially feared. If anything, the Seahawks exploited Jean Francois and Aldon Smith’s inexperience by running out of shotgun formations, a trend that the 49ers can work to improve, or so I’d imagine.

As for the pass rush, the 49ers production didn’t take a significant hit with Justin Smith’s absence. In the 14 games with Smith, the 49ers averaged 14.85 quarterback pressures per game. Against Seattle, they managed 13. In all, they pressured Russell Wilson on 37% of his snaps, which is only slightly less than what Seattle typically allows.

And so the the problem wasn’t Smith’s absence, it was Wilson’s presence–pocket presence, that is. It wasn’t that the 49ers weren’t getting there, it was that Wilson was able to scramble and elude rushers. Though he’d certainly have some impact, I don’t think Justin Smith would have remedied the 49ers over-pursuit of Wilson.

Pinning the defense’s meltdown against the Seahawks on Justin Smith’s absence would be to oversimplify the problem. The simple truth is the 49ers were outplayed and outcoached. They were unprepared for certain run schemes and for Russell Wilson’s scrambling ability. And they paid for it, dearly. If they happen to meet again in the Playoffs, I’d expect a much different outcome, even if Justin Smith is on the sidelines.

Information and charts for this post were provided by Pro Football Focus.