The San Francisco 49ers — now coming off back-to-back losses that saw convincing first-half leads evaporate after the break — have been here before.

A year ago, the 49ers entered Week 4 reeling after consecutive losses of 20-plus points at the hands of the Seahawks and Colts. San Francisco’s offense put up a combined 10 points in those contests while turning the ball over a whopping seven times. Serious questions were raised about Colin Kaepernick, the coaching staff, and whether the 49ers’ offense could possibly get them back to the playoffs. Somehow the 49ers kept on playing, won 11 of their final 13 regular season games, and eventually wound up in their third straight NFC Championship Game.

Last season alone is not reason enough to simply ignore San Francisco’s 1-2 start and assume they’re bound to produce the same result in 2014. However, it should be enough to make you hesitant to press the panic button without thinking about how the 49ers got where they are and how likely those causes are to continue. There has been no shortage of reasons given to explain the 49ers’ early-season woes. Let’s take a few of the most prominent and attempt to figure out whether it’s just early-season noise or if it could be the start of a season-long problem.

Blame It On The Refs

If you came here expecting paragraph after paragraph detailing how terrible the referees are and how the 49ers have gotten screwed by the NFL, you’ve come to the wrong place. Guess what? Refereeing in the NFL is a terrible, inconsistent mess across the board. There’s not a game played that goes without a poor call and inevitably there will be games where it feels like the men in stripes are piling on one team over the other. It’s an unfortunate part of the game, but one that every team will deal with at some point.

This is not to say that penalties cannot have a significant impact on the game. There’s no question they can and penalties in key moments can swing the outcome of games. But to suggest the refs have an agenda and are out to get a specific team is to be…well, any sports fan of any sports team, ever.

Putting aside the merits of individual penalties, there is some valuable information we can gain by digging deeper into the 49ers’ penalty situation. Through the first three games of the season, the 49ers have committed 36 penalties, the most in any three-game stretch under Jim Harbaugh. (The second-highest three-game total? The 29 penalties in Weeks 1-3 of last season.) Even worse has been the timing of those penalties.

By my count 15 penalties, or five per game, have resulted in a first down for the opponent with half of them (8) coming on third down. Going back to 2003, only one team has managed to average over three such penalties per game over the course of an entire season, the 2011 Raiders. Prior to this season, under Harbaugh the 49ers have averaged 1.7 penalties per game that have given their opponent a free set of downs, a rate less than the league average over that time.

Even if you believe that the NFL’s increased focus on illegal contact and defensive holding penalties will result in an uptick in penalty totals over the entire season, there’s no way that the 49ers will continue to hand opposing offenses five free first downs per game. Cut that number in half (or possibly by more than that) and all of the sudden you have an extra drive or two in which the 49ers’ defense is off the field rather than giving the opposition a second chance at points.

Where’s The Killer Instinct?

San Francisco’s lackluster offense in the second half has perhaps shouldered even more of the blame than the referees in the aftermath of the Arizona game. Numerous fans and members of the media have cited the 49ers "taking their foot off the accelerator" or "lacking a killer instinct" as reasons for the team’s issues. This one is a notion that extends well beyond the last three weeks. The problem is there is very little evidence to support this being a long-term issue.

For the All About The W’s crowd, under Harbaugh, the 49ers have taken a lead into halftime 43 times; they are 36-7 (.837 winning percentage) in those games. Make that lead more than a touchdown and San Francisco is 23-2 (.920), having never lost a halftime lead of eight or more points prior to the last two weeks.

Those of you who require a little more evidence that simply wins and losses, we shall turn to the incredibly handy Football Outsiders Premium Database. Because DVOA examines the NFL on a play-by-play basis, there are a number of various splits that can be used to evaluate a team’s performance, including by half. Here’s a look at the 49ers’ offensive DVOA splits by half since 2011:

2013 2012 2011 1st Half 11.8% 20.1% -6.1% 2nd Half 6.2% 13.6% -1.1% Late & Close 14.3% 29.2% -11.1%

Outside of 2011 — when the Alex Smith-led offense was slightly better in the second half, albeit with a significantly worse offense overall — there has been a slight decrease (roughly six percentage points in each season) in the 49ers’ offensive efficiency from the first half to the second half under Harbaugh. Most of that can be explained away by the fact San Francisco has spent more time playing with a lead than anyone in football over the last three seasons and have therefore spent many second halves running the ball into stacked boxes to eat up clock, not exactly the most efficient tactic in the world. It’s the final row of the table that is more meaningful.

In late and close situations — defined as any play run in the second half when the score is within eight points — the 49ers’ offense has actually improved over their first half performance in the last two seasons. In other words, when the outcome of the game was still in flux in the second half, Kaepernick and co. have been up to the challenge, raising their level of performance on a per play basis.

There’s no denying that San Francisco has collapsed in the second half in each of the last two weeks. However, in no way does the outcome of two games outweigh multiple seasons worth of evidence pointing the other direction. The 49ers didn’t suddenly forget how to close out games and they don’t lack killer instinct. Defenses aren’t going to keep the 49ers out of the end zone in the second half for the entire season and once it stops, people will forget this conversation even took place.

Fire Greg Roman!

Closely tied to the previous section is the group calling for offensive coordinator Greg Roman’s job. The reasoning here comes in many forms: terrible playcalling, poor gameplans, a lack of halftime adjustments, you name it. San Francisco could put up a 50-point, 500-yard performance on offense and people will find fault in Roman somewhere.

Listing and attempting to refute the many claims of Roman’s supposed incompetence is better saved for a separate post, but what many are failing to see during the first three weeks of the season is that the 49ers are in a clear transition period on offense. Harbaugh and Roman’s offense is evolving from one that sought to protect its quarterback to one that is looking to showcase it.

To oversimplify things a bit, going back to that first season under the current regime in 2011, there have been three phases of the 49ers offense:

Phase I: The Alex Smith phase. Hyper-conservative and looking to avoid turnovers at all costs, the 49ers were content to take a sack or throw the ball away in an effort to avoid throwing the ball downfield into coverage. Overly reliant on the run game in nearly all situations.

The Alex Smith phase. Hyper-conservative and looking to avoid turnovers at all costs, the 49ers were content to take a sack or throw the ball away in an effort to avoid throwing the ball downfield into coverage. Overly reliant on the run game in nearly all situations. Phase II: The early Colin Kaepernick phase. Similar to Phase I in a lot of ways but with more read option and more of a willingness to push the ball down the field. Less reliant on the run game early in the game and when the score is close, but quick to throw extra offensive lineman on the field and run power into a nine-man box once they had built up a double-digit lead.

The early Colin Kaepernick phase. Similar to Phase I in a lot of ways but with more read option and more of a willingness to push the ball down the field. Less reliant on the run game early in the game and when the score is close, but quick to throw extra offensive lineman on the field and run power into a nine-man box once they had built up a double-digit lead. Phase III: Whatever the hell is happening right now.

Finally equipped with receiving targets consisting of more than Vernon Davis and a single competent wide receiver, the 49ers have made 11 personnel (1 RB, 1 TE, 3 WR) their primary grouping over the first three weeks of 2014. I don’t have updated numbers as of this writing, but there’s a reasonable chance San Francisco put four wide receivers on the field at the same time for more snaps in the Arizona game than the previous three seasons combined.

The 49ers put all of those receivers to good use, spreading the field with an empty backfield set and speeding up the tempo. It was a completely new wrinkle in San Francisco’s offense and it offered a couple of notable benefits against a very good Cardinals defense. First, it prevented the Cardinals from using the exotic pre-snap looks they love to run, forcing them into more vanilla coverages. In addition, it exposed the weakest part of Arizona’s defense: the linebackers and safeties in the middle of the field. The 49ers were able to get Stevie Johnson, Michael Crabtree, and Anquan Boldin open over the middle, often times getting them matched up on one of those linebackers or safeties. This led to several easy throws underneath for Kaepernick and gave him quick outlets if the Cardinals decided to blitz. It was a great change-of-pace look for the 49ers offense and their success from that look should give them the confidence to continue to go to it in the future.

From more of a big picture view, Roman is putting the offense on Colin Kaepernick’s back. In the first half of the Cardinals game, the 49ers ran 35 offensive plays and Kaepernick threw or ran on 28 of them. Against the Bears it was a similar story as Kaepernick was responsible for the outcome of 23-of-31 first half plays. You might argue that San Francisco should be giving Frank Gore and Carlos Hyde more of those touches, but it’s clear this is the direction the 49ers are headed on offense.

This transition to an offense that is reliant on its quarterback to win games from the offense that only hoped he wouldn’t screw it up is not going to take place overnight. Growing pains are to be expected, but this is a change that I believe is the right thing for San Francisco’s long-term success.

The 49ers’ formula for success over the past three seasons is a difficult one to sustain. If you look at the teams who have experienced the most success since the turn of the century, the common thread is an offense that runs through the quarterback. The 49ers believe they have a quarterback capable being that type of player and they’ve finally handed him the keys to the offense. It’s on Kaepernick to not crash it into a tree.