Stanford football has an identity crisis.

For most of the first three quarters and the final two plays on Saturday, Stanford looked a team that was simply lost. A Pac-12 champion cannot go 45 minutes without scoring a point and expect to win.

Speaking of Stanford being a Pac-12 champion, I’m sure I’m not the only one who noticed that Utah’s offensive game plan Saturday was almost identical to UCLA’s in the Pac-12 championship game last season. Yet due to injuries, poor tackling and a suspect defensive game plan, it took the Cardinal three quarters to figure out how to slow the Utes down.

But the most frustrating aspect of the loss wasn’t that Stanford struggled mightily for three quarters, it was that, even after those early-game struggles, the Cardinal should have won the game. Yet, for some inexplicable reason, Stanford decided not to punch it in on third-and-2 from the 6 but instead throw two pass plays.

I’m sure that head coach David Shaw had his reasons for calling a pass — maybe there was some matchup advantage he liked on tape — but that is over-thinking a very simple situation. The Stanford Cardinal runs the football. Since Jim Harbaugh arrived on the Farm to take over the head coaching job in late 2006, bringing Shaw with him, the Cardinal has been a team that will out-physical opponents for those yards on the ground.

On Oct. 12, 2013, that identity disappeared. Through the first five games of the 2013 season, Stanford had faced third- or fourth-and-2 three times. In all three situations, the Cardinal ran the ball, and all three times the Cardinal picked up the first down. Against Utah, Stanford faced that same situation three more times, and all three times Stanford threw the ball, only converting one of the three.

I know that’s a small sample size, but if you expand it outwards by accepting a bit more generality (third or fourth downs with three yards or fewer remaining), it’s staggering what the numbers say.

With Hogan in the game at quarterback (equivalently, in non-garbage time), Stanford has faced 30 such situations this season (including against Utah). Stanford has thrown the ball 10 times, with two completions for first downs and eight incompletions. You don’t need to be a statistician to figure out that those numbers are not very good.

On the other hand, when Stanford ran the ball (the other 20 times), the Cardinal picked up a first down or a touchdown 18 times, a whopping 90 percent conversion rate. And the two times Stanford didn’t pick up the first down? The bootleg by Hogan at the end of the Washington game — why didn’t Stanford run power? — and a third-and-1 against Washington State when Stanford converted on fourth-and-1 a play later by, you guessed it, running the football again.

Shaw tried to justify his decision Saturday, at least partially, in his postgame press conference by saying that he didn’t want to use his final timeout after the play if the run failed. Are you kidding me? On the 6-yard-line with over a minute to go, Shaw was concerned about running the ball because he thought the Cardinal would run out of time? I find it hard to believe that was actually the reasoning, but if it was, that would be truly remarkable.

Now I’m not a football coach, and I’ve never had to make a crunch-time decision like Shaw had to against the Utes, but taking all of this into consideration, I just can’t understand why Stanford would throw the ball. Shaw may claim that he had confidence in those passing plays, but the decision smells more like Shaw saying that he doesn’t have confidence in his running game; if I were a Stanford offensive lineman, those play-calls would feel like a slap in the face.

And while Stanford never should have let the game be so close, that decision is a big reason why the Cardinal could not escape with a victory. After talking about a BCS Championship Game appearance for the past few months, Stanford is facing a brutal stretch of must-win games to keep the hope of any BCS berth alive. That is a real shame.

Sam Fisher was clearly ambivalent to Stanford’s loss to the Utes. Remind him how important football really is at safisher ‘at’ stanford.edu, and follow him on Twitter @SamFisher908.