"There's adversity," Harbaugh said Monday. "There's an opportunity to stare it in the face and whip it. That's our approach."
Availability of best players
Every team has players who can't suit up. The 49ers have missed or will be missing their best players. The team's top wide receiver, Michael Crabtree, might miss the entire season. Tight end Vernon Davis missed Sunday's loss to the Colts, and linebacker Patrick Willis left with a groin injury. Willis looks unlikely to play Thursday night against the St. Louis Rams.
The 49ers traditionally just play 12 players-per-game on defense, so losing starting nose tackle Ian Williams for the season is a big problem.
Linebacker Aldon Smith was placed on the non-football injury list Monday, opening up a roster spot for the team. NFL Media Insider Ian Rapoport reports that Smith has checked into rehab, according to a team source. He's out indefinitely.
San Francisco's depth is being tested. The 49ers have boasted some of the best talent in the league over the last few years, but no team can survive losing so many of their very best players.
San Francisco is 30th in team scoring, in large part because of their running game. Frank Gore couldn't get anything done in the first two games, and then the 49ers oddly didn't give him the ball in the second half on Sunday. Defenses have done a nice job containing Colin Kaepernick on the ground. Speaking of which ...
Read option not a big factor
Can't get open against man coverage
Perhaps all that worrying about the 49ers' wide receiver position was warranted. Anquan Boldin was a great acquisition, but he's not a true No. 1 receiver. Kyle Williams, the nominal No. 2 receiver, has 87 yards this season. The rest of the 49ers wideouts have one catch for six yards combined. As we mentioned on our Week 3 recap podcast, this is a group that just can't appear to get open.
Defense no longer a difference-maker
The Chronicle notes that the 49ers have given up more rushing yards in consecutive games than any Niners team since Dennis Erickson's 2-14 squad in 2004. The 49ers miss Williams. They have given up 10 touchdowns in 14 red-zone trips. Harbaugh's team prides itself on its toughness, but the 49ers have been steam-rolled on more than one occasion this season. We knew the secondary was going to be a problem. It's surprising that the front seven has had so many issues, and life is only going to get tougher now that Smith has left the team indefinitely.