Can Nolan and Smith coexist with the 49ers?

Does Mike Nolan have it out for Alex Smith, the golden-boy quarterback he made the No. 1 pick in the 2005 NFL draft? Did Nolan undermine his third-year QB before teammates in the San Francisco locker room? Has Nolan created a public relations nightmare by taking some thinly-veiled shots at a young player that's linked to Nolan's future with the 49ers probably more than anybody else on the roster?

Is Smith soft? Does he still have the respect of his teammates? Did Smith make a mistake by publicly inferring that a string of poor performances was the result of an injured throwing wing that he decided to go ahead and play with anyway? Did he make an even bigger mistake by lashing out at Nolan when it was suggested that criticism of Smith was mounting in the locker room?

These are some of the questions and issues that are swirling around the beleaguered 49ers as they attemp to eke out a few more victories over the next three weeks to conclude a hugely disappointing season.

But the biggest question now facing the team as the season nears its finish is if coach and quarterback still can coexist as the 49ers move forward.

And that could be a big if.

There are several outside observers who are suggesting that fragile relationship already is fractured and scarred beyond repair.

But Nolan says that just isn't the case. There is no irreparable rift between the two central-figure 49ers, the coach claims.

"I totally disagree. I really don't feel that way," Nolan said this week. "You don't want the truth to stand in the way of a good story, but I'm just telling you there's nothing between us."

But what really is the truth of the matter? Is the bond between Nolan and Smith, which appeared so firm and strong just a few short months ago, cracked and on the verge of breaking after the latest episode of the Nolan/Smith saga?

That saga began in the middle of November when Smith - after three dismal outings in losses to New Orleans, Atlanta and Seattle - revealed that his shoulder and forearm injuries were worse than the team was letting on. Smith suffered a Grade III separation of his throwing shoulder in Week 4 against Seattle, then attempted a comeback four weeks after the injury.

At that time, the usually low-key Smith let it be known he was upset that Nolan continually referred to Smith's problems as mere soreness. Nolan, for his part, was perturbed that Smith broke the chain of command by taking his problems to the media and apparently not discussing them with Nolan first.

For weeks afterward - as Smith rested his injured throwing wing, sought other medical opinions and contemplated season-ending shoulder surgery - Nolan couldn't resist taking a few digs at Smith while talking with reporters.

As Smith's status stood in limbo, Nolan continued to characterize Smith's separation as "not very severe" while also continuing to praise the toughness, passion and leadership qualities of Trent Dilfer, Smith's replacement as the team's starting quarterback.

While it's not overt and most players refuse to even go near the subject, there is a sense in the locker room that Smith made a mistake by not keeping his injury-related problems in house, and his courage and toughness are now questioned by some of his peers.

When approached by a reporter regarding that subject, Smith indicated he wasn't bothered by any public controversy regarding his injury, but that Nolan took it a little too far by making it an issue within the San Francisco locker room.

"He came out and said some things to the team," Smith was quoted in the San Jose Mercury News. "It was like he was telling his side of it, and I didn't want to get into it …That was my biggest concern when he did that: I felt it was trying to undermine me with my teammates."

Smith went on: "I think if (teammates) would have heard what I actually said (about his injury) out there that day (in November), it wouldn't have been an issue. But all of a sudden Nolan spins it as I was making excuses for an injury."

Nolan and Smith met Tuesday on the day that article was published, and later that afternoon, the team released a joint statement from player and coach. In it, Smith said he reacted out of frustration, the article did not reflect how he really felt and he never intended this to be a distraction to the team. Smith also said he understands how an article of this type could be damaging, "but I know my relationships with coach Nolan and my teammates are stronger than that."

Nolan, in the statement, likewise said, "The relationship Alex and I have developed over the past three years is stronger than a negative news story."

The skeptics remained unconvinced, and Nolan faced a media horde intent on fueling the controversy after Wednesday's practice - the same day Smith flew to Alabama to have season-ending surgery on his shoulder. Smith addressed his teammates before leaving for Alabama and apologized to them for being a distraction.

And that's where it stands today as the 49ers prepare for the final weeks of the season, beginning with Saturday's game against the Cincinnati Bengals at Monster Park. Which is to say, several of these issues still are standing on edge and simmering below the surface.

With Smith now out for the season, everyone is left to wonder whether this month-long spat will carry over into 2008 and have ripple effects as the team attempts to regroup.

And that begs the question whether the 49ers can go forward and fix their problems with Smith as their quarterback and Nolan as their coach. Nolan's job security, already shaky as the team continues to implode in December, appears contingent on how well he can hold together and strengthen his once-solid relationship with Smith.

"We have continued to communicate all along," Nolan said. "It's all about communication, and I do believe that we communicate. But everyone has to be honest in the communication process all the time and up-front."

Despite some growing public sentiment that either Smith or Nolan - or both - should be jettisoned, it appears that both will return next year. Nolan has two years remaining on his contract, and though team ownership isn't talking publicly, sources within the organization suggest that the York family is leaning toward giving Nolan a fourth season to fix the mess the 49ers have become.

For his part, Smith is unlikely to be going anywhere in 2008. He signed a $49.5 million deal as the No. 1 overall pick in 2005, and his departure would deliver a damaging blow to the team's salary cap. And, despite the problems that have hit Smith during his lost 2007 season, he still is a developing young quarterback with promise, and those things are difficult to find in the NFL.

Nolan insisted Wednesday that, in the big scheme of things, this is just a little miscommunication/misunderstanding that will blow over with time and be forgotten about as the 49ers move on to more important things. And, Nolan said, he still believes in Smith as his quarterback.

"From the very beginning, when we drafted him, I was very confident at that time and I still am," Nolan said. "The things I said about him then, I have not changed (my beliefs) since. And in building the things around him, we've stayed true to that from the beginning."

Nolan then was asked if he was 100 percent certain Smith would be on the team in 2008.

"There's no reason for me to believe that he will not right now, no reason whatsoever," Nolan replied.

Then, perhaps cryptically, he added, "But I can't foretell the future."

With this sort of thing surfacing between quarterback and coach, nobody can. But if it so happens either Nolan or Smith doesn't return to the 49ers next season, this incident surely will be among the reasons why.

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