“In terms of things like that, it sounds juvenile to say guys picking up their trash in the locker room helps create a culture that doesn’t have off-the-field issues, it does. But, you look back in history, you look at New York City, there was crime ridden in the 1980s and you look at what the people did there of fixing broken windows, fixing graffiti, fixing little things like that and it’s amazing how that has a big effect on a larger issue and larger violent crime. So, you look at those things, little things matter. When you’re talking about winning a Super Bowl, it’s not about having the most innovative scheme on this side of the ball or that side of the ball. It’s not about having the best player here. In basketball, one player that’s 20 percent of your team. That makes a big difference. One player in football, that’s 1/22nd of your team, 1/25th, 1/30th when you’re talking about special teams and guys that really contribute on a daily basis. So, it’s a bunch of collections of little things that make the difference.”

This little pearl of wisdom regarding championship “culture” (a corporate buzzword I detest, but will use throughout this post to stay consistent with Jed York’s language) came courtesy of the 49ers CEO on Jan. 15, the day he and Trent Baalke introduced Jim Tomsula as the team’s new head coach. While York was explaining his reasoning for choosing Tomsula — who made good on York’s promise to help keep the locker room tidy — the comparison he made was clear.

Jim Harbaugh was David Dinkins or Ed Koch, and Tomsula is Rudy Giuliani.

That’s a questionable premise, for two reasons.

For starters, Giuliani was all-too-willing to take all the credit for New York’s cleanup efforts, which started before he took office. But that’s not relevant to the 49ers.

A more problematic part of the team’s “culture” — a propensity for betrayal and calculated leaks to major media outlets — was the reason why Harbaugh was rendered toothless by the front office before his final season with the 49ers began. How could a head coach have the power to keep his players flying right, when everyone on the team knew the head coach’s days were numbered?

The “culture” of leaks was in place before Harbaugh arrived. Just ask Mike Singletary about rats. Harbaugh is gone, but the emotional and mental vandalism is still prevalent in the 49ers’ shiny new locker room. And that’s where we get to Colin Kaepernick, who isn’t blameless at all, but in certain ways is a victim just the same.

Jay Glazer drops a Kaeperbomb

Just about everyone heard about this over the weekend:

“His confidence is completely shot,” Glazer said on Sunday. “It’s not that (the players) don’t like him. But he’s just alone, on an island in that locker room. There’s not a lot of people he connects with. “Confidence-wise he’s just buried right now.” Kaepernick signed a team-friendly, seven-year, $126 million contract before the start of the 2014 season, but that doesn’t mean the 49ers plan to move from him, according to Glazer. “They can move on from him at the end of the year provided he is not injured,” Glazer reported. “That’s not the team’s mindset. They look at him and say, ‘This is the same guy that took us to the Super Bowl.'”

Here’s what Ray Ratto had to say about that:

So Jay Glazer of Fox Sports, who is typically an excellent barometer of the inner workings of the San Francisco 49ers front office all the way up to the owners’ suite, reported Sunday that Colin Kaepernick’s aloofness and production are reasons much of the locker room has turned lukewarm on him. This of course led to the obvious raft of “This explains the following things I want to explain about why the 49ers suck.”

And if you don’t think Ratto is completely accurate when he describes Glazer as an organizational mouthpiece of sorts, consider this: Glazer was the first (right at the beginning of the 2014 season) to report that Harbaugh would be gone after last year ended, even if the team won the Super Bowl. And just check out that last Glazer quote in his Kaepernick story, the one about “the team’s mindset,” which only serves to bolster whatever remaining trade value Kaepernick has left.

Kyle McLorg’s story from Sunday

McLorg heard rumblings about the Aldon Smith/Nessa/Kaepernick love triangle and its effects on the 49ers locker room (Smith has made his feelings clear to several people on his current team in Oakland, too) for several weeks. He filled in some of Glazer’s blanks with a report on the team’s reaction to the Nessa story. Some might think it’s nothing but tabloid fodder, but if this lingering story is compounding the situation between Kaepernick and his teammates, it shouldn’t be ignored.

Quarterbacks are held to an extremely high standard. Press conference apparel/demeanor is one thing, but Kaepernick’s decision to date an ex-girlfriend of one of his (now former) teammates is a terrible look. The highest-paid player on the team, the guy with the most endorsements and opportunities to enjoy off-the-field perks of all kinds, almost has to spend most of his non-football hours gaining the trust of his coaches and teammates … unless he’s won multiple Super Bowls, in which case his standing among his teammates was probably high to begin with.

This trust idea goes both ways. A former 49ers assistant told Niners Nation that “it wasn’t that Kaepernick couldn’t read or couldn’t make the throws, but he lacked the ability to trust his receivers to be there before he could see them.” If Kaepernick doesn’t trust his teammates to block and get open, there’s a good chance they’ll respond with uninspired play.

This is a team with trust issues all over the place. The front office buried Harbaugh and hired a successor that Harbaugh himself seemed to believe was undermining him behind the scenes. Now Kaepernick is getting the same Glazer treatment, and it appears that he’s acting in ways that aren’t befitting what is expected from a franchise quarterback.

Would Kaepernick have broken “the code” and gone after Nessa if he was on a team that lived by an one-for-all-and-all-for-one mindset and displayed that kind of character from the owner down to Joan in Payroll? If he felt he could trust his teammates and his teammates trusted him?

Who knows. Affairs of the heart are impossible to explain — even when you have intimate knowledge of the participants and the situation. But this all seems symptomatic of a team that’s a sinking ship, with everyone fighting to get on the few seaworthy lifeboats.

As much as I chide Ted Robinson for glossing over the team’s failures in areas York doesn’t want highlighted, I have to credit him for alluding to this Kaepernick thing for weeks. Not the Nessa story per se, but after the Green Bay loss, Robinson openly questioned whether the players would fight for their quarterback. He referenced the body language he saw on the field and sidelines from frustrated receivers and downtrodden offensive linemen, but Robinson could’ve been speaking with behind-the-scenes knowledge that he couldn’t explain on the air.

The players-only meeting that turned into an Italian dinner table (oh boy)

From Matt Maiocco:

On Monday, CSNBayArea.com reported that one player called out Kaepernick in a players-only meeting approximately a month ago. Another player defended Kaepernick, and the exchange became heated. Tomsula said he called the meeting in the week before the 49ers’ game at the New York Giants and had some choice words for his team before leaving the room to allow the players to address each other. “The other one, with a ‘players only meeting,’ they must be referring to the meeting I had after the Packers game. I had a very pointed meeting,” Tomsula said. “I’m obviously not going to use the language I used in the meeting. And I’m obviously not going to get into the particulars of the meeting. “I did have a heated meeting. That does happen in this business. When you become 2-5, that starts to become headlines. But it was a very productive meeting. It was a meeting where it was truthful, and dealt with facts and reality. “As I finished what I had to say and the conversations we were having, I walked out and said, ‘Now you guys, get talking.’ I think that was a heck of a meeting.” As reported on Monday, Tomsula said the individuals who were at odds with each other during the meeting cleared up their differences in the days that followed. “The biggest thing I said to them was, ‘Guys, it’s like an Italian dining room table,'” Tomsula said. “‘Everybody’s sitting around the table and sometimes it gets heated, dishes get broken, people leave. (But) everybody’s got to come back to the table to eat. And when it’s all said and done, we’re hugging and kissing and we’re eating good food again. OK? I mean that with all due respect. I’m saying that complimentary.”

Other than Tomsula sounding like some sort of mob boss caricature you’d see on The Sopranos, kissing grown men on the cheek (“Eh, so yous guys are gonna play a little football, then we have a spicy meatball. Capiche?”), the part that sticks out is how he describes a situation in which one player is openly questioning the quarterback, and another is defending him, as normal.

Well, of course they “cleared up their differences in the days that followed.” What’s the other option, fighting every single day until one player gets released? And from what I’ve heard, the two combatants have both been with the team for quite some time (here are the details) … so they’re all-too-familiar with this 49ers “culture” that teaches players, coaches and execs to walk over one another to get what they desire.

York has created a “culture” that encourages anonymous complaining and breeds insecurity. He tacitly pinned the blame for all of the locker room anarchy (including the arrests) on Harbaugh, but the stains are too embedded to clean with one coaching change. If anything, the Harbotage perpetrated by York led to a feeling of unrest that has shifted players’ thoughts from on-the-field competition to gossiping and backstabbing, the only areas where the 49ers have truly excelled above all other teams over the last decade.