There’ve been some weird goings-on in Congress around the Kerry-Boxer clean energy bill over the past few days. So let’s take a step back and try to get a handle on how the story is unfolding.

In the House, the development of the Waxman-Markey bill was a relatively orderly process. Waxman took control of the Energy committee early in the session and selected Markey, who’d been fleshing out a progressive bill in his special committee, as his wingman. Together they introduced a bill and then worked it past the committee members, making concessions when necessary, mostly behinds closed doors, always tightly in control of the process. The idea was to do the bulk of the negotiating in-committee so that the resulting bill could pass on the floor without undue fuss. In the end that’s just what happened.

Boxer desperately wanted to play the same role in the Senate. It didn’t work out in early 2008 with the Lieberman-Warner bill, but she’s been working overtime to make it work this go-round. One recurring theme of last week’s three-day hearing marathon was Boxer’s refrain that she’s going to work with other senators, that the bill will change, that she’s open to feedback. She practically hung out an “Open for Business” sign. She clearly wants to run this bill and emulate Waxman’s success.

Just as badly, lots of other people don’t want her to. Baucus made it clear early on that his committee would mark up a bill too, and then other committees jumped in. Inside EPW, James Inhofe desperately wants to give Boxer a black eye. That’s why he and the rest of the committee Republicans boycotted the markup of the bill on Tuesday and Wednesday and show every sign of carrying on with that boycott. It now looks like EPW is going to pass a bill out of committee without a Republican ever having touched or debated it and without substantial markup of any kind. [UPDATE: Yep, the bill passed out of committee on Thursday morning without any GOP involvement.]

That bill will be a dead letter. Already there’s an undercurrent of anxiety in Washington that a bill can never pass as long as it’s associated with an unpopular lady senator who runs one of the body’s most liberal committees. The Senate isn’t like the House. There is no party discipline among Democrats; in fact, Democratic senators are fond of explicitly disclaiming party discipline. It’s a chamber full of large, jostling egos and not a little old-boy sexism. They’re not about to let a combative liberal woman run the show.

So a bill that’s Pure Boxer won’t fly. That’s why you saw, on Wednesday, the Senate’s perceived centrists — Kerry, Graham, and their new buddy Joe Lieberman — swoop in and and open a “dual track” of negotiations, in consultation with the White House. (Lieberman lives to do this kind of thing.) Graham seemed to rebuke his colleagues on the EPW Committee: “If you can’t participate in solving the problem, then why are you up here?” he asked. But at the same time he, along with fellow moderates Gregg, Snowe, and Collins, signed a letter to EPA chief Lisa Jackson reiterating the Republicans’ essentially preposterous demand for another five weeks of study of the bill.

An EPA official testified to EPW on Tuesday that such a study would be expensive, time-consuming, and utterly unnecessary. There’s no substantive rationale whatsoever for demanding it. Remember, though, this isn’t about substance — it’s the Senate. It’s about perception. And what moderate Republicans are signaling here is: “Whoa, slow down the crazy liberal lady!”

Similarly, by stepping in, Kerry, Graham, and Lieberman are letting the political establishment know that the Very Serious grown-ups are back in charge. (It’s pretty telling that Kerry feels the need to craft another bill alongside the one with his name on it.) They will go to the White House, close the door, and hash out what kind of bill can really pass.

In short, it seems that Boxer’s high-water mark of influence on the bill has passed, and with a fizzle rather than a bang.

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Addendum: I should emphasize: this is all perception. Is Boxer really a crazy liberal? No. Was she jamming a liberal bill through her committee too quickly? No, the bill was relatively modest, similarly to the intensely analyzed House bill, and she was being almost absurdly solicitous of the feedback of the committee’s Republicans. Is Boxer too abrasive to do the delicate work of shepherding a bill through the Senate? Well, there may be something to that. In Congress it’s all about staff, and D.C. rumor has it that Boxer’s staff director, Bettina Poirier, is a controlling and alienating presence. EPW has been hemorrhaging key staff for a while now, and more than one Senate staffer has a tale of being misled or bypassed entirely by Boxer’s staff during negotiations over the bill. All those stories feed the general sentiment that Boxer just shouldn’t be the one running this. Fair or not, that’s the perception, and perception is reality in the Senate.