Eventually, the Justice Department did step away from Yoo’s defense — although Yoo’s personal lawyer, former GOP judicial nominee Miguel Estrada, is still being paid by U.S. taxpayers.

Now, despite having already filed briefs on Yoo’s behalf in the district court arguing that as a former DOJ lawyer he should not be held liable for the consequences of his legal advice sanctioning torture, the Justice Department has filed yet another brief in the case, making essentially the same argument, this time on the government’s own behalf.

In an amicus (friend-of-the-court) brief filed to the appeals court yesterday (the lower court had refused to dismiss the case), the Justice Department argues that the court should not allow a lawsuit against a government lawyer providing advice to the executive branch where the case implicates national security and war powers. Such liability “could deter frank and full discussions within the Executive Branch regarding such matters.”

Of course, if the executive branch had actually had a “frank and full discussion” about the legality of torture with more than just a couple of hand-picked lawyers who believed in absolute executive power in the first place, John Yoo and the rest of the country wouldn’t be in the mess we’re in now. But set that aside for a moment.

Footnote 1 of the brief implicitly acknowledges the weird conflict involved in the DOJ’s even filing this brief, though without explicitly noting that the DOJ already made these same arguments on Yoo’s behalf earlier.

The first footnote essentially says that the Justice Department is going to repeat only some of its earlier arguments this time but not others. Specifically, it’s not going to make the argument now that Yoo didn’t do anything wrong because the right not to be tortured wasn’t clear at the time he approved it. That’s because since filing that first brief making just that argument, the department realized that, whoops, Yoo is under an internal ethics investigation, so maybe we should just stay out of this.

Dave Hoffman at Concurring Opinions interprets the footnote this way: “We’d like to join and expand on Yoo’s arguments about his good faith behavior. But other parts of us are still holding onto a report which may call into question the accuracy of that claim. Coincidentally and luckily, that report continues to be delayed, making it unnecessary for us to commit to a position that would be internally incoherent.  Do us a favor and resolve this on constitutional grounds, would ya?”

To be sure, that hasn’t stopped the Justice Department from making the argument elsewhere that torture wasn’t clearly illegal when Yoo sanctioned it. In the case of Rasul v. Rumsfeld, for example, that’s precisely the argument the Obama administration is still making. In fact, as I noted recently, the administration is going even further than that. In a brief recently filed to the U.S. Supreme Court, the Obama Justice Department argued that under its own interpretation of the law, there is no constitutional right not to be tortured by U.S. authorities in U.S.-run prisons abroad.

Yoo, of course, is the former Deputy Attorney General in the Office of Legal Counsel and primary author of the so-called “torture memos” – memos that defined torture so narrowly as to approve a broad range of interrogation techniques, at least one of which — waterboarding, or simulated drowning — had been deemed torture repeatedly by the United States in the past.

Padilla claims he was subjected to a range of harsh and arguably illegal interrogation techniques, such as sleep deprivation, exposure to extreme hot and cold temperatures in his prison cell, threats to torture and kill him, stress positions, and much more, during his more than three years held in isolation without charge at a U.S. military brig. (Padilla was eventually transferred to civilian custody and tried in federal court on criminal conspiracy charges. He was sentenced to 17 years in prison.) Represented by a Yale Law School clinic, Padilla and his mother are now suing Yoo, among others, for his treatment by U.S. officials. (A parallel case is pending in the South Carolina against former Attorney General John Ashcroft and Donald Rumsfeld.)

Yoo, represented by the U.S. government because he was sued for his official acts (although whether the Justice Department ought to be representing him is questionable), argued that he is immune from suit because, among other things, it wasn’t clear at the time that the abusing Padilla was unlawful, and because in any event Padilla can’t connect the abusive conditions of his detention to Yoo’s actions writing memos that authorized brutal treatment. Yoo also argued that the court should not review the adequacy of his legal memos, because that’s the role of the executive branch or Congress.

The court rejected that argument, noting that it’s still the role of the courts to judge whether the government met constitutional standards in its treatment of detainees.  The court also denied Yoo’s argument that he is entitle to immunity from suit because Padilla’s rights as an “enemy combatant” were not clear at the time — the same claim Bush officials have made in several other cases. “The Court finds that the complaint alleges conduct that would be unconstitutional if directed at any detainee, and therefore finds that the rights allegedly violated were clearly established at the time of the alleged conduct,” wrote Judge White.

That Yoo only wrote the legal authorization for the abuse and didn’t carry it out himself didn’t help him any with the court. “Like any other government official, government lawyers are responsible for the foreseeable consequences of their conduct,” wrote Judge White, an appointee of President George W. Bush. That mistreatment would follow from an authoritative legal memo advising the executive branch that those specific acts of abuse were lawful is not a stretch. The legal complaint also specifically charges that Yoo helped develop the government’s policy in the “war on terror”, and specifically sanctioned the treatment of Padilla as an “enemy combatant,” and the court found that if true, that would give rise to Yoo’s liability for Padilla’s treatment.

One factor weighing in favor of Padilla’s right to sue is that the United States had not afforded him an alternative remedy for the abuse he claims he suffered. The court quoted news reports such as one in The New York Times saying that “President Obama has shown little interest in prosecuting officials of the previous administration, and it is not clear whether there will be a government sponsored investigation of Bush administration policies.”

Padilla’s lawyers are thrilled.

“This ruling gives hope that the courts will not shy away from accountability for those who designed and implemented the last administration’s torture policy,” said Jonathan Freiman, lead counsel for Padilla, in an e-mail over the weekend. He added:

The Court noted what it called “the irony” of Yoo’s position: that Padilla alleges “that Yoo drafted legal cover to shield review of the conduct of federal officials” who tortured Padilla, and that Yoo’s response was “that the very drafting itself should be shielded from judicial review.” Even if, as Judge White notes, the political branches may currently lack the will to hold accountable those who were responsbile for the torture policy, the judiciary has the duty not to avert its eyes.

The case is very similar to the lawsuit filed by U.S. citizen and former enemy combatant Jose Padilla against former Deputy Assistant Attorney General John Yoo, which I’ve been following. The plaintiffs in Rasul v. Rumsfeld allege that former Defense Secretary Donald Rumsfeld and other senior Bush officials are responsible for their torture; prolonged arbitrary detention; cruel, inhuman or degrading treatment; cruel and unusual punishment; denial of liberties without due process, and preventing the exercise and expression of their religious beliefs.

According to their legal complaint, Shafiq Rasul, Asif Iqbal and Rhuhel Ahmed claim they traveled to Afghanistan in October 2001 to offer humanitarian relief to civilians. In late November, they were kidnapped by Rashid Dostum, the Uzbeki warlord and leader of the U.S.-supported Northern Alliance. He turned them over to U.S. custody – apparently for bounty money that American officials were paying for suspected terrorists. In December, without any independent evidence that the men had engaged in hostilities against the United States, U.S. officials sent them to Guantanamo Bay. Over the next two years, they claim — as does a fourth British man — that they were imprisoned in cages, tortured and humiliated, forced to shave their beards and watch their Korans desecrated, until they were returned to Britain in 2004. None were ever charged with a crime.

Dismissed at the urging of the Bush administration, the case was appealed to the U.S. Supreme Court. In December, the case was sent back to the U.S. Circuit Court of Appeals in Washington for reconsideration, because the Supreme Court had ruled in Boumediene v. Bush that Guantanamo detainees have the right to challenge their detentions. It wasn’t clear what effect that ruling might have on the Rasul case.

Although some civil rights lawyers had hoped the Obama administration would change the government’s position — or at least try to settle this case, which is at the very least an embarrassment to the United States –  the former prisoners had no such luck. Today, the Justice Department filed a brief arguing, as it did in Padilla’s case against Yoo, that government officials are not liable for torture, abuse, denial of due process or religious rights, because the right of Guantanamo prisoners not to suffer those abuses at the hands of the U.S. government was not clearly established at the time.

That would seem to contradict previous statements by President Obama and Attorney General Eric Holder that torture (including waterboarding) and other abuses are clearly illegal, now and always, and that the president can’t simply override that prohibition. It also may discourage those who are hoping the president will eventually support prosecutions of former Bush officials for exactly those crimes.

Reached today, the lead lawyer on the case, Eric Lewis, a partner at the Washington-based law firm, Baach Robinson & Lewis, said he was “disappointed” but “not surprised.”

However, as I’ve pointed out before in the context of the Yoo case, the defense does raise some serious questions about whether the Obama Justice Department really ought to be defending Donald Rumsfeld and his former colleagues in this case at all.

I’ll be writing more about this case and others like it, as well as their implications, in the coming week.

That’s because fundamental to any argument on behalf of a government official being sued for things he did in government is the claim of “qualified immunity” — essentially, the official is immune if it wasn’t clear at the time that what he was doing violated established rights.

Now, lots of people will claim that we all knew that U.S. citizens have a right not to be tortured or detained indefinitely without access to counsel and incommunicado, so Yoo should really lose that argument. Still, it’s probably the best argument he has — that the president’s wartime authority at least arguably overrode all those rights we thought we knew we had, but didn’t know the administration had quietly revoked.

In fact, much to the dismay of some of its supporters, the Obama administration is making just that argument. In its brief moving to dismiss the case that Padilla and his mother filed against Yoo, the government argues that “Defendant Yoo is entitled to qualified immunity as a matter of law.” Not only was he not personally responsible for what happened to Padilla, they claim (although Padilla’s lawyers claim Yoo participated personally in formulating the plan for Padilla’s detention and treatment), but the government claims that the claims all fail because “Plaintiffs have not alleged a violation of any constitutional rights.”

As long as Padilla was an “enemy combatant,” the government argues, it wasn’t clear he had any legal rights at all. That was, of course, what the Bush administration argued, too.

But doesn’t that claim contradict others made by President Obama and Eric Holder — that torture, for example, is and always was illegal? (Notably, as I wrote recently about the al-Marri case, the Obama administration has not claimed that indefinite detention of U.S. residents or citizens within the United States is unconstitutional.) Do they really want to be claiming now that they’re not so sure?

In Ratner’s view, that’s a bad thing all around.

“The more I think about it, representing Yoo puts the administration in a potential contradiction,” he wrote to me in an e-mail after our phone conversation. “They should not be arguing that there was not a clearly established right to be free from detention without trial, court access or abuse under the Fifth and Eighth amendments. If they do, or have, it would be a grave disappointment and justify many of the nasty Bush administration practices.”

Ratner added: “They need to get Yoo another lawyer, or better, cut him loose, as continued representation is contrary to government interests. A lawyer should represent Yoo who can take positions that they [the Obama administration] should not.”

Likewise with Donald Rumsfeld, added Ratner. The Center for Constitutional Rights is representing alleged torture victims in a case against the former secretary of defense, among others, now pending in the U.S.Court of Appeals for the D.C. Circuit, on remand from the U.S. Supreme Court. As in the Yoo case, the Bush administration tried to dismiss the case against Rumsfeld on the grounds of qualified immunity. Now that the Obama administration has taken over, it will be interesting to see whether that argument changes.

The Justice Department’s brief in the Rumsfeld case is due later this week. Stay tuned.

When the Center for Independent Media’s own Ed Brayton put the question to me on his radio show last week, I had to admit I wasn’t really sure of the answer. Like many people, I assumed that the government was required to defend a former employee being called to account for something he did while in government office. But does the DOJ always have to defend government employees, or are there limits? If that former employee has broken — or at the very least twisted — the law, can the Justice Department refuse?

I asked Justice Department spokesman Charles Miller yesterday, who responded by sending me a lengthy excerpt from the relevant section of the Code of Federal Regulations. (I’ll spare you the seven pages of fine print.) The quick answer is, according to 28 C.F.R. § 50.15, a former federal employee “may be provided representation in civil, criminal and Congressional proceedings in which he is sued, subpoenaed, or charged in his individual capacity . . . when the actions for which representation is requested reasonably appear to have been performed within the scope of the employee’s employment and the Attorney General or his designee determines that providing representation would otherwise be in the interest of the United States.”

That of course begs the question: when is providing such representation “in the interest of the United States”?

The Justice Department wouldn’t comment on that one, which should come as no surprise: chances are it’s a matter of heated internal debate right now. I’m just speculating here, but given the recent reports that the Justice Department’s Office of Professional Responsibility is sitting on a classified report that analyzes John Yoo’s opinions and, according to Justice Department officials that have been leaking all over the media, the report will slam Yoo’s legal research and reasoning, and how he arrived at his conclusions. If it does, it wouldn’t be the first such criticism: former Bush Justice Department official Jack Goldsmith, now a Harvard Law professor, withdrew Yoo’s memos when he took over OLC in 2003, and later wrote in his book that he was “astonished” by their “deeply flawed” and “sloppily reasoned” legal analysis. Since then, many more legal scholars have agreed.

According to lawyer and writer Scott Horton in The Daily Beast yesterday, the OPR report will also include “detailed disclosure of Yoo’s dealings with the White House in connection with the preparation of the memos,” which are widely suspected to have been requested as “as after-the-fact legal cover for draconian policies that were already in place (“CYA memos”).”

A source in the Justice Department wouldn’t give me any more details about the forthcoming report, but confirmed that what’s been reported about it in the media so far is accurate.

So it sounds like the report is going to conclude that Yoo crafted the memos using shoddy legal research and reasoning to justify policies that were, objectively, legally indefensible. That would seem to constitute, at the very least, an ethical violation, if not worse. (In addition to being sued in the lawsuit by Padilla, Yoo is one of the Bush officials most often discussed as a target of a possible U.S. prosecution — even, by implication, Senator Arlen Specter (R-Penn.), who recently expressed outrage at some of the more extreme Office of Legal Counsel memos produced earlier this month.)

All of which calls into doubt how much longer Attorney General Eric Holder will be able to continue to say that defending former OLC lawyer John Yoo from claims that he’s responsible for torture is “in the interest of the United States.”