As Sotomayor put it to Jonathan Cohn, the Justice Department lawyer arguing the case before the Second Circuit Court of Appeals: “So the minute the executive raises the specter of foreign policy or national security, it is the government’s position that that is a license to torture anyone, a U.S. citizen or a foreign citizen? License meaning you can do so without any financial consequence. That’s your position?”

Oddly, The New York Times and most media outlets have largely ignored Sotomayor’s questioning at that tense and controversial two -hour-long oral argument in December.  When The Times did report on it, however, the reporters used the exchange not to reveal an insight about Sotomayor’s grasp of the issue or concerns about torture or the abuse of executive power, but to illustrate a point that Jeffrey Rosen had first made in a New Republic article citing anonymous lawyers calling Sotomayor “a bully on the bench.”

Under the headline “Sotomayor’s Blunt Style Raises Issue of Temperament,” (the headline earlier in the day, as Canadian blogger Juliet Waters points out, was “Sotomayor’s Sharp-Tongue Brings Up Issues of Temperament”), reporters Joe Becker and Adam Liptak used the exchange in the Arar case to say that Sotomayor “has a blunt and even testy side” which “was on display in December during an argument before the federal appeals court in New York.”

The reporters largely ignored the substance of the exchange, but characterized Sotomayor has “pepper[ing] a government lawyer with skeptical questions.”

Here’s the Times’ description of Sotomayor’s exchange with the government lawyer:

“So the minute the executive raises the specter of foreign policy, national security,” Judge Sotomayor asked the lawyer, Jonathan F. Cohn, “it is the government’s position that that is a license to torture anyone?”

Mr. Cohn managed to get out two and a half words: “No, your hon—— .”

Judge Sotomayor cut him off, then hit him with two more questions and a flat declaration of what she said was his position. The lawyer managed to say she was wrong, but could not clarify the point until the chief judge, Dennis G. Jacobs, stepped in, asking, “Why don’t we just get the position?”

The Times went on to say that “some lawyers have described her as ‘difficult’ and ‘nasty’” and that this “raises questions about her judicial temperament and willingness to listen.”

In fact, if you listen to the entire two-hour argument, or even just to the complete hour-long section in which the judges question the government’s lawyer, Sotomayor, in context, is mild-mannered compared to many of her colleagues, and far less argumentative.

Judge Calabresi, for example, whose own skepticism of the government’s argument was obvious, dominated the questioning of the government’s lawyer, interrupting him at least ten times to force him to clarify his position and its implications. Other judges, such as Judge Rosemary Pooler (also clearly disturbed by Cohn’s position) and Judge Reena Raggi also interrupted the government’s lawyer repeatedly. And Chief Judge Dennis Jacobs, who was evidently more sympathetic to the government’s position than were many of his colleagues, stepped in at least three more times to ask the other judges to back off and let the lawyer make his case.

“Excuse me, I think all these questions are out of order” Jacobs said at one point, interrupting Judge Parker, one of several judges who was challenging the lawyer with difficult procedural questions in what was an extremely complex and unusual case. “I don’t even know what the question is that’s pending,” he added, with obvious irritation that his colleagues weren’t letting the government’s lawyer present his case.

Of course, in an en banc appellate court argument where 12 judges are questioning a single lawyer at a time, that’s the role of the court — not to sit passively for a lecture from the lawyer, but to challenge the lawyers on all sides to address the difficult and complicated procedural and substantive legal issues that have led the court to take on a full-court argument in the first place. (Most courts of appeals choose to re-hear only one or two cases a year in this manner, and then only the most controversial and important ones.) To argue that Sotomayor was inappropriately abrupt or “testy” makes no sense in the context of the actual court argument.

Putting the lawyers to the test is exactly what the judges are supposed to do, and it’s a role that Judge Sotomayor played extremely well in the case of Maher Arar.

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Judge Sonia Sotomayor (Zuma Press)

Most commentators and reporters have assumed that when it comes to Judge Sonia Sotomayor’s record, there’s little to suggest how she might rule on critical matters of executive power and national security that are sure to be among the most controversial issues before the court in the next few years.

One exception to that is a Fox News report on Tuesday, which cites Sotomayor’s March 2003 lecture to a class at Indiana University Law School, where she said, “We have suspected enemy combatants detained in secret and given different process than criminals. One can certainly justify that type of detention under precedents and current law.”

Illustration by: Matt Mahurin

To Lee Ross at Fox News, this was a pronouncement “that could draw criticism from liberal groups.” But in the context of the entire lecture, which Sotomayor provided, along with a mass of other materials, to the Senate Judiciary Committee on Monday evening, the statement appears to be simply an explanation to law students of where the courts had come down on the issue so far. The issues would eventually reach the Supreme Court, which would affirm the government’s right to detain certain enemy combatants indefinitely. But at that time only a district court from the Southern District of New York and the U.S. Court of Appeals for the Fourth Circuit had addressed the questions.

Notably, The New York Times on Wednesday focuses on a different part of the lecture in which Sotomayor expresses skepticism about the government’s authority under the USA Patriot Act “to impose nationwide wiretaps with little judicial supervision” and to monitor use of the Internet.

While reporters and bloggers have noted that Sotomayor has never worked in the federal executive branch and has sat on courts that don’t hear many executive power challenges, her record from the bench is not a blank slate. In fact, just last year, she joined two other judges in ruling that sections of the USA Patriot Act regarding national security letters are unconstitutional. And in the case of the Canadian former detainee Maher Arar, arrested while changing planes at John F. Kennedy airport and rendered by U.S. authorities to Syria to be tortured, he claims, Judge Sotomayor played an active role in a heated two-hour argument before the full 2nd Circuit Court of Appeals in December. (The court has not yet issued its opinion.) Both of those cases — largely overlooked by the media as indicators of Sotomayor’s inclinations on executive power — suggest that Sotomayor will be no wallflower in cases challenging unchecked executive authority in matters of national security.

What Judge Sotomayor actually believes the law is when it comes to the treatment and detention of suspected terrorists, and the type of justice they’re afforded, is critically important to how the Supreme Court will rule on these issues in the coming years, however. As Charlie Savage wrote recently in The New York Times, the impact of a new justice on presidential power could make all the difference. “Important rulings on executive authority — striking down military commissions and upholding habeas corpus rights for Guantanamo detainees — have been decided by a five-vote majority, including Justice Souter, on the nine-member court,” Savage explained. Justice Souter was a strong proponent of limits on executive power, voting to strike down the first incarnation of military commissions created by President Bush, and voting in favor of providing Guantanamo detainees’ habeas corpus rights. A new judge could swing the majority the other way. And both of those issues — the new Obama military commissions and habeas rights for detainees at other U.S. prisons abroad, such as Bagram — are likely to reach the Supreme Court in the next few years.

“To my mind, this is the most significant issue for the court, especially given the radicalism of Roberts and Alito on presidential supremacy,” wrote Andrew Sullivan on his blog at The Atlantic recently.

In the 2008 ruling Doe v. Mukasey, Judge Sotomayor joined an opinion written by Judge Jon Newman that struck down parts of the USA Patriot Act. The law put a “gag order” on companies that received a National Security Letter from the FBI requiring the company to turn over information about their customers, and required the recipient of the letter to go to court to have the gag order lifted. The three-judge panel of the 2nd Circuit, including Sotomayor, ruled that it was the government’s burden to justify to a court why it had to silence an NSL recipient. The court also invalidated sections of the Patriot Act that required judges to assume as true the FBI’s claims about what would harm national security.

As the court wrote: “There is not meaningful judicial review of the decision of the Executive Branch to prohibit speech if the position of the Executive Branch that speech would be harmful is ‘conclusive’ on a reviewing court, absent only a demonstration of bad faith. … The fiat of a governmental official, though senior in rank and doubtless honorable in the execution of official duties, cannot displace the judicial obligation to enforce constitutional requirements. ‘Under no circumstances should the Judiciary become the handmaiden of the Executive.’”

While it’s hardly a radical position for a federal court to reject a government’s arguments that its positions are unreviewable by any court, it does suggest that Sotomayor is willing to stand up to broad executive claims of unreviewable power in matters of national security. That’s likely to come up in cases raising the matter of state secrets, “preventive detention” of suspected terrorists and the creation of military commissions.

Sotomayor herself was explicit about her suspicion of the government’s assertion of unreviewable power in the national security context during the argument in Arar v. Ashcroft. Sotomayor wasn’t physically present in the courtroom, but her larger-than-life image was beamed on a screen via satellite teleconferencing technology, giving her what one blogger called “a Star Trek immensity.”

The government’s lawyer, Jonathan Cohn, was attempting to argue that the case is so “inextricably bound” with matters of foreign policy and national security that the courts should just stay out of it, since those are the exclusive domains of the executive branch.

Sotomayor, like many of her colleagues, was skeptical. In her most striking exchange with the government’s lawyer, she asked, “are you saying that there should be no Bivens action [a right to sue federal officials] for any torture by a federal agent?”

Cohn quickly said no, that’s not the government’s position, unless the issue is “fraught with national security implications.”

Sotomayor pressed the point: “So the minute the executive raises the specter of foreign policy or national security, it is the government’s position that that is a license to torture anyone, a U.S. citizen or a foreign citizen? License meaning you can do so without any financial consequence. That’s your position?”

Although Cohn claimed again that he was not saying that, Sotomayor had correctly seized upon the implication of his argument — that the government cannot be sued for torture so long as it claims that the suit raises foreign policy or national security concerns. And the nature of her questioning suggested strongly that she did not agree.

A slew of lawsuits isn’t hard to imagine. About 750 people have been detained as suspected terrorists at Guantanamo Bay. Thousands more have been held around the world. Many claim they were tortured, and we know from the Bush administration’s own documents that tactics such as waterboarding, stress positions, extreme hot and cold, blaring music and sleep deprivation, and sexual and religious humiliation were all among the tactics used to wring information out of them.

Although the Military Commissions Act tries to preclude lawsuits filed by enemy combatants, many of the people held were never determined to be enemy combatants, or were still held after they were cleared for release. Of the lawsuits already filed against US officials by detainees, none of them were ever deemed enemy combatants. The Second Circuit heard arguments in the case of Maher Arar this week, and lawyers on the other case (Rasul v. Rumsfeld) have asked the US Supreme Court for review. The court will consider the request when it meets on Friday.

Although all sorts of immunities protect US officials from wrongdoing on the job, there’s a strong argument to be made that torture can never be considered part of a government official’s job, so those immunities shouldn’t apply. And the Religious Freedom Restoration Act, which protects against violations of detainees’ religious rights, such as having their Koran flushed down the toilet or being forcibly shaven, is very broad. (That didn’t stop the DC Circuit from dismissing four British detainees’ claims under it earlier this year, though, as I’ve written about before.)

But as I was talking to Carolyn Patty Blum the other day, an emeritus law professor at Berkeley and consultant to the International Center for Transitional Justice, she mentioned that a commission set up to investigate torture and other abuses perpetrated by Bush officials could also recommend, in addition to prosecution, a means by which torture victims can be compensated. Even if Bush were to pardon himself and his officials, a topic of much recent discussion, that wouldn’t shield anybody from future civil lawsuits demanding monetary compensation. But a statute that set up an investigative commission that had the power to, among other things, recommend compensating victims of torture and arbitrary detention, could also protect the US government from some costly future litigation.

“If a commission led to the creation of some sort of process that allows people to clear their name and apply for some sort of monetary compensation for being arbitrarily detained, one of the benefits is it would foreclose the ability for people to pursue another remedy,” Blum explained. “That would be a net gain in terms of cost savings for the new administration.”

Although that’s not the primary reason why Obama should create an investigative commission — Scott Horton at Harper’s has made the case for one quite well — it’s yet another argument in its favor.