There is a fierce battle going on over what kind of a CIA director Barack Obama should appoint, when he should close the prison camp at Guantanamo, and whether there should be a full scale investigation (and possible prosecution) of the torture advocates in the Bush administration.

If you’ve only been reading The New York Times, you’re probably aware of these battles—but almost everyone you have seen quoted about them has similar points of view. Most of the Times’s sources don’t think that anyone who formulated or acquiesced in the current administration’s torture policies should be excluded as a candidate for CIA director, or prosecuted for possible violations of criminal law.

The story on the front page of Wednesday morning’s New York Times provides the most recent and the most dramatic example of this syndrome. The story, by Mark Mazzetti and Scott Shane, noted that John O. Brennan had withdrawn his name from consideration for CIA director after liberal critics attacked his role in the agency’s interrogation program, even though Brennan characterized himself as a “strong opponent” within the agency of harsh interrogation techniques. Brennan’s characterization was not disputed by anyone else in the story, even though most experts on this subject agree that Brennan acquiesced in everything that the CIA did in this area while he served there.

Brennan’s self-defense was followed by a quote from another ex-CIA man, Mark Lowenthal, who claimed that Brennan’s downfall “sent a message that ‘if you worked in the C.I.A. during the war on terror, you are now tainted,’ and had created anxiety in the ranks of the agency’s clandestine service.”

“I was aghast reading this,” said Scott Horton, a professor of human rights law at Hofstra and a contributing editor at Harper’s, whose blog was instrumental in framing the opposition to Brennan’s appointment. “The Times doesn’t even do a reasonable job of presenting the conflicts—their principal source today was John O. Brennan. They have not reached out to the other side. It looks like Mark and Scott have decided that it’s payback time for a couple of their sources at the agency.”

Horton also disputed the idea that an investigation of agency abuses would “would demoralize the line officers of intelligence and the military.” The people saying that are “very very skillfully pointing to the interrogators as being the targets—because they know they would not be the targets. The people who would be the targets are policy makers like [Cheney chief of staff David] Addington, who have the same ability to attract sympathy from the public as cockroaches. I’m not sure that the early part of the story is going to be so embarrassing to the company. There was push back at the beginning; you had pretty high level opposition and Cheney decided to cram it down, which is why they went to get that Department of Justice memo” authorizing the torture of prisoners.

Horton added that people in the CIA say Brennan is “absolutely correct he wasn’t responsible for shaping this policy; but when he suggests he was a vigorous opponent, they laugh.”

Asked by Full Court Press about Horton’s suspicions that the piece he had co-authored was payback for his sources at the CIA, Mark Mazzetti replied, “What am I going to say to that? It’s like absurd.”

The Times piece also framed the debate as a contest between CIA veterans and the “left flank of the Democratic Party.” But the only opponent to the Bush administration’s torture policy quoted in the piece was retired general Paul D. Eaton, who oversaw the training of Iraqi forces for the Army in 2003 and 2004.

Eaton, who is one of a group of forty retired admirals and generals opposed to torture, told the Times, “This administration has set a tone problem for the military. We’ve had eight years of undermining good order and discipline.”

I asked Mazzetti if he thought Eaton and his fellow retired generals and admirals regarded themselves part of the “left flank” of the Democratic Party. The Times reporter replied, “I wouldn’t want to comment on that. I think our piece pretty much stands for itself.”

A veteran human rights advocate in Washington explained the press’s dilemma this way:

The people who are doing the transition aren’t talking to anyone. And the people who are talking don’t really know what’s going on. The reporters are under enormous pressure to write stories; so what they inevitably do is go to these people outside of the circle who are either exaggerating their knowledge to make themselves look important, or are advancing an agenda.

(Scott Horton also observed that another piece in the Times Week on Review last Sunday, about how Americans should think about Guantanamo, relied almost exclusively on quotes from supporters of the current administration.)

The piece on the front page of Wednesday’s Times struck me as so unbalanced, I sent this e-mail to four top editors there: “This morning’s torture story on the front page is 1174 words long, of which 147 words are devoted to the anti-torture position, which the reporters writing the story obviously disagree with. I would like to know on what basis you believe this equation meets traditional New York Times standards for fairness and balance.”

Executive editor Bill Keller replied:

Your e-mail is 67 words long, of which zero are devoted to the substance of the story. The story is not a roundup of the debate over the use of torture. It is about the dilemma facing the Obama administration as it seeks a new head of the C.I.A. and tries to decide what level of association with the recent past might disqualify a candidate. One potential choice to head the agency has already withdrawn his name after coming under attack. Now, the piece reports, “Mr. Obama’s search for someone else and his future relationship with the agency are complicated by the tension between his apparent desire to make a clean break with Bush aministration policies he has condemned and concern about alienating an agency with a central role in the campaign against Al Qaeda.” This is a balancing act Obama has not yet resolved, and the article in no way rescribes how he should resolve it…It’s a little unfair to criticize an article for not being some altogether different article you might have written.

Washington bureau chief Dean Baquet told me, “Your take is sort of ridiculous. Your’re reading a point of view on the part of the reporters that is not there. You should read their past stories before jumping to conclusions.”

Since torture is the subject that I have written about more frequently than anything else since I started this blog one year ago, I have indeed read previous stories in the Times about torture, including a particularly egregious one last spring by Scott Shane, which suggested a kind of moral equivalency between opponents and proponents of torture: “Certainly the debate is rich in emotion, with each side claiming the moral heights: You approve torture! You’re coddling terrorists! But the arguments have been scant on science to back them up.”

Then Shane revealed the crucial science which had been ignored in the debate: “…[T]he [Army Field] manual’s inherited wisdom has not been updated to reflect decades of corporate analysis of how to influence consumers. Behavioral economists have dissected decision-making, and academic psychologists have studied political persuasion, but their lessons have not informed the interrogator’s art either.” (I told Baquet that this was one of the oddest observations I had ever read in a newspaper.)

In that same piece, Shane also quoted Benjamin Wittes, a fellow at the Brookings Institution and a longtime defender of the Bush Administration: “We don’t have any idea — other than anecdote or moral philosophy — what really works.”

That is flatly false.

The one story on this subject that should be required reading for everyone is the piece by a former senior interrogator in Iraq in last Sunday’s Outlook section of The Washington Post, entitled “I’m Still Tortured by What I Saw in Iraq.”

Like every one of those retired generals and admirals who has fought against the current administration’s torture policies, the author of the Post piece DOES know what works:

I taught the members of my unit a new methodology — one based on building rapport with suspects, showing cultural understanding and using good old-fashioned brainpower to tease out information. I personally conducted more than 300 interrogations, and I supervised more than 1,000. The methods my team used are not classified (they’re listed in the unclassified Field Manual), but the way we used them was, I like to think, unique. We got to know our enemies, we learned to negotiate with them, and we adapted criminal investigative techniques to our work (something that the Field Manual permits, under the concept of “ruses and trickery”). It worked. Our efforts started a chain of successes that ultimately led to Zarqawi. Over the course of this renaissance in interrogation tactics, our attitudes changed. We no longer saw our prisoners as the stereotypical al-Qaeda evildoers we had been repeatedly briefed to expect; we saw them as Sunni Iraqis, often family men protecting themselves from Shiite militias and trying to ensure that their fellow Sunnis would still have some access to wealth and power in the new Iraq. Most surprisingly, they turned out to despise al-Qaeda in Iraq as much as they despised us, but Zarqawi and his thugs were willing to provide them with arms and money. I pointed this out to Gen. George Casey, the former top U.S. commander in Iraq, when he visited my prison in the summer of 2006. He did not respond.

This piece also includes the best description anywhere of the immorality—and absolute counter-productivity—of the single worst policy in which the United States has engaged since it annihilated most of the Native American population in the 18th and 19th centuries:

Torture and abuse are against my moral fabric. The cliche still bears repeating: Such outrages are inconsistent with American principles. And then there’s the pragmatic side: Torture and abuse cost American lives. I learned in Iraq that the No. 1 reason foreign fighters flocked there to fight were the abuses carried out at Abu Ghraib and Guantanamo. Our policy of torture was directly and swiftly recruiting fighters for al-Qaeda in Iraq. The large majority of suicide bombings in Iraq are still carried out by these foreigners. They are also involved in most of the attacks on U.S. and coalition forces in Iraq. It’s no exaggeration to say that at least half of our losses and casualties in that country have come at the hands of foreigners who joined the fray because of our program of detainee abuse. The number of U.S. soldiers who have died because of our torture policy will never be definitively known, but it is fair to say that it is close to the number of lives lost on Sept. 11, 2001. How anyone can say that torture keeps Americans safe is beyond me – unless you don’t count American soldiers as Americans.

Those are the words Barack Obama needs to remember—and those are the ideas and the facts that you have not read in The New York Times.

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Charles Kaiser is the author of The Gay Metropolis and 1968 in America. He has been media editor for Newsweek, a member of the metro staff of The New York Times, and a reporter for The Wall Street Journal, where he covered the press and book publishing. To learn more, visit charleskaiser.com.