Leading candidates for CIA director include, from left, retired Adm. Dennis Blair, former Rep. Tim Roemer and Rep. Jane Harman. (Wikimedia Commons; Flickr: miraclebaby; house.gov)

President-elect Barack Obama has enjoyed a surprisingly smooth presidential transition, with nearly all his appointees to Cabinet-level posts receiving widespread acclaim. But the exception has been the intelligence community. The abrupt departure of Obama’s probable nominee to lead the CIA has caused a bout of consternation in both intelligence and progressive circles at a time when the community is viewed as plagued with structural turmoil despite near-fundamental reorganization since 2004.

“Reform of the intelligence community is far from complete,” said Rep. Rush Holt (D-N.J.), chairman of the House Select Intelligence Oversight Panel. “There are still major gaps in basic product — intelligence.”

Illustration by: Matt Mahurin

John Brennan, a longtime intelligence official and key adviser to Obama, formally withdrew from consideration Nov. 25 after Salon’s Glenn Greenwald posted Brennan quotes expressing support for the practice of rendition, in which terrorism suspects are sent to foreign countries for interrogation, many of which employ torture. When the Bush administration ordered the CIA to engage in torture after 9/11, Brennan — then a deputy to CIA Director George Tenet — was considered, for the most part, an opponent of torture, according to several intelligence officials. “I have been a strong opponent of many of the policies of the Bush Administration, such as the preemptive war in Iraq and coercive interrogation tactics, to include waterboarding,” he wrote in a letter to Obama. Yet a New Yorker 2007 story by Jane Mayer identified Brennan as a “supporter” of coercive interrogation methods.

“I don’t know John Brennan very well, but he certainly has an excellent reputation,” said Bob Graham, the retired Florida senator and governor who chaired the Senate intelligence committee from 2001 to 2002 and who served as its vice chairman until 2004. “When he said he was not supportive of those initiatives — and inside the agency was a voice of restraint and reform — I would give him a strong presumption of correctness.”

Brennan’s abrupt withdrawal from consideration for the CIA post caused an explosion of concerns among former intelligence officials. For the past two weeks, many of them have vented anonymously — and bitterly — to reporters that Obama had thrown them under the bus to appease progressives. They worry that the illegality of the Bush era has made CIA operatives, analysts and bureaucrats radioactive, in effect holding the bag in the next administration for the crimes of the current one. “Brennan’s hands were not very dirty at all,” went one typical quote, given to Jeff Stein of Congressional Quarterly last week. “He was apparently thrown under the bus because some ill-informed bloggers thought they were [dirty], and the transition folks didn’t have the will to explain that they were wrong.”

Sources within the Obama transition say that Brennan volunteered to withdraw from consideration without any pressure from the Obama team. Brennan still leads the transition’s effort at finding a new Director of National Intelligence (DNI) and CIA director.

Some progressives were struck by the intensity of the CIA defense of Brennan and the invective of some ex-officials toward the left. “I am puzzled that certain parts of the CIA now consider objections to an open defender of torture, which contributes to the decline in our nation’s national security standing, as evidence of bad faith on the part of a group of ordinary citizens,” said Matt Stoller, a Democratic political activist and co-founder of the influential progressive blog OpenLeft. “I can’t imagine that these anonymous sources represent the entire intelligence community.”

Graham urged agitated CIA officials to regain calm. “There’s been some tension [with] the CIA chafing under what’s thought to be the influence of the new administration,” he said. “People need to put those kinds of concerns behind them. There’s a need to focus on how to get the intelligence community to overcome the problems of the recent past — like 9/11 and the run-up to the Iraq war — and focus on making America more secure and giving us advance warning [of] our enemies’ action.”

With Brennan out of the picture, several names have emerged to lead the intelligence community, which has been under near-constant political fire since the 9/11 attacks. Obama is said to be considering retired Adm. Dennis Blair, a former commander of U.S. forces in the Pacific; former Rep. Tim Roemer (D-Ind.), a 9/11 commissioner; Rep. Jane Harman, former chairwoman of the House intelligence committee; and Jack Devine, a longtime CIA official and former acting CIA director. The Obama transition declined to comment on any of these individuals. Nor would it give a timeline for any announcement.

Some intelligence veterans agree with progressives that members of the Tenet era should be disqualified from consideration. “It’s just too big a cloud that hangs over [the community] — the WMD, the torture issues, it’s just too much,” said one former senior intelligence official who requested anonymity. “That has to be unwound for the agency to do well.”

Graham distinguished between the skills necessary to be CIA director and those to be director of national intelligence. “One of the principal objectives is to move the community to a more mission-orientation [model] from a functional [one],” he said, emphasizing that the intelligence community is still short on linguists fluent in the languages of the Middle East and South Asia. Another responsibility for the DNI, he said, was “to rebuild the very frayed relations between the intelligence community, the executive branch and Congress.” The CIA director, by contrast, “is more of a manager of a large, complex organization, and I think that probably calls for someone who’s had some operational experience in the intelligence community.”

Others such as Paul Pillar, a retired senior intelligence analyst, called for stability, arguing that the past four years’ worth of politically-charged restructuring has exacerbated problems it meant to solve. “Change for the sake of change is not good,” said Pillar, who as chief Middle East analyst questioned whether Saddam Hussein had ties to Al Qaeda and blasted the administration’s manipulation of intelligence in a famous Foreign Affairs article. “We have had so much disruption and turmoil associated with reorganization. The reorganization associated with the 2004 legislation creating the office of the DNI is still being shaken out with regard to whose responsibilities lie where.” Pillar added that he had no expectation that the current intelligence chiefs — DNI Mike McConnell and CIA Director Michael Hayden — would keep their jobs.

The 2004 legislation represented one of the largest overhauls in the 60-year history of the modern intelligence community. While separating the leadership of the intelligence community from its historic home in the CIA, it do not specify what the new leader’s statutory and budgetary authority are. As a result, several new arrangements have arisen. For one, the DNI and Secretary of Defense Robert Gates made a deal in 2007 to designate the Pentagon’s top intelligence official as the chief of defense intelligence, a measure to undo efforts by former Defense Secretary Donald Rumsfeld to create an intelligence czar within the Pentagon, which controls nearly 90 percent of the $48-billion annual defense budget.

Holt, who is one of the main overseers of the intelligence community on Capitol Hill, said he is in the dark about how the joint DNI-Pentagon initiative has fared. “It’s hard to say for sure,” Holt said. “Congress doesn’t have the visibility it needs, which is a longstanding problem. Most members of Congress feel that even if and when the intelligence leaders subject themselves to questioning, members of Congress have to play 20 Questions before they can actually pry out the information they need.”

Another source of concern emerging from the 2004 legislation is a recent directive that makes intelligence officials at overseas embassies directly responsible to the DNI, even though the National Clandestine Service is supposed to be under the control of the CIA. “It’s madness, it’s just crazy,” said a former intelligence official. “This is like two competing institutions. The DNI’s not [supposed to] have these resources. If every time he makes a demand on CIA there’s resentment and pushback, it’s a huge problem.” Such a resource struggle is especially unwelcome given Obama’s stated emphasis on killing or capturing Osama bin Laden in Pakistan, a mission that will require a significant effort on the part of the intelligence community’s clandestine service.

Similarly, many have worried that the DNI’s office has been neglectful of long-term analysis, instead emphasizing responsiveness to the immediate needs of policymakers. One of the earliest actions taken by John Negroponte, the first director of national intelligence, was to shutter the CIA’s Strategic Assessments Group — its in-house office for long-term analysis — and move significant numbers of analysts from CIA into the DNI’s office.

Pillar cautioned that balancing short-term needs with long-term analysis has plagued the intelligence community for generations. “There’s no structural fix,” he said. “The inbox, the demands of the day and the crisis of the day — and not just in intelligence — are always going to overwhelm and push aside longer-term missions and projects.” Another ex-official said that the CIA was losing older analysts, particularly those who took a longer view of foreign challenges, and likened the Langley Starbucks to a college campus hangout.

Holt was agnostic on whether the new leadership of the intelligence community ought to be an intelligence veteran, as some have suggested. He focused instead on other criteria. “You need somebody who has vision and administrative ability,” Holt said. “Someone who’s experienced — just to learn the acronyms of community can take a year — who knows the territory and is capable of getting intellectual distance from it. I think that you need someone who’s not timid when it comes to international interactions and even distasteful encounters, but you don’t want someone who revels in warfighting.”

We’ve also long known that the Justice Dept., at the behest of a Central Intelligence Agency deeply fearful about its legal vulnerabilities, endorsed the torture techniques that CIA leadership desired. And we’ve recently learned that George W. Bush’s principal aides, including Condoleezza Rice, were aware of all the Spanish Inquisition-derived instruments of cruelty that the government was rehabilitating — as was Bush himself.

But now The Washington Post reports that in 2003 and 2004 — after those detainees had already been waterboarded — the White House explicitly authorized waterboarding in a pair of still-classified memoranda.

The memos were the first — and, for years, the only — tangible expressions of the administration’s consent for the CIA’s use of harsh measures to extract information from captured al-Qaeda leaders, the sources said. As early as the spring of 2002, several White House officials, including then-national security adviser Condoleezza Rice and Vice President Cheney, were given individual briefings by Tenet and his deputies, the officials said. Rice, in a statement to congressional investigators last month, confirmed the briefings and acknowledged that the CIA director had pressed the White House for “policy approval.”

Marcy Wheeler at FDL has the right follow-on question: Whose signature is on the memos? Wouldn’t it have to have been Bush’s? If it didn’t suffice to have Alberto Gonzales’ signature on the authorization for warrantless surveillance in March 2004 (instead of the attorney general’s), wouldn’t the president have had to be the one ordering the CIA to subject detainees to an unambiguously illegal activity?

Certainly that’s the logic of the CIA fears that undergirded the memoranda.

Consider what The Post reports:

“The suggestion that someone from CIA came in and browbeat everybody is ridiculous,” said one former agency official familiar with the meeting. “The CIA understood that it was controversial and would be widely criticized if it became public,” the official said of the interrogation program. “But given the tenor of the times and the belief that more attacks were coming, they felt they had to do what they could to stop the attack.”

The CIA’s anxiety was partly fueled by the lack of explicit presidential authorization for the interrogation program. A secret White House “memorandum of notification” signed by Bush on Sept. 15, 2001, gave the agency broad authority to wage war against al-Qaeda, including killing and capturing its members. But it did not spell out how captives should be handled during interrogation.

I know we’ll never ever have the war-crimes trial for Bush that is so obviously warranted. But if we did, these memos would make for powerful evidence.

Bush, Cheney, Gonzales, Yoo, Addington, Rice, George Tenet and the rest of them should think about tearing up their passports, because more and more nations are acknowledging universal jurisdiction for war crimes offenses.