There’s just one problem. American Muslims simply don’t see Brennan’s perspective informing FBI and other law enforcement interactions with them.

“At the principal level, there’s a recognition of the need to respect our constitutional rights,” said Farhana Khera, the president and executive director of Muslim Advocates, a San Francisco-based civil rights group, “but what we see in the ground, by the agencies, is not the same reality.”

Khera is in town to testify this afternoon to a House Judiciary subcommittee. Along with other civil rights groups, her intention at the hearing is to raise awareness of the rise of racial and religious profiling among law enforcement. Muslim Advocates has collected stories from American Muslim communities about patterns of harassment: surprise visits at home and at work from FBI agents who don’t ask questions tied to evident criminal investigations. “They’re about religious practices, political views, involvement in community organizations,” Khera said. At border crossings and customs checkpoints, Department of Homeland Security agents ask about “what mosque you pray in, how often you pray, opinions on the Iraq war, thing that have nothing to do with international travel.”

That’s consistent with intelligence gathering — giving rise to suspicions that the FBI is treating American Muslim communities as an intelligence target. Khera’s prepared testimony to the House Judiciary subcommittee calls the FBI’s Domestic Intelligence Operations Guide a blueprint for “unprecedented, massive data gathering”:

This type of data collection is based on perceived characteristics and activities of racial and ethnic communities, not individualized suspicion of criminal activity. The DIOGs allow for this racial and ethnic information to be mapped, heightening the concern that this information will be used by law enforcement agencies to unlawfully target innocent Muslim Americans for further investigative activities.

“It’s a real concern,” Khera said. “In the America I grew up in, your religious practices were your own personal business. The government is encroaching on longstanding values of our country.” And — if you believe John Brennan — that’s a counterterrorism liability.

“We are in the midst of re-thinking and re-drafting our counterterrorism strategy,” Flournoy said in response to an audience question. “And one of the discussions we’re having in that context is what are the root causes of extremism, and what are the historical conditions that gave rise to this. How do we understand the cycle of radicalization?” She anticipated work continuing on that study for “the next several months.” So much for “the terrorists hate us for our freedom.”

Consider it tomorrow’s political headache today. Led by counterterrorism adviser John Brennan, the administration has aggressively denied any linkage between al-Qaeda-like extremism and Islam, out of a stated desire to prevent playing into the terrorist group’s rhetorical frame. It’s earned Obama scorn from the right. So will any effort in the forthcoming strategy document to say that U.S. policy has any role, however inadvertent, in contributing to radicalization — despite reams of evidence indicating that to be the case.

Good David Ignatius column on What James Clapper’s Nomination Means:

The DNI flap has been fascinating in what it shows about Obama’s approach to intelligence. He wants facts, not commentary; he mistrusts aides such as Blair who let their personal opinions show, and he correspondingly values low-key colleagues such as Gates; he wants to oversee intelligence not from a separate fiefdom but from inside the White House, where former CIA official John Brennan serves as deputy national security adviser.

Sen. Dianne Feinstein (D-Calif.), read this column. Ignatius’s insightful observation indicates that your problem isn’t whether Clapper is an obstacle to a strong director of national intelligence. It’s whether John Brennan and President Obama are those obstacles. Institutional powers matter. They matter a lot. But unless the structure of the intelligence community changes radically, the strongest you can make the job is akin to a powerful congressional committee chair, not a cabinet secretary, to use the formulation of Defense Secretary Robert Gates, a former CIA director. More radical changes would require a presidential commitment, and clearly Obama would prefer intelligence to be ultimately answerable to John Brennan at the White House. Accordingly, that’s going to be the official to whom the leadership of the intelligence agencies look to for their cues, whether or not Clapper gets confirmed and no matter what Clapper tells Feinstein when they parley in the coming days.

But a forthcoming study, led by Brian Glyn Williams, an associate professor at the University of Massachusetts, finds that the civilian death toll from the drones is lower than most media accounts present. “We came to the conclusion that the drones have a unique capability for targeting militants, as opposed to civilians,” Williams said in an interview.

Williams’ study, which he provided to The Washington Independent, has yet to be published. A writer for a blog affiliated with the International Herald Tribune, Farhat Taj, blogged some of the key details of his research today, but prematurely stated that the Combatting Terrorism Center at West Point will be publishing Williams’ work. Erich Marquardt, the editor of the center’s journal, said that he hasn’t even begun to review Williams’ submission yet.

Much like the New America Foundation study, Williams’ team relied on English-language media accounts of the drone strikes in Pakistan to compile a data base of how many civilians and militants were reported to be killed. He conceded from the start that such a reliance is a “serious limitation” of the study — news reports can, after all, be incorrect — but the tribal areas of Pakistan where the strikes occur are often off limits to Western researchers, and even their Pakistani counterparts. (Still, Williams plans on traveling to the tribal areas on June 10 to attempt a poll of local attitudes about the strikes.) His team took measures to mitigate that limitation: they only considered strikes that had been reported by multiple independent outlets and they erred on the side of treating the deaths of people in disputed militant status as either civilians or “unknown.”

Williams’ results, which he said have been peer-reviewed, are as follows:

According to our database, as of 1 April 2010, there have been a total of 127 confirmed CIA drone strikes in Pakistan, killing a total of 1,247 people. Of those killed only 44 (or 3.53%) could be confirmed as civilians, while 963 (or 77.23%) were reported to be “militants” or “suspected militants.”

That leaves just over 19 percent of reported deaths out of either category, as their status as civilians or combatants can’t be rigorously determined under Williams’ methodology. But he writes that “even if every single ‘unknown’ is assumed to in fact be a civilian, the vast majority of fatalities would remain suspected militants rather than civilians – indeed, by approximately a 3.4:1 ratio.”

Williams insists that he went into the study with an open mind. “We didn’t know what to think” about the drone program, he said, and he considers his research agnostic on the wisdom of the drone strikes (to say nothing of their legality). “We’re not necessarily trying to alter policy on this,” he said.

Both of the principle authors of New America’s drone strike survey, Peter Bergen and Katherine Tiedemann, are on vacation, but they both still (generously) addressed my questions. All three researchers — Bergen, Tiedemann and Williams — appeared to agree that New America was more methodologically aggressive than Williams in counting as civilians all who could not be clearly identified as militants, which perhaps accounts for the variance in their results.

Bergen observed in a Blackberried message that although his civilian death tallies are higher than Williams’, he has observed that the drone program has increased its accuracy over time, “so the later the the date that the study begins the lower the rate [of civilian deaths] will be.” That’s in line with Brennan’s intimation (he never actually uses the word “drones”) that the drone strikes “are more precise and more accurate than ever before.”

Accordingly, Bergen now pegs the civilian death rate from the drone strikes at 20 percent. Williams pegs it at 3.53 percent. What no one knows, however, is how many outraged Pakistanis take up arms against the U.S. or its allies as a result. There are media reports suggesting that Faisal Shahzad, the naturalized U.S. citizen of Pakistani origin accused of attempting to detonate a car bomb in Times Square, claimed to investigators that his attempted terrorist act was vengeance for civilians killed by the drones. Leaving aside the question of the legality of the drones — which the State Department’s legal adviser claims to result from a September 2001 act of Congress that doesn’t mention the program — only policymakers can determine if the benefits of the drones outweigh the risks of blowback.

Several recent incidences of violent extremists in the United States who are committed to fighting here and abroad have underscored the threat to the United States and our interests posed by individuals radicalized at home. Our best defenses against this threat are well informed and equipped families, local communities, and institutions. The Federal Government will invest in intelligence to understand this threat and expand community engagement and development programs to empower local communities. And the Federal Government, drawing on the expertise and resources from all relevant agencies, will clearly communicate our policies and intentions, listening to local concerns, tailoring policies to address regional concerns, and making clear that our diversity is part of our strength—not a source of division or insecurity.

The Department of Homeland Security has documented increased attempts by al-Qaeda and those inspired by it in recent months to attempt what John Brennan, Obama’s chief counterterrorism adviser, calls attacks of “low sophistication” within the United States. That creates a choice for intelligence and law enforcement. One answer is to apply counterinsurgency principles of population protection. That entails treating host communities as essentially “at-risk” cohorts that run the risk of infection by radical recruitment techniques. By partnering with community leaders, you give financial and political support to the recognized and legitimate authority figures so they can prevent extremism from taking hold — and to isolate, marginalize, identify and target for law enforcement those people who might still fall under its sway. This is what the NYPD’s old counterterrorism chief, Mike Sheehan, did in Muslim communities in New York City early last decade. It was as often as simple — and as crucial — as showing up to mosque meetings and letting people vent their grievances.

And this is the approach the National Security Strategy embraces: one that distinguishes between the extremists and the communities that they emerge from and exploit; treats the communities as under threat; and empowers those communities to handle that threat at the most immediate, legitimate and basic levels.

There’s another approach. You could treat the communities as the threat. Andy McCarthy, the most influential conservative legal authority on national security at the moment, ridicules the very idea of “Muslim ‘moderates’” as a “hopelessly ill-conceived construct.” His new book portrays Islam itself as a threat to America. The natural remedy is to empower law enforcement to target those Muslim communities in the United States. Subject them to surveillance. Detain them when necessary. If every Muslim who looks to their faith to inform their politics — which is all the wide, varied, catch-all term “Islamist” means — is on a slippery slope to swearing fealty to Osama bin Laden, then that approach makes sense.

Except that it doesn’t. And as John Brennan explained yesterday, it’s the exact strategy that bin Laden wants the U.S. to pursue, because it will guarantee that greater numbers within those communities turn to extremism in their frustration, precisely the outcome the strategy seeks to prevent. It’s worth quoting extensively from Brennan’s remarks:

Finally, remaining faithful to our values requires something else – that we never surrender the diversity and tolerance and openness to different cultures and faiths that define us as Americans. Several months ago, I had the opportunity to speak at NYU, where I was hosted by the university’s Islamic center and the Islamic Law Students Association. The audience included people of many faiths – Muslim, Christian, Jew, Hindu and Sikh. I was there to have a dialogue on how, as Americans, we can all work together to keep our country safe from the terrorists who seek to drive us apart.

After I was finished speaking, person after person stood up to share their perspective and to ask their questions. Mothers and fathers, religious leaders and students, recent immigrants and American citizens by birth. One after another, they spoke of how they love this country and of all the opportunities it has afforded them and their families. But they also spoke of their concerns, that their fellow Americans, and at times, their own government, may see them as a threat to American security, rather than a part of the American family. One man, a father, explained that his 21-year-old son, an American born and raised, who was subjected to extra security every time he boards a plane, now feels disenfranchised in his own country.

This is the challenge we face. Even more than the attacks al-Qaida and its violent affiliates unleash or the blood they spill, they seek to strike at the very essence of who we are as Americans by replacing our hard-won confidence with fear and replacing our tolerance with suspicion; by turning our great diversity from a source of strength into a source of division; by causing us to undermine the laws and values that have been a source of our strength and our influence throughout the world; by turning a nation whose global leadership has meant greater security and prosperity for people in every corner of the globe into a nation that retreats from the world stage and abandons allies and partners.

That is what al-Qaida and its allies want – to achieve their goals by turning us into something we are not. But that is something they can never achieve, because only the people of America can change who we are as a nation. Al-Qaida can sew explosives into their clothes or park an SUV with explosives on a busy street. But it is our choice to react with panic or resolve. They can seek to recruit people already living among us, but it is our choice to subject entire communities to suspicion, or to support those communities in reaching the disaffected before they turn to violence. Terrorists may try to bring death to our cities, but it is our choice to either uphold the rule of law or chip away at it. They may strike our communities, but it is our choice to either respond wisely and effectively or lash out in ways that inflame entire regions and stoke the fires of the violent extremism.

John Brennan (UPPA/ZUMApress.com)

“We will destroy al-Qaeda.”

That’s how John Brennan capped his presentation Wednesday morning on counterterrorism’s role in the forthcoming National Security Strategy, and the often intense White House senior counterterrorism adviser smiled a bit as he said it. His exploration of the administration’s pathway for getting there was mostly familiar. “A broad, sustained integrated campaign” making use of “every tool of American power: military, civilian, kinetic and diplomatic, and indeed, the power of our values and partnerships,” will sustain “pressure” on al-Qaeda in “Afghanistan, Pakistan, Yemen, Somalia and beyond” while addressing the “political, economic and social forces” that can create either demand for extremism among populations or acquiescence to it. Judge for yourself how that fits within the broader National Security Strategy.

[Security1] But Brennan did highlight a new development the Obama administration faces — and subtly defended a controversial tactic that he says contributed to it. Al-Qaeda and its affiliates have entered a “new phase” of their campaign against the United States, relying on operatives with “little training” who don’t fit “the traditional profile of a terrorist” for attacks of “little sophistication but with very lethal intent.” English-speaking al-Qaeda allies like California metalhead-turned-extremist Adam Gadahn and Yemen-based radical preacher Anwar al-Awlaki, both American citizens, seek to inspire people already in America to execute their own independently planned terrorist attacks.

All of these moves, Brennan said, are tactical responses from al-Qaeda to a successful pressure campaign from the U.S. and its allies abroad to reduce its safe havens and to hardened U.S. homeland security measures by law enforcement and at ports of entry, for which the Bush administration deserves some credit. And in only the vaguest terms, without making an explicit reference, he suggested that the drone strikes the administration has accelerated and exported in Pakistan, Yemen and Afghanistan are a principle reason for al-Qaeda’s adjustment. Limited by an ability to speak publicly about a classified program, Brennan signaled as well that the administration is concerned that blowback from civilians killed by the drones could turn tactical success into strategic failure — but thinks the problem is under control.

In all efforts, we will exercise force prudently, recognizing that we often need to use a scalpel and not a hammer. When we know that terrorist networks are plotting against us, we have a responsibility to take action to defend ourselves, and we will do so. At the same time, an action that eliminates a single terrorist but causes civilian casualties can in fact inflame local populations and create far more problems. A tactical success but a strategic failure. So we need to ensure that our actions are more precise and more accurate than ever before. This is something that President Obama not only expects but demands.

It’s difficult, if not impossible, to independently verify Brennan’s claims. Anecdotal reporting indicates that the drone program is expanding beyond precisely targeted top extremist leaders to mid-level operatives and below. There’s also a low-level rumbling in intelligence circles that the CIA’s drone strikes cause fewer civilian casualties than those executed by the military, particularly in Afghanistan, and the agency doesn’t like the media conflating two different programs. But any differences in impact on local populations are extraordinarily difficult to verify.

Brennan’s forecast of success against al-Qaeda rested on another foundation: It’s in America’s power to determine how it will react to terrorism. Al-Qaeda’s enduring strategy is to get America to “overextend” itself and compromise its values, thereby weakening the sources of its strength and isolating it internationally, until it retracts its overall global posture. “We must be honest with ourselves,” Brennan warned. “No nation, no matter how powerful, can prevent every attack from coming to fruition.” But just as the U.S. has an obligation to destroy al-Qaeda proactively, he said, it also has a responsibility not to overreact in the event of a successful attack.

“Al-Qaeda can sew explosives into their clothes, and can place explosives in an SUV, but it is our choice how to react,” he said. “They can seek to recruit people already living among us but it is our choice to treat those communities with suspicion or to support those communities.”

I asked Brennan if the Obama administration was counterproductively compromising American values by retaining policies of indefinite suspension without charge at Guantanamo Bay and beyond. “When this administration came in, in January of last year, we dealt with a number of legacy situations that we wanted to make sure we were able to deal with appropriately without compromising the security of the American people,” Brennan said.

I think as everybody recognizes, on both sides of the political spectrum, the situation at Guantanamo is a very, very difficult and challenging one. I think that even as the president said he was determined to close Guantanamo within one year, it still remains open because the president is determined not to do anything that would compromise America’s security. It is something that we are working very closely with the Congress on. We are trying to do things in a very thoughtful manner. We have transferred about 50 of those detainees over the past year and a half, and we’re continuing to look at their situations there. But this is a challenge that we need to look at from a policy perspective, from a legal perspective as well as from a security perspective.

Assistant to the President for Counterterrorism and Homeland Security John Brennan (EPA/ZUMApress.com)

John Brennan has a tough rhetorical job ahead of him Wednesday morning. Speaking to the Center for Strategic and International Studies, Brennan, President Obama’s most influential terrorism and intelligence adviser, will attempt to reconcile the harder edges of Obama’s escalation in Afghanistan and his enthusiastic embrace of drone-enabled assassinations of terrorists with the broader approach to grand strategy that the White House will finally unveil this week. Some wonder if that reconciliation is even possible.

The National Security Strategy will be formally unveiled on Thursday. And Brennan won’t be the only senior official previewing it and amplifying its themes. Secretary of State Hillary Rodham Clinton, just back from a wide-ranging trip to China, will present it to the Brookings Institution. Vice President Biden will do the same on Friday, to the graduating class of Navy midshipmen at Annapolis. Jim Jones, Obama’s national security adviser, has said that the “defining feature of our foreign policy” is that the U.S. is “willing to commit to a new era of engagement based on mutual interests and mutual respect.” He’s finalizing the details of his own National Security Strategy-related speech.

Brennan tried this once before — at CSIS, in fact, last August. But back then, Brennan was more interested in articulating discontinuities with the Bush administration in how Obama handled terrorism, such as eschewing a war-centric construct for viewing the conflict and taking it away from Islam. One senior administration official, Dan Benjamin, the State Department’s counterterrorism chief, has urged an expansion of that critique, arguing last June that U.S. strategy needs to “shift away from a foreign and security policy that makes counterterrorism the prism through which everything is evaluated and decided.” The National Security Strategy is supposed to be that prism, but it remains to be seen how the administration’s counterterrorism efforts can be viewed through it.

Marc Lynch, a professor at George Washington University and a non-resident scholar at the Center for a New American Security, grapples with that reconciliation in a forthcoming paper for the influential think tank, and doesn’t come away with particularly easy answers. “The problem they face is they make a series of pragmatic decisions, each on its own terms, and you can see the logic behind any of them,” Lynch said. “But add it all up, and you see the implementation is clearly at odds with the philosophy.”

All of which are unilateral actions that have met with significant opposition overseas. None easily fit within the framework of “a new era of engagement based on mutual interests and mutual respect.” A senior Republican congressional aide agreed that that framework was the “essence” of Obama’s foreign policy. “There are norms and there are laws and ways of doing things in the world that we in the U.S. have in large part put into place, and sustain,” summarized the aide, who declined to speak for attribution. “Those laws, norms and ideas are above every nation and every nation has a responsibility to uphold them. So we need to do better at meeting our responsibilities and so too, incidentally, does the Iranian government.”

Obama’s approach to Afghanistan might not be such an anomaly, even if the recipient of the Nobel Peace Prize inherited the war he has escalated. That’s because even though Obama has nearly tripled the number of troops in Afghanistan, by July 2011 the so-called “extended surge” will begin to give way to more of a supporting role for U.S. forces. What’s more, as Afghan President Hamid Karzai’s visit to Washington two weeks ago highlighted, Obama has recast relations with both Afghanistan and Pakistan in terms of long-term diplomatic, economic and security cooperation, beyond just counterterrorism. What’s more, not only is military action in Afghanistan a multinational affair operated by NATO and not the U.S. alone, it is specifically legally authorized by the U.N. Security Council. Lynch, a former Obama campaign adviser and a critic of the Afghanistan war, observed, “Afghanistan is a big hole in the strategy in all kinds of ways of ways that matter, but not in a conceptual way.”

Heather Hurlburt, an administration ally at the progressive National Security Network, said that the problem is indicative of an inherent tension between a rules-based international order and the prerogatives of a superpower. “What any administration says is the strategy and what the national-security apparatus does on a day-to-day basis are not necessarily the same thing, especially early on,” Hurlburt observed. The role of a National Security Strategy isn’t necessarily to eliminate those tensions, but rather to bring the military and the intelligence services into rough alignment with the broader vision. “It’s a very powerful signaling mechanism across the government and outside of it, to say ‘We’re serious about this rules-based multilateralism, this human rights stuff, this non-proliferation stuff, and you can’t outlast it.’”

But if the administration keeps granting itself exceptions to following the international order for the exigencies of terrorist emergencies, Lynch said, it will be left without the intellectual underpinnings — and, accordingly, the public support — for an appropriate response if a terrorist attack ultimately succeeds. “What i’m afraid of is that as soon as you get turbulence — like an actual terrorist attack — there’s going to be a big backlash and you can’t hold the overall structure in place,” Lynch said. “Right now, Obama’s got the rhetoric, but they’ve done precious little to institutionalize it and put on durable legal foundations.”

Jeff Stein of The Washington Post wants to dislodge Leiter from that comfort — and, for that matter, his job.

If U.S. intelligence hasn’t completely eluded accountability — and there’s widespread doubt about that — then somebody’s got to take the fall.

Why not start with Leiter?

Hosenball:

The report is based principally on an analysis of online postings of Sada al-Malahim, described as Al Qaeda in the Arabian Peninsula’s (AQAP) online magazine. According to the report, before last October the magazine mainly talked about AQAP’s interest in promoting jihad and subversion in the region where the group is based: Saudi Arabia and Yemen. In an edition posted last Oct. 29, however, the document says, AQAP signaled a shift in its objectives, indicating it had now become interested in “targeting the U.S. homeland.” In the Oct. 29 posting, the intelligence analysis says, an article by one of AQAP’s leaders, Nasser al-Wuhayshi, in what the paper says was an “attempt to appeal to a broader audience” beyond the Arabian subcontinent, sought to encourage readers to launch violent jihad against the West. According to the intelligence paper, Al-Wuhayshi asserted in his posting that little effort and material support would be needed to reach this goal. He suggested that readers should use any means possible to launch attacks, including knives, and to target the “airports of the Western crusader countries … or in their aircraft, residential compounds or in the train tunnels, etc.”

Hey Mark, I see what you did with your headline…

The warning is commensurate with White House counterterrorism chief John Brennan’s January assessment that AQAP has made a strategic decision to strike in the U.S. homeland. And it’s also commensurate with the fear that’s driving administration officials to want to kill Anwar al-Awlaki, the U.S. citizen and Yemen-based extremist preacher.

The opposing argument, made by Rahm Emanuel, is a political one. (And apparently not shared by David Axelrod.) It’s that the trial is a political headache and the cost of closing Guantanamo Bay, another administration priority, is the vote of Sen. Lindsey Graham (R-S.C.) — and the cost of Graham’s vote is to try KSM in a military commission. Graham showed his utility to the administration yesterday, going to bat for Obama’s right to try at least some terrorism detainees in civilian court after his close political allies, Sens. Joe Lieberman (I-Conn.) and John McCain (R-Ariz.), released a bill providing for indefinite detention without trial for terrorism suspects.