Most counterterrorism scholars will never meet Ayman al-Zawahiri, the leader of al-Qaida, let alone pray with him. As a teenage extremist, Tawfik Hamid did.

Back when Hamid was a youth in Cairo, studying at a medical school, his religious fervor compelled him to associate with terrorists. "One of the mosques at the school was reserved for Gemaa Islamiyah," Hamid casually explains over a burger in Arlington, Virginia. Before Hamid decided that he'd prefer not to assassinate the police officer that Gemaa Islamiyah wanted him to kill, he shared mosque time on a few more occasions with the man who would succeed Osama bin Laden. Now senior U.S. generals refer to him as a "treasure."

Similarly, most counterterrorism analysts will never interview one of the seminal figures in Islamic extremism. Yet Abu Walid al-Masri, an associate of al-Qaida figures stretching back to the 1980s Afghanistan jihad, eagerly exchanged e-mails with an obscure Australian academic named Leah Farrall. al-Masri didn't grant the interview with a major newspaper or television network. He wanted it posted on her blog.

Hamid and Farrall don't have much in common; he's working on a new translation of the Koran, she's writing essays for Foreign Affairs. But they're united in their rigor, and their structural focus, when it comes to studying terrorism. That puts them – Farrall more than Hamid – in line with a rising group of counterterrorism scholars, many of whom are under 40 and are more likely to debate on Twitter than on the New York Times op-ed page.

"A lot of us have either lived in the region or we've also got at least one of the languages – Arabic, French, which helps [study] North Africa, and many of us come from a non-political science or terrorism studies or security studies background," explains Aaron Zelin, a Brandeis graduate now at the Washington Institute for Near East Policy. "Many of us either did history or did area studies in the Middle East or Islam in terms of our actual academic background.... We understand it's not just 'This is Islam'; we've studied what Islam actually is."

Leah Farrall lectures at the University of Sydney's 9/11 symposium, June 2011. Photo: University of Sydney Leah Farrall lectures at the University of Sydney's 9/11 symposium, June 2011. Photo: University of Sydney

There is a competing school of thought, one with more purchase in official Washington. It holds that the problem of terrorism is actually the problem of Islam. As a Danger Room series has explored, adherents of that viewpoint have instructed counterterrorism professionals within the FBI, the Justice Department and the military. Last week, a military college run by the Joint Chiefs of Staff removed an Army lieutenant colonel who taught senior officers that the United States ought to attack Muslim civilians.

That approach is the polar opposite of the perspective taken by this rising crowd of scholars. While the FBI's William Gawthrop, the Army's Lt. Col. Matthew Dooley and the freelance consultant Stephen Coughlin lay the blame for terrorism at the feet of Islam itself, this new crowd goes granular, studying minute distinctions between different terrorist groups and movements, or among individual terrorists within the same organization. Some are tied to the Combatting Terrorism Center at West Point, which the FBI enlisted for help ridding its training of anti-Islam bias. They consider terrorism a perversion of Islam, not a consequence of it.

But these scholars don't have the same influence – yet. They're just beginning to consult for government agencies. Some, like Farrall, prefer not to, as she's leery of compromising her scholarship by getting it into the policy realm. None of them are easily classifiable into the partisan research tribes that masquerade as scholarship in institutional Washington, where the mark of intellectual merit is how politically salient a study is. Daveed Gartenstein-Ross, for instance, works for the conservative Foundation for the Defense of Democracies, but he's anything but a reliable Republican.

"As time goes on," Zelin says, "you'll see more and more individuals like ourselves doing more training sessions, or filling positions in an administration." But as the Obama administration seeks to wind down the post-9/11 wars and keep them out of sight, they may be too young and too late for their own good.

Any administration looking to hire them will have a long online record to wade through. Many of their debates occur on blogs like Zelin's Jihadology, Will McCants' Jihadica and Farrall's website, which was called All Things Counterterrorism until she renamed it in protest of "violation[s] of universal human rights and democratic principles" that she argues pass for counterterrorism. Even more occur on Twitter, sometimes as light-hearted, bravado-filled fights in full view of the professional communities they seek to join. "Twitter Fight Club is a great example," Farrall says, referring to a goofy March Madness-style competition in which bloggers, scholars and journalists fake-battle each other through "twisticuffs." (Full disclosure: I made the Final Four in 2011; this year, I didn't even crack the Elite Eight.)

But re-tweets aren't endorsements. When a U.S. drone strike killed al-Qaida second-in-command Abu Yahya al-Libi, Farrall, now a research associate at the University of Sydney's United States Studies Centre, feared that the United States had inadvertently taken a moderating figure off the board. McCants – a former State Department consultant and reigning Twitter Fight Club champion – challenged her through his @will_mccants account. They began a days-long colloquy drawing out exceedingly precise distinctions, based on publicly available if obscure information, to isolate precisely what it meant to think of al-Libi as a "moderate" or if Farrall's assessment was valid. When the Twitter back-and-forth failed to yield a consensus, McCants blogged another 1,100 words about why Farrall was wrong.

That exchanged was a microcosm of how this cohort of counterterrorism scholars operates. They go into exacting detail about the extremist movements they study. They draw accordingly fine distinctions. And they do it online.

Muslims protest the 2008 Mumbai terrorist bombings. A rising group of counterterrorism scholars draws rigorous distinctions between varieties of extremism and the average Muslim. Photo: Flickr/ Anuradha Sengupta Muslims protest the 2008 Mumbai terrorist bombings. A rising group of counterterrorism scholars draws rigorous distinctions between varieties of extremism and the average Muslim. Photo: Flickr/ Anuradha Sengupta

Hamid is somewhat different. You won't find him getting into Twitter debates. He's older and more established, ensconced at the Potomac Institute for Policy Studies and occasionally consulting for federal law enforcement and intelligence agencies. Hamid's view is that Islam isn't responsible for terrorism, but he frets that the way Islam is "taught today in most communities is perverted and destructive," he wrote in a 2008 book, Inside Jihad. He's caused confusion on that point, however, by saying in a radio interview that "the majority of Muslims are passive terrorists."

Expressing views like that got him invitations from U.S. organizations – which he declines to name – that he later came to see as harboring a "bias" against Islam, something that chagrins him as a Muslim. Asked about the "passive terrorist" quote, he backs away from it as inelegantly expressing a frustration with what he thought was a "passive attitude" in the Muslim world about terrorism, something he now feels has been overtaken by a more assertive, outspoken Muslim attitude against it.

In an interview, Hamid draws far more exacting distinctions when discussing radical Islam and terrorism than he did in his book, speaking of "concentric circles" of extremism that distinguish at several different levels between al-Qaida and even those who might espouse similarly intolerant views – let alone everyday Muslims. He learned for himself about those distinctions when he and his educated peers got swept up in radical enthusiasm in Egypt after the Soviets invaded Afghanistan, but balked after Gemaa Islamiyah told him to shoot a police officer.

Hamid has big backers within the U.S. military. "I have known Dr. Tawfik Hamid about two years. He is a great scholar whose knowledge of terrorism is extremely valuable," ret. Army Lt. Gen. Mick Kicklighter, the former Pentagon inspector general, tells Danger Room. "There is no doubt about his first-hand experience and depth of knowledge. He is truly a treasure."

Hamid says his next project is designed to keep young Muslims who might be misled by extremist preachers from going down a similar path. It's a "new translation of the Koran, a modern one" that intends to reclaim verses often cited by those extremists.

"You see this verse, 'Kill the infidels wherever you find them,'" Hamid explains. "Is it generalizable to every infidel, or is it only specific to some group of people who fought Muhammad at the early stage of Islam? Based on the [Arabic] suffix, you can the meaning only to this stage in human history. Then I ask: Why was the Koran against them? Because according to the Koran, they discriminated against the [Islamic] believers, they tortured them, and they burned some of them alive. What is the common theme of those infidels? Discrimination against a small religious minority. So what we should learn from this is not to discriminate against small religious minorities or against dissenting views, otherwise we'll be like those infidels."

It's an open question whether Hamid's version of the Koran will catch on, since he's not a theologian. Another open question is whether any of these newer counterterrorism scholars will go from Twitter personalities to senior government officials. It may simply be too late.

The decade after 9/11 was a boom time for counterterrorism scholars and pseudo-scholars alike. Since so few inside the government and the media had studied al-Qaida, both institutions tended to latch on to whomever passed themselves off as an expert, especially as the wars in Iraq and Afghanistan ground on. But now the Iraq war is done and the Afghanistan war is fading away. Their successors, the "shadow wars" fought with drones and commando forces, are seemingly enduring, but don't lend themselves to similar public scrutiny. Government officials confidently predict that al-Qaida itself will soon be a spent force, and much of their time and emphasis is shifting to Asia policy. What's a terrorism scholar to do?

Zelin, who was only 15 years old on 9/11, has an answer.

"There's definitely an issue with getting funding to do this kind of work," he says. "But the thing that people have to remember is that, while of course Asia's important, as is the rise of China and helping our allies there, we're still very much tied and embroiled in the issues of the Middle East, even if we don't want it to be that way. We've got military personnel in Yemen, everything that's going on in Syria [looks like] the more things go on the more we'll be pushed in, Israel and Palestine.... I don't think it's going to necessarily go away because of the way things are going in the Middle East and how there's upheaval. It's going to be a long process for the region to get out of what it's going through – a decade, two decades, three decades."

Update, 1:45 p.m.: It appears I misremembered my 2011 Twitter Fight Club performance. I didn't make it to the Finals. I was bested in the Final Four by my friend Jeremy Scahill of The Nation, as Daveed Gartenstein-Ross is delighting to remind me on Twitter by using the hashtag #StolenTFCValor. I regret my error.