So now, Bush looked into the camera and spoke solemnly: “Good evening. I appreciate you giving me a few minutes of your time tonight so I can discuss with you a complex and difficult issue, an issue that is one of the most profound of our time.”

That issue was stem cell research.

Two-and-a-half years later, as Bush’s national security advisor Condoleezza Rice appears before the 9/11 commission, she is being questioned about whether the White House could have acted on the terrorist threat more decisively. But perhaps the most intriguing and least discussed what-if is this: What if, during the first eight months of the Bush administration, the president had showered terrorism with as much personal time and attention as he did stem cell research?

“In hindsight knowing now what we should’ve known then, the importance of terrorism and national security certainly should have bypassed any huge focus on stem cell research,” says Monica Gabrielle, whose husband was killed in the World Trade Center attacks. “The contrast is astounding,” she says.

In the wake of 9/11 and the war in Iraq it’s hard to remember that the summer of 2001 for the White House was the summer of stem cell research. It was a time when this relatively obscure issue dear to the hearts of Bush’s Christian conservative political base rose to dominate the administration’s agenda and, according to his aides, certainly the president’s time and attention. In fact, aides went out of their way to portray the president as “obsessed” and “consumed” about the issue, soaking up any scrap of information he could. According to Bush’s own Aug. 9 address, he had consulted “scientists, scholars, bioethicists, religious leaders, doctors, researchers, members of Congress, my Cabinet, and my friends.”

That White House talking point was distributed everywhere. USA Today reported, “Bush agonized in public, surprised guests at social gatherings by soliciting their views, debated the issue with advisers, listened to passionate advocates on all sides, read everything that landed on his desk on the topic. And he prayed.” Bush’s senior political advisor, Karl Rove, told members of Congress that the president believed his stem cell research decision was “no less important than a decision to commit troops to war.”

During the summer of 2001 the press’s portrayal of Bush “agonizing” over the intricacies of scientific research served the White House’s purpose of establishing the new president as intellectually curious, thoughtful about policy and in control. In retrospect, the idyllic picture of a president “consumed” with stem cell research, of buttonholing all sorts of experts to draw out their opinions, while showing little or no curiosity about al-Qaida, is not a White House talking point.

“Is it too bold to suggest the Bush administration was distracted by domestic politics during the summer of 2001?” asks Matthew Nisbet, an assistant communications professor at Ohio State University who studies the stem cell debate. “What the Bush White House did was to take a minor issue, administratively, and make it into a major political one that captured a lot of time and attention during the summer of 2001. And it didn’t necessarily have to be that way. Nobody could have predicted that Bush’s first nationally televised address to the country would be about stem cell research.”

For months prior to 9/11, Bush’s counterterrorism chief could not get a meeting scheduled to brief the president about the mounting al-Qaida threat, despite the fact that, according to the one 9/11 commissioner who’s had full access to the library of 2001 intelligence briefings, the growing terrorism warnings “would set your hair on fire.” According to a 9/11 commission staff report, during those very same three months in 2001, the National Security Agency, which eavesdrops on communications around the world, reported 33 messages suggesting “a possibly imminent terrorist attack.”

Yet during the summer of 2001, Bush’s aides painted an image of an Oval Office bursting with outside experts queued up to discuss stem cells face-to-face with Bush in a process that seemed to stretch for weeks at a time.

“He, during the months of May, June and July, frequently asked people, even in the context of completely different meetings, about stem cell research and about their opinions,” Karen Hughes, Bush’s then-top communications aide, told the New York Times in an Aug. 11, 2001 article. Not even Hughes, who has just published a new book, “Ten Minutes from Normal,” and has been making the media rounds adamantly defending Bush’s handling of terrorism, has suggested that during the months of May, June, July and August 2001, Bush was distracted from his stem cell “obsession” by al-Qaida.

In the August 2001 Times article, Hughes read back her notes to Times reporters from one of three separate July 9 Oval Office meetings Bush had that day regarding stem cell research: “I must confess I am wrestling with a difficult decision,” Bush told an invited doctor. To date, neither Hughes nor anyone else in the White House has produced any notes from a 2001 meeting in which Bush expressed to outside experts how he was agonizing over terrorism threats.

Even Rice, Bush’s national security advisor, was drawn into the administration-wide debate over stem cells that summer. Scientists at Stanford University, where Rice once served as provost, contacted her and asked her to intervene on behalf of unrestricted scientific research. But she refused.

The issue surrounding embryo stem cell research came to the forefront because President Clinton permitted federally funded medical researchers to perform research using stem cells as long as they did not destroy the embryos themselves. Clinton argued the cell lines did not fall under a law passed by Congress prohibiting government funding of research that would harm or destroy embryos. The Department of Health and Human Services ruled that cells were not themselves embryos and therefore the National Institutes of Health could fund grants involving their use.

During the campaign, Bush said he would overturn Clinton’s decision, saying he opposed federal funding for research. In office just one week, after an early antiabortion initiative which included a ban on foreign aid to overseas family planning groups that used their own funds to support abortion, and his promise to review federal approval of the RU-486 abortion pill, Bush indicated he would not support any funding of research involving human embryos. Many observers thought the final decision would simply be handled through a statement from the Department of Health and Human Services. But when Bush’s own HHS secretary, Tommy Thompson, as well as prominent, conservative members of Congress came out in support of continuing the federally funded research, arguing it could hold key medical breakthroughs for juvenile diabetes, Alzheimer’s and Parkinson’s diseases, Bush’s decision became more politically difficult.

“The one thing we saw in Bush’s first months in office was he was consumed with the agenda of his base: tax cuts, missiles defense and critical social issues that energized the religious constituencies,” says Thomas Mann, political analyst at the Brookings Institution.

After months of deliberation, Bush decided that he would not permit federal money to be used for research on new lines of stem cells, but would allow it for existing lines. He insisted 60 such existing lines were available to researchers.

The final decision, spun as a compromise, upset some stalwart antiabortion activists. But for the most part Bush’s move pleased his political base. Focus on the Family president Dr. James Dobson praised the president, insisting he had “courageously upheld his promise to protect unborn children.” The Revs. Jerry Falwell and Pat Robertson also heaped praise on Bush.

Over time, Bush’s assertion regarding the 60 stem cell lines has proven to be untrue. The Council on Bioethics, created by Bush himself, reported that by September of 2003, just 12 eligible stem lines — not 60 — were available to federally funded researchers.

“They were trying hard to thread a very small needle and they did it the way they often do such things,” says David Seldin, communications director for National Abortion and Reproductive Rights Action League. “They made something up.”

With his first televised speech to the nation on an urgent issue, Bush successfully established an image, constructed by the White House and broadcast by the media, of a president who had thought long and hard about a significant matter, been deeply involved in the making of policy, consulted far and wide, and achieved a savvy political position that was popular with public opinion. After his Aug. 9 speech, Bush spent the rest of the month at his Crawford ranch, not returning to the White House until Aug. 31.

No one, except for the president and his national security team, knew of the al-Qaida threat warnings they were receiving.

Apologists for the tarnished military commissions, like Attorney General Eric Holder and the sixth and current chief prosecutor Brigadier General Mark Martins, acknowledge that our regular federal courts are best suited for terrorism trials. Holder told an audience at Northwestern University in March:

Simply put, since 9/11, hundreds of individuals have been convicted of terrorism or terrorism-related offenses in Article III courts and are now serving long sentences in federal prison.  Not one has ever escaped custody.  No judicial district has suffered any kind of retaliatory attack. These are facts, not opinions.  There are not two sides to this story. Those who claim that our federal courts are incapable of handling terrorism cases are not registering a dissenting opinion – they are simply wrong.

After singing the praises of the federal courts – which really have been swift, severe and successful in comparison to the six and-a-half dubious trials completed over the past decade at Guantanamo – Martins and Holder pivot to polishing the image of the tarnished military commissions they argue are well-suited for a small category of cases. Martins told an audience at Harvard in April:

It is perfectly reasonable to ask why – with concurrent jurisdiction over offenses that can be characterized as both federal civilian crimes and violations of the law of war and with comparable procedural protections – we should invest great energy and resources in military trials. The answer is that there is a narrow but important category of cases in which the pragmatic and principled choice among the lawful tools available to protect our people and serve the interests of justice is a reformed military commission.

Beltway bureaucrats are prone to using buzzwords to shade the truth. For example, rather than saying “yes, it makes us look bad when we lock people away in prison for a decade without a trial,” some might soften it up by using more subtle Beltway language: “The optics are not optimal.”  The word “pragmatic” has become a favorite of the spinmeisters. In truth, being pragmatic has become a synonym for being a wuss. When a bureaucrat capitulates instead of confronting barriers standing in the way of doing the right thing, and then cites the barriers as an excuse for choosing the easier path, he is lauded for making the “pragmatic choice.” Others might say he simply wussed out. President Obama has been “pragmatic” far too often on national security choices in his first three years in office.

There is nothing pragmatic or principled about undermining America’s reputation as a champion of the rule of law and a supposed model for the world to follow. The apologists for Obama’s decision to embrace military commissions call attention to similarities between the commission rules and the rules in federal courts, and they claim those rules are essentially the same. They argue that the two systems are virtually identical and that trial observers will find trials in the two forums nearly indistinguishable. In some things, however, close is just not good enough. An O’Doul’s looks like a beer and has a beer-like flavor, but a real beer drinker would never argue that an O’Doul’s is virtually indistinguishable from a Sam Adams. Just as a near-beer is not practically the same as a real beer, neither is near-justice the equivalent of real justice. The apologists may think they are fooling the rest of the world when they say at long last military commissions do real justice, but they are wrong.

Holder and Martins justify the need for a second-rate military commission system by talking up the alleged realities of the battlefield that they say make it impracticable for troops to worry about doing rights advisements and establishing a chain of custody for evidence while in the midst of a war. Their general principle is entirely valid … but also totally irrelevant in the cases they intend to prosecute before military commissions. Few of the 779 men ever held at Guantanamo were captured by members of the U.S. armed forces and even fewer still were apprehended on the battlefield as that term is commonly understood by ordinary human beings. Khalid Sheikh Mohammed, for instance, was rousted from a sound sleep and arrested in Rawalpindi, Pakistan, by the Pakistani Inter-Services Intelligence Directorate based on information developed by our civilian Central Intelligence Agency. Abd al Rahim al Nashiri, the alleged USS Cole bomber, was apprehended in Dubai, a bustling global business center in the United Arab Emirates that no one considers a battlefield. Hambali was arrested near Bangkok, Thailand, by Thai authorities and later turned over to the CIA. The truth is that not a single one of the 14 so-called high-value detainees was captured by members of the U.S. armed forces on a battlefield; in fact, none were even apprehended in Afghanistan. The perception of some inexperienced 19-year-old Army private trying to read Miranda rights to a captured al Qaeda fighter while hunkered down in a foxhole with bombs exploding nearby and bullets whizzing past overhead is a canard.

Military commission apologists should have the integrity to stand up and tell the public the truth about the small category of cases they believe are best-suited for the second-rate procedures of the tarnished military commissions. The truth is the reason the apologists want a second-rate military commission option is because of what we did to the detainees, not because of what the detainees did to us. This is not about the exigencies of the battlefield and the problems our soldiers face trying to fight a war; this is about torture, coercion, rendition and a decade or more in confinement without an opportunity to confront the evidence – abuses that would have us up in arms if done to an American citizen by some other country – that make the tarnished military commissions uniquely suited to try and accommodate the small category of cases where we crossed over to the dark side. A military commission may be a justice-themed theatrical production – complete with a script, actors, a sound stage and costumes that create a passable courtroom-like atmosphere – but beneath that facade is a ‘heads we win, tails you lose’ charade where, as the government admits, even if a KSM or a Nashiri is found not guilty he returns to a cell to continue serving what is likely a life sentence. That should not inspire anyone to wave the flag and shout USA! USA! in celebration of our vaunted exceptionalism.

Lloyd Cutler was the youngest member of the prosecution team in the trial of eight Nazi saboteurs captured, convicted by a military commission and executed in a span of six weeks in the summer of 1942. He wrote an op-ed in the Wall Street Journal on December 31, 2001, nearly 60 years after his military commission experience ended and 10 days before the first detainees arrived at Guantanamo Bay. Mr. Cutler said that how we prosecute alleged al Qaeda terrorists will say as much about us as it does about al Qaeda. He warned that success will be judged by our ability to show the world that justice is in fact being done.

Had we heeded Mr. Cutler’s advice back in 2001 we would not be where we are now in 2012, fumbling along more than a decade later still trying to mold a second-rate process to fit around sets of bad facts we created when we turned our backs on the law and our values.  In normal practice, cases are developed to conform to the court. Here, because of how we mistreated some of the detainees, we are trying to develop a court to conform to the cases. We are setting an example for the world, but not a good one.

Some similar exemption must also be made for the Canadian citizen Omar Khadr, who was 15 years old when he was found, badly injured and barely alive, after a 2002 firefight between U.S. troops and Taliban forces in Afghanistan. (Khadr’s father, an al-Qaida supporter and fundraiser, had apparently dropped him off at a Taliban compound a few weeks earlier.) Based on what we see in the painful, revealing documentary “You Don’t Like the Truth: 4 Days Inside Guantánamo” — the first film to show actual interrogation footage from inside the secret American military prison at Guantánamo Bay, Cuba — Khadr became a sort of ritual sacrifice by the Canadian government, an offering to its American allies and/or overlords. His case became a hot political issue north of the border, where Canadians pride themselves on a society that is more egalitarian, and more civilized, than that of their American neighbors.

Following a Canadian Supreme Court decision, most of Khadr’s seven-hour interrogation at Gitmo by CSIS officers — the approximate Canadian equivalent of the CIA — has been declassified, and veteran lefty documentarians Luc Côté and Patricio Henríquez use that claustrophobic, low-resolution 2003 footage as the basis for “You Don’t Like the Truth.” That sounds like something the interrogators might have said to Khadr, but it isn’t. It’s what he tells them after realizing they don’t want to hear his allegations that he was tortured by American forces, and that all his supposed confessions about knowing Osama bin Laden and attending al-Qaida barbecues were made up on the spot, to stop the pain.

You won’t see Khadr suffer physical torture on these surveillance tapes, although the interrogators rely on time-honored tactics of psychological abuse, alternately berating him and plying him with Big Macs. You will see a teenager who speaks idiomatic North American English, and who is obviously relieved to see fellow Canadians, whom he naively assumes have come to help him. And you’ll see him go through a near-total breakdown, sitting alone in the room weeping for his mother, after he realizes that no one cares about what happens to him and that he’s only interesting to his interrogators as long as he keeps making up stories about Osama and al-Qaida.

I have no idea whether Khadr actually threw a grenade that killed a U.S. Delta Force soldier, as was alleged after his capture. (Khadr has consistently denied it, and photographic evidence suggests that he had been shot through the back and was out cold before the soldier’s death.) But the Canadian interrogators barely mention it, and it feels suspiciously like an inflammatory distraction, thrown in mostly to alienate all possible North American sympathy. At best it’s an ancillary question. If Khadr was a genuine military combatant, then he can’t be prosecuted for killing an enemy soldier in battle. Furthermore, he would have to be considered a child soldier under international law, which theoretically immunizes him even for war crimes. Convicting him on such charges, as the government eventually did in a secret court on secret evidence, required the finding that he wasn’t a soldier but a civilian terrorist (even though he was supposedly linked to two organizations, al-Qaida and the Taliban, with whom the U.S. government has repeatedly said it’s at war).

Côté and Henríquez intersperse brief and highly effective interview segments between snippets of the interrogation tape, with subjects ranging from former U.S. military officers (including Khadr’s lawyer and psychiatrist) to former Guantánamo inmates (including Moazzam Begg, now a leading British activist for other detainees) to Khadr’s mother and sister (wearing full-face Islamic veils) to Damien Corsetti, the much-demonized former soldier who knew Khadr as a guard at Bagram. What comes through repeatedly is that questions of law and reason, or guilt and innocence, played no role in the case of Omar Khadr. He was a vulnerable and confused kid whose own government turned its back on him, which made him a perfect candidate to become one of the few Gitmo detainees convicted of something. He was 15 when he was captured, and will be 31 when he (supposedly) gets out.

“You Don’t Like the Truth: 4 Days Inside Guantánamo” is now playing at Film Forum in New York, with more cities and dates to follow.

He was apparently killed by a CIA drone strike in Pakistan’s lawless tribal areas, though officials would not describe the method since the program is classified. A drone strike was reported by locals on Sunday night.

The officials say al-Shahri worked closely with the Pakistani Taliban to carry out attacks inside Pakistan, and was also a contender to assume some duties of al-Qaida’s second in command, Atiyah Abd al-Rahman. Al-Rahman was killed by a CIA drone strike in late August.

U.S. officials believe they can cripple the core al-Qaida organization if they take out the top four or five figures, following the killing in May of al-Qaida chief Osama by Laden by Navy SEALs. Eight of the network’s top 20 leaders were killed this year alone, according to the Pentagon’s undersecretary for defense intelligence, Michael Vickers, in remarks this week. Vickers predicted that with sustained counterterrorist operations, “within 18-24 months, core al-Qaida’s cohesion and operational capabilities could be degraded to the point that the group could fragment and exist mostly as a propaganda arm.”

But Vickers and CIA director David Petraeus said al-Qaida’s offshoots will remain a serious threat to the U.S.

A Pakistani intelligence official says Pakistani operations chief al-Shahri was a Saudi national, who had lived in the tribal regions of Pakistan, bordering eastern Afghanistan, since 2002.

One of the U.S. officials said the same individual is No. 11 on Saudi Arabia’s top-85 most wanted terror suspects, where his full name is listed as Osama Hamoud Gharman Al-Shihri. The official said the same person is No. 68 on Interpol’s most wanted list, where his name was spelled “Al-Shehri” and his birthdate was listed as Sept. 17, 1981.

Al-Shahri engaged in liaison mainly with Pakistan’s Tehrik-e Taliban Pakistan to conduct coordinated attacks against targets inside Pakistan, one of the U.S. officials said. But al-Qaida also inspired the Pakistani Taliban to undertake its first known overseas attack, when a U.S. based operative tried and failed to detonate a car bomb in Times Square last year.

Al-Shahri’s killing was first reported by NBC News.

Al-Qaida’s senior planner of global terror operations, Adnan Shukrijumah, remains at large.

AP writer Matt Apuzzo contributed from Washington, and AP writer Riaz Khan contributed to this story from Peshawar.

David S. Cohen, Treasury’s point man for terrorism and financial intelligence, said Iran entered a “secret deal with al-Qaida allowing it to funnel funds and operatives through its territory.” He didn’t provide any details of that agreement, but said the sanctions seek to disrupt al-Qaida’s work in Iraq and deny the terrorist group’s leadership much-needed support.

“Iran is the leading state sponsor of terrorism in the world today,” Cohen said in a statement. “We are illuminating yet another aspect of Iran’s unmatched support for terrorism.”

Treasury said the exposure of the clandestine agreement would disrupt al-Qaida operations by shedding light on Iran’s role as a “critical transit point” for money and extremists reaching Pakistan and Afghanistan.

“This network serves as the core pipeline through which al-Qaida moves money, facilitators and operatives from across the Middle East to South Asia,” it said..

Treasury said a branch headed by Ezedin Abdel Aziz Khalil was operating in Iran with the Tehran government’s blessing, funneling funds collected from across the Arab world to al-Qaida’s senior leaders in Pakistan. Khalil, the department said, has operated within Iran’s borders for six years.

Also targeted by the sanctions is Atiyah Abd al-Rahman, appointed by Osama bin Laden as al-Qaida’s envoy in Iran after serving as a commander in Pakistan’s tribal areas. As an emissary, al-Rahman is allowed to travel in and out of Iran with the permission of government officials, the statement claimed.

The sanctions block any assets the individuals might have held in the United States, and bans Americans from doing any business with them.

No Iranian officials were cited for complicity in terrorism. The others targeted were Umid Muhammadi, described as a key planner for al-Qaida in Iraq’s attacks; Salim Hasan Khalifa Rashid al-Kuwari and Abdallah Ghanim Mafuz Muslim al-Khawar, Qatar-based financial supporters who’ve allegedly helped extremists travel across the region; and Ali Hassan Ali al-Ajmi, a Kuwait-based fundraiser for al-Qaida and the Taliban.

The action comes a day after the top U.S. commander for special operations forces said al-Qaida is bloodied and “nearing its end,” even as he warned that the next generation of militants could keep special operations fighting for a decade to come.

Navy SEAL Adm. Eric T. Olson said bin Laden’s killing on May 2 was a near-fatal blow for the organization created by bin Laden and led from his Pakistan hide out. He said the group already had lost steam because of the revolts of the Arab Spring, which proved the Muslim world did not need terrorism to bring down governments, from Tunisia to Egypt.

Treasury’s public allegations against Iran may reflect part of a strategy to expand the pressure on smaller, less well-established offshoots of al-Qaida as the weakening of the group’s leadership threatens to make its activities more disparate. Washington already has re-focused much attention on al-Qaida’s Yemen-based branch, which has attempted to bomb a U.S.-bound jetliner and cargo planes in recent years.

But the exact nature of Iran’s relationship with al-Qaida remains disputed in Washington, with different branches of the intelligence community disagreeing about whether Iran is supporting al-Qaida as a matter of policy, according to one U.S. official. The official spoke on condition of anonymity to discuss intelligence matters.

Some hardline militants backing al-Qaida, members of Islam’s majority Sunnis, see the Shiite Islam dominant in Iran as heretical, and they view Tehran’s regional ambitions as a greater threat than the West. Sunni insurgents in Iraq have used car bombs and suicide attacks against Shiite targets, killing thousands since 2003, as well as targeting Shiite militias allied to Iran.

Since 2001, Iran has appeared a somewhat reluctant host for senior al-Qaida operatives who fled there after the U.S. invasion of Afghanistan, keeping them under tight restrictions. After an initial period of cooperation with the West, Iran now seems to be a more comfortable haven even if it remains on the edge of al-Qaida’s orbit.

Western officials point to the release earlier this year of an Iranian diplomat who was held for 15 months after being kidnapped by gunmen in Pakistan.

In negotiations for the diplomat’s freedom, they say Iran promised better conditions for dozens of people close to Osama bin Laden who were being held under tight security. These included some of the terror chief’s children and the network’s most senior military strategist, Saif al-Adel.

Still, the life of the al-Qaida-linked exiles in Iran continues to be very much a blind spot for Western intelligence agencies. Few firm details have emerged, such as how much Iran limits their movements and contacts.

Last week the officials were talking to the Wall Street Journal. They told the paper that Al-Qaida would likely be shifting the focus of its attacks to Western targets outside of the United States. They said this was because it had become too difficult for them to strike inside the United States.

The Wall Street Journal said the U.S. officials had come to this conclusion based on evidence gleaned from flash drives found in the compound where bin Laden was killed. Much of the information we are learning about bin Laden and Al-Qaida, in fact, is said (by U.S. officials) to be coming from those flash disks, as well as a computer.

It was from the computer, for instance, that U.S. officials learned that bin Laden liked porn. Everyone ran with that story. It was great story. Not only was it sure to drive traffic, combining two of the most searched items on the internet these days (porn and bin Laden), but it also tweaks the legacy of a man who claimed that a strict adherence to Islam is what guided him in his global campaign of terror.

It is reminiscent of the news, also released by U.S. officials, immediately following the raid that led to bin Laden’s death that, in a vain attempt to protect himself, bin Laden used his wife as a human shield. Not so heroic. That detail turned out to be false. As was news that bin Laden was armed.

The news that bin Laden liked porn also came from U.S. officials. They leaked it anonymously to Reuters and then everyone else reported the Reuters report (including GlobalPost). In fact, all the details about the raid, what transpired and what was found after, has come from U.S. officials.

The New York Times reported on May 6 that the details surrounding the raid and the discoveries that followed have been fluid in their accuracy. It partly blamed a ravenous media, itself included. But it also blamed a desire by the United States to spin facts in order to diminish bin Laden’s legacy.

Was the revelation that bin Laden liked porn part of that spin? What about everything else we are learning from U.S. officials? Is that spin too?

If it’s not spin, all the reports surely play into the hands of the U.S. government. Not only did the Wall Street Journal story infer that our defense measures are working but it justified our continued pursuit of Al-Qaida militants all over the world, both through the war in Afghanistan and the ramping up of drone attacks in Yemen and Somalia.

The Washington Post story, meanwhile, suggests that we have been successful in Pakistan, where drone strikes have been plentiful, but Al-Qaida remained strong in Yemen, where the U.S. plans to increase its use of unmanned drones.

Other things we learned recently about bin Laden: He was planning an attack on the 10-year anniversary of Sept. 11, he had a “direct” role in the planning of the July 7 bombings in London, a belief that runs counter to previous reports, and he was actively planning any number of other attacks as well — all according to “U.S. officials.”

If you say so.