On November 18, as the Musharraf régime’s hold on power began to look more tenuous, The New York Times published an article by David Sanger and William Broad on a “secret program” of U.S. nuclear security aid to Pakistan. It was the day’s big story, played above the fold:

Over the past six years, the Bush administration has spent almost $100 million on a highly classified program to help Gen. Pervez Musharraf, Pakistan’s president, secure his country’s nuclear weapons, according to current and former senior administration officials. …

The American program was created after the Sept. 11, 2001, attacks, when the Bush administration debated whether to share with Pakistan one of the crown jewels of American nuclear protection technology, known as “permissive action links,” or PALS, a system used to keep a weapon from detonating without proper codes and authorizations.

The eleventh paragraph held another revelation: The Times had known details of the story for “more than three years,” but had agreed to keep it from readers after the Bush administration argued disclosure would jeopardize the program. The article raises the possibility that the White House’s Pakistan request came before the 2004 presidential election, at the same time as another, more famous hold, also on a sensitive matter of national security: the National Security Agency’s warrantless wiretapping program.

And as with that hold, the Times’s Pakistan decision helped keep a legally controversial initiative and nuclear policy debate from full public light.

As time passed, the decision to keep the hold seems increasingly odd, since the article’s biggest points came out in reports by NBC and in The New Yorker.

In February of 2004, the NBC Nightly News had an “exclusive” on what Tom Brokaw called “an American program to protect Pakistan’s nuclear arsenal.” While the script left out technical language and many details—inevitable in stopwatch-timed broadcast writing—the point was clear. The United States was spending millions, in cooperation with Pakistan, to protect that country’s nuclear weapons. And some of that money, NBC reported, was helping the Pakistanis develop “secret authorization codes”—a vernacular phrase experts would know meant PALs.

Steve Coll wrote about the plan for The New Yorker in February of 2006. While his article stopped short of saying that the Pakistanis had accepted the aid, it described, in about as much detail as the Times would twenty-one months later, the sort of basic dual-use equipment (“Kevlar blankets, high-grade fencing”) being offered, and also described administration struggles over the legality of going further and sharing PALs.

Even after these two pieces—which mostly let the cat out of the bag—the Times stayed quiet. As a result, Times readers missed out on a significant policy and legal debate.

The administration’s internal debate over PALs centered around two questions: Would sharing the technology be a security risk? And would it be in violation of U.S. or international non-proliferation law?

To understand the debate, you need to know something about PALs. Writing on PALs involves some guesswork, but all indications suggest the devices are some combination of advanced cryptography equipment, cleverly assembled and protected so as to avoid tampering. In theory, bombs with PALs won’t cause harm without the right code, and can’t be short-circuited. Experts agree that they have no real use besides the protection of nuclear weapons.

And that’s the tricky fact. Ever since the U.S signed the nuclear non-proliferation treaty in 1968, the government has entered into a complicated series of international obligations that in many cases prohibit the transfer of nuclear knowledge and technology. Some of these obligations are echoed in domestic law.

It’s a complicated legal arena, but there’s one red line. Sharing equipment that has some non-nuclear weapons usage—like radiation detectors or fencing—is often allowed. But sharing equipment that can only be used in weapons is verboten, even if that technology is, like PALs, intended to improve nuclear safety.

On first read, there seem to be shades of disagreement between the reports on what exactly the U.S. decided to do on the PALs question. While Coll and the Times are in agreement that the government concluded that sharing PALs equipment would be legally problematic, the 2004 NBC report said that the that the United States was, in fact, “helping Pakistan develop” PALs.

The Times leaves this possibility open. Without being clear about the time period, or if it is referring to China, Russia, Pakistan, or some other state, the Times reported that officials say the United States “has shared ideas—but not technologies—about how to make the safeguards that lie at the heart of American weapons security.”

There’s linguistic (and perhaps legal) wiggle room between “ideas” and “technologies”, lying in the difference between providing the actual physical devices and providing briefings on their logic and construction.

“I think it’s basically a semantic argument,” says Robert Windrem, who co-wrote a 1994 book on weapons proliferation, and was the NBC producer behind the 2004 report. He says he knew at the time from multiple U.S. and Pakistani sources that the countries had engaged in “table top” discussions on the mechanics and logic behind PALs, and emphasizes that a “a former very high ranking CIA official” confirmed the assistance to him just two days before the Times published.

Windrem says that if a country can build a nuclear weapon, it can easily manufacture PALs. So to him, the distinction between sharing ideas and technology is not significant from a security standpoint. “You always have to be careful with semantics with these guys. What they have to do is get the job done,” he says.

On November 6, a week before the Times story, MSNBC published a web piece by Windrem definitively stating that in 2003, “the U.S. secretly provided technology and training to Pakistani nuclear scientists so they could develop ‘permissive action links.’”

The Times piece is carefully worded, and does not to definitely rule out U.S. participation in such information sharing. But it’s vague enough that one could be excused for thinking it does.

George Bunn, a nuclear law expert who helped draft the non-proliferation treaty (NPT) as the top lawyer at the U.S. Arms Control and Disarmament Agency, says that treaty is unclear on the legality of such assistance. But he thinks the Nuclear Suppliers Group (NSG), a closely aligned multinational body, “would never approve” such nudge-nudge, wink-wink talks, and he’s “reasonably confident” that other strictures in U.S. law and international agreements would also prohibit it.

It’s a complicated area of international law. But if the Times knew that PALs information had been exchanged with Pakistan, as seems likely, that means the paper deprived its readers of a chance to learn about a potential violation—as well intentioned as it may have been—by the Bush Administration of U.S. laws and international nuclear non-proliferation obligations.

Bunn, who began work on nuclear non-proliferation under Kennedy, says that elements of the Bush administration—by loosely interpreting NSG rules, by negotiating an outside framework with India, and working to undermine the comprehensive test ban treaty and international NPT conferences—has been the “worst I’ve ever known” at maintaining the arms control status quo.

“Its not a trivial point, violating the NPT,” says Coll, who’s been reporting on nuclear issues for over a decade. Coll says that some administration officials were worried that if the U.S. was seen to be playing fast and loose with the non-proliferation framework with Pakistan that they’d be deprived of powerful leverage in their nuclear struggle with Iran. “The whole Iranian equation rests on challenging their argument inside this NPT framework,” he says.

Despite repeated CJR requests over the past two weeks, the Times declined to provide a staff member to explain or discuss the hold. In an email, spokesperson Diane McNulty explained that the “editors involved said the discussions were long ago, and hard to separate from other related conversations with the White House.”

That—and the article’s admission that the hold had been honored for “more than three years”—suggest that the request may have come before the 2004 elections, at roughly the same time the Times agreed, at the request of the White House on the grounds of national security, to hold off reporting on the administration’s warrantless domestic wiretapping. The Times waited over a year before publishing that story on December 16, 2005. Editor Bill Keller and Publisher Arthur Sulzberger initially refused to discuss the timing of that story, which came just before the information would appear in a book by James Risen, a co-author of the Pulitzer-winning article, or discuss other aspects of the story with anyone, including the paper’s public editor.

The Times’s explanation for why it finally ran the November 18 Pakistan piece also seems thin. In early November, the Times wrote that the paper let the administration know it was “reopening” its look at the program “in light of” the turmoil in Pakistan, discussions about the program in Pakistani news media, and a vague disclosure in a Pakistani official’s public remarks “late last year.” That last part seems to reference presentations that took place in Washington last October, and is an odd explanation for an action taken more than a year later.

When the Times contacted the White House in early November, the paper reported the administration said it was no longer worried about the story, and the piece ran.

The November 18 article doesn’t give a lot of information on why the paper agreed to stay quiet for three years, except to say that the Bush administration had “argued that premature disclosure could hurt the effort to secure the weapons.”

That makes sense. Ample publicity for the program could have been uncomfortable for Musharraf, who struggles with virulently (and occasionally violent) anti-American domestic opposition.

There are cases where journalists and their editors may be better off keeping some information they uncover to themselves. But those decisions should be tempered with the right of the public to know about relevant policy debates—and potential illegality—before it’s too late to do anything about them.

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Clint Hendler is the managing editor of Mother Jones, and a former deputy editor of CJR.