ANDREA SEABROOK, host:

This is ALL THINGS CONSIDERED from NPR News. I'm Andrea Seabrook.

The political turmoil in Pakistan is riveting the world's attention not just because Pakistani President Pervez Musharraf has been an ally in the U.S. war on Islamist militants, it's also a great source of concern because Pakistan has nuclear weapons that could potentially fall into the wrong hands.

Today, the New York Times reports that the U.S. has been secretly helping Pakistan safeguard its nuclear arsenal. One of the reporters on that story is David Sanger and he joins me now.

David Sanger, how exactly has the U.S. helped Pakistan guard its nuclear arms?

Mr. DAVID SANGER (Reporter, New York Times): Whether the U.S. has been quite limited in what it has been allowed to go do with the Pakistanis, partly because of legal restrictions at our end and partly because of Pakistan's own hesitance to let us know where or even how many nuclear weapons they have or let us get in to their nuclear laboratories.

So most of the $100 million program that we wrote about on the Sunday paper concerns helping the Pakistanis learn how to fence off and separated much of their nuclear material to psychological profiling for the workers who is working on them. Presumably, there is some testing of their political loyalties as well but we don't know that for a fact. Helping them with helicopters, night vision goggles, all kinds of things that they might need to repel a terror attack against either the arsenal or one of the laboratories.

SEABROOK: It's the Nuclear Non-Proliferation Treaty that prohibits countries from sharing actual nuclear technology and it's that that the U.S. is trying to work around, isn't that right?

Mr. SANGER: That's right. Pakistan is one of the three countries that never signed the Nuclear Non-Proliferation Treaty - the other two are India and Israel, and North Korea pulled out of the treaty. So when you have a country that's not a signatory, it becomes more difficult to deal with them. And then we have all kinds of legislation in the United States putting prohibitions on cooperation with the countries that don't sign the NPT.

But even if we offered the Pakistanis the crown jewels of our security system -which is something called PAL, the permissive action link system, which is the series of codes that would be needed to authorize use of a warhead and so forth - it's doubtful that the Pakistanis would even accept it, because they're quite concerned that we would slip in a kill switch that would enable us enable us to turn off their nuclear weapons.

SEABROOK: I thought this was actually one of the most fascinating parts of your story - was about how the U.S. has developed this technology that would allow officials to keep some amount of control, at least kill a weapon's functionality if the weapon were to fall into the wrong hands.

Mr. SANGER: That's right and that's helpful if the terrorists grabbed an actual weapon. I think that the weapon side of the Pakistani arsenal people believe are pretty well-protected. What worries them the most are the labs including the famous Khan nuclear laboratory - named for A. Q. Khan, who was one of the fathers of the Pakistani bomb, but then went off to build the world's greatest proliferation network. He's now under house arrest in Pakistan and has been since 2004.

But it was the laboratories which he ran that were the source of the great proliferation. And so laboratories today that still produce highly enriched uranium. And if you're a terrorist, it's probably easier to try to get a portion of the AGU or other technology out of those labs than it is to actually steal a weapon.

SEABROOK: David Sanger, why is this hundred million dollar appropriation been buried in, you know, secret classified portions of the federal budget? The money spent to secure Russian nuclear weapons after the Soviet Union collapse was public.

Mr. SANGER: In the case of Pakistan, the American concern was that the Pakistan's president, President Musharraf, would be accused by his enemies -including some of the terror groups - of letting the United States get its hands on Pakistan's most valuable asset, its weapons.

And only recently, as details of the program have come out and as the Pakistanis have begun to discuss a little bit about their program to allay fears in Pakistan that it could be vulnerable. That began to breakdown and eventually, we went back from the administration and said, look, we're talking about it in Pakistan, there's no reason not to talk about it here.

SEABROOK: Yeah. The Bush administration asked you not to publish the story for three years.

Mr. SANGER: That's right. As you know, it's quite rare that the New York Times will hold the story out of national security concerns. But in this case, the Times decided that the early argument that the administration made, that the program was not yet fully in place, and thus it would reveal vulnerabilities of the Pakistani nuclear program and, secondly, the arguments about General Musharraf. They may have been applicable at that time. But when we went back to the administration and said, you know, we really don't think this apply anymore, the administration agreed and actually lifted its request.

SEABROOK: Do you think the Bush administration wants people to know about this now?

Mr. SANGER: Well, certainly, there is heightened concern because of the instability in Pakistan now about the fate of Pakistan's nuclear weapons. And so I would guess, and this only a guess, that one of the calculations that the administration made was that it is now important that they offer some reassurances that something has been done to help secure those weapons.

SEABROOK: David Sanger's the chief Washington correspondent of the New York Times.

Thanks very much.

Mr. SANGER: Thank you, Andrea.

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