Of the many ironies apparent in the flap over China’s nuclear spying, none is so glaring as the government’s plans to rely more heavily on lie detectors to root out future moles — even though Wen Ho Lee, the Chinese-American scientist suspected of supplying nuclear weapons secrets to Beijing, passed a polygraph test in November 1998.

A close second on the irony-meter is official Washington’s professed alarm over Beijing’s espionage, when it was the CIA’s own spy inside China who first showed up with evidence that U.S. nuclear arms laboratories may have been penetrated. In yet another twist, the CIA eventually decided that its Chinese spy was actually a double agent under Beijing’s control.

Despite months of investigation and partisan recriminations over who’s responsible for the alleged success of Chinese espionage, which extends over four administrations reaching back to Jimmy Carter, no one has yet been arrested. Only one outcome is already clear: Untold millions of dollars are going to be spent to bolster security at government arms labs — well after China has already acquired U.S. weapons designs.

Among the measures will be a dramatic expansion of employee polygraph tests, even though their reliability has come under increasing scrutiny in recent years.

Wen Ho Lee was not the only alleged spy to pass a lie detector test. Other notorious moles who beat the machine include Aldrich Ames and Larry Wu-Tai Chin, another Chinese American spy. Ames was Moscow’s agent inside the CIA for eight years, until he was caught in 1995. Larry Chin, a 20-year intelligence analyst, spied for Beijing for untold decades until he was arrested in 1985. Both, as well as Wen Ho Lee, first passed, and then eventually failed polygraphs, but only after mountains of other evidence had been compiled against them. Chin committed suicide in jail before he was tried. Scores of the CIA’s Cuban agents, who turned out to be really working for Fidel Castro, also fooled U.S. government polygraphers for years. The same happened with CIA spies dispatched to the Soviet Union and North Vietnam. In most cases they were given, and passed, polygraph tests.

“Well, they don’t work,” Ames told retired Sen. Dennis Deconcini, D-Ariz., chairman of the Senate Intelligence Committee. An FBI polygrapher once told a scientific conference he could teach his teenage son how to beat the machine “in a few minutes.”

Wen Ho Lee’s case seems to come right out of the pages of John Le Carre. In 1978 the diminutive China-born scientist was hired by the Los Alamos Laboratory, where the atomic bomb was born in 1945. Sometime in the early 1980s, according to reports, he began helping the FBI on at least one case of suspected espionage. In 1987 Lee’s wife, Sylvia, a secretary at Los Alamos, herself became an informant for the FBI, providing information on visiting Chinese delegations. During this time her husband traveled to China to give scientific lectures on U.S. arms developments.

The FBI, meanwhile, had suspected that U.S. nuclear warhead secrets were leaking from Los Alamos for a while. In 1997 it began to zero in on Lee, and asked the Justice Department for permission to wiretap Lee, but was rebuffed. In November 1998 Lee was given, and judged to have passed, a polygraph examination. Subsequently, counterintelligence agents got more information on Lee and in February 1999, when he was polygraphed again, he failed.

Despite mixed results in this and other high-profile cases, the U.S. Senate Defense Authorization Bill includes funds for expanding polygraph tests to 20,000 employees of the Department of Energy, where the China spying flap is centered.

Responding to the exploding China spy scare, C. Bruce Tarter, Director of the Lawrence Livermore National Laboratory of the University of California, on May 5 told Congress that its plans to protect itself from future threats would “focus primarily on the need to expand the DOE’s current polygraph program …”

This despite Senate testimony from a senior FBI scientist that the tests were virtually no better than tea leaves, Ouija boards, and witchcraft in ferreting out spies. The tests have “a complete lack of validity,” testified Supervisory Special Agent Drew C. Richardson. The government’s reliance on them may actually endanger national security, he said.

“I believe that there is virtually no probability of catching a spy with the use of polygraph screening techniques,” Richardson, a Ph.D. physiologist, testified. “To the extent that we place any confidence in the results of polygraph screening, and as a consequence shortchange traditional security vetting techniques, I think our national security is severely jeopardized,” he added.

For the first time, the views of Richardson and other polygraph skeptics in the scientific community are being heard. Last week the Senate Intelligence Committee asked the FBI and CIA to “come up with alternatives to polygraph testing” within 90 days, according to committee spokesman Bill Duhnkey.

“Given the potential unreliability of the polygraph system, the committee believes the alternatives to the polygraph should be explored,” the committee reported on May 11.

“I don’t think they know yet what the alternatives are,” said a government scientist who follows the issue closely. “They just know the polygraph is screwed up.” The committee’s directive, however, won’t affect the DOE’s plans to expand its reliance on polygraphs.

Sen. Charles Grassley, R-Iowa, a severe critic of FBI laboratory practices, has also been examining reported abuses in the FBI’s polygraph screening program for employee applicants, with an eye toward hearings.

Polygraph alternatives include full background checks of employees and closer monitoring of travel and spending habits. An FBI study of convicted espionage felons, called Project Shadow, also recommended co-workers take note of dramatic personality changes in their colleagues, due to divorce or being passed over for promotion. Better control of classified information is also a more effective way to reduce vulnerability to spies than polygraph tests, and specialists say agencies must work harder to limit access to secrets to employees to with a genuine need to know. Ironically, many security experts say the government should drastically curtail the number of documents it classifies, to make sure harmless information isn’t being treated with the time-consuming care that true secrets deserve.

Counterintelligence agents were appalled by the loose security at Los Alamos and other labs, according to reports, with classified papers strewn about desks and uncleared visitors frequenting the installation.

“Some feel Wen Ho Lee was not guilty of anything, that he’s a scapegoat for a sloppy environment, and that various minor security allegations were trumped up against him,” said a government agent whose expertise is unchallenged. “The polygraph really didn’t support anything one way or another.” While his take on Lee’s culpability could not be corroborated, it was a sign that there is skepticism about the Lee case even within the security community.

Meanwhile, the difficulty of nailing moles with the polygraph is compounded when foreign nationals are involved, experts agree. The emotional pull of the homeland tends to skew answers to certain questions.

“You don’t ask an ethnic: Are you loyal to a government other than the United States?” a retired deputy chief of counterintelligence for the FBI told Salon. “In fact, that’s one the agency [CIA] used to ask. Most ethnics will flunk that, because if they’re first-generation ethnics, they have ties to the homeland, even if they’ve fled. The question shouldn’t be if they’re loyal to a country, but if they’re working for another country’s government.”

Further complicating the security challenge is the fact that Chinese-American scientists may not know they are helping Beijing’s spies when they hand over scientific papers. Chinese intelligence also sends “sleeper agents” to the United States, such as college students, where they may remain dormant for years before being activated, a CIA source said.

Polygraphs can also boomerang on innocent employees, tie an agency’s security personnel in knots, and end up giving employers a legal and public relations headache. As Salon reported exclusively last June, a 28-year-old CIA lawyer named Adam Ciralsky was put on paid leave last year after flunking an agency polygraph even though he had passed three previous tests. His lawyer, former Justice Department Nazi hunter Neal Sher, is preparing a suit against the CIA.

Scientists outside the close-knit brotherhood of polygraph operators say the only way a “lie detector” can be completely reliable is when a suspect is being interrogated about information only he and the investigators could know — the combination to a safe, say, or a closely held code word.

Meanwhile, no one is yet predicting the fate of Wen Ho Lee, the figure at the center of the scandal, who was suspended from his job at Los Alamos after classified documents were found in his private computer files. He has not been charged with anything.

In all the hue and cry over allegations in the Cox Report, it has largely gone unnoticed that evidence of Beijing’s theft of U.S. nuclear secrets came in the form of a Chinese document that fell into the hands of the CIA. According to a New York Times account, the document was in a “suitcase” full of material handed over by a Chinese spy who “walked into the CIA’s arms” in Taiwan. Later, however, the man was judged to be under the control of Beijing. Puzzled CIA experts don’t know what to make of the incident, but they still regard the document as genuine.

In yet another irony relevant to the case, little notice was taken recently of a security violation similar to Lee’s by one of the CIA’s own past chiefs. Agents making a routine inspection discovered the home computers of former CIA Director John M. Deutch filled with classified documents that he was unauthorized to possess. A referral was made to the Justice Department, which declined to prosecute.

Closer to home, the Washington Post reported recently that the CIA itself had unloaded scores of its own laptops for sale — while they were still filled with CIA documents. One of the newspaper’s columnists is running a tongue-in-cheek contest for readers to guess what was in the files.

The cloud that’s been hanging over New Mexico Gov. Bill Richardson recently, and cost him his shot at being Commerce secretary, appeared to be lifted yesterday. That’s when the Associated Press broke the news that Richardson won’t face charges stemming from a federal probe of pay-to-play allegations. Now, the cloud is back.

On Thursday, a Richardson spokesman, Gilbert Gallegos, took a little victory lap, saying in a statement that the governor is “gratified that this yearlong investigation has ended with the vindication of his administration.”

New Mexico Gov. Bill Richardson appears to have successfully weathered the federal investigation that cost him a spot as secretary of Commerce. The Associated Press reports that Richardson and former top aides will not be charged in the investigation, which was looking into an alleged pay-for-play scheme.

Decisions about charging high-ranking political figures are generally made in consultation with main Justice back in Washington, D.C., which typically has final say. That appears to be what happened here, as the AP reports the decision “was made by top Justice Department officials.” The AP’s source doesn’t appear to be happy about it, saying, “It’s over. There’s nothing. It was killed in Washington.”

Update: Clinton’s mission was successful, and Kim Jong Il has pardoned the two journalists. See this post for more.

In a surprise visit, former President Bill Clinton arrived Tuesday in Pyongyang, North Korea, to meet with the isolated nation’s leader, Kim Jong Il. While North Korea’s nuclear program and recent spate of missile tests have caused growing consternation around the world, the main purpose of Clinton’s trip was to negotiate for the release of two U.S. journalists currently imprisoned there.

President Obama struck out with his first two picks for Commerce secretary, as both New Mexico Gov. Bill Richardson and Sen. Judd Gregg (R-N.H.) withdrew their nominations for the post. Now, he’s reportedly hoping to do better with a fairly obscure choice — former Washington Gov. Gary Locke.

Locke, who left in office in 2005, served two terms and opted not to run for a third; he was the first Chinese-American governor in U.S. history.

One day after the sudden announcement that New Mexico Gov. Bill Richardson’s nomination to be commerce secretary was being withdrawn, Richardson offered additional details during a press conference. It did not go off without a hitch.

Richardson maintained that the decision to withdraw was his, and said he came to make that choice because an investigation into state contracts given to CDR Financial Products Inc., whose president is a Richardson donor, had gone on longer than he expected it to — he’d hoped it would be done in December, removing the cloud from over his head before confirmation hearings were to begin. The governor said, as he had in a statement on Sunday, that the country couldn’t afford any delay in confirming a new head for the department. “Sometimes your own dreams and plans must take a back seat to what is best for the nation,” he told reporters.