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On the fringes of Interstate 85, where the highway snakes through Atlanta's inner city, researchers from Emory University came to study the off-road behaviour of long-haul truckers.

There, amid the empty lots, nudie bars and by-the-hour motels, they set up their living lab -- and landed in one of the ugly morality debates dogging American science.

The project was inspired by research in Africa, where the mix of truckers and sex workers on the Kinshasa Highway is infamous for spreading AIDS along the continent's spine. Emory's experts wondered if the same would be true in North America.

Preliminary field work showed that long-haul truckers (close to four million in the United States, including half a million Canadians) are at the centre of a desperate network of truck-stop hustlers.

Prostitutes, drug dealers and truck chasers -- gay or bisexual men who idolize truckers as "the last of the cowboys" -- vie to eke out a living off the drivers, who may bring home something worse than cargo.

In 2002, the U.S. National Institutes of Health, the government's prime funder of medical research, agreed it was worth learning more. It awarded the Emory scientists a $1.1-million (U.S.) grant.

But a year later an official called to warn them their project was on an ominous list circulating in Washington.

The Traditional Values Coalition, which lobbies on behalf of 43,000 U.S. churches, spotted the study on the NIH website: "Wait until you see how angry the American people get," its president wrote to Democratic Rep. Henry Waxman, "when they discover that NIH have been using federal tax dollars to study 'lot lizards' -- prostitutes who service truckers in parking lots."

The group deemed the project and 200 others an immoral or "nonsensical" waste.

With Congress threatening action, the NIH undertook a review of all its behaviour-related studies. Although attempts to strip funding failed, the episode spawned a chill that shows no sign of thaw.

With the re-election of President George W. Bush and the Republican congressional majority, scientists across the United States have found themselves in a surreal era of self-censorship. Conservatives used key-word Internet searches to compile their watch lists, so researchers are hunting for euphemisms for homosexuals and prostitutes (replaced with "high-risk population").

"Many STD/HIV researchers who are seeking federal funding are reconsidering details down to the level of how they title their grants, so as not to draw unwanted --ideologically and certainly not intellectually driven -- scrutiny," said Jeanne Marrazzo, who researches sexually transmitted diseases at Washington State University. "It's scary."

Such measures might sound more like Soviet-era paranoia than modern American science. But there is no mistaking the degree of mistrust many U.S. researchers feel in this political climate. "I think folks are worried this smacks of McCarthyism 50 years later," said David Celentano, an AIDS researcher at Johns Hopkins University.

Dr. Celentano described grant-review hearings attended by religious-group members and political appointees. He said it was the NIH that has advised researchers to take projects "underground" -- to replace lesbians, for example, with "prospective mothers."

NIH officials would not discuss the policy on the record. But a recent article in the Johns Hopkins alumni magazine included comments from an unnamed official pressed to explain the ambiguous-language directive. "Don't make me speak to you about this in public," she said. "There are spies everywhere!"

Politics and science have clashed before in the United States, and around the world, on issues such as nuclear arms or, most recently, stem cells.

But never before has the U.S. scientific community been embroiled in such a broad, sustained battle with political leaders.

The government ignored the protests of its top geologists in 2003 when it decided to allow the sale of a book at Grand Canyon National Park claiming that Noah's biblical flood created the chasm 4,500 years ago -- an estimate scientists suggest is short by six million years.

Most publicly, even Congress intervened to prolong the life of Terri Schiavo, a Florida woman who had lived in a "persistent vegetative state" for 15 years. Despite medical evidence of severe brain damage and no hope of recovery, religious groups took up the case as a right-to-life issue.

Mr. Bush interrupted his Texas vacation to sign the bill, and his brother Jeb, the governor of Florida, sought to have the state take custody of Ms. Schiavo's care. The U.S. Supreme Court six times turned down requests to consider the case before she died on March 31.

Controversy over the treatment of science has erupted around national security, myriad environmental issues and endangered-species programs. Medical research in particular has been caught in the crossfire. Whenever it involves issues of sexuality, such as STD prevention, AIDS policies or reproductive issues, critics charge, morality trumps medical evidence.

"It's part of an anti-scientific revolution," said Columbia University professor Peter Bearman, commenting on the push to keep safe-sex education out of schools. "There's a lot of hostility toward science in America right now."

Over the past year, the Union of Concerned Scientists (UCS), a non-profit advocacy group based in Cambridge, Mass., has documented dozens of alleged cases where it argues that the Bush administration has sacrificed scientific integrity in the interests of big business, big oil and the religious right. It cites censored data, altered websites and the appointment of under-qualified extremists as science advisers while other candidates are asked if they voted for Mr. Bush.

Last February, the UCS drafted a petition to "restore scientific integrity" to government policymaking and 62 prominent scientists signed on. That number swelled to 4,000 before last fall's U.S. election, and the protest now bears more than 6,300 signatures, including 48 Nobel laureates and former presidential science advisers dating back to the Eisenhower administration.

Government supporters suggest that scientists are traditionally liberal secularists, and simply resentful that the balance of power has tilted out of their favour.

Bill Pierce, a spokesman for the Department of Health and Human Services, the powerful government body that oversees medical research, argued that scientists who backed Democrat John Kerry for president are the ones who "have politicized" issues. Asked why scientists felt such opposition, he replied: "We don't spend a lot of time thinking about that. . . . There's no shortage of researchers who are ready to roll up their sleeves and do hard work. So that's fine, we don't want 'em."

Founded in 1969, the UCS does have a history of protesting against conservative-leaning government policy, but it hardly stands alone in its criticisms of the Bush administration. Leading scientific journals, professional societies and mainstream media, including The New York Times and The Washington Post, have featured editorials, speakers and articles noting the alleged abuses.

"Scientists are not known for signing [petitions]like this," said UCS spokesman Lexi Schultz. But the current situation, she said, "is different, qualitatively and quantitatively, than anything we've seen before."

The Emory team, led by sociologist Yarghos Apostolopoulos and Sevil Sonmez, now has the results of its truck-stop study in hand and believes more than ever in its merits.

They found that truck drivers, often exhausted and lonely, are undoubtedly "bridges" ferrying infections back to their wives and partners at home. Blood tests at three Atlanta truck stops turned up STDs from Hepatitis C to HIV, in some cases in people who had no idea they had been infected.

Dr. Sonmez stressed that not all truckers are involved in risky behaviour. "But even if it were 10 per cent or 5 per cent of the four million truckers . . . you are looking at quite a disaster" in terms of chains of transmission. "Unless you understand what is going on, the dynamics of the infection, you cannot do anything to prevent it."

The Emory group hopes to win a second grant to survey truckers across the country. Given the evidence, Dr. Sonmez remains optimistic that "efforts will not pay off to stop this kind of research."

But scientists offer numerous examples of cases where ideology has eclipsed empirical evidence. Felicia Stewart, former deputy assistant secretary of population affairs under Bill Clinton, noted that scientists have struggled before under conservative leadership, but she said previous cases tended to be about money. "We've not had this level of religiosity before," she said.

Dr. Stewart, now co-director of the University of California's Center for Reproductive Health Research and Policy, cites the ongoing battle at the U.S. Food and Drug Administration over over-the-counter emergency contraception.

Research suggests that allowing women faster, non-prescription access to Plan B, a high-dose contraceptive best taken within 72 hours after having unprotected intercourse, could halve the country's number of unintended pregnancies and abortions.

Social conservatives have voiced concerns that Plan B is tantamount to an abortion pill, while others fear greater access to it will promote promiscuity.

Two independent FDA panels voted overwhelmingly (23 to 4) to allow the change, finding that the move made sense and the drug seemed remarkably safe. But in a highly unusual move, the FDA leadership overruled its own panels. The agency's director said more information was needed to ensure the drug's safety in young teens. Now, more than seven months after the drug maker agreed to restrict non-prescription sales to those over 16, no decision has been made.

One of the FDA's own panel experts, James Trussel at Princeton University, told the UCS that there were no age-related concerns. The issue, he said, is "nothing more than a made-up reason intended to sound plausible. From a scientific standpoint, it is complete and utter nonsense."

The Center for Reproductive Rights, an advocacy group, is suing the FDA over the delayed decision.

"We are really coming against the fact that data doesn't matter. . . . If you don't like what the data says, well then you don't have to pay attention to it," said Kirsten Moore, president of the Reproductive Health Technologies Project, a non-profit group that lobbied to make the pill available.

"That's not to say scientists have all the answers. . . . But I think what we find so frustrating are bogus scientific arguments to justify a political position."

David Hager, an obstetrician and gynecologist at the University of Kentucky, was one of the few who voted against easier access to the so-called morning-after pill. "What we heard today," he said at the time, "was frequently about individuals who did not want to take responsibility for their actions and wanted a medication to relieve those consequences."

The author of As Jesus Cared for Women, Dr. Hager is known widely for having refused to prescribe contraception to unmarried women, and recommending Bible-reading to relieve PMS. His placement on the FDA Reproductive Health Drugs Advisory Committee is one of many controversial appointments Mr. Bush has made.

One of several contentious picks for the Presidential Advisory Council on HIV/AIDS, for example, was the outspoken Christian conservative tapped to be its co-chair in 2002. Former Republican congressman Thomas Coburn, an Oklahoma obstetrician and now a senator who advocates the death penalty for abortion doctors, had certainly been active on the AIDS issue, spearheading legislation to commit $1-billion to treat and prevent the disease. But he also distinguished himself as an abstinence-only crusader, insisting that condoms carry warning labels about failure rates.

Mr. Bush's top science adviser, John Marburger, has defended White House appointments, noting that he himself is a lifelong Democrat. But critics charge that the administration has often bypassed those with the best scientific credentials for ideological reasons.

The administration's Mr. Pierce acknowledged that "these are people who may well hold different ideas than [the critics]do." But, he said, "If you want to receive good advice, you need to have competing ideas. If you want to receive bad advice, then get five people in a room who all think the same thing."

Yet last winter, 170 scientists wrote an open letter of protest to the White House charging that world-renowned biologist Elizabeth Blackburn had been dismissed from the President's Council on Bioethics because she did not support government policies on embryonic-stem-cell research.

Lewis Branscomb, a Harvard University professor who directed the National Bureau of Standards under Richard Nixon's Republican administration, was particularly critical of the government's record on these matters: "I'm not aware that [Mr. Nixon]ever hand-picked ideologues to serve on advisory committees, or dismissed from advisory committees very well-qualified people if he didn't like their views," he has said.

"What's going on now is in many ways more insidious. . . . I don't think we've had this kind of cynicism with respect to objective scientific advice since I've been watching government, which is quite a long time."

When the Traditional Values Coalition prepared its list of "questionable" research projects, it proudly described the endeavour as targeting a "sacred cow." That sentiment hints at a larger problem -- a significant conversion in a society that once seemed to embrace science as tantamount to a new religion.

From the Second World War to the close of the millennium, miracles seemed to spring from laboratories -- moon landings, heart transplants, commercial jets, the polio vaccine, nuclear power, computers, antibiotics and a decoded human genome (a feat Mr. Clinton likened to learning the language of God).

But now all around are mysteries it struggles to solve, from cancer to mad-cow disease, from antibiotic resistance to SARS. Wonder drugs have been exposed as killers. Cold fusion has flopped. Even the flu looms as an insurmountable foe. People are losing faith.

"Science is not viewed as nearly as infallible as it once was," said Alan Leshner, chief executive officer of the American Association for the Advancement of Science. "The relationship between science and society is rockier than it's been for quite a while."

Dr. Leshner pointed to a study in Europe that found the number of people who believe that the benefits of science outweigh the risks dropped more than 10 percentage points from 1992 to 2001, from 61 to 50 per cent.

He links those figures to statistics from the U.S. National Science Bureau that suggest 61 per cent of Americans believe in ESP and 41 per cent think astrology is scientific: "It's not that Americans don't understand scientific facts, but rather that they don't like them and they don't want to hear them."

Just last month, movie theatres in Texas, Georgia and the Carolinas refused to run an IMAX film about volcanoes, fearing that it might offend people who do not believe in evolution.

Meanwhile, recent advancements in science have left people not just skeptical, but uneasy, Dr. Leshner said. The life-saving potential of stem cells, for example, could mean the destruction of countless human embryos, forcing the public to make moral choices about the beginnings of life. "When you get on issues that border towards religion, you get the feeling that science is making people uncomfortable. And where they're uncomfortable, that's when we're seeing this increasing overlay of politics, or moralizing, or ideology."

Critics suggest that the Bush government is not simply catering to society's most conservative members, but capitalizing on its wider scientific discomfort. With little fear of paying a political price -- particularly in its second and last term in office -- the administration, they allege, feels free to alter a major federal report finding human activity contributes to global warming; to freeze the NIH research budget for the first time in more than five years; or to disregard environmentalists' concerns about drilling for oil in the pristine Arctic wildlife refuge.

As Dr. Stewart framed it, "If you believe the world is going to end soon, then you don't need to worry about conservation. It's bizarre, but there's a deep lack of respect and hostility toward science."

Certainly the administration's Mr. Pierce speaks with spit-fire impatience about "these guys, these scientists" who steadily lob accusations at the Bush administration. But as he sees it, the problem is theirs: "There is no real tension in the public's mind. This is a blip on the radar."

Some conflicts have spilled out of the laboratories and into the courts. Like the sad saga of Terry Schiavo, a recent Florida environmental controversy has reached the bench of a federal judge.

In the state's southwest, one of the fastest-developing areas in the United States, the prized Florida panther has struggled to survive in its shrinking habitat, the Western Everglades. Shopping malls, roads and golf-course communities have devoured the roaming grounds of the endangered big cat at a rate of 30,000 acres a year.

Andy Eller, a biologist with the U.S. Fish and Wildlife Service, wrote six "biological reports" in his 18-year career warning of threats that could quicken the panther's extinction. But Mr. Eller alleges that in December, 2001, as he set out to pen the seventh, he and his colleagues received astonishing high-level instructions to stop writing reports on risks to the region's 68 threatened species -- the Miami blue butterfly and the American crocodile among them.

But with only 80 Florida panthers remaining, Mr. Eller could not help but log his concerns. He was fired last November, three days after Mr. Bush was re-elected. In a public complaint, he alleged that his disobedience was the reason.

"The tension that comes from pro-development interests has always been there," Mr. Eller said in an interview, "but if there are no reports on threats [to a species] then there is no reason to say no to development."

Federal officials maintain that they sacked Mr. Eller for poor job performance. But last August, a federal judge reviewing a limestone mine proposal in the area ruled that the Fish and Wildlife Service had indeed failed to properly assess the impact of development on the endangered panther.

Last month, an independent federal investigation found that the FWS had actually relied on faulty science in shaping its policies, neglecting to evaluate the panther's movements when the animal is most active.

Mr. Eller, now widely lauded as a whistle blower, worries that he is just one of many who have been silenced into not doing their jobs to the best of their abilities. "This administration has proven itself so impervious that people are afraid to speak out."

The most serious charge scientists direct at the White House is that it chokes the free flow of accurate information to the public, particularly on matters of sexual health. They accuse the government of spin and censorship, for example, in nothing less than a "war against condoms."

It began with a congressional request, instigated by abstinence-only proponents, to have federal agencies investigate the efficacy of condoms in preventing the transmission of sexually transmitted diseases. The July, 2001, report found condoms highly effective in preventing STDs when used consistently and correctly, and a notable success rate of more than 90 per cent in shielding against HIV.

Birth-control opponents viewed the less-than-perfect score as evidence that using condoms is like "playing Russian roulette." The results ushered in a new era of abstinence promotion at the U.S. Centers for Disease Control and Prevention, which helps to focus health research and clinical care across the United States.

A fact sheet on the CDC website that promoted condoms as an effective means to protect against STDs was replaced with information that emphasizes their failure rate. Information about how to run sex-education programs has also disappeared.

"The focus on everything has to be abstinence," said a long-time CDC scientist, who asked not to be identified. "The language has to be very scrutinized and approved at 3,000 levels. The general sense is that propaganda has taken precedence over science."

The government's Mr. Pierce argued that the condom review simply produced results that showed the CDC website was inaccurate: "So they took it down.

"They put up that most recent, up-to-date information -- based on science, the thing, the Holy Grail they keep raising up," he said sarcastically. "What's wrong with that? Nothing. . . . There's just no denying the fact, if you practise abstinence, you're not going to get pregnant and you're not going to get STDs."

Morale has plummeted at the Atlanta-based CDC, one of the world's foremost public-health authorities. "You want an environment of open inquiry, but you see policy driven more by ideology than science," said John Santelli, a former CDC scientist who worked for 13 years in STD prevention.

Now a professor at Columbia University, Dr. Santelli said he left the agency for both personal and professional reasons last summer: "It was becoming increasingly difficult to do good science in the federal system. The CDC wasn't being as bold as it could in looking at issues that should have been explored."

A Washington Post article last month estimated that between retirements and widespread discontent, 40 CDC top managers had left the agency, or were about to do so.

Dr. Stewart argues that it will take federal agencies a long while to recover from the loss of good people. As well, she said, "bright graduate students aren't going to be attracted to public-health areas. . . . They will see the controversy, and say, 'I think I'll go into X-rays.' "

True to his campaign promise to spend as much on abstinence-only programs as on programs that deal with contraception, Mr. Bush has doubled spending on the area since taking office, with $170-million earmarked for the cause this year.

Leslee Unruh, president of the Abstinence Clearinghouse based in Sioux Falls, S.D., has received a $2.7-million grant that will allow her group to police abstinence-only programs to make sure they mention condoms only in reference to their failure rates, with no instruction as to their proper use.

"This is his baby," Mrs. Unruh said admiringly of the President's push for abstinence. "This is what he wants to see."

Ever since her son came home from a Grade 5 sex-ed class "sick to his stomach" in 1984, Mrs. Unruh has argued that telling youths about contraceptives confuses the message. "The problem is we've got two worldviews in America. Some think we should give kids birth control and pay for their abortions, and some don't. Some of us believe you can control yourself -- some believe you can't."

No public-health official opposes teaching abstinence. But they argue that emphasizing it over other prevention ignores the fact that different people require different approaches. The vast majority of the roughly 40,000 new HIV infections in the United States each year, for example, involve gay men. But if sex outside marriage is considered wrong, and gays cannot marry, the implicit and unrealistic message is that gays should never have sex.

"When the morality mandate is driving what are the best interventions, you will undermine prevention efforts," said Dr. Marrazzo at Washington State.

Meanwhile, a report released in December by California representative Henry Waxman, a fierce critic of the government's science record, found some federal abstinence-only programs taught young people that touching a person's genitals could result in pregnancy, that abortion often led to suicide or sterility and that half of gay teens in the United States had AIDS.

A key federal study is under way to evaluate the abstinence-only approach. But researchers argue that evidence to date suggests it doesn't work. Some have found it may even be harmful.

Prof. Bearman, director of Columbia's Institute for Social and Economic Research Policy, discovered that STD rates among 12,000 teens who took virginity pledges were the same as for non-pledgers. While some pledgers delayed sex for 18 months longer, had fewer sexual partners and married earlier, Dr. Bearman found they were unprepared or uneducated when the heat of the moment was unexpectedly upon them. What's more, they were more likely to engage in risky sexual behaviour -- such as unprotected anal sex -- to "technically remain a virgin."

"Kids who take these pledges are less likely to go see a doctor, less likely to be diagnosed with an STD and less likely to think they have an STD. If you actually care about public health, these are programs that are, at best, neutral, and are possibly dangerous."

David Guston, associate director of science, policy and outcomes at Arizona State University, said the mix of politics and science is a necessary one that keeps research socially relevant. Conflicts have always arisen. Richard Nixon, for example, fired his presidential science advisers in 1973 after they spoke out publicly against his plans for a supersonic transport program.

Prof. Guston said he is not convinced Mr. Bush is any more anti-science than previous presidents. Rather, he said, Mr. Bush's style of "governance and the application of power" clashes with scientific culture.

He cited recent published accounts that paint the President as a man whose faith imbues him with unflinching certainty in setting policy -- despite doubts others may cast his way.

Jeff Ruch, executive director of the Public Employees for Environmental Responsibility, an advocacy group based in Washington, described the Bush administration as a sophisticated machine able to secure the results it is after.

"The Clinton administration was not well-organized," he said. "The Bush administration is highly organized and centralized. And in many instances, the directives are coming from political appointments right down to the field officers."

Mr. Ruch's organization, along with the UCS, conducted a survey last fall of scientists who work for the Fish and Wildlife Service and found that the experience of Florida panther biologist Andy Eller was not unique: One in five of the nearly 300 who responded said they had been asked to exclude or alter technical information in a scientific document.

In the past three months, two non-partisan entities have taken direct aim at the practices of the U.S. Environmental Protection Agency. Both the EPA inspector-general and the Government Accountability Office issued reports that found EPA staff received high-level instructions to distort its analysis of how to reduce mercury emissions from power plants.

As Ms. Schultz of the UCS explained, "EPA scientists were actually given the end policy result of how much mercury could be controlled from power plants -- and told to make the science justify the figures."

It is too early to gauge what impact the current conflict will have on American science, but there is little doubt it has accelerated a cultural shift in the scientific community. Scientists are stepping down from their ivory towers to defend their work and, more significantly, to win public support.

In California, scientists have done an end-run around the President's restrictive funding policies on stem-cell research, winning a statewide ballot last fall to raise $3-billion for the cause with a public bond-offering.

In December, the UCS bypassed Washington and wrote directly to Prime Minister Paul Martin, warning the U.S. Ballistic Missile Defence program was based on flawed science and a dubious plan to weaponize space.

In March, Rick Piltz, a former senior associate with the federal Climate Change Science Program, resigned from his job of 10 years. He said he wanted to contribute "to public understanding of the problem of what happens when scientific assessments of climate change are misused in the political arena."

Mr. Piltz alleged in an interview that the government has "essentially suppressed the use of the most substantial scientific assessment undertaken by the program in its 15-year history."

The administration was displeased with its findings, he alleged, so that the National Assessment of the Potential Consequences of Climate Variability and Change compiled by hundreds of U.S. scientists was sent "into a black hole," playing no role in strategy planning or reports to Congress.

Dr. Leshner, of the American Association for the Advancement of Science, believes firmly that scientists must expand their public role: "When all of this politics, ideology and moralizing started, everybody in the scientific community's initial reaction was to lament the situation. But whining doesn't help.

"What I believe, and what many of my colleagues believe, is that you need to go out to people where they are, not where we are."

That means talking to reporters "as much as we can," he said, and writing commentaries in the mass media.

"It's about finding out what [the public's]concerns are and trying to find common ground," Dr. Leshner said. "We need to change our strategy and engage with the public."

And that means scientists mounting a political campaign of their own. Dr. Leshner said the AAAS now has an elaborate plan to develop "a cadre of ambassadors of science," to fan out across the country and visit "religious groups, churches, synagogues, mosques, Boys' and Girls' Clubs, Kiwanis and Rotary Clubs . . . to go to where the people are, listen to what they are thinking about . . . let them help shape the research agenda.

"The truth is," he said, "they're paying for this [research] They ought to get something out of it."

Carolyn Abraham, The Globe and Mail's medical reporter, was recently nominated for a National Newspaper Award in feature writing.

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