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Physicists became enmeshed with national security when they built the atomic bomb in World War II and then committed themselves to maintaining nuclear superiority during the Cold War. The key object of control was information: how to obtain fissionable fuel for atomic bombs, and the workings of the bombs themselves. No one disputed that research on nuclear weapons or access to such research had to be restricted to scientists who would not risk national security by releasing classified information, either inadvertently or through espionage.

That logic was sensible on its face, but how to make it operational was highly disputed in the tense, early years of the Cold War. Communism was understood to be an international conspiracy, demanding loyalty to the Soviet Union from its adherents everywhere. The revelations of the espionage committed by the nuclear physicists Alan Nunn May and Klaus Fuchs indicated that the conspiracy reached into the heart of the nuclear-weapons enterprise in Canada and the United States. In 1947, to defend against Communist infiltration of the government, the Truman administration began requiring loyalty checks for all federal employees. The policy affected almost 60,000 U.S. scientists and engineers.

In that politically fraught climate, which yielded Senator Joseph McCarthy’s reign of ideological terror, the line between liberalism and Communism was blurred, often making liberals suspect as security risks and opening their activities to scrutiny by FBI investigators. Lengthy security-clearance investigations could cost scientists months of anguish and unemployment. For some, past or present political associations led to the denial of clearances or to confinement to unclassified research. For others, they produced public castigation, like the House Un-American Activities Committee’s unwarranted denunciation of the physicist Edward U. Condon, the head of the National Bureau of Standards, as “one of the weakest links in our atomic security.”

Worries about security led the government even to cloud the distinction between practitioners of classified and unclassified research. In 1950, some conservative congressmen tried to require security clearances for all researchers receiving fellowships from the proposed National Science Foundation. They failed, but that same year the Joint Committee on Atomic Energy successfully imposed the requirement on all applicants for Atomic Energy Commission fellowships, whether they would be engaged in classified research or not. There is always the chance, declared the conservative Republican senator William Knowland, that some student, even if engaged in nonsecret studies, might “hit upon a super-duper atom bomb and be off to Russia.” The State Department, determined to protect U.S. atomic secrets against suspicious foreigners, denied the Nobel laureate Paul Dirac, a member of the British atomic-energy effort but in the 1930s a frequent visitor to the Soviet Union, a visa to attend scientific congresses in the United States. It also refused the homegrown chemist Linus Pauling, an outspoken liberal, a visa for travel abroad.

Some scientists protested the assaults on civil liberties. “The opportunity of the young scientist to develop his ideas should not be purchased at the expense of his human dignity,” Albert Einstein said. But the security issue left President A. N. Richards of the National Academy of Sciences cowed. Explaining the academy’s refusal to come vigorously to Condon’s defense, Richards said that “the most unfortunate outcome would be to jeopardize our relations with government.” And as the Cold War intensified, many scientists came to consider Communism a sufficient threat to U.S. security to warrant the curtailment of civil liberties.

Harvard University president James B. Conant, a key figure in atomic policymaking and a liberal on most domestic matters, was typical. Conant waffled on the Condon case, and in December 1948, several months after the Communist takeover of Czechoslovakia, he said, “It must be recognized that quite apart from the possibility that some individuals might be connected with this [Communist] conspiracy, others who are quite innocent of any such ties are nevertheless temperamentally naive and indiscrete and cannot be trusted with confidential information in spite of their excellent intent and high ability. The government, in resolving doubts on these matters about employees, including scientists, must settle the case in favor of the government rather than the individual. If a shadow of doubt exists, the individual should be prevented from having access to confidential information.”

Like physicists during and after World War II, many biomedical scientists today are eager to help strengthen national security. In June 2002, a committee of the National Research Council published Making the Nation Safer: The Role of Science and Technology in Countering Terrorism, which laid out a variety of research agendas, including one in the area of human and agricultural health. Microbiologists have often been casual in managing lethal agents, keeping anthrax, for example, in glass tubes on bench tops in unlocked labs. Most biologists today seem to consider reasonable the requirement that anthrax samples be inventoried and locked up.

But many microbiologists worry that the new security regulations may be counterproductive not only to basic research and biotechnology but even to the defense against bioterrorism. Ronald Atlas, president of the American Society for Microbiology, has noted that “some researchers are now afraid to be anywhere near an anthrax culture,” and that many academics are destroying their restricted agents to be sure of avoiding prosecution. Gary Bass, executive director of the nonprofit OMB Watch, which advocates greater access to government information, has observed, “We have a basic principle of right to know in this country. It is shifting, ever so subtly, to becoming one based on a need to know.” Robert Iuliano, acting vice president and general counsel at Harvard, told me recently that many faculty members worry how the restrictions on foreigners may affect the openness of the campus-for example, the accustomed freedom of undergraduates, no matter their national origins, to visit any laboratory. An essential and troubling question facing American scientific leaders is how to help defend the country without damaging the vitality of basic research, biotechnology, and, indeed, higher education.

The National Academy of Sciences has been far more publicly active in dealing with the question now than in the postWorld War II decade. The American Society for Microbiology has also weighed in powerfully on security issues. It has commanded attention by reason of its size-42,000 members-and of the tireless outspokenness of Atlas, an environmental biologist with experience at the intersection of science and policy. After September 11, Atlas was inundated with inquiries from scientists, government officials, and the media. “At the height of the anthrax attacks,” he told me in a recent e-mail, “I was handling 70 press calls a day. I had to have two secretaries working full time to screen calls.” Academic scientists were not consulted when security restrictions were inserted into the USA Patriot Act; Atlas felt they ought to have been.

Still, U.S. scientists are not toiling in the same atmosphere of suspicion that they endured during the Cold War. None is accused of being a risk to national security, the way some physicists were in the heyday of McCarthyism; none needs fear being branded a subversive simply for speaking out in defense of open and accessible biomedical science. And so they have been able to publicly take issue with the new restrictions.

But in several ways today’s biologists face more difficult obstacles than physicists did in the early Cold War. Then, a scientist was made suspect by his or her political affiliations. In principle, suspicion could be allayed by repudiations of past political behavior and renunciation of current allegedly dubious activity. In contrast, what makes a scientist suspect today is his or her nationality, which is difficult to modify, or ethnicity, which is unchangeable. There is no appeal against the denial of access to selected biological agents on the basis of nationality; it applies absolutely without exception.

Foreign students are now subjected to close scrutiny in applications for visas. The State Department reportedly asks all male applicants between the ages of 16 and 45 whether they have any experience with biological weapons or have participated in armed conflicts. (Of course, a would-be terrorist would just lie, but discovery of the lie would provide grounds for prosecution and expulsion from the country.) Requests for visas, especially by male students from Arab and Muslim countries, and by anyone bound for scientific activities, often meet with lengthy delays. A number of foreign students home on vacation after having been previously admitted to the United States have found themselves stuck awaiting reentry; one doctoral candidate at Yale University who went home for the holidays in December 2002 had to wait so long for a visa that he missed the spring semester.

Visa delays and denials have already interfered with or caused the cancellation of important international conferences, disrupted careers, and slowed research projects-including, according to media reports, an anti-HIV drug, a vaccine against the West Nile virus, and sensors to detect biowarfare agents. In the long term, they could jeopardize the nation’s research and training programs, which depend heavily on foreign students, and ultimately its economic competitiveness. According to 1997 figures, the latest available, foreign-born students represent a quarter of all U.S. PhDs in biology. The U.S. biotechnology industry draws abundantly on these trainees: between 8 and 10 percent of its employees are visa-holding foreigners, four out of five of whom trained at American universities.

Even if they negotiate the visa gauntlet, foreign students may find themselves investigated by the FBI if they are working in potentially dangerous biomedical research. Critics worry that under the broad terms of the USA Patriot Act, the government might claim authority to pry into student records and e-mail accounts. Visa-holding Muslim students have been complaining of harassment on their return to the United States from vacations. Students from countries believed to sponsor terrorism are fingerprinted, photographed, and required to check in periodically with the government. In an interview with the Chronicle of Higher Education, Omar Afzal, who advises Muslim students at Cornell University, said, “They are terrified. They come from a culture where if a policeman shows up at the door, you are being targeted to be sent to prison for a long time.”

Beyond visa considerations, biomedical scientists have found especially disturbing the prospect of restrictions on the practice and publication of so-called sensitive research. In nuclear research, a line could be drawn between research that was and was not integral to national security. If the investigation of fissionable nuclei was crucial to national defense, research into the nuclei in most of the periodic table was not. It remained open and unclassified.

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