Noboru Hashimoto/Corbis

The death cult Aum Shinrikyo, which used sarin gas to horrific effect in the Tokyo subway system in 1995, had also sought to weaponize anthrax.

The White House wanted to know: How much safer are Americans today than they were on October 4, 2001? That was the day when a photo editor in Florida became the first reported case of inhalation anthrax in America in decades. In what became biology’s 9/11, five letters containing less than a quarter-ounce of anthrax total—the equivalent of two pats of butter—killed five people, infected 17, put more than 20,000 on antibiotics, and traumatized thousands more. Decontamination alone, including at the Hart Senate Office Building in Washington, took over three years and cost some $200 million.

With these disturbing facts in mind, and keenly aware that al-Qaida and other terrorist groups have sought germ weapons, the White House in 2006 quietly directed the Department of Homeland Security to commission studies from teams of researchers on what Americans had received for the billions of dollars spent on preparing for a bioterrorist attack since 2001. Taken together, the papers—whose contents remain secret and whose authors have been asked by the DHS not to discuss them—constitute what officials call the first “net assessment” to focus exclusively on the issue. Though many of the papers were delivered to the DHS months ago, the net assessment remains unfinished and is likely to be handed over to the next administration, officials say. Still, its thrust is that while the estimated $50 billion spent since 2001 on countering bioterrorism has left us far better prepared for a bioterrorist attack, we remain vulnerable and, in some ways, may even be losing ground.

President Bush himself is said to have privately expressed frustration with the pace of biosecurity progress. At a meeting with cabinet members and other senior biodefense officials in the White House situation room on June 30, the president was briefed on yet another internal review of the administration’s biodefense effort. After hearing that his agencies were unlikely to complete most of their 56 assigned tasks by the end of his term in office, says one official who was told about the meeting, Bush echoed the old Nike ad, in a display of irritated determination: “Just do it!”

Officials and independent analysts agree that much has been done to prepare for an attack and mitigate its consequences. One of the most important advances is the least quantifiable. “We understand the problem far better than we did before the anthrax mailings,” says Kenneth Bernard, a former White House biodefense advisor in both the Clinton and Bush administrations. “We now see the risks and our vulnerabilities far more clearly and have spent billions addressing them.” Scientists know much more today than they did seven years ago about the importance of timely detection in any suspicious outbreak of disease, for example, and about the difficulty of delivering drugs and vaccines quickly and cheaply to affected populations.

They also know more about the genomic structure of pathogens. Federally funded research has vastly improved scientific understanding of many entries in the government’s list of some 70 “select agents,” the world’s most contagious or lethal bacteria and viruses. Between 2001 and 2008, research funding by the National Institutes of Health on bioweapons agents increased from $53 million to $1.6 billion. At the same time, the Pentagon more than doubled its investment in biodefense research, to over $1 billion.

Bioforensics, too, has seen great advances. Using techniques that hadn’t even been invented when the anthrax letters arrived in 2001, for instance, scientists working with the FBI’s “Amerithrax” investigation broke ground in microbial forensics, decoding the anthrax genome to trace the powder used in the letters to a flask labeled RMR-1029 that was stored at the Army Medical Institute of Infectious Diseases, the military’s main biodefense lab, in Fort Detrick, Maryland.

Another source of pride is the Strategic National Stockpile, a repository of drugs and antibiotics stored at sites throughout the country that can be sent to any city within 12 hours. Launched nearly a decade ago under the Clinton administration, the stockpile now contains enough antibiotics to treat more than 40 million Americans who might be exposed to anthrax, as well as other vaccines and drugs to combat a wide range of illnesses.

One of these, smallpox, used to be a major concern. The World Health Organization had declared the disease eradicated in 1980, but scientists have long suspected that countries or labs might be hiding samples of the deadly virus that could fall into terrorist hands. But the Strategic National Stockpile has virtually removed the disease from the list of America’s bioterrorism concerns, according to James W. LeDuc, associate director of the University of Texas’s Galveston National Laboratory. The number of smallpox-vaccine doses in the stockpile has increased from 90,000 before 9/11 to 300 million today. “In the event of a smallpox outbreak today, we would have access to enough vaccine for every American,” LeDuc says. “It cost close to $1 billion, but it is a tremendous insurance policy.”

Yet another advance is the crown jewel of the Department of Homeland Security’s biodefense effort: a vast research complex at Fort Detrick, an hour’s drive from the capital, centered on the new National Biodefense Analysis and Countermeasures Center. The NBACC already operates in temporary offices; its state-of-the-art, $150 million, 160,000-square-foot headquarters is scheduled to be completed by March 2009. It will contain a large Biosafety Level 4 (BSL-4) laboratory, authorized to work on the world’s most dangerous germs, such as Ebola and Marburg, for which neither vaccines nor cures yet exist. Its 150 scientists will characterize existing biological threats—the bulk of its research—identify future sources of potential vulnerability, and conduct the kind of bioforensic research that was used in Amerithrax in the event of future bioterrorist attacks.

The agency’s original plan was to operate the NBACC mostly in secret by classifying the entire center as a Sensitive Compartmented Information Facility (SCIF, pronounced “skiff”)—a place where top-secret information and materials could be stored and discussed. But the NBACC’s new director, J. Patrick Fitch, says that he intends to operate the lab with the greatest possible transparency. “Eighty percent of our projects and their results will be unclassified, and we will encourage our scientists to publish,” he says. While his facility would be “SCIFable” in an emergency, he intends to encourage as much interaction as possible between NBACC scientists and their American and foreign counterparts. “In such a fast-moving area,” he explains, “it’s self-defeating to isolate yourself.”

Fitch also denies reports that the lab plans to invent new superbugs just to see if it can be done. “Our research must be grounded in indications of a real threat and in science,” he says. And in another course correction, Fitch has appointed a panel of seven independent scientists to review the lab’s work three times a year to ensure that its research is not only safe, but in compliance with the 1972 international treaty banning the acquisition, production, and development of germ weapons for anything other than defensive purposes. The panel has allayed some of the concerns of Tara O’Toole, director of the University of Pittsburgh’s Center for Biosecurity, formerly a forceful critic of the lab and now a panel member. Fitch has made “earnest efforts to be responsible and transparent and must continue on this path,” says O’Toole.

Taken together, all these achievements have dramatically altered the biodefense landscape since the anthrax letter attacks, many analysts agree. “I don’t think there’s any doubt that we are safer today than we were seven years ago,” said Michael Chertoff, the secretary of the Department of Homeland Security, at a forum on September 10, though he also warned Americans against complacency. “Getting the ship of state to move 10 degrees to port is a big deal,” says Bernard. “You can always show how it might have been done better. But this has been tantamount to putting a man on the moon”—an exercise in “imperfect incrementalism,” as one administration official calls it. “I really don’t think we went down any major wrong roads,” Bernard ventures. “The perfect is inevitably the enemy of the good.”

But many experts believe that the government has taken detours from the highway to better biosecurity. Some even question what had looked like unqualified successes. Consider the Amerithrax investigation. The impressive scientific achievement that enabled the FBI to trace the anthrax in the letters back to the RMR-1029 flask has been largely overshadowed by allegations that the bureau once again rushed to judgment in blaming Bruce E. Ivins, one of more than 100 researchers at the Army’s biodefense lab who had access to the flask. Ivins committed suicide before he could be indicted.

According to several analysts who attended the bureau’s classified briefings on its investigation, the case is based largely on the kind of circumstantial information that led the FBI to finger Steven J. Hatfill as the likely culprit five years ago, and would have been unlikely to hold up in court. Hatfill, who doggedly fought his designation as a “person of interest” in the press and the courts for five years, was recently vindicated when the FBI paid him $5.8 million for the damage done to his reputation and career.

Moreover, while there is no doubt that Ivins had psychological problems that ultimately prompted his suicide, his attorney and family say that being subjected to such intense federal scrutiny was also partly to blame. And those who worked most closely with the eccentric scientist at Fort Detrick have openly challenged the bureau’s claim that Ivins was the perpetrator. Critics have called for more congressional hearings and even an independent commission to examine the entire Amerithrax investigation. In any event, the controversy over the case highlights the continuing difficulty of “attribution”—identifying the source of an attack so that its sponsors can be punished and future strikes deterred—even in an age of sophisticated bioforensics.

Some scientists—though they’re in the minority—view the proliferation of high-containment, top-security labs as a liability. Government officials like Anthony S. Fauci, the National Institutes of Health official who heads biodefense research, maintain that there was a critical shortage of such labs in 2001 and that the expansion will eventually result in better diagnostics and next-generation drugs. But Elisa D. Harris, a biosecurity expert at the University of Maryland, warned in the New York Times that the increase of high-containment labs and undertrained personnel was creating the very threat that it was intended to thwart. “The correct response to the anthrax letter attacks,” agrees Richard H. Ebright, a biochemist at Rutgers, “should have been to curtail the number of people and institutions with access to the deadliest agents and to dramatically increase security surrounding such research.”

Keith Rhodes, chief technologist at the Government Accountability Office, also warned Congress last October that the nation was at “greater risk” because of the increase of BSL-4 labs from five before 2001 to 15 today. His agency estimated that at least 15,000 technicians were working with dangerous pathogens in BSL-3 and BSL-4 labs—the vast majority of them for the first time—and that, though no one knew exactly how many public and private BSL-3 labs were in operation, the number was “surely in the thousands.” Moreover, he added, articulating a more widely shared concern, though 12 federal agencies were involved in some aspect of biological research, no single agency was responsible for monitoring the labs and managing the risks. While most of the scientists in the field welcome the additional lab capacity, they do worry about the lack of direct federal oversight and insufficient safety and security standards at these new labs. “We have not wildly expanded over what we need,” O’Toole says. “But we do need better training and to ensure that the labs and people in them conform to rigorous standards.”

As for the Strategic National Stockpile, its drugs will help combat bioterrorist attacks only if they can be delivered and distributed rapidly enough—and at present, the government doubts that they can be. “When we began in 2001, we could get antibiotics to people in 2.5 weeks,” says a senior official. “Today it takes four days, but that’s still not good enough. We need to do it in two days. We’ve moved mountains, but not enough of them.”

Among the recommendations that President Bush endorsed in the June meeting was a proposal to support additional testing of drug and vaccine delivery by mail and other methods. For example, instead of using mainly public buildings as PODs (points of distribution), as New York and other cities currently plan, government might also use large commercial enterprises like Wal-Mart. But even then, who would administer the drugs after an attack? A federal scheme in 2003 to inoculate half a million health-care workers against smallpox foundered after Washington failed to provide guarantees that workers who fell ill because of the vaccine would be compensated; only 40,000 workers volunteered to be vaccinated, 8 percent of the target.

Supplying the Strategic National Stockpile is another challenge. BioShield is a multibillion-dollar fund to encourage the development of vaccines and other drugs for the stockpile. But major pharmaceutical companies have proved reluctant to develop drugs whose main customer would be the government, fearing that the market for such drugs is likely to be limited, absent an attack, and that research costs wouldn’t be recouped. As for smaller firms, the government was forced in 2006 to cancel its contract with VaxGen, a biotech start-up that had never produced a vaccine before. VaxGen was to help supply 75 million more doses of a safer, second-generation anthrax vaccine, but repeatedly missed its deadlines.

Even if drugs can be manufactured sufficiently and delivered promptly, they depend on our ability to detect an attack in the first place. In a project called “BioWatch,” Washington has deployed equipment in more than 30 cities to sniff out deadly germs in the air—but because the sniffers’ filters must be checked manually and transported to labs for diagnosis, detecting the germs can take up to 36 hours. New York City has been testing six automated sensors that detect the existence of an unwelcome pathogen more quickly—the only such units yet deployed in the nation. “We want to know when something happens as soon as it happens,” says Dani-Margot Zavasky, an infectious-disease specialist who advises the NYPD on WMD-related medical issues.

But the Department of Homeland Security has rejected the city’s appeal for more units, which last September led police commissioner Raymond W. Kelly, for whom counterterrorism is a religion, to berate BioWatch’s “anemic budget” and the “low priority” that the federal government places on biosurveillance. (Amy Kudwa, a DHS spokesperson, counters that the department’s investment of almost $400 million in BioWatch proves its commitment to the detection effort.)

Then there are the federal government’s bureaucratic mistakes. Numerous officials, advisors, and independent analysts criticize what they say is the government’s lack of emphasis on the personnel needed to staff labs, produce drugs, and create and operate detectors and other expensive technology. “It is our passion for things, for quick technical fixes, gadgets and more labs, better detectors, that obscures our real needs and vulnerabilities,” says Colonel David R. Franz, a former commander of the defense lab at Fort Detrick. Federal budgetary decisions have reflected this bias, health officials complain, with cuts almost invariably targeting not equipment but nurses, lab technicians, and other “first responders” critical in the immediate aftermath of an attack.

Complaints about the government’s episodic focus on biosecurity are also common. While Washington threw money at biosecurity soon after the anthrax letter attacks, it took the White House almost three years to produce a “blueprint” for the nation’s future biodefense program—and that blueprint mandated that the net assessment be completed in four more years. Further, the White House didn’t lay out a strategy for public health and medical preparedness for catastrophes until last October, O’Toole says. “Although we’re in better shape than we were before the anthrax attacks, biosecurity no longer seems to have national priority,” says Richard Falkenrath, the NYPD’s deputy commissioner for counterterrorism, who previously coordinated biodefense in the Bush White House.

A lack of coordination among federal agencies in biodefense preparations is another problem, critics say. The federal government has no single, central oversight to ensure that its departments’ many grants are financing research likely to result in useful drugs, vaccines, and equipment. It has, in sum, no obvious way to determine if the billions allocated to biodefense are being spent wisely. “There is clearly a need to rethink how we would respond to a major terrorist event,” says Penrose “Parney” Albright, a former senior defense official and national security expert, “and for a biodefense management system that sets requirements and oversees agency programs to ensure they are responsive to those needs.”

Stories about federal turf battles abound, too—in particular, the dysfunctional split between the Department of Health and Human Services (DHHS) and that younger, bureaucracy-bound behemoth, the Department of Homeland Security. At a conference in Baltimore last August, scientists from the Centers for Disease Control and Prevention, a notoriously independent fiefdom within DHHS, disclosed that they no longer had confidence that the BioWatch monitors would detect the presence of germs other than anthrax and plague—a concern that they had not previously shared with Homeland Security, which is responsible for the monitors.

And two key papers in the net assessment—one by Robert P. Kadlec, a physician who is now the White House’s senior director for biological defense policy, and another by Albright—say that America remains vulnerable partly because its early plans rested on unrealistic assumptions about the federal government’s role in responding to bioterrorism. “After the anthrax mailings, we initially thought that because all crises are local, our states and high-value-target cities would be able to manage a serious or sustained attack if they received enough federal dollars to help them prepare,” says an official privy to the ongoing debate in Washington. “We now know, as Hurricane Katrina demonstrated, that the federal government would have to take the lead in a true bioterror emergency.”

But the feds aren’t yet prepared for taking that lead. While they are ready to deliver an emergency supply of vaccine from the stockpile to a state, say, they still have no plans in place to deploy the army or order governors to send the National Guard to help with distribution of the vaccine. DHS officials say that they have “plans and guidelines in place” to help cities respond to bioterrorism, but city officials call these plans vague and “nonoperational.”

Two of the papers written for the “net assessment” discuss New York City in particular, and their conclusions are apparently grim. One, a 50-page study of New York’s response plans and its “decision sequence” in the event of an attack, was written by Edward Hamilton, a former New York deputy mayor, and Terrance Leighton, a scientist at Children’s Hospital Oakland Research Institute in California. According to experts who described the study, it found that despite New York’s extensive plans and preparations, the city would be severely challenged by a major anthrax attack and would have difficulty recovering.

Officials who had read the papers said that neither New York nor any other American city had plans that could manage a true catastrophe. The city would struggle to distribute drugs and transport public health emergency workers, since contamination would probably close its subways. The city has no decontamination plans; decontaminating skyscrapers would be a forbidding challenge; and there are no federal standards on how clean an area must be before it can be reoccupied. “No locality can set such standards,” one expert says. “This is yet another federal function that has not been done, and it is not trivial.”

The Hamilton-Leighton study builds on earlier work by Lawrence Wein, a Stanford University business school professor. In 2003, he calculated that a large aerosolized anthrax attack in New York might result in 100,000 deaths, even if early cases were successfully diagnosed and drugs quickly delivered and taken. Two years later, he calculated that decontaminating New York by traditional methods could cost well over $20 billion and take 314 years. Wein has also argued that current plans for distribution of antibiotics from PODs could result in delays costing up to 10,000 lives a day.

In a new study for the net assessment, experts say, Wein urges the government to consider distributing antibiotics before an attack, or after one, through a variety of alternative methods—including by mail to people’s homes, the approach he endorsed in his earlier work. The government could encourage postal workers to come to work—a recent DHHS study predicts absentee rates of some 40 percent during a severe pandemic—by guaranteeing them and their families early doses of antidotes. New York officials, however, doubt that drugs could be delivered by the postal system; they fear that postal workers would stay home regardless, and that New York would be unable to provide sufficient security for those who did show up.

One bright spot is that New York has bolstered the federal BioWatch initiative by investing heavily in its own biological surveillance programs. The city electronically monitors everything from over-the-counter drug sales to hospital entries to emergency-clinic visits, says Isaac B. Weisfuse, New York’s deputy commissioner of public health, and the city’s 6,000-person health department is widely regarded as among the nation’s best. But technologically speaking, most public health networks lag a decade behind New York’s and can afford neither the technology nor the personnel in which the city has invested.

The challenge grows larger each day as the biotech revolution spreads skills and knowledge around the globe. Margaret Hamburg, a physician who served in senior health posts in the federal government and in New York City, calls the explosion of biotechnology “frightening.” In a speech last September, she speculated on a variety of weapons, some already existent and others still being researched, that foes might deploy one day: aerosol technology to deliver infectious agents more efficiently into the lungs; gene therapy vectors that could cause a permanent change in an infected person’s genetic makeup; “stealth” viruses that could lie dormant in victims until triggered; and biological agents intentionally engineered to be resistant to available antibiotics or evade immune response.

Those who regard such weapons as permanently beyond terrorists’ capability should bear in mind that techniques that were theoretical just a decade ago can now be performed by high school chemistry students. Recent research by former Navy secretary and now Barack Obama advisor Richard J. Danzig drives the point home. While it was known that Aum Shinrikyo, the Japanese group that released nerve gas into the Tokyo subway in 1995, had experimented with botulism and anthrax and had sought to obtain Ebola, scientists once believed that the group’s efforts to weaponize anthrax had failed because it had relied on a harmless vaccine strain. But Danzig’s recent interviews with cult members in Japan suggest that over a decade ago, Aum nearly succeeded in making a benign strain lethal through genetic modification. “No one should take comfort in Aum’s failure,” said Hamburg. “The tools of biotechnology have jumped light-years since then.”

Hamburg’s observation underscores the ongoing need for intelligence about America’s rivals and enemies—in fighting bioterrorism, an ounce of prevention really is worth a pound of cure, and our first line of defense against a devastating biological attack is still the intelligence community, whose knowledge of what is being cooked up in foreign laboratories remains inadequate. “In bioterrorism,” warns Franz, “intentions are more important than capabilities.”

Should an attack occur, there is no question that our capacity to respond, while improved, would still fall short. “What we’ve been trying to prepare for is obviously unprecedented,” says one senior official. “Pandemics are tough enough, and for those there are precedents—the 1918 flu and even seasonal outbreaks. It’s so much harder to prepare for something you’ve never experienced. You’re obviously going to make some mistakes.”