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A U.S. Army scientist stands near the letters used in the 2001 anthrax attacks (Photo courtesy of FBI).

This story is a joint project with ProPublica, PBS Frontline and McClatchy. The story will air on Frontline on Oct. 11. Check local listings.

WASHINGTON – Months after the anthrax mailings that terrorized the nation in 2001, and long before he became the prime suspect, Army biologist Bruce Ivins sent his superiors an email offering to help scientists trace the killer.

Part 1: New Evidence Adds Doubt to FBI’s Case Against Anthrax Suspect

Part 2: Did Bruce Ivins Hide Attack Anthrax From the FBI?

Part 3: Was FBI’s Science Good Enough to ID Anthrax Killer?

Video: The Anthrax Files

Interactive: Read and annotate the case documents

Editor’s Note: About the Case of the Anthrax Letters

Already, an FBI science consultant had concluded that the attack powder was made with a rare strain of anthrax known as Ames that’s used in research laboratories worldwide.

In his email, Ivins volunteered to help take things further. He said he had several variants of the Ames strain that could be tested in “ongoing genetic studies” aimed at tracing the origins of the powder that had killed five people. He mentioned several cultures by name, including a batch made mostly of Ames anthrax that had been grown for him at an Army base in Dugway, Utah.

Seven years later, as federal investigators prepared to charge him with the same crimes he’d offered to help solve, Ivins, who was 62, committed suicide. At a news conference, prosecutors voiced confidence that Ivins would have been found guilty. They said years of cutting-edge DNA analysis had borne fruit, proving that his spores were “effectively the murder weapon.”

To many of Ivins’ former colleagues at the germ research center in Fort Detrick, Md., where they worked, his invitation to test the Dugway material and other spores in his inventory is among numerous indications that the FBI got the wrong man.

What kind of murderer, they wonder, would ask the cops to test his own gun for ballistics?

To prosecutors, who later branded Ivins the killer in a lengthy report on the investigation, his solicitous email is trumped by a long chain of evidence, much of it circumstantial, that they say would have convinced a jury that he prepared the lethal powder right under the noses of some of the nation’s foremost bio-defense scientists.

PBS’ Frontline, McClatchy and ProPublica have taken an in-depth look at the case against Ivins, conducting dozens of interviews and reviewing thousands of pages of FBI files. Much of the case remains unchallenged, notably the finding that the anthrax letters were mailed from Princeton, N.J., just steps from an office of the college sorority that Ivins was obsessed with for much of his adult life.

Bruce Ivins
Bruce Ivins

But newly available documents and the accounts of Ivins’ former colleagues shed fresh light on the evidence and, while they don’t exonerate Ivins, are at odds with some of the science and circumstantial evidence that the government said would have convicted him of capital crimes. While prosecutors continue to vehemently defend their case, even some of the government’s science consultants wonder whether the real killer is still at large.

Prosecutors have said Ivins tried to hide his guilt by submitting a set of false samples of his Dugway spores in April 2002. Tests on those samples didn’t display the telltale genetic variants later found in the attack powder and in sampling from Ivins’ Dugway flask.

Yet records discovered by Frontline, McClatchy and ProPublica reveal publicly for the first time that Ivins made available at least three other samples that the investigation ultimately found to contain the crucial variants, including one after he allegedly tried to deceive investigators with the April submission.

Paul Kemp, who was Ivins’ lawyer, said the government never told him about two of the samples, a discovery he called “incredible.” The fact that the FBI had multiple samples of Ivins’ spores that genetically matched anthrax in the letters, Kemp said, debunks the charge that the biologist was trying to cover his tracks.

Asked about the sample submissions, as well as other inconsistencies and unanswered questions in the Justice Department’s case, lead federal prosecutor Rachel Lieber said she was confident that a jury would have convicted Ivins.

“You can get into the weeds, and you can take little shots of each of these aspects of our vast, you know, mosaic of evidence against Dr. Ivins,” she said in an interview. But in a trial, she said, prosecutors would have urged jurors to see the big picture.

“And, ladies and gentlemen, the big picture is, you have, you know, brick upon brick upon brick upon brick upon brick of a wall of evidence that demonstrates that Dr. Ivins was guilty of this offense.”

Scientists who worked on the FBI’s case do not all share her certainty. Claire Fraser-Liggett, a genetics consultant whose work provided some of the most important evidence linking Ivins to the attack powder, said she would have voted to acquit.

“I don’t know how it would have been possible to convict him,” said Fraser-Liggett, the director of the University of Maryland’s Institute for Genome Sciences. “Should he have had access to a potential bio-weapon, given everything that’s come to light? I’d say no. Was he just totally off the wall, from everything I’ve seen and read? I’d say yes.

“But that doesn’t mean someone is a cold-blooded killer.”

The Justice Department formally closed the anthrax case last year. In identifying Ivins as the perpetrator, prosecutors pointed to his deceptions, his shifting explanations, his obsessions with the sorority and a former lab technician, his penchant for taking long drives to mail letters under pseudonyms from distant post offices and, after he fell into drinking and depression with the FBI closing in, his violent threats during group therapy sessions. An FBI search of his home before he died turned up a cache of guns and ammunition.

Most of all, though, prosecutors cited the genetics tests as conclusive evidence that Ivins’ Dugway spores were the parent material to the powder.

Yet, the FBI never could prove that Ivins manufactured the dry powder from the type of wet anthrax suspensions used at Fort Detrick. It couldn’t prove that he scrawled letters mimicking the hateful rhetoric of Islamic terrorists. And it couldn’t prove that he twice slipped away to Princeton to mail the letters to news media outlets and two U.S. senators; it could prove only that he had an opportunity to do so undetected.

The $100 million investigation did establish that circumstantial evidence could mislead even investigators armed with unlimited resources.

Before focusing on Ivins, the FBI spent years building a case against another former Army scientist. Steven Hatfill had commissioned a study on the effectiveness of a mailed anthrax attack and had taken ciprofloxacin, a powerful antibiotic used to treat or prevent anthrax, around the dates of the mailings. Then-Attorney General John Ashcroft called Hatfill a “person of interest,” and the government eventually paid him a $5.8 million settlement after mistakenly targeting him.

Ivins’ colleagues and some of the experts who worked on the case wonder: Could the FBI have made the same blunder twice?

Did Ivins have a motive?

Growing up in Ohio, the young Bruce Ivins showed an early knack for music and science. But his home life, described as “strange and traumatic” in a damning psychological report released after his death, left scars that wouldn’t go away.

The report, written by a longtime FBI consultant and other evaluators with court-approved access to Ivins’ psychiatric records, said Ivins was physically abused by a domineering and violent mother and mocked by his father. Ivins developed “the deeply felt sense that he had not been wanted,” the authors found, and he learned to cope by hiding his feelings and avoiding confrontation with others.

Ivins attended the University of Cincinnati, staying there until he earned a doctoral degree in microbiology. In his sophomore year, prosecutors say, the socially awkward Ivins had a chance encounter that influenced his life: A fellow student who belonged to the Kappa Kappa Gamma sorority spurned him.

For more than 40 years, even as a married man, Ivins was obsessed with KKG, a fixation that he later admitted drove him to multiple crimes. Twice he broke into chapters, once climbing through a window and stealing the sorority’s secret code book.

After taking a research job at the University of North Carolina at Chapel Hill, Ivins discovered that a doctoral student, Nancy Haigwood, was a KKG alumna, and he tried to strike up a friendship. When she kept him at a distance, Ivins turned stalker, swiping her lab book and vandalizing her fiance’s car and the fence outside her home. Two decades later, when Haigwood received an FBI appeal for scientists nationwide to help find the anthrax mailer, she instantly thought of Ivins and phoned the FBI. Investigators didn’t home in on him for years.

When they did, the mailbox in Princeton, which also was near the home of a former Fort Detrick researcher whom Ivins disliked, loomed large.

“This mailbox wasn’t a random mailbox,” said Edward Montooth, a recently retired FBI agent who ran the inquiry. “There was significance to it for multiple reasons. And when we spoke to some of the behavioral science folks, they explained to us that everything is done for a reason with the perpetrator. And you may never understand it because you don’t think the same way.”

Ivins was a complicated, eccentric man. Friends knew him as a practical jokester who juggled beanbags while riding a unicycle, played the organ in church on Sundays and spiced office parties with comical limericks. William Hirt, who befriended Ivins in grad school and was the best man at his wedding, described him as “a very probing, spiritual fellow that wouldn’t hurt a fly.”

Ivins gained self-esteem and status in his job as an anthrax researcher at the U.S. Army Medical Research Institute of Infectious Diseases at Fort Detrick in Frederick, Md.

Even so, his fixations wouldn’t quit.

He became so obsessed with two of his lab technicians that he sent one of them, Mara Linscott, hundreds of email messages after she left to attend medical school in Buffalo, N.Y. Ivins drove to her home to leave a wedding gift on her doorstep. When she left, he wrote a friend, “it was crushing,” and called her “my confidante on everything, my therapist and friend.”

Later, after snooping on email messages in which the two technicians discussed him, Ivins told a therapist that he’d schemed to poison Linscott but aborted the plan at the last minute.

USAMRIID was once a secret germ factory for the Pentagon, but the institute’s assignment shifted to vaccines and countermeasures after the United States and Soviet Union signed an international treaty banning offensive weapons in 1969. A decade later, a deadly leak from a secret anthrax-making facility in the Soviet city of Sverdlovsk made it clear that Moscow was cheating and prompted the United States to renew its defensive measures.

Ivins was among the first to be hired in a push for new vaccines.

By the late 1990s, he was one of USAMRIID’s top scientists, but the institute was enmeshed in controversy. Worried that Iraqi leader Saddam Hussein had made large quantities of anthrax before the 1991 Persian Gulf War, President Bill Clinton had ordered that all military personnel, not just those in war zones, be inoculated with a 1970s-era vaccine. But soldiers complained of ill health from the vaccine, some blaming it for the symptoms called Gulf War Syndrome.

Later, Karl Rove, political adviser to new President George W. Bush, suggested that it was time to stop the vaccinations. Further, a Pentagon directive—although quickly reversed in 2000—had ordered a halt to research on USAMRIID’s multiple anthrax-vaccine projects.

Federal prosecutors say these developments devastated Ivins, who’d devoted more than 20 years to anthrax research that was now under attack.

“Dr. Ivins’ life’s work appeared destined for failure, absent an unexpected event,” said the Justice Department’s final report on the anthrax investigation, called Amerithrax. Told by a supervisor that he might have to work on other germs, prosecutors say Ivins replied: “I am an anthrax researcher. This is what I do.”

Ivins’ former bosses at Fort Detrick call that Justice Department characterization wrong. Ivins had little to do with the existing vaccine; rather, he was working to replace it with a better, second-generation version, they say.

In the summer of 2001, Ivins shouldn’t have had any worries about his future, said Gerard Andrews, who was then his boss as the head of USAMRIID’s Bacteriology Division. “I believe the timeline has been distorted by the FBI,” Andrews said. “It’s not accurate.”

Months earlier, Andrews said, the Pentagon had approved a full year’s funding for research on the new vaccine and was mapping out a five-year plan to invest well over $15 million.

Published reports have suggested that Ivins had another motive: greed. He shared patent rights on the new vaccine. If it ever reached the market, after many more years of testing and study, federal rules allowed him to collect up to $150,000 in annual royalties.

If that was his plan, it didn’t go well. After the attacks, Congress approved billions of dollars for bio-defense and awarded an $877.5 million contract to VaxGen Inc. to make the new vaccine but scrapped it when the California firm couldn’t produce the required 25 million doses within two years.

Ivins received modest royalty payments totaling at least $6,000. He told prosecutors he gave most of the money to others who had worked with him on the project, said Kemp, his defense attorney.

Kemp said prosecutors told him privately that they’d dismissed potential financial returns as a motive. That incentive wasn’t cited in the Justice Department’s final report.

Did Ivins have an opportunity?

The relatively lax security precautions in place at U.S. defense labs before the mailings and Sept. 11 terrorist attacks offered many opportunities for a deranged scientist. Prosecutors said Ivins had easy access to all the tools needed to make the attack spores and letters.

Researchers studying dangerous germs work in a “hot suite,” a specially designed lab sealed off from the outside world. The air is maintained at “negative pressure” to prevent germs from escaping. Scientists undress and shower before entering and leaving.

Watch the video report
Like many of his colleagues at Fort Detrick, Ivins dropped by work at odd hours. In the summer and fall of 2001, his night and weekend time in the hot suite spiked: 11 hours and 15 minutes in August, 31 hours and 28 minutes in September and 16 hours and 13 minutes in October. He’d averaged only a couple of hours in prior months. Swiping a security card each time he entered and left the suite, he created a precise record of his visits. Rules in place at the time allowed him to work alone.

Sometime before the mailings, prosecutors theorize, Ivins withdrew a sample of anthrax from his flask—labeled RMR-1029—and began to grow large quantities of the deadly germ. If so, his choice of strains seemed inconsistent with the FBI’s portrait of him as a cunning killer. Surrounded by a veritable library of germs, they say, Ivins picked the Dugway Ames spores, a culture that was expressly under his control.

Using the Ames strain “pointed right at USAMRIID,” said W. Russell Byrne, who preceded Andrews as the chief of the Bacteriology Division and who’s among those convinced of Ivins’ innocence. “That was our bug.”

Federal prosecutors have declined to provide a specific account of when they think Ivins grew spores for the attacks or how he made a powder. But the steps required are no mystery.

First, he would have had to propagate trillions of anthrax spores for each letter. The bug can be grown on agar plates (a kind of petri dish), in flasks or in a larger vessel known as a fermenter. Lieber, then an assistant U.S. attorney and lead prosecutor, said the hot suite had a fermenter that was big enough to grow enough wet spores for the letters quickly.

To make the amount of powder found in the letters, totaling an estimated 4 to 5 grams, Ivins would have needed 400 to 1,200 agar plates, according to a report by a National Academy of Sciences panel released in May. Growing it in a fermenter or a flask would have been less noticeable, requiring between a few quarts and 14 gallons of liquid nutrients.

Next was drying. Simple evaporation can do the job, but it also would expose other scientists in a hot suite. Lieber said the lab had two pieces of equipment that could have worked faster: a lyophilizer, or freeze dryer; and a smaller device called a “Speed Vac.”

Investigators haven’t said whether they think the Sept. 11 attacks prompted Ivins to start making the powder or to accelerate a plan already under way. However, records show that on the weekend after 9/11, Ivins spent more than two hours each night in the hot suite on Friday, Saturday and Sunday.

The next afternoon, Monday, Sept. 17, 2001, he took four hours of annual leave but was back at USAMRIID at 7 p.m. Because of their Sept. 18 postmarks, the anthrax-laced letters had to have been dropped sometime between 5 p.m. Monday and Tuesday’s noon pickup at a mailbox at 10 Nassau St. in Princeton.

If Ivins did make the seven-hour round-trip drive from Fort Detrick, he would’ve had to travel overnight. Investigators said he reported to USAMRIID at 7 a.m. Tuesday for a business trip to Pennsylvania.

Did Ivins have the means?

Colleagues who worked with Ivins in the hot suite and think that he’s innocent say he’d never worked with dried anthrax and couldn’t have made it in the lab without spreading contamination.

Andrews, Ivins’ former boss, said Ivins didn’t know how to use the fastest process, the fermenter, which Andrews described as “indefinitely disabled,” with its motor removed. He said the freeze dryer was outside the hot suite, so using it would have exposed unprotected employees to lethal spores.

Without a fermenter, it would have taken Ivins “30 to 50 weeks of continuous labor” to brew spores for the letters, said Henry Heine, a former fellow Fort Detrick microbiologist who’s now with the University of Florida. Prosecutors and a National Academy of Sciences panel that studied the case said the anthrax could have been grown as quickly as a few days, though they didn’t specify a method.

FBI searches years later found no traces of the attack powder in the hot suite, lab and drying equipment.

Fraser-Liggett, the FBI’s genetics consultant, questioned how someone who perhaps had to work “haphazardly, quickly” could have avoided leaving behind tiny pieces of forensically traceable DNA from the attack powder.

Lieber, the Justice Department prosecutor, said the FBI never expected to find useable evidence in the hot suite after the equipment had been cleaned multiple times.

“This notion that someone could have stuck a Q-tip up in there and found, you know, a scrap of ‘1029’ DNA, I think is, with all due respect, it’s inconsistent with the reality of what was actually happening,” she said.

Yet, in 2007, six years after the letters were mailed, the FBI carefully searched Ivins’ home and vehicles looking for, among other things, anthrax spores. None were found.

The first round of anthrax letters went to an eclectic media group: Tom Brokaw, the NBC anchor; the tabloid newspaper the New York Post; and the Florida offices of American Media Inc., which publishes the National Enquirer. Just over two weeks later, on Oct. 4, jittery Americans were startled to learn that a Florida photo editor, Robert Stevens, had contracted an extremely rare case of inhalation anthrax.

Stevens died the next day. As prosecutors tell the story, Ivins would hit the road to New Jersey again as early as Oct. 6, carrying letters addressed to the offices of Democratic Sens. Patrick Leahy, the Judiciary Committee chairman from Vermont, and Tom Daschle of South Dakota, the Senate majority leader.

Unlike the brownish, granular, impure anthrax in the earlier letters, this batch was far purer, with tiny particles that floated like a gas, making them more easily inhaled and therefore deadlier.

Just a few hours before those letters were dropped at Nassau Street, investigators had a scientific breakthrough: Paul Keim, an anthrax specialist at Northern Arizona University, verified that the spores in Stevens’ tissues were the Ames strain of anthrax.

“It was a laboratory strain,” Keim recalled later, “and that was very significant to us.”

On Oct. 15, an intern in Daschle’s office opened a nondescript envelope with the return address “4th Grade, Greendale School, Franklin Park, NJ 08852.” A white powder uncoiled from the rip, eventually swirling hundreds of feet through the Hart Senate Office Building, where dozens of senators work and hold hearings. It would take months and millions of dollars to fully cleanse the building of spores.

Ill-prepared to investigate America’s first anthrax attack, the FBI didn’t have a properly equipped lab to handle the evidence, so the Daschle letter and remaining powder were taken to Fort Detrick.

Among those immediately enlisted to examine the attack powder: Bruce Ivins.

The FBI would turn to Ivins time and again in the months and years ahead. At this early moment, he examined the Daschle spores and logged his observations with scientific exactitude. The quality, he determined, suggested “professional manufacturing techniques.”

“It is an extremely pure preparation, and an extremely high concentration,” Ivins wrote on Oct. 18, 2001. “These are not ‘garage’ spores.”

Part 2: Did Bruce Ivins Hide Attack Anthrax From the FBI?

In early 2002, federal agents who were hunting the anthrax killer were trying to winnow a suspect list that numbered in the hundreds. They knew only that they were looking for someone with access to the rare Ames strain of anthrax used in research labs around the world. Profilers said the perpetrator probably was an American with “an agenda.”

The powder-laced letters, which killed five people, contained no fingerprints, hair or human DNA but did offer one solid microscopic clue: The lethal spores in the powder were dotted with genetically distinct variants known as morphs.

So agents set out on an arduous task: Collect samples from Ames anthrax cultures around the world, sort through them and find one with morphs that matched the attack powder. Then they’d have a line on where the murder weapon was made and, perhaps, the identity of the killer.

Bruce Ivins, an Army scientist at Fort Detrick, Md., had a good idea where the inquiry was headed. In the months after the attacks, he’d schooled federal agents in the intricacies of anthrax, explaining how the telltale morphs can arise from one generation to the next.

In April 2002, Ivins did something that investigators would highlight years later as a pillar in the capital murder case that was being prepared against him before he committed suicide in 2008: He turned over a set of samples from his flask of Ames anthrax that tested negative, showing no morphs. Later, investigators would take their own samples from the flask and find four morphs that matched those in the powder.

Rachel Lieber, the lead prosecutor in a case that will never go to trial, thinks that Ivins manipulated his sample to cover his tracks. “If you send something that is supposed to be from the murder weapon, but you send something that doesn’t match, that’s the ultimate act of deception. That’s why it’s so important,” Lieber said.

However, a re-examination of the anthrax investigation by Frontline, McClatchy and ProPublica turned up new evidence that challenges the FBI’s narrative of Ivins as a man with a guilty conscience who was desperately trying to avoid being discovered.

Records recently released under the Freedom of Information Act show that Ivins made available a total of four sets of samples from 2002 to 2004, double the number the FBI has disclosed. And in subsequent FBI tests, three of the four sets ultimately tested positive for the morphs.

Paul Kemp, Ivins’ lawyer, said the existence of Ivins’ additional submissions was significant because it discredits an important aspect of the FBI’s case against his client. “I wish I’d known that at the time,” he said.

Heroes and suspects

To understand how investigators eventually came to see almost everything Ivins did or said as proof of his guilt, you have to return to the fall of 2001.

The FBI wasn’t equipped to handle deadly germs, so the attack powder was rushed to Fort Detrick, the home of the U.S. Army Medical Research Institute of Infectious Diseases.

From the beginning, Fort Detrick researchers played a prominent role in the inquiry. Ivins was among the most voluble, offering advice and a steady stream of tips about co-workers, foreign powers and former employees who might have carried out the attacks.

Investigators quickly recognized they were in an awkward situation. Any of the scientists could be the killer. Agents canvassed the tight-knit laboratory, inviting the researchers to finger their colleagues. “We were heroes in the morning and suspects in the afternoon,” recalled Jeffrey Adamovicz, at the time the deputy chief of the Bacteriology Division, where Ivins worked.

At 8:45 a.m. on Dec. 16, 2001, Ivins typed out an email to colleagues offering to provide Ames strain “for genetic analysis or sequencing by whomever.” He offered a sample of the original Ames anthrax taken in 1981 from a Texas cow and a collection of spores sent to Fort Detrick in 1997, mostly from the U.S. Army base in Dugway, Utah. Seven years later, prosecutors announced that they were certain the attack powder had been grown with germs from the Dugway flask Ivins was offering for scrutiny.

John Ezzell, a USAMRIID scientist at the time who assisted the FBI, said in an interview that Ivins likely didn’t think the technology could distinguish among Ames variants. But the record suggests otherwise.

On Jan. 23, 2002, Ivins gave an FBI agent a detailed tutorial on how to spot morphs in anthrax colonies. He also volunteered the names of two people who had the “knowledge and character” to have prepared and sent the letters while explaining that he’d never worked with powdered anthrax.

Ivins then showed the agent photos of anthrax morphs and said that “DNA sequencing should show the differences in genetics,” the mutations that make morphs grow differently. Ivins had good reason to understand the biology of morphs: One of his best friends at the lab, Patricia Worsham, had published a pioneering paper on the subject several years earlier.

In suggesting that the FBI use morphs to catch a killer, Ivins was proposing some cutting-edge science. No one had ever attempted to genetically fingerprint morphs, and the researchers advising the FBI weren’t even sure it could be done. Such genetic detective work, now commonplace, was in its infancy. Today, this technique is recognized as a precise but not foolproof method of identification.

A few weeks later, Ivins gave several people the sort of evidence he seemed to be suggesting they collect. He provided a sample to a colleague who wanted to look at the spores under a microscope. Then, on Feb. 27, Ivins drew anthrax from his flask, which he labeled RMR-1029, and provided it to investigators who were assembling the FBI’s worldwide library of anthrax. If prosecutors are right, the murderer had handed over his gun for testing.

But then the narrative took a strange twist. Perhaps deliberately, perhaps by chance, Ivins placed the spores in the wrong type of glass vessel. Investigators rejected the sample and told him to try again.

Sometime in the next few weeks, prosecutors contend, Ivins figured out for the first time that the morphs might trap him. Until then, they assert, he’d assumed that the anthrax in his flask was pure and therefore without morphs. But Paul Keim, the scientist who helped the FBI identify the attack strain, said it seemed implausible that Ivins thought his spores were morph-free. The Dugway culture included dozens of separate batches, most of which were grown at the Utah Army base in fermenters, an ideal breeding ground for morphs. Ivins, Keim said, was likely to have understood this.

In April 2002, Ivins prepared a third sample from RMR-1029. This time, his lawyer said, he plucked a sample using a technique called a “single colony pick,” a method biologists use to maintain purity when growing bacteria. Ultimately, this sample tested negative for the morphs. Prosecutors said they’re not even sure that the sample Ivins submitted came from the flask. If it did, they said, he obstructed justice, since their subpoena instructed scientists to capture diverse samples of spores that would be sure to reproduce any morphs. Ivins told investigators he’d followed standard procedures for microbiologists when he sampled just one colony.

Investigators eventually seized and tested the germs Ivins turned over to his colleague for microscopic examination, and found they tested positive for the morphs. Separately, they stumbled across a duplicate first submission from February: the material that had been rejected. It, too, was positive.

Curious conduct in the lab

In late April 2002, investigators confronted Ivins about reports that he’d been furtively testing for anthrax spores in his office and other areas outside the “hot suites,” the sealed rooms where researchers worked with deadly pathogens.

Ivins said that that was true and volunteered that he’d also conducted cleanups in the lab not once but twice — in December 2001, when he bleached over areas he’d found to be contaminated, and again in mid-April, when he conducted a search for errant anthrax spores.

These acts violated the lab’s standard procedure, which called for the safety office to investigate and clean up any contamination.

Ivins offered curious explanations. He said that in December, he had been trying to address the worries of a junior technician that sloppy handling of the attack powder had spread deadly spores through the lab. In April, against the advice of his supervisor, he launched his own tests after two researchers accidentally spilled a small amount of anthrax in the hot suite.

Asked why he didn’t inform safety officials of the possible dangers, Ivins told investigators he didn’t want to disrupt the FBI inquiry or alarm colleagues.

Whatever his motivation, subsequent tests showed Ivins had a point about failures to contain anthrax in the labs. His sampling showed that tiny amounts of anthrax of various strains had somehow seeped out of the hot suite and into his office. The Army ordered an investigation into why the lab’s safety procedures weren’t followed.

Despite Ivins’ puzzling behavior, investigators wouldn’t focus on him for years.

The anthrax inquiry was following another course and had zeroed in on a virologist named Steven Hatfill. A blunt character who boasted of his years in Rhodesia, Hatfill had a penchant for publicity, holes in his résumé and an unpublished novel that featured a Palestinian terrorist who attacks Washington with the bubonic plague. The evidence against him was entirely circumstantial.

Investigators remained on Hatfill’s trail until late 2006. By then, they’d searched his home, deployed anthrax-sniffing dogs and even emptied a pond, from which they removed a suspicious contraption. It was a turtle trap. No evidence of anthrax turned up. (Hatfill sued the government and received $5.8 million to settle the case).

A new Ivins sample

In early April 2004, Ivins was asked to help the FBI collect a complete set of cultures from Fort Detrick. Earlier, FBI agents had found 22 vials of anthrax that hadn’t been turned over. On April 6, a lab assistant found a test tube of material that appeared to have been removed from Ivins’ flask.

The assistant gave the germs to Henry Heine, a colleague of Ivins’ who happened to be in the building. Heine said he checked with Ivins, who told him to send a sample from the tube to the FBI. In an April 6 email, Ivins thanked Heine, acknowledging that the anthrax “was probably RMR-1029.”

Heine views this moment as a sign of his colleague’s innocence, pointing out that Ivins willingly turned over a sample he thought had originated from his flask. In an interview, Heine said there were no cameras in the building, that FBI agents weren’t monitoring the search and that Ivins easily could have prepared the sample himself and tampered with the evidence.

A day later, investigators seized Ivins’ flask, locking it in a safe double-sealed with evidence tape.

What happened next raises questions about the reliability of the FBI’s method for detecting morphs. The bureau separately ordered tests on Heine’s sample and a second one drawn from the same test tube. Records show conflicting results, one negative and one positive.

Does this mean the FBI’s tests for morphs were unreliable?

An FBI scientist said Ivins had told investigators the anthrax in the refrigerator had been diluted. This perhaps made the morphs undetectable in testing, said the scientist, who was made available to discuss the matter on the condition of anonymity.

Heine said the sample he sent wasn’t diluted.

“We can only go by what Bruce told us,” the FBI scientist replied.

Heine said he sent the FBI at least two additional samples from RMR-1029 that Ivins had shared with him. He said the FBI later told him both had tested negative for the morphs. The FBI scientist said the bureau could find no record of this.

Ivins’ hidden obsessions come out

In September 2006, the FBI assigned Edward Montooth to lead the anthrax inquiry. Montooth looked at the evidence through fresh eyes, and his attention quickly focused on the background and conduct of Ivins. By December, he told FBI Director Robert Mueller that Ivins had emerged as the prime suspect.

Investigators saw mounting evidence that the Fort Detrick scientist was hiding something.

They learned about his lifelong obsession with the Kappa Kappa Gamma sorority and discovered that the Princeton, N.J., mailbox into which the letters had been dropped was just yards from a KKG office. Ivins had mailed packages under assumed names, and his email messages expressed fears that he was paranoid, delusional or suffering from a split personality.

“When I get all steamed up, I don’t pout. I push Bruce aside, then I’m free to run about!” one read.

The genetic evidence seemed persuasive. Investigators had tested 1,059 Ames samples from U.S. and foreign labs and found only 10 with three or more of the morphs that genetically matched the letter powder. All traced back to Ivins’ flask.

The FBI identified 419 people at Fort Detrick and other labs who could have had access to the material. Prosecutors say each was investigated and cleared of possible involvement.

All of Ivins’ actions in the early days of the investigation were reinterpreted as signs of his guilt. Investigators recovered a portion of his first sample from RMR-1029—the test tubes that had been rejected because they were the wrong kind—and found that they contained the incriminating morphs. They contrasted that with the second sample from 2002—no morphs—and saw it as proof that Ivins had learned before submitting it that the Ames strain could be traced to his flask.

Asked about the April 2004 sample turned up by PBS Frontline, McClatchy and ProPublica that tested positive, prosecutor Lieber said it could be easily explained. Ivins had no choice: FBI agents were swarming through Fort Detrick looking for cultures of anthrax that hadn’t been submitted for genetic testing.

The unauthorized cleanup of the lab, the Justice Department said in its report last year, reflected a “guilty conscience.”

“The evidence suggests that Dr. Ivins knew where to swab because he knew where he had contaminated the building,” prosecutors wrote.

Even Ivins’ defenders had questioned his actions at the time. “I said, ‘Bruce, do you realize how bad this looks?’ And he was a little bit puzzled,” Adamovicz said. “I said, ‘This makes you look suspicious because it looks like you’re trying to hide something.’ Bruce, of course, denied that he was trying to hide anything. And again, in my view, I don’t think he was trying to hide anything. I think he couldn’t keep a secret if he had to.”

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The Army’s report on the incident didn’t portray it as nefarious. It confirmed the presence of Ames anthrax and two other anthrax strains in Ivins’ office. Ames also was found near a “pass box” through which Ivins had transferred one of the letters to the hot suite, the men’s changing area and Ivins’ office. But investigators were unable to nail down an original source for the contamination. They determined that it was unrelated to the minor spill in the hot suite and speculated that it could have resulted from the handling of the anthrax letters.

Investigators executed a search warrant at Ivins’ home and office. They found guns, a shooting range in his basement and Tasers. But swab after swab taken from every conceivable nook and cranny found not a single spore from the attack powder. Lieber said that was to be expected with a microbiologist trained to handle dangerous germs.

Claire Fraser-Liggett, a key genetics consultant for investigators, found such a dismissal troubling. “You think about all the efforts that had to go into decontaminating postal facilities, and the volatility of those spores and the fact that they were around for so long,” she said. “I think it represents a big hole, really gives me pause to think: How strong was this case against Dr. Ivins?”

Ivins sat down for detailed interviews with prosecutors in early 2008 and volunteered a series of damaging admissions with his lawyer present. He acknowledged making long drives at night while his wife slept and calmly recounted his obsession with Kappa Kappa Gamma, blindfolding and bondage. Sometimes his answers were incoherent, FBI summaries show. He couldn’t explain, for example, why he had spent so many late nights in the lab in the weeks before the letter attacks.

By the summer of 2008, Ivins was coming apart. He told his group therapy session, which he’d begun attending in recent months, that he was planning to get a gun so he could kill his enemies. The FBI searched his home again and seized several guns, bulletproof vests and 250 rounds of ammunition.

Ivins was briefly committed and then released. On July 26, he took an overdose of over-the-counter medication. Three days later, he was dead at 62. Neither he nor the prosecutors would ever have their day in court.

‘This was not an airtight case’

A week later, Justice Department officials called a news conference to describe their evidence against Ivins as some in Congress called for an independent investigation of the case.

“We believed that based on the evidence we had collected, we could prove his guilt to a jury beyond a reasonable doubt,” U.S. Attorney Jeffrey Taylor told reporters at the time. “Based on the totality of the evidence we had gathered against him, we are confident that Dr. Ivins was the only person responsible for these attacks.”

Prosecutors and investigators patiently laid out the case against Ivins. At its heart, they said, was the revolutionary science that had improbably traced the attack powder to a single flask.

“RMR-1029 was conclusively identified as the parent material to the anthrax powder used in the mailings,” the Justice Department wrote in its summary of the case.

Fraser-Liggett, who did some of the pioneering genetics work for the investigation, remains unconvinced.

“This was not an airtight case, by any means. You know, I think that, for an awful lot of people, there is a desire to really want to say that ‘yes, Ivins was the perpetrator. This case can reasonably be closed. And we can put this tragic chapter in U.S. history behind us,’ ” she said. “But I think part of what’s driving that is the fact that, if he wasn’t the perpetrator, then it means that person is still out there.”

Part 3: Was FBI’s Science Good Enough to ID Anthrax Killer?

WASHINGTON — In March 2007, federal agents convened an elite group of outside experts to evaluate the science that had traced the anthrax in the letters to a single flask at an Army lab in Maryland.

Laboratory work had built the heart of the case against Bruce Ivins, an Army researcher who controlled the flask. Investigators had invented a new form of genetic fingerprinting for the case, testing anthrax collected from U.S. and foreign labs for mutations detected in the attack powder.

Out of more than 1,000 samples, only eight had tested positive for four mutations found in the deadly germs sent to Congress and the news media.

Even so, the outside scientists, known as the “Red Team,” urged the FBI to do more basic research into how and when the mutations arose to make sure the tests were “sound” and the results unchallengeable.

Jenifer Smith, a senior manager at the FBI’s laboratory, shared the team’s concerns. Smith recalled that she was worried the FBI didn’t have a full understanding of the mutations and might see a trial judge throw out the key evidence.

“The admissibility hearing would have been very difficult,” Smith recalled in an interview. “They had some good science, but they also had some holes that would have been very difficult to fill.”

The FBI rebuffed the Red Team’s suggestion, describing it as “an academic question with little probative value to the investigation.”

Ivins committed suicide in July 2008 as prosecutors were preparing to charge him with capital murder in the cases of the five people killed by the anthrax mailings. Prosecutors announced that Ivins was the sole perpetrator and the parent material for the letters had come from his flask.

Three years later, that assertion remains an open question. A separate panel, from the National Academy of Sciences, found that prosecutors had overstated the certainty of their finding. Committee members said newly available testing methods could prove the FBI’s case much more definitively or lead to other potential suspects. But federal investigators, who closed the case more than a year ago, have expressed no interest in further scientific study of the evidence.

A re-examination of the anthrax case by PBS Frontline, McClatchy and ProPublica has raised new questions about some of the evidence against Ivins. The reporting uncovered previously undisclosed tensions between researchers who were trying to create a new form of forensic science and criminal investigators whose boss was under intense pressure from the president of the United States to crack a case that had few leads and hundreds of plausible suspects.

Paul Keim, an anthrax expert at Northern Arizona University who assisted in the FBI investigation, said he had qualms about whether the bureau’s groundbreaking laboratory method would have survived a rigorous legal review.

“I don’t think that it was ready for the courtroom at the time Bruce committed suicide,” Keim said.

If Ivins hadn’t killed himself, he said, the FBI would have launched a “hard push” for additional data that showed the method was reliable. Such research, he said, also could have shown it wasn’t valid.

Keim, a member of the Red Team who attended the March 2007 meeting in Quantico, Va., said he didn’t find out that the team’s call for further research had been rejected until a year later, after Ivins had committed suicide and prosecutors were hastily organizing a news conference to describe the science.

Keim and other scientists involved in the case said the strictures of a criminal investigation prevented them from talking to one another or sharing information as they would on a typical research effort.

“The investigation was being driven by a small group of bureau scientists and investigators,” Keim said. “Broader engagement with an expert panel sworn to secrecy would have been good. Having the best scientific consultants embedded would have been good.”

Jenifer Smith was the section chief of the Intelligence and Analysis Section in the FBI’s Weapons of Mass Destruction Directorate until 2009, and she observed the process from inside. During the anthrax case, she said, the FBI lab departed from its traditional procedures and allowed top investigators to influence how the science was conducted.

“They deviated from traditional lab practice in this particular case,” Smith said. “There were some political things going on behind the scenes, and it was embarrassing not to have this solved. Yes, it was a long, drawn-out investigation. But that’s when you don’t deviate from your practices.”

Rachel Lieber, the lead prosecutor, said law-enforcement officials did try to make sure the science was rigorously vetted. But Lieber said there were limits and that the science was only a piece of a much larger mosaic of evidence against Ivins.

“You look at the lines of a trial and where do we spend our resources,” Lieber said. “Are we doing a science project or are we looking for proof at trial? These are two very different standards.”

Unprecedented effort on science

Questions about the definitiveness of the scientific findings began to arise soon after prosecutors said Ivins was the anthrax mailer. U.S. Attorney Jeffrey Taylor declared without equivocation in August 2008 that the FBI had proved that Ivins’ flask, RMR-1029, “was the parent flask for the spores” used in the mailings — “effectively the murder weapon.”

At a briefing a few weeks later, the FBI’s lab director, Christian Hassell, was asked to give a “level of confidence” for the findings. “It’s very high,” he replied. “This whole exercise shows that they were traced back to a single flask.”

Another official at the briefing, who spoke on condition of anonymity as a ground rule, claimed that the Red Team of outside experts had vetted and approved the work and the FBI had heeded its calls for further research.

“We invited a cadre of scientists to conduct a Red Team review of the science that we performed, and we took their suggestions,” the official said. “We made additional experiments and the data available to the Red Team at their suggestion. And so all of the science that went behind this was well-reviewed.”

Critics on Capitol Hill weren’t mollified. Sen. Patrick Leahy, a Vermont Democrat and one of the intended recipients of an anthrax letter, said he didn’t believe that Ivins had acted alone. So FBI Director Robert Mueller announced in September 2008 that a panel of the National Academy of Sciences would conduct an independent review of the scientific findings.

The FBI didn’t wait for the outcome of those deliberations. In February 2010, with the panel still taking testimony, prosecutors announced that the case was closed, Ivins was the sole perpetrator and RMR-1029 was “conclusively identified as the parent material to the anthrax powder used in the mailings.”

Nearly a year to the day later, the outside committee looked at the same evidence differently, saying scientific data “provided leads” as to where the spores had come from but “alone did not rule out other sources.”

The tests that identified the flask as the source of the parent spores for the attack showed an association but didn’t “definitively demonstrate such a relationship,” the panel said.

When the case of the anthrax mailings broke in late 2001, genetic sequencing was in its early days. It was only a year earlier that two teams of American scientists had announced that they’d mapped the human genome. Work on anthrax was under way but incomplete.

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A fortuitous lab miscue may have provided the biggest break. Early in the investigation, a colleague of Ivins’ at the Army research facility in Fort Detrick, Md., left spores from one of the letters growing in a dish longer than she’d planned. When she next looked, the researcher, Terry Abshire, noticed something potentially significant: The cultures had small numbers of visually distinguishable colonies, or morphs, which are caused by genetic mutations.

One of the leading scientists in the field describes morphs this way: Imagine a jar of M&M’s that are almost all chocolate — the anthrax spores — but sprinkled with a few blues and reds — the morphs. Scoop out a big enough portion of spores, grow the anthrax on plates, and a morph or two probably will appear.

Morphs that look the same can be caused by different mutations. To create a true genetic fingerprint of the attack powder, scientists had to find and sequence the mutations that spawned the morphs.

Once they had that fingerprint, investigators could look for a match with the stocks of anthrax in bio-defense labs. The Ames strain used in the letter attacks had been cultured from a dead cow in Texas in 1981, and the Army frequently used it for animal testing of vaccines.

More than 1,000 samples tested

The attack powder had multiple morphs. Over several years, contractors developed tests for four morphs that produced what the FBI said were reliable results.

It was no easy task. Just a year before the anthrax attacks, it would have been inconceivable, Keim said. By late 2001, it was merely revolutionary.

When the anthrax samples from U.S. and foreign bio-weapons labs were screened, only 10 out of more than 1,000 tested positive for three or more of the morphs. All came from Ivins’ flask, RMR-1029.

In its report earlier this year, the National Academy of Sciences panel raised numerous questions about this finding, some of which had been posed by the Red Team back in 2007.

The panel also noted that the FBI didn’t have a complete understanding of how temperature or other growth conditions might affect how many morphs appeared. Perhaps a particular morph would become visible only under certain growth conditions. It was this question that the Red Team had suggested for additional research in 2007.

The FBI’s own records show that the tests didn’t always deliver reliable results. In trying to prove that a sample Ivins provided from his flask in April 2002 was deceptive because it contained none of the morphs from the attack powder, investigators sampled the flask 30 times. All came back with at least one morph, and 16 came back with all four. Six of them showed only two or fewer, even though they were grown directly from the Ivins culture.

The National Academy of Sciences panel’s report raised the possibility that some of the morphs could arise through the process of “parallel evolution,” in which identical mutations occur in separately growing colonies of bacteria.

Richard Lenski, a Michigan State University professor and specialist in this field, said the FBI faced a significant challenge. In what he termed a “dream world” with unlimited resources, researchers could separately grow hundreds of colonies of the anthrax in both Ivins’ flask and the attack powder and compare the morphs that evolve.

Such an experiment, of course, would be an expensive long shot, because the person who made the powder did so in secret with methods that remain unknown.

Claire Fraser-Liggett, a pioneering genetics researcher, was part of the effort to track the morphs. In August 2008, she sat onstage alongside senior FBI science officials as the findings were presented. By then, she said, the technology had leapfrogged far beyond the techniques used in 2001 and 2002 to compare morphs.

Beginning in about 2006, she said, “next generation” sequencing came on line. What cost $250,000 and took one to two months of work in 2001 now could be done for about $150 in a week. With price no longer an issue, the DNA in a colony of anthrax could be sampled over and over and over, assuring accuracy. And you wouldn’t be limited to four morphs; you could test as many as you felt were useful.

Fraser-Liggett doesn’t fault the FBI for not switching to an untried technique in 2006. But she said the enhanced precision now available could bring new evidence to light, confirming investigators’ original conclusion or pointing in other directions.

Chemical signals never fully explained

For now, the case remains a matter of dispute, with prosecutors and law-enforcement officials insisting that the combination of science and circumstantial evidence would have been more than sufficient to win a conviction.

One area of contention is whether the killer tried to add a chemical to make the spores float more easily, so they’d have a better chance of being inhaled. McClatchy first reported last spring that the FBI had failed to explain the presence of unusual levels of silicon and tin in two of the letters, since those elements aren’t part of the process of growing spores.

Scientists pressing for answers to those questions published a paper in a scientific journal this month. The FBI says the silicon was present through a natural process, not from any special treatment by Ivins.

David A. Relman, vice chairman of the National Academy study committee and a professor at the Stanford University School of Medicine, said the scientific picture remained incomplete.

Relman said, for example, that the high level of silicon measured in the letter sent to the New York Post remained a “big discrepancy,” one for which the panel received no explanation. None of the spores in Ivins’ now-infamous flask contained any silicon.

Relman said the panel questioned FBI officials about whether the high silicon measurement had arisen from an anomaly in the testing.

“We asked: ‘Is it nonrepresentative sampling?'” he said.

“And they said, ‘No, we don’t think that’s the answer.’ ”

“There is no answer,” Relman said, “That’s why we said it’s not resolved.”

Lieber, the prosecutor, said she would have moved to exclude the high-silicon reading at trial since it came from a single measurement.

According to the FBI, the anthrax from RMR-1029 was used as starter germs for the attack powder. Investigators suspect that there were at least two separate production runs. The powder sent to the media was relatively coarse; the anthrax mailed to Congress had much smaller particles and floated like a gas.

The germs in the flask were a mix of anthrax grown by Ivins and the Army base in Dugway, Utah. During the growth phase, the anthrax killer introduced several impurities, including silicon, trace elements of tin and, in two of the letters, an unusual strain of another bacterium, Bacillus subtilis.

Had Ivins not committed suicide, his trial very likely would have included vigorous sparring over the scientific evidence. Experts probably would have offered conflicting testimony about the reliability and certainty of the genetic tests.

Relman said a trial would have been the only way in which the prosecution’s evidence “could have been weighed and challenged by experts.”

It’s worth considering whether an independent panel should evaluate the full case against Ivins, looking at the science, the evidence investigators gathered and all other relevant material, Relman said.

“We have to decide … how important this case is to us as a society, and I’m not presupposing it is,” he said.

Fraser-Liggett and Lenski said it would be valuable to continue testing the anthrax samples in the case as new, more sensitive technologies come on line.

“Speaking as an individual citizen,” Lenski wrote in an email, “I think it would benefit the public. Even if it didn’t resolve the Amerithrax case with respect to criminal culpability, it would be a valuable test run of what science could contribute if a similar terrorist event were to occur.”

by Stephen Engelberg, ProPublica, Greg Gordon, McClatchy, Jim Gilmore and Mike Wiser, PBS Frontline, Oct. 10, 2011, 11:04

Find the story at 10 October 2011 part 1

Find the story at 10 October 2011 part 2

Find the story at 10 October 2011 part 3

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