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

Ivins said he had several variants of Ames anthrax - the rare strain that an FBI science consultant concluded was used in the attack - that could be tested to find the origins of the powder that had killed five people.

Seven years later, as federal investigators prepared to charge him with the same crimes he had offered to help solve, Ivins committed suicide at age 62.

Prosecutors voiced confidence that Ivins would have been found guilty, announcing that years of cutting-edge DNA analysis proved that his spores were "effectively the murder weapon."

To many of Ivins' former colleagues at the U.S. Army germ research center in Fort Detrick, Md., his invitation to test anthrax in his own inventory is among many indications the FBI got the wrong man.

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

Ten years after the attack, an in-depth examination of the case against Ivins by PBS' "Frontline," McClatchy Newspapers and ProPublica raises fresh doubts about the government's evidence and questions whether, despite a $100 million investigation, the real anthrax killer remains on the loose.

Doubts about evidence

The news organizations conducted dozens of interviews and reviewed thousands of pages of FBI files over the past year.

While not exonerating Ivins, a gifted but tortured scientist with a history of obsessive behavior, the documents and accounts are at odds with some of the science and circumstantial evidence that the government said would have convicted Ivins for capital crimes:

Prosecutors have said Ivins tried to hide his guilt by submitting a false sample of his anthrax that didn't contain telltale genetic mutations found in the attack powder. But records reveal publicly for the first time that Ivins made available at least three other samples for testing between 2002 and 2004. Those samples did match the anthrax in the attack letters - a discovery that Ivins' lawyer said debunks charges that he was covering his tracks.

Prosecutors argued Ivins was motivated by signals from the White House and Pentagon that the Fort Detrick lab's anthrax-vaccine projects could be curtailed, saying his "life's work appeared destined for failure, absent an unexpected event."

But Ivins' former bosses say he shouldn't have had any worries about his future, because he knew that the Pentagon had approved a full year's funding for his and others' research on a new vaccine, and was mapping out a five-year plan to invest well over $15 million.

As the FBI zeroed in on Ivins in March 2007, an elite group of outside scientists urged investigators to do more basic research - about how and when the genetic mutations arose - to make sure the results were unchallengeable. FBI officials rebuffed that recommendation, saying it addressed "an academic question with little probative value to the investigation."

After collecting swabs from Ivins' home, office and vehicles and finding not a single spore from the attack powder, prosecutors said a microbiologist trained to handle dangerous germs would have been able to hide its traces.

But Claire Fraser-Liggett, a genetics consultant who oversaw work that provided some of the most important evidence linking Ivins to the attack powder, found that dismissal troubling. She questioned how someone who perhaps had to work "haphazardly, quickly" could have avoided leaving behind tiny pieces of forensically traceable DNA.

"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?"

Prosecutors defend case

Prosecutors continue to vehemently defend their case, arguing the inconsistencies and unanswered questions are trumped by a long chain of evidence they think would have convinced a jury that Ivins prepared the lethal powder that was mailed to news media outlets and two U.S. senators.

"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," lead federal prosecutor Rachel Lieber said in an interview. But in a trial, she said, prosecutors would urge 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."

Genetic tests

Prosecutors cited genetics tests as conclusive evidence that Ivins' spores, most grown for him at an Army base in Dugway, Utah, were the parent material to the powder. In January 2002, Ivins himself gave an FBI agent a detailed tutorial on how to spot the genetically distinct variants, known as morphs, that serve as a kind of microscopic fingerprint for anthrax spores.

Ivins first submitted a set of samples in February 2002 that was rejected for being in the wrong type of glass vessels. The Justice Department later alleged that he then manipulated a second set of samples in April 2002 so they wouldn't show the distinct variants matching the attack powder.

Records recently released under the Freedom of Information Act show Ivins ultimately made available to investigators a total of four sets of samples from 2002 to 2004 - double the number the FBI has disclosed.

Questionable methods

Prosecutors contend that Ivins at first thought his anthrax spores were pure and therefore morph-free.

But Paul Keim, an anthrax expert at Northern Arizona University who helped the FBI identify the attack strain, said that was implausible.

The Dugway culture that Ivins provided included dozens of separate batches, most of which were grown in fermenters, an ideal breeding ground for morphs. Keim said Ivins likely understood this.

At the time Ivins committed suicide, Keim said, the groundbreaking lab method that the FBI used to trace the attack powder to Ivins' flask wasn't "ready for the courtroom."

A member of the "Red Team" of experts the FBI convened in March 2007, Keim didn't learn that its call for further research had been rejected until a year later, after Ivins had killed himself and prosecutors were hastily organizing a news conference to describe the science.

The strictures of the FBI's investigation prevented scientists from talking to each other or sharing information as they would on a typical research effort, Keim and other scientists said.

They described tension between scientific best practices and investigators whose boss was under intense pressure to crack a case with few leads and hundreds of plausible suspects.

Silicon in spores unexplained

Another area of contention is whether the killer tried to add a chemical to make the anthrax 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 - and none of the spores in Ivins' flask contained any silicon.

David A. Relman, a Stanford University School of Medicine professor and vice chairman of a National Research Council committee that studied the investigation, said the scientific picture remained incomplete.

High levels of silicon in the letter sent to the New York Post was a "big discrepancy," he said.

Lieber, the prosecutor, said she would have argued for excluding the high-silicon reading at trial because it had come from a single measurement.

One week after Ivins died following an overdose of over-the-counter medication in July 2008, U.S. Attorney Jeffrey Taylor proclaimed at a news conference: "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."

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

"This was not an airtight case, by any means," she said. "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.'

"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."