The FBI used science to make its case that Bruce Ivins was behind the deadly anthrax attacks of 2001 — but FOX News has learned that the scientific evidence in the case isn't as straight-forward as it first appeared.

When the FBI told reporters in August that its investigation had led to only one suspect, Ivins, the federal prosecutor in the case backed up the evidence against the defense researcher.

"We have a flask that's effectively the murder weapon from which those spores were taken that was controlled by Dr. Ivins," U.S. Attorney Jeffrey Taylor said. "Anthrax in that flask was created by Dr. Ivins."

The science clearly is the backbone of the FBI case against Ivins, who committed suicide last year as investigators closed in, and much of the evidence is based on highly sophisticated and specialized research by people like Joe Michael, who works at the Sandia National Labs in New Mexico.

But when Michael compared the bacterial spores in three letters, sent to the New York Post and Sens. Patrick Leahy and Tom Daschle on Capitol Hill, with the bacteria found in Ivins’ flask, he reached a striking conclusion: They do not share the same chemical fingerprint.

"I don’t think this exonerates (Ivins) at all,” Michael told FOX News, adding, "I don’t think it's not enough to say that he did it, as well."

Click here to see video.

Michael said the powder in the letters contains silicon, oxygen, iron and tin; the flask does not. But there is a good explanation for the lack of a chemical match, he said.

"What the FBI believes happened, and I think the evidence helps support them, is that this material was taken out of that flask and then re-grown before it was put in the letters," Michael said.

FBI investigators think there were at least two “re-growths” by Ivins. This, they say, accounts for the difference between the New York Post powder, which was darker and more granular than the batch sent to Capitol Hill. But the exact recipe or method used remains a mystery.

The FBI case centers on Ivins and his work as a military bio-defense researcher at Fort Detrick in Maryland. Some skeptics still question whether Ivins, as the FBI maintains, was the only person who created the anthrax and controlled access to the flask. Five people died in the attacks.

"When you do an investigation, you have what is called a chain of custody," terrorism expert Neil Livingstone told FOX News. "And the evidence always has to be in that chain of custody. You have to be able to explain it. And it doesn't appear that the FBI has an iron-clad chain of custody here."

At Quantico, Va., home to the FBI Laboratory's Chemical-Biological Sciences Unit , a bureau microbiologist told FOX that the chemical mismatch is of no consequence because the powder and the spores share the same DNA.

"There is no expectation they should have the same chemical profile," Jason Bannan, the FBI forensic examiner , told FOX News, adding, "we don't know what method was used to grow the spores."

The FBI has promised an independent review of their findings by the National Academy of Sciences, though, according to some reports, it has not yet begun. This week, two Democratic congressmen, Jerry Nadler and Rush Holt, whose districts were affected by the attacks, introduced legislation calling for the creation of a 9/11-style commission to independently investigate the attacks because they say the nation deserves to know whether the case is truly solved.

"All of us — but especially the families of the victims of the anthrax attacks — deserve credible answers about how the attacks happened and whether the case really is closed," Holt said in a written statement. "The commission, like the 9/11 Commission, would do that, and it would help American families know that the government is better prepared to protect them and their children from future bioterrorism attacks."

Friday afternoon, the FBI released a detailed statement about the anthrax powder's chemical signature and other elements of the bureau's scientific work.

Click here to read the full statement.