updated 10/5/2011 10:49:58 AM ET 2011-10-05T14:49:58

The poor handling of DNA evidence played a starring role in the appeal of American student Amanda Knox this week and led to her release from a prison in Perugia, Italy.

An Italian appellate court judge ruled that the prosecutors used substandard methods and contaminated the evidence. Prosecutors had alleged that evidence of Knox's blood was found on a knife used to kill her roommate, British college student Meredith Kercher.

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Knox and her boyfriend at the time, Raffaele Sollecito, were sentenced to 25 years for the murder of the 21-year-old Kercher, who shared an apartment with Knox.

But the microscopic amounts of DNA found on the knife, as well as on a bra clasp, were thrown into doubt after a report from independent experts criticized the Perugia police's handling and analysis of the materials.

"The tragedy of this case is that bad science, like bad surgery, caused most of the damage after the initial murder," said Greg Hampikian, a professor of biology at Boise State University and a forensic science expert who was part of Knox’s defense team. "The crime was an obvious one. It was one man whose DNA was found at the murder scene. It was a very simple case."

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Hampikian and 19 other U.S. forensic experts reviewed the DNA evidence in the Knox case in 2009 and found it shaky. Their letter to the Italian judge outlined their concerns that police mishandled their collection of blood samples from a kitchen knife found in the apartment of Knox and Kerchner, as well as Kercher's bra clasp.

The U.S. experts' letter was not used in the original trial of Knox, in which she was found guilty. But its conclusions were upheld by two Italian independent experts who testified in the appeals trial in September. An eight-person jury found Knox and Sollecito not guilty on Monday.

Hampikian reviewed the case for Discovery News.

"What (the Italian forensic experts) found was that the knife recovered from Raffaele's apartment not only did not have traces of human blood, but it had not been cleaned in the way the prosecution said. They had said that Amanda bleached the knife. Instead, what experts appointed by the judge said was that the blade had potato starch on it. It was a typical kitchen knife. It was found in a kitchen drawer with other knifes. It wasn’t well cleaned and it wasn't used as a murder weapon."

The Italian prosecutors used a DNA detection limit far below that of the independent U.S. experts or the FBI in determining the presence of blood DNA on the blade, Hampikian said, which made contamination a much more likely source of the genetic material.

The second piece of evidence was Kercher's bra clasp that allegedly had Sollecito's DNA but was inconclusive, according to Hampikian. Police investigators found no DNA from Sollecito or Knox on the rest of the bra, other items of Kercher's clothing, objects collected from Kercher's room, or in samples from her body. However they did find large amounts of DNA from Rudy Guede, a drifter from the Ivory Coast who was separately convicted of Kercher's murder and is serving 16 years in prison.

There were also issues with the storage of the DNA evidence in plastic bags, where scientists say moisture builds and degrades the sample.

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"If you have one piece of evidence with a weak result, and dozens of pieces of evidence with strong results, you should doubt that one piece of evidence," Hampikian said. "The real take-home story is that you should use your gut feelings as a hypothesis, but when the data contradicts the hypothesis, you have to give it up and declare it as wrong. That’s the scientific method."

Elizabeth Johnson, an independent consultant and DNA forensic scientist who co-wrote the 2009 letter with Hampikian, said the Knox case was based on the hubris of the prosecution team.

"This should have been the verdict at the (original) trial," Johnson said. "But for political reasons they had to admit their own experts and prosecutors were wrong."

While Knox's family in Seattle raised money for her defense, neither Johnson nor Hampikian were paid by the defense. Hampikian is also director of the Idaho Innocence Project, which works to free prisoners using DNA evidence.

© 2012 Discovery Channel


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