Sunday, February 21, 2010

Farah Jama and forensic DNA contamination

Part VIII in a series on the Knox/Sollecito case

I have previously posted on DNA contamination issues and subsequently used this post as a starting point to examine the bra clasp and knife as evidence in the murder of Meredith Kercher. I would like to give an additional example of DNA contamintion, that of Farah Jama, an Australian convicted of rape. He spent sixteen months in prison before being released (

The twenty year-old Mr. Jama’s DNA profile was found in connection with a possible rape that occurred at a club for those over 28. The woman had no memory of the night. Mr. Jama claimed that he had been reading passages from the Koran to his critically ill father on the evening of the alleged crime. His brother and a friend gave supporting evidence (

According to an article in the Herald-Sun on 7 December 2009, ‘The same forensic officer who conducted the tests on the alleged rape victim had done another unrelated test the day before that involved Mr Jama's DNA.” This is the key point; as we have seen before in other cases, when two samples are run at almost the same time, there exists a real possibility for contamination. Another important take-home message is the need to weigh DNA forensics against other evidence (,,26542662-27197,00.html).

Sunday, February 14, 2010

The Monster of Florence and the Tragedy in Perugia

Part VII in a series on the Knox/Sollecito case

There are connections between the Knox/Sollecito trial in the murder of Meredith Kercher and the “Monster of Florence” case. The latter was a string of murders mainly in the 1970s and 1980s. A series of couples on lovers’ lanes were shot and the female bodies mutilated. Although several people were suspected, it is unlikely that the true culprit was ever found. Knox prosecutor Guiliano Mignini became involved in the Florence case well after the murders. He and an investigator, Michele Giuttari, were seeking a connection between the Monster case and the death of a certain Dr. Narducci in 1985 (p. 208, The Monster of Florence). Mr. Giuttari believed that the lack of an autopsy was evidence that the body in Dr. Narducci’s grave was not really his. On 6 April 2002 the body was exhumed and confirmed to be that of Dr. Narducci (p. 213). Mr. Giuttari and Mr. Mignini then argued that the bodies had been swapped twice, the second time just before it was exhumed.

Mr. Mignini claimed to believe that Mario Spezi, Mr. Preston’s coauthor for the book The Monster of Florence, planted evidence in the Monster of Florence case. Later he and Mr. Giuttari made Mr. Spezi into a suspect in the murders (p. 239). Mr. Spezi was indicted for obstruction of justice in the Narducci case and held in isolation for five days in 2006. Mr. Preston was himself interrogated by Mr. Mignini, after which he left the country because he was indagato for the crimes of reticence and making false statements (p. 259).

It is a shame that Mr. Mignini harassed Mr. Preston and especially Mr. Spezi. Their theory of the crime and their identification of a suspect made much more sense than the baroque conspiracy theory Mr. Mignini and Mr. Giuttari favored. The Committee to Protect Journalists said that their, “research and interviews with Italian journalists, some of whom asked to remain anonymous for fear of official retaliation, show a pattern of official harassment against Spezi in connection with his investigation of the ‘Monster of Florence’ case.”

“Mignini filed a request with the preliminary investigation judge of Perugia, Marina De Robertis, to invoke a rarely used law under Italy's criminal code to deny Spezi access to a lawyer for five days, Spezi's lawyer Alessandro Traversi told CPJ. The law is typically applied to the most dangerous criminals, yet Judge De Robertis authorized the measure, and for five days Spezi was denied legal counsel and held incommunicado.”

“An appeals court that day ordered that Spezi be released immediately, but it did not issue an explanation as to why it overruled the judge who authorized the imprisonment. Spezi, 60, spent 22 days in prison after being taken into custody on April 7.”

Now let us move on to the Knox/Sollecito case, starting with something that happened to Mario Spezi (from the new afterward to Douglas Preston’s book The Monster of Florence, pp. 325-326):

“A few moments later a timid and exceedingly nervous young woman approached.

“I’m a fellow journalist here in Perugia,” she said quietly. Could I speak with you a moment?”

Spezi invited her to sit at his table.

She looked about furtively, as if to check if she were being followed. Then she lit a cigarette with a trembling hand and, stumbling over her words, blurted out, “I hope they don’t see us together.”

“Excuse me, Spezi asked, but who is ‘they’?”

“Them, the police. Mignini’s men.”

“And why can’t we be seen together? What are you afraid of?

“My name is Francesca Bene,” she said all in a rush, “and I work for a small newspaper here, the Giornale dell’Umbria. Last July I made what I thought was a real scoop in the case of Meredith Kercher.” [Francesca tells the story of a drug addict’s suspicious behavior on the night of the murder.]

“Then what happened? Why wasn’t there any follow-up?”

“I’ll tell you what happened. “ Francesca Bene looked around again. “The very day I published that story, I was summoned to the prosecutor’s office and interrogated by Mignini’s men—in particular that big policewoman, the same one who interrogated Amanda Knox.” (The one Amanda says struck her.)” “She’s violent; she scares me.”

“What was there to interrogate you about?” Spezi said. “You say your story was corroborated by many witnesses who went on the record.”

“Of course. But that didn’t stop them from indicting me for the crime of inciting public alarm by publishing false information.”

“But that’s absurd.”

“I was afraid. I’m the only one who works in my family and if I lose my job…I was afraid. So I dropped the story.”

My hunch is that the drug addict in question is unrelated to the murder of Meredith Kercher. However, from this information it should be possible to identify the policewoman who allegedly hit Ms. Knox. This incident also says much about Mr. Mignini’s character and the power of the prosecutors in Italy to intimidate journalists.

With this background in mind, I would like to offer Douglas Preston’s insights from the interview he gave to blogger Candace Dempsey: “One other detail that American readers might like to know: in Italy, prosecutors are firmly in charge. They tell the police what to look for, where to go, what evidence to analyze, what evidence not to analyze. In America, the police work independently and are specifically trained in evidence gathering and criminal investigation. In Italy, the police must do what the prosecutor tells them. As a result, many criminal investigations in Italy are botched by prosecutors who are judges, trained in the law, who have no background in criminal investigation, police work, or forensic science.”

Ms. Dempsey has also written about the connections between this case and the Monster of Florence case. Her highlighting of Preston’s and Spezi’s dissection of the word “compatible,” a word applied to certain forensic evidence in the Knox/Sollecito case, is worth pondering.

Friday, February 5, 2010

An ordinary kitchen knife or a murder weapon?

Part VI in a series on the Knox/Sollecito case

Let’s reexamine the problems with the electropherogram of DNA allegedly arising from the knife first, then interpret the profile in light of these problems.

There are three basic problems with the profile of DNA culled from the knife. The first is the weakness of the signals, as discussed in the previous post on the knife (Amanda Knox and Raffaele Sollecito and the Murder of Meredith Kercher, Part I). The signals one typically observes are in the many hundreds or thousands of RFUs, yet 22 of 29 peaks in this electropherogram fall below 50 RFU. Dr. Tagliabracci, a defense expert witness, noted in a document on DNA and paternity testing that the lower limit of detection is not less than 50 RFU ( In Darkness Descending, the first book on the Kercher murder, one of Italy’s top forensic scientists, General Luciano Garofano, noted that 100-150 RFU is usually considered to be the minimum. There is a suggestion in the forensic literature to set two thresholds that are related to the average noise level, as opposed to a fixed value of RFUs (Gilder et al., Journal of Forensic Science, 2007, 52(1), 97-101). Two of the coauthors are signers of the open letter on the forensics of this case (

Thus there is no universal threshold, but the lowest I have been able to document is 50 RFU, with one suggestion that peaks to 40 RFU may be interpreted with caution. Moreover, there ought to be consistency within one lab. Were the other DNA samples in the lab analyzed with the same threshold or a different one? Indeed, an equally serious issue is that one should always set the threshold before doing the experiment. The machine that Dr. Stefanoni used had a preset limit of 50 RFU (, and changing the limit after the experiment was done opens the door to bias, as discussed in the previous post on the knife (

The second problem with this DNA profile is the appearance of two extra peaks in locus D3S1358, both of which have a signal-to-noise ratio (S/N) of about 20*. They have fifteen and sixteen repeats, respectively, and neither of which is part of Meredith’s profile, which has fourteen and eighteen repeats at this locus. There is one peak in locus D7S820 with a S/N ratio of only 15, which is interpreted to be part of Meredith’s profile. Why should this latter peak be treated as part of Meredith’s profile and the two other peaks ignored?

The third problem with this profile is that eight loci, D7S820, D16S539, D19S433, vWA, TPOX, D18S51, D5S818, FGA, have pairs of peaks in which the smaller peak is less than 70% of the height of the larger one. This value is typically 70-100% in a single source sample, and there are two peaks because there are usually two different alleles, one from each parent (Butler, Forensic DNA Typing, 2nd ed., pp. 155-156). Ordinarily, peaks below 70% that are not stutters (a type of artifact) are thought to indicate that the DNA arises from more than one person (is a mixture). In this case, a reasonable alternate explanation is that the peak heights are different because there are very few copies of the DNA template, perhaps 10-20. The special issues with low copy number DNA will be the subject of a future post. The problems noted above all support taking a conservative interpretation of the profile, as the signers of the open letter did. They refer to it as a “partial profile.” I lean toward referring it as a possible partial profile.

If the profile is Meredith’s, the question is how did it arise. Dr. Elizabeth Johnson said, “if someone had a knife covered in blood and they tried to

clean it very well, they would remove their ability to detect the DNA before they removed the ability to detect the chemical traces of blood.” The segment can be viewed at Therefore, the lack of blood makes it impossible for there to be DNA on the knife, and the DNA that was observed has to arise from contamination from mechanisms similar to those documented in the previous post, “Forensic DNA Contamination,” such as the Mixer murder. General Garofano said, “they say it was cleaned with bleach. If an object is cleaned with bleach, there is no DNA left. And if any were left there would be the same amount of DNA belonging to Amanda Knox as to Meredith Kercher. Next to nothing…So the fact that there is a lot of Amanda Knox's DNA and a little of Meredith's doesn't sound logical to me.”

Dr. Johnson’s words on the ABC segment are more adamant than in the open letter. One might instead argue that it is only improbable that some DNA would remain on the knife. If so, then one would be left with choosing between two events, contamination or DNA somehow escaping removal, and deciding which seems more likely.

Dr. Donald Riley wrote (

(1) A partial profile essentially proves that one is operating outside of well-characterized and recommended limits.
(2) Contaminating DNA usually presents as a partial profile, although not always. For this reason, the risk that the result is a contaminant is greater than for samples that present as full profiles.
(3) A partial profile is at risk of being incomplete and misleading. The partial nature of it proves that DNA molecules have been missed. There is no way of firmly determining what the complete profile would have been, except by seeking other samples that may present a full profile.

Recall that we appear to be dealing with a partial profile in this instance.

The Italian forensics team might have made a stronger case for the DNA profile originating from blood on the knife, not contamination, had they done several things differently. General Garofano said**, “Did they open the knife to see if blood had dripped between the metal part of the handle and the plastic? No? Pity. That would have been a sure place to find blood if there was blood." Checking the knife more thoroughly for blood is the first thing that the forensics team should have done.

Second, the forensics team failed to perform a control experiment that would have shed light on whether or not the profile arose from contamination. Recently, I was fortunate enough to discuss this case with a graduate of our department who is now a forensic scientist in a municipal police department. When I told her about the knife, she asked whether or not they had checked other knives from the drawer for DNA (a good example of thinking like a scientist). If other knives had shown DNA from Meredith (or the other flatmates, for instance), then contamination certainly occurred.

Third, the prosecution has not released the fsa files, an almost unheard of occurrence in DNA forensics. These files allow independent forensic scientists to analyze the data. The open letter of 19 November 2009 noted their absence. Examination of these files might shed light on possible contamination and also give information on how signals were accepted or rejected as artifacts. To sum up, the lack of blood, the failure to look for DNA on other knives, and the lack of independent review greatly reduce the value of this DNA profile.

The authors of the open letter wrote, “There exists the real possibility that the low level, partial profile attributed to the knife blade is a result of unintended transfer in the laboratory during sample handling… No credible scientific evidence has been presented to associate this kitchen knife with the murder of Meredith Kercher.” That statement is more than sufficient to create reasonable doubt that this knife is a murder weapon, in addition to the many other problems associated with this knife ( Sometimes a kitchen knife is just a kitchen knife.

*Update 11 February 2010. The words "signal-to-noise ratio" should be changed to "peak height" in this paragraph. All of the numbers are in RFUs. I am sorry about this error; however, their interpretation is not changed by this correction. **Update 17 February 2010. Corrected the spelling of General Garofano's name.