Part XIV in the Knox/Sollecito case
(updated three times on 4/27/10, once on 5/6/10, and once on 5/20/10)
One of the first things that drew me to the Knox/Sollecito case was the open letter on two items of evidence, the kitchen knife and the bra clasp. The two coauthors, Drs. Elizabeth Johnson and Gregory Hampikian are forensic DNA scientists. A one-paragraph appendix to the open letter was co-signed by seven additional experts in the forensic DNA field, including Dan Krane and Jason Gilder. The open letter completely dismissed the DNA evidence linking the knife to the crime and said. “Handling and movement of this sample [the clasp] has compromised its probative value.”
Dr. Johnson was initially approached by someone close to the defense team about looking into this case, but I have no information on how the other individuals became involved. The defense gave Drs. Johnson and Hampikian the limited materials that were released in discovery; however, the other seven did not have these data, owing to time. The seven co-signers wrote, “…While I have not had the opportunity to review all of the case-specific data in this matter, I agree that the scientific evidence that they describe does not convincingly associate the kitchen knife with the murder of Meredith Kercher. I also agree that the handling and movement of the bra clasp that they describe would have compromised its probative value, and that the presence of a DNA profile does not speak in any way to the time frame or the circumstances under which DNA became associated with this sample…” The seven names appear at this website but not on the pdf file of the letter itself; however, several of them have confirmed their involvement in the case in email correspondence.
One portion of the open letter made specific mention of the lack of release of the electronic data files. Drs. Johnson and Hampikian both requested the release of the electronic files used to construct the DNA electropherograms (for one manufacturer, these are called .fsa files), according to Jason Gilder. Dr. Krane did so on multiple occasions, according to Jason Gilder, who is one of the seven co-signers of the open letter. Dr. Krane had previously put electronic data files to very good use in the Leskie case; therefore, it is no surprise that he would request them here. The requests were made via the defense lawyers, but the prosecution steadfastly refused the requests. According to Dr. Krane, the release of electronic files is the almost universal norm. Dr. Norah Rudin provides on her website a standard form, DNA discovery request, for cases involving DNA forensics. From this document:
“2. Items #7 and #8 listed in the Discovery Request refer to electronic data, also known as raw data.
a. Electronic data is considered standard discovery and is critical to an independent review.
b. Electronic data must be received prior to commencing an independent review.
c. The laboratory will typically provide you with a CD containing electronic data.”
According to Amanda’s stepfather Chris Mellas, the defense team had asked for the DNA forensic data (this would be expected to include the electronic files and machine logs) but was told that they did not exist. Then the defense learned that the Kercher family’s lawyer had some of this information and demanded that the judge order the release of the data in the summer of 2009. The prosecution released some data, but not what was asked for. The lack of release of these data was one of the reasons for a mistrial motion in the fall of 2009. In April of 2010 Bob Graham wrote, “It has also emerged that the prosecution has failed to deliver to the defence all the paperwork and documentation related to the forensic testing. Chris Mellas, Knox's step-father who is currently in Perugia, said yesterday: ‘Our lawyers asked for everything, every file and record relating to the forensic testing. We were given some of the stuff, like what was on Meredith's shoes or a juice glass but not the full reports on the knife used or the bra-clasp.’ Deputy prosecutor Manuela Comodi brushed off the request for all forensic documentation and added: ‘They have everything they need. That is enough.’” Ms. Comodi’s words imply that the defense did not receive everything, just what the prosecution claims is enough.
The news reports from last summer and fall are consistent with Mellas’s recounting of the events. The defense did not know until last July that Patrizia Stefanoni had written the words, “Too low” on files relating to the DNA profile culled from the knife. ABC news reported in September of 2009, “The trial reopened with an attempt to have the case thrown out, but it was rejected after the judge and the jurors deliberated for 90 minutes. Lawyers for Knox and Sollecito became animated in their assertion that evidence had been withheld from them. Sollecito's lawyer, Giulia Bongiorno, addressed the court for 20 minutes arguing that the defense was not provided with crucial details of Sollecito's DNA allegedly found on Kercher's bra hook until July 30, 2009. The rights of the defense were damaged, she said, when ‘documents regarding the quantity of biological material on the bra hook and documents regarding the procedure used to attain DNA results were not made available to the defense.’”
Sara Gino, a defense expert witness, still did not have the dates on which the samples were run as of September of 2009. Frank Sfarzo reported in October of 2009 that the defense also asked the judge for an independent review of the forensics, which was not granted. Bob Graham reported in December of 2009, “Other forensic experts in several countries – including two from Britain – have started to study the DNA results but have delayed giving a verdict until they have received precise details on the methodology used by their Italian counterparts. The failure of the prosecution to provide these details to Knox and Sollecito’s defence teams is one of their central complaints.”
Do the defense team and the experts it consults have a right to obtain the data in electronic form? Release is clearly routine in the United States, consistent with the principle of transparency, enunciated by Keith Inman and Norah Rudin. Good science does not change when one crosses the border between nations. As an anonymous DNA forensic expert speaking about paper copies of the DNA forensic data said, “Certain parameters have irrevocably been applied to the data; as such it represents an interpretation by the laboratory rather than the original data.” A defendant should have the right to see and to challenge the evidence against him or her, and that principle is at risk in the Knox/Sollecito case.
Update I, 4/27/10: I corrected a minor typographical error in the first paragraph, where Dr. Johnson's name appeared twice.
Update II, 4/27/10: According to Chris Mellas by the time the defense learned that Mr. Maresca, the attorney representing the Kerchers, had some of the DNA forensic data, they had already requested it twice, before the pretrial and before the trial itself. Their third request in the summer of 2009 resulted in a court order that was not followed. To the best of my knowledge the additional DNA experts associated with the open letter made their requests after this time.
Update III, 4/27/10: Joy Halverson and Marc Taylor have confirmed that they signed the appendix to the open letter. Marc Taylor wrote, “We have discovered numerous manipulations of the data analysis or the actual physical analysis of the evidence by reviewing the electronic data…The electronic data is clearly the ‘best evidence’ in the legal system.”
Update IV, 5/6/10: In response to my query to another person who signed the letter, Simon Ford confirmed that he signed the letter and replied, “In my opinion, it is always important to review the electronic data underlying a test result, if only to confirm the integrity of the data set. In low level DNA cases such as this, in which the slightest contamination could compromise the test result, it is absolutely essential to review the electronic data for the key samples and the associated controls to check for low level contamination. I cannot think of any valid reason why the prosecutor would chose not to provide the electronic data. In my experience, forensic DNA analysts in the US are invariably happy to turn over the data to support their findings.”
Update V, 5/20/10
The Irish Times - Saturday, February 27, 2010
DNA testing project offers fresh hope to the wrongfully convicted
A forensic genetics expert, Dr Hampikian’s expertise is called on by the Innocence Project all over the US and further afield. He is currently working with the family of Amanda Knox, the American student jailed in Italy last year for the murder of British student Meredith Kercher.
A professor of genetics at the University of Boise, Idaho, Dr Hampikian’s role with the Innocence Project is voluntary, but one he takes seriously. He has been involved in four exonerations over the past decade, though, ironically, his DNA testing has confirmed guilt in two further cases.
“I can’t tell who is telling the truth or who is lying, but the DNA can tell,” he says. “Sometimes the Innocence Project is a bit of a misnomer. In two of the four exonerations, I developed evidence that led to the arrest of somebody new for the crime, so for some people we are the Guilty Project – and that’s an important part of what we do.”
This documents that Dr. Hampkian, like Dr. Johnson, is a consultant for the Knox defense team.
Monday, April 26, 2010
Sunday, April 18, 2010
Things said and left unsaid: Barbie Nadeau’s coverage of the Knox/Sollecito case (Part XIII)
Ms. Barbie Nadeau’s book on the murder of Meredith Kercher is now out and will be reviewed here soon. A reading of some of her Newsweek and Daily Beast articles may give a glimpse of what to expect. Early in the article Ms. Nadeau wrote, “Just days after Kercher's body was found last November in the villa Knox shared with the victim, security camera footage showed the couple buying lingerie in a local store, with Knox giggling and telling Sollecito, ‘Afterwards I'm going to take you home so we can have wild sex together.’” Ms. Nadeau’s account is misleading in several respects. Ms. Knox did not have access to her own belongings at this time (her flat was a crime scene) and needed to buy underwear and borrow jeans. The security camera did not have sound, and witnesses say that the store has very loud music, making it difficult to overhear someone’s conversation. Whether the merchant, who was a paid interviewee and the actual source of the quote, spoke English or not is disputed. However, the couple did kiss in the store, and their demeanor appears playful.
Ms. Nadeau went on, “And by her own account in a prison diary leaked to the media, she details her sexual escapades with at least seven men she'd been with in her three months in Italy before her arrest. She even wrote that she might have HIV and then she uses a process of elimination to narrow down who might have given it to her. The diary is part of the collection of evidence and could be damaging to Knox in a court trial. Recently leaked segments of her continuing tome paint a disturbing picture of her state of mind. In one entry, she writes: ‘I think it's possible that Raffaelle went to Meredith's house, raped her, then killed her and then when he got home, while I was sleeping, he pressed my fingerprints n the knife.’”
Mark Waterbury rightly took Ms. Nadeau to task for the many problems with her assertions. Ms. Knox wrote of having seven intimate partners her whole life because she was told that she was or might be HIV-positive. Ms. Knox’s diary shows her emotional distress, and to claim that it “details her sexual escapades” is so blatantly wrong that it leaves one wondering what Ms. Nadeau could possibly have been thinking. Some of the most problematic assertions, including the incorrect description of the night of the murder, were based on an English translation of an Italian translation of her diary, instead of the original. When she was contacted about the mistranslation, Ms. Nadeau claimed that there was a second diary, but she is the only reporter who has made this claim to the best of my knowledge.
The last portion of the article says as much about Ms. Nadeau as about the case. “To complicate things further, Sollecito and Knox's reported break up prompted speculation that they would testify against each other. But Sollecito's flowers may be a signal that their defense teams may actually work together to pin the blame on Guede. If that strategy succeeds, the cipher of Amanda Knox may never truly be decoded.” Ms. Nadeau’s use of the word “pin” suggests that she believed Knox and Sollecito were guilty. Her linking the potential success of their blaming Mr. Guede to the potential failure to decipher Ms. Knox leaves little doubt about her opinion on their culpability. Why Newsweek entrusted their coverage of this case to her is the real mystery.
Let us consider some of her entries at The Daily Beast more briefly and with comments interspersed. In a recent article Nadeau wrote, “Shortly after her arrest, Knox admitted to being at the Perugian villa when Kercher was murdered. The confession was later thrown out of the body of evidence because of allegations of police brutality and coercion, but much of what she said in that original statement coincides with known elements of the case, including evidence gathered by CCTV footage from a nearby parking garage.” The CCTV footage may be of Meredith entering her cottage for the last time. Yet it is what this article does not say that is at least equally troubling. Nothing about the police giving out false information and only a little to on the British press, which sometimes behaved outrageously. Meredith’s father, John Kercher, was part of the British tabloid press corps, and this may explain some of the contempt the British press exhibited toward Ms. Knox.
Shortly after the conviction, Ms. Nadeau began an article, “Is the real Amanda Knox the sex-obsessed, cold-blooded murderer that the prosecution depicted? Or worse?” This question and the title of her article are truly egregious, worthy of comparison to the Newsweek mug shot cover on the Duke lacrosse case in 2006, and that is saying something. Clearly Ms. Nadeau had access to Edda Mellas and Curt Knox, which undercuts her claim about being shut out in the article about how the media got the case wrong (see above). The rest of the article lacks a critical appraisal of the forensics. “They [the jury] wondered why Amanda’s DNA and Meredith’s blood was wiped away and recovered with Luminol. They thought it was Raffaele’s bloody footprint on the bathroom rug and his DNA on Meredith’s bra clasp. They believed the prosecutor’s testimony that Meredith’s DNA was on the blade of the knife that had Amanda’s DNA on the handle.” There is no reason to assume that a substance that tests positive with Luminol is blood; it is a presumptive test that needs to be confirmed with one that is more specific for blood.
Immediately after the conviction Ms. Nadeau wrote, “At one point the stepmother of Raffaele Sollecito, Knox’s former boyfriend who was sentenced to 25 years for his part in the murder, yelled out ‘F@#k you,’” Ms. Nadeau is the only reporter who heard this; others heard, “Forte, Raffaele,” which just means strength, Raffaele. “But in the end, the two judges and six lay jurors trusted the sanctity of the DNA evidence, and doubted the words of Knox and Sollecito….For those who believed that Knox was guilty, the most damning evidence was the presence of her DNA mixed with Kercher’s blood in the house, and her statement that she was in the house at the time of the murder.” Ms. Nadeau has never written about the open letter signed by nine DNA forensics experts, but even if she is unaware of their views, she should know that the quality of the DNA evidence is very much in dispute.
Ms. Nadeau wrote about the jury’s report on its reasons for conviction, “A spot of Knox and Kercher’s mixed blood in one of the bedrooms, found using Luminol, and four additional spots in the small bathroom the girls shared also swayed the jurors.” The claim that finding Knox’s DNA mixed with Kercher’s blood means that their blood was mixed is dubious.
Quoting prosecutor Mignini Nadeau wrote, “’The window was broken from the inside, not the outside. The glass was on top of the clothes that had been strewn around the room, not under them. The break-in was staged and Knox is the one who did it.’ He also hinted that Knox and Sollecito might have been in a drug-fueled frenzy when they allegedly killed Kercher. He outlined the effects of cocaine and acid, and told the judges and jury how Knox and Sollecito ran with a crowd that often used these ‘stupificante,’ or stupefying drugs.” What drugs? Knox and Sollecito acknowledge smoking marijuana but no evidence of other drugs was presented. The notion that the window was broken from the inside is not convincing. Ms. Nadeau presents this closing argument without commenting on its many problems. This is only a reasonable approach if we accept this blog entry as pure reporting (with Ms. Nadeau reporting and editorializing are sometimes mixed. And yet after the introductory paragraph, eight of the nine succeeding paragraphs cover Mr. Mignini’s summation, whereas only one covers the defense’s summation.
“Other evidentiary problems include the lack of video or audio tapes of Knox’s original interrogation and the scientific police forgetting to pick up a bra clasp for nearly six weeks. That clasp is said to have Sollecito’s DNA on the metal hook and is the only material evidence police have tying Sollecito to the crime. While these obvious errors might well establish reasonable doubt in an American courtroom, it is unlikely they will have the same effect here in Italy, where defendants often seem to be presumed guilty until proven innocent.”
“Last July, testimony by noted forensic specialist Adriano Tagliabracci was abruptly suspended after the defense discovered that they had not been given all the prosecution’s evidence reports. Specifically, they did not have crucial evidence about Sollecito’s DNA found on the clasp of the bloodied bra that was cut from Kercher after she was stabbed.”
“Saturday’s hearing ended with a dramatic exchange about whether the prosecution had given the defense key documents regarding the DNA on Kercher’s bra. The charge was seen as a blatant attempt by the prosecution to throw the defense’s witness, and it worked. The exchange ended with Sollecito’s lawyers accusing the prosecution with illegality—a move many thought was primarily to set the stage for an appeal if one or both are convicted.” These three examples show that Ms. Nadeau does report on some aspects of the case that create sympathy for the defendants.
Ms. Nadeau wrote an article about Rudy Guede, who was the only person at that time convicted of Meredith Kercher’s murder. “’He has never changed his story,’ Guede’s lawyer, Valter Biscotti, told The Daily Beast this week. Biscotti would not supply any details about the version of events Guede gave at his own, closed-door trial, but he did say, ‘He has always maintained that they were all there, but that he is not the one who killed her.’” Ms. Nadeau did not comment on this remarkable assertion. When he was in Germany, the police intercepted one of Mr. Guede’s skype conversations in which he said that Amanda was not there. The first months after his arrest he said that an unidentified man murdered Ms. Kercher when Guede was on the toilet. Months later he began to claim that the man was Raffaele Sollecito and that Ms. Knox was at least present. ABC news reported that “Guede, 25, has at different times said the Knox, 22, of Seattle, was and was not at the house the night of the murder. At one point, he also implied that Knox's co-defendant Raffaele Sollecito was at the murder scene.”
Finally, I will expand upon a point I raised in the comments section of the previous article. In response to a question during a live chat, Ms. Nadeau said, “I think it is important to remember that the same scientific police and laboratories tested the DNA for all three suspects. That is to say, if the DNA matches Rudy and is accepted, then the DNA that matches the other two should also be accepted. How she may have left so little DNA if she was actually in the room is very hard to square.”
Ms. Nadeau is asserting implicitly that all DNA evidence is equal, but this is false. We know that the knife profile is weak, has drop-ins, and has considerable imbalance in intensity between most of the pairs of alleles. We know that the bra clasp was left in an insecure location for 47 days and handled poorly when it was finally collected. As Dan Krane said, “The science of DNA profiling is sound. But, not all of DNA profiling is science.” The evidence against Guede has never been released, and one cannot pass judgment on its quality without seeing it. There is second problem with Ms. Nadeau’s assertion. Rudy Guede was only identified as a suspect after the forensics came back, but Raffaele Sollecito and Amanda Knox were already suspects (first on the basis of demeanor, then on the basis of their interrogations) before the forensics was completed. This problem is particularly acute for the bra clasp, and one has to consider the problem of confirmation bias or even outright fraud when weighing the forensic evidence. The third problem is that even within a lab, the quality of work may not be uniform. For one thing lab contamination can be a sporadic event, as it was in the Jaidyn Leskie case. For another, there may be a lone sloppy or dishonest technician in a lab full of competent, ethical ones.
Update 20 April 2010
I added a hyperlink to the Newsweek story in paragraph 1 and the word "to" in paragraph 6, line 4.
Ms. Nadeau went on, “And by her own account in a prison diary leaked to the media, she details her sexual escapades with at least seven men she'd been with in her three months in Italy before her arrest. She even wrote that she might have HIV and then she uses a process of elimination to narrow down who might have given it to her. The diary is part of the collection of evidence and could be damaging to Knox in a court trial. Recently leaked segments of her continuing tome paint a disturbing picture of her state of mind. In one entry, she writes: ‘I think it's possible that Raffaelle went to Meredith's house, raped her, then killed her and then when he got home, while I was sleeping, he pressed my fingerprints n the knife.’”
Mark Waterbury rightly took Ms. Nadeau to task for the many problems with her assertions. Ms. Knox wrote of having seven intimate partners her whole life because she was told that she was or might be HIV-positive. Ms. Knox’s diary shows her emotional distress, and to claim that it “details her sexual escapades” is so blatantly wrong that it leaves one wondering what Ms. Nadeau could possibly have been thinking. Some of the most problematic assertions, including the incorrect description of the night of the murder, were based on an English translation of an Italian translation of her diary, instead of the original. When she was contacted about the mistranslation, Ms. Nadeau claimed that there was a second diary, but she is the only reporter who has made this claim to the best of my knowledge.
The last portion of the article says as much about Ms. Nadeau as about the case. “To complicate things further, Sollecito and Knox's reported break up prompted speculation that they would testify against each other. But Sollecito's flowers may be a signal that their defense teams may actually work together to pin the blame on Guede. If that strategy succeeds, the cipher of Amanda Knox may never truly be decoded.” Ms. Nadeau’s use of the word “pin” suggests that she believed Knox and Sollecito were guilty. Her linking the potential success of their blaming Mr. Guede to the potential failure to decipher Ms. Knox leaves little doubt about her opinion on their culpability. Why Newsweek entrusted their coverage of this case to her is the real mystery.
Let us consider some of her entries at The Daily Beast more briefly and with comments interspersed. In a recent article Nadeau wrote, “Shortly after her arrest, Knox admitted to being at the Perugian villa when Kercher was murdered. The confession was later thrown out of the body of evidence because of allegations of police brutality and coercion, but much of what she said in that original statement coincides with known elements of the case, including evidence gathered by CCTV footage from a nearby parking garage.” The CCTV footage may be of Meredith entering her cottage for the last time. Yet it is what this article does not say that is at least equally troubling. Nothing about the police giving out false information and only a little to on the British press, which sometimes behaved outrageously. Meredith’s father, John Kercher, was part of the British tabloid press corps, and this may explain some of the contempt the British press exhibited toward Ms. Knox.
Shortly after the conviction, Ms. Nadeau began an article, “Is the real Amanda Knox the sex-obsessed, cold-blooded murderer that the prosecution depicted? Or worse?” This question and the title of her article are truly egregious, worthy of comparison to the Newsweek mug shot cover on the Duke lacrosse case in 2006, and that is saying something. Clearly Ms. Nadeau had access to Edda Mellas and Curt Knox, which undercuts her claim about being shut out in the article about how the media got the case wrong (see above). The rest of the article lacks a critical appraisal of the forensics. “They [the jury] wondered why Amanda’s DNA and Meredith’s blood was wiped away and recovered with Luminol. They thought it was Raffaele’s bloody footprint on the bathroom rug and his DNA on Meredith’s bra clasp. They believed the prosecutor’s testimony that Meredith’s DNA was on the blade of the knife that had Amanda’s DNA on the handle.” There is no reason to assume that a substance that tests positive with Luminol is blood; it is a presumptive test that needs to be confirmed with one that is more specific for blood.
Immediately after the conviction Ms. Nadeau wrote, “At one point the stepmother of Raffaele Sollecito, Knox’s former boyfriend who was sentenced to 25 years for his part in the murder, yelled out ‘F@#k you,’” Ms. Nadeau is the only reporter who heard this; others heard, “Forte, Raffaele,” which just means strength, Raffaele. “But in the end, the two judges and six lay jurors trusted the sanctity of the DNA evidence, and doubted the words of Knox and Sollecito….For those who believed that Knox was guilty, the most damning evidence was the presence of her DNA mixed with Kercher’s blood in the house, and her statement that she was in the house at the time of the murder.” Ms. Nadeau has never written about the open letter signed by nine DNA forensics experts, but even if she is unaware of their views, she should know that the quality of the DNA evidence is very much in dispute.
Ms. Nadeau wrote about the jury’s report on its reasons for conviction, “A spot of Knox and Kercher’s mixed blood in one of the bedrooms, found using Luminol, and four additional spots in the small bathroom the girls shared also swayed the jurors.” The claim that finding Knox’s DNA mixed with Kercher’s blood means that their blood was mixed is dubious.
Quoting prosecutor Mignini Nadeau wrote, “’The window was broken from the inside, not the outside. The glass was on top of the clothes that had been strewn around the room, not under them. The break-in was staged and Knox is the one who did it.’ He also hinted that Knox and Sollecito might have been in a drug-fueled frenzy when they allegedly killed Kercher. He outlined the effects of cocaine and acid, and told the judges and jury how Knox and Sollecito ran with a crowd that often used these ‘stupificante,’ or stupefying drugs.” What drugs? Knox and Sollecito acknowledge smoking marijuana but no evidence of other drugs was presented. The notion that the window was broken from the inside is not convincing. Ms. Nadeau presents this closing argument without commenting on its many problems. This is only a reasonable approach if we accept this blog entry as pure reporting (with Ms. Nadeau reporting and editorializing are sometimes mixed. And yet after the introductory paragraph, eight of the nine succeeding paragraphs cover Mr. Mignini’s summation, whereas only one covers the defense’s summation.
“Other evidentiary problems include the lack of video or audio tapes of Knox’s original interrogation and the scientific police forgetting to pick up a bra clasp for nearly six weeks. That clasp is said to have Sollecito’s DNA on the metal hook and is the only material evidence police have tying Sollecito to the crime. While these obvious errors might well establish reasonable doubt in an American courtroom, it is unlikely they will have the same effect here in Italy, where defendants often seem to be presumed guilty until proven innocent.”
“Last July, testimony by noted forensic specialist Adriano Tagliabracci was abruptly suspended after the defense discovered that they had not been given all the prosecution’s evidence reports. Specifically, they did not have crucial evidence about Sollecito’s DNA found on the clasp of the bloodied bra that was cut from Kercher after she was stabbed.”
“Saturday’s hearing ended with a dramatic exchange about whether the prosecution had given the defense key documents regarding the DNA on Kercher’s bra. The charge was seen as a blatant attempt by the prosecution to throw the defense’s witness, and it worked. The exchange ended with Sollecito’s lawyers accusing the prosecution with illegality—a move many thought was primarily to set the stage for an appeal if one or both are convicted.” These three examples show that Ms. Nadeau does report on some aspects of the case that create sympathy for the defendants.
Ms. Nadeau wrote an article about Rudy Guede, who was the only person at that time convicted of Meredith Kercher’s murder. “’He has never changed his story,’ Guede’s lawyer, Valter Biscotti, told The Daily Beast this week. Biscotti would not supply any details about the version of events Guede gave at his own, closed-door trial, but he did say, ‘He has always maintained that they were all there, but that he is not the one who killed her.’” Ms. Nadeau did not comment on this remarkable assertion. When he was in Germany, the police intercepted one of Mr. Guede’s skype conversations in which he said that Amanda was not there. The first months after his arrest he said that an unidentified man murdered Ms. Kercher when Guede was on the toilet. Months later he began to claim that the man was Raffaele Sollecito and that Ms. Knox was at least present. ABC news reported that “Guede, 25, has at different times said the Knox, 22, of Seattle, was and was not at the house the night of the murder. At one point, he also implied that Knox's co-defendant Raffaele Sollecito was at the murder scene.”
Finally, I will expand upon a point I raised in the comments section of the previous article. In response to a question during a live chat, Ms. Nadeau said, “I think it is important to remember that the same scientific police and laboratories tested the DNA for all three suspects. That is to say, if the DNA matches Rudy and is accepted, then the DNA that matches the other two should also be accepted. How she may have left so little DNA if she was actually in the room is very hard to square.”
Ms. Nadeau is asserting implicitly that all DNA evidence is equal, but this is false. We know that the knife profile is weak, has drop-ins, and has considerable imbalance in intensity between most of the pairs of alleles. We know that the bra clasp was left in an insecure location for 47 days and handled poorly when it was finally collected. As Dan Krane said, “The science of DNA profiling is sound. But, not all of DNA profiling is science.” The evidence against Guede has never been released, and one cannot pass judgment on its quality without seeing it. There is second problem with Ms. Nadeau’s assertion. Rudy Guede was only identified as a suspect after the forensics came back, but Raffaele Sollecito and Amanda Knox were already suspects (first on the basis of demeanor, then on the basis of their interrogations) before the forensics was completed. This problem is particularly acute for the bra clasp, and one has to consider the problem of confirmation bias or even outright fraud when weighing the forensic evidence. The third problem is that even within a lab, the quality of work may not be uniform. For one thing lab contamination can be a sporadic event, as it was in the Jaidyn Leskie case. For another, there may be a lone sloppy or dishonest technician in a lab full of competent, ethical ones.
Update 20 April 2010
I added a hyperlink to the Newsweek story in paragraph 1 and the word "to" in paragraph 6, line 4.
Monday, April 5, 2010
The utility of electronic data files in DNA forensics cases
Part XII on the Knox/Sollecito case
“Full disclosure allows a thorough independent review of results and thereby helps assure that the underlying scientific methods are strong and appropriate, and that the laboratory’s interpretations are fair and accurate. Until the electronic data are made available, I cannot say that I have performed a complete review of the underlying evidence in this matter.”
-William Thompson, Victoria State Coroner’s Inquest into Death of Jaidyn Leskie
In a previous post (http://viewfromwilmington.blogspot.com/2010/03/interim-evaluation-of-evidence-against.html) I wrote:
Why are the .fsa files important? Technical bulletin 40-035 from Chromosomal Laboratories, Inc., is a checklist of what the laboratory is expected to provide, and it states, “Copies of all data files used and created in the course of performing tests and analyzing data in this case, including .fsa files, if applicable. These files should include all data necessary to independently reanalyze the raw data.” In response to a question on this subject, Professor Dan Krane wrote, “The biggest concern that I personally have regarding this case is the refusal of the prosecution to provide the defense with a copy of the electronic data that underlies the DNA test results -- that is virtually unheard of world-wide today and it would be especially important to review that data in a case such as this which seems to involve such low level samples.” According to a knowledgeable source, “Each tested sample has its own file. The file contains the full electropherogram trace information along with other information about the testing conditions (e.g., date, time, injection time, voltage, temperature, current, the RFU threshold used by the analyst). If you have the electronic data, you can use the DNA analysis software (GeneScan & Genotyper or GeneMapper ID) to independently analyze the electronic data. That allows you to examine the results as closely as possible (zoom in on the electropherogram to evaluate low-level results) and establish the RFU threshold of your choosing.” (emphasis added)
The knowledgable source I quoted above is Jason Gilder, and he and Dan Krane are cosigners of the open letter from a total of nine forensics scientists that is critical of the evidence in this case. I would like to reexamine this issue with respect to how these files are useful. I will have more to say about circumstances of their being withheld from the defense in the future.
Contents of fsa files
The fsa files are created by the DNA analysis instruments of Applied Biosystems, and the program GeneScan can read them. These files contain the times of and dates on which samples were (runhttp://www.nfstc.org/pdi/Subject06/pdi_s06_m01_02.htm). They also contain the peak detection threshold in relative fluorescence units. Perhaps most importantly, they contain the electronic information needed to recreate a DNA electropherogram with the parameters chosen by the analyst.
Electronic data files and the Leskie case
I would like to examine this case more extensively, both for what it tells us about contamination and what it tells us about electronic data files. Jaidyn Leskie was a young boy in Australia who was murdered n 1997. DNA from an alleged rape victim, Ms. P, was found on two items of his clothing, a bib and track pants. There is general agreement that this was the result of contamination (http://viewfromwilmington.blogspot.com/2010/01/forensic-dna-contamination.html), despite the fact that contamination did not show up in the negative control (reagent blank or no-template) samples. It is helpful to know that Jaidyn’s body was submerged in water for several months before its discover, and these conditions are not at all conducive to the stability of DNA. None of Jaidyn’s own DNA was found, only Ms. P’s.
Professor Thompson provided a report for the Leskie case (quoted above). Professor Thompson wrote (http://www.bioforensics.com/articles/index.html), “When I review the casework of forensic DNA laboratories in the United States, I typically ask for and receive copies of the electronic data collected by laboratory instruments during DNA testing. These data show the actual results of the DNA tests. By examining these data, an independent expert can check whether the forensic laboratory interpreted its results correctly and can detect a host of potential problems that would not be apparent from examining the laboratory notes. Electronic data would be particularly helpful in evaluating the present cases. Beyond allowing a cross check of the analysts’ interpretations, it would allow a detailed independent assessment of whether there is evidence of low- level contamination in any samples.”
Professor Krane provided two reports; the supplemental report was written after he was given access to the electronic data files. With respect to the negative controls not showing contamination his first report state, “there is no good reason to expect that contamination would uniformly affect all samples if and when it does occur. In much the same way, Salmonella-tainted meat placed on one part of a countertop at the beginning of food preparation does not mean that all food subsequently prepared for the same (or even a later) meal will be similarly tainted – just those items that also come in contact with the same portion of the countertop can be reasonably expected to have a chance of being tainted.” In previous posts, I have noted that the amount of DNA after it has been amplified by the polymerase chanin reaction (PCR) makes it a serious potential contaminant. However, professor Krane explained why the PCR process itself was not likely to be the source of the contamination in this instance. Professors Thompson and Krane both indicate that substrate controls would have been appropriate in this case.
It is Dr. Krane’s second report that is especially pertinent to the utility of access to the electronic data. He wrote, “My subsequent review of the underlying electronic data associated with the testing performed by the VFSC during their investigation of the death of Jaidyn Leskie in particular leaves me even more convinced that the STR-DNA profile match observed between the condom of the rape investigation and the bib in the Jaidyn Leskie abduction investigation is the result of contamination.” He went on to say, “Now that I have had an opportunity to review the electronic data from the Leskie investigation I, like Professor Thompson, do indeed find low levels of signal that are consistent with Ms. P’s DNA profile and lend substantially more credence to the already compelling proposition that she is the source of the DNA associated with the Leskie bib and track pants.” Professor Krane subsequently wrote in response to one of my inquiries that the observation of these peaks “helped strengthen the case that contamination had occurred by several orders of magnitude.” (emphasis added)
Professor Krane noted that there was a systematic difference in the peak heights depending on the software one used and the analysis options one chose: “However, I thought it might also be helpful to consider the output as it was seen by the testing laboratory primarily for two reasons: 1) no-smoothing with the Macintosh versions of the software systematically makes peak heights larger; and 2) the peak heights generated in this way should be more directly comparable with the threshold established by the testing laboratory in the course of their validation studies. As Professor Thompson points out, “Most laboratories establish a peak height threshold for reporting alleles and make it a practice to ignore peaks falling below that threshold.” I, like him, feel that this practice is appropriate but that low-level signals may also contain useful information in investigations such as this one.” It is possible that peaks could fall above the threshold in the hands of one analyst and below it in the hands of another. The sizes of the peaks in the two figures in this report vary from less than one hundred RFUs to many hundreds of RFUs, documenting the fact that profiles arising from contamination can easily be mistaken for samples arising from genuine contact.
Justification for the release of electronic files in another case
An anonymous DNA forensic expert unaffiliated with the present case had this to say in a case from several years ago:
“The laboratory has provided hard copy printouts of the data that do not allow the possibility of reanalysis by an independent expert. Certain parameters have irrevocably been applied to the data; as such it represents an interpretation by the laboratory rather than the original data. Of additional concern is the fact that the documents provided by the laboratory are represented as fully complying with the discovery request.” The expert gave several areas where independent review requires the electronic data files, including.
1. Determination of the threshold. “Not all qualified experts would necessarily apply the same threshold given identical data…The possibility of false inclusions as well as false exclusions exists if real data that happen to reside below an artificial threshold are ignored.”
2. Scale of viewing. “This ability is an important element in determining whether a particular peak represents and authentic DNA fragment.”
3. Proprietary concerns. “The data itself, as the work product of a government laboratory in a criminal matter, is clearly in the public purview.”
“Honest differences of opinion by qualified experts should be welcomed by the Court. This can only be accomplished if the independent expert is provided full and complete discovery by the government.”
Electronic data files and the Knox/Sollecito case
In response to a question, Dan Krane wrote me to say, “I would like to see that data primarily for two reasons: 1) to determine the actual heights and data collection points of all the peaks (for purposes of mixture resolution and the possibility that some are associated with pull up, respectively), and 2) to calculate a limit of detection from the data in the controls so as to determine if the lab was reliably distinguishing between signal and noise in the evidence samples.”
Professor William Thompson wrote (Tarnish on the 'gold standard:' Understanding recent problems in forensic DNA testing. The Champion. 30(1):10-16, January/February 2006), “A key aspect of discovery in DNA cases is the electronic data produced by the computer-controlled genetic analyzers that are currently used to “type” DNA samples. Analysis of the computer files can not only reveal undisclosed problems and support alternative interpretations of the findings, but also, as discussed above, these files can be crucial for detecting instances of scientific fraud, such as that committed by Jacqueline Blake and Sarah Blair.” Jacqueline Blake was an employee of the FBI whose two-year record of contamination-free work was the result of dumping a portion of the negative control down the sink. Sarah Blair repeatedly substituted a file of a contamination-free blank for the actual blank.
I can think of several things I would look for using the electronic data files. The first is what peak threshold was used for the 400+ runs and whether or not it was the same threshold as the knife blade profile. The second is to zoom in on the small peaks in the bra clasp, as Jason Gilder implied. It is conceivable that the identities of the three additional people who contributed DNA to the clasp could be ascertained. The third is to examine the negative control runs for evidence of fraud, as Professor Thompson noted could be done. The negative controls are the most common place for fraud to be detected.
State of Michigan
One exception to the general rule of complete disclosure of the electronic data files was the state of Michigan (http://www.bioforensics.com/articles/Thompson_Champion_Tarnish.pdf). In 2005 the Michigan State police Issued a statement saying that, “it is the position of the Michigan State Police Forensic Science Division that any release of this (sic) data for processing with non-validated parameters is tantamount to evidence tampering.” Thompson refutes this position: “By analogy, if the police disclosed digital photos of the crime scene, it would hardly be ‘data tampering’ for a defense expert to manipulate the digital images in an effort to enhance them or bring specific details into focus…The use of proper analysis parameters might well become an issue if and when the defense decided to offer into evidence the results of its analysis of the electronic data. But to deny access to digital data on grounds that the defense might analyze it improperly eviscerates the right to discovery.” (emphasis added) I will update this post if I am able to learn whether or not the State of Michigan has changed its policy.
“Full disclosure allows a thorough independent review of results and thereby helps assure that the underlying scientific methods are strong and appropriate, and that the laboratory’s interpretations are fair and accurate. Until the electronic data are made available, I cannot say that I have performed a complete review of the underlying evidence in this matter.”
-William Thompson, Victoria State Coroner’s Inquest into Death of Jaidyn Leskie
In a previous post (http://viewfromwilmington.blogspot.com/2010/03/interim-evaluation-of-evidence-against.html) I wrote:
Why are the .fsa files important? Technical bulletin 40-035 from Chromosomal Laboratories, Inc., is a checklist of what the laboratory is expected to provide, and it states, “Copies of all data files used and created in the course of performing tests and analyzing data in this case, including .fsa files, if applicable. These files should include all data necessary to independently reanalyze the raw data.” In response to a question on this subject, Professor Dan Krane wrote, “The biggest concern that I personally have regarding this case is the refusal of the prosecution to provide the defense with a copy of the electronic data that underlies the DNA test results -- that is virtually unheard of world-wide today and it would be especially important to review that data in a case such as this which seems to involve such low level samples.” According to a knowledgeable source, “Each tested sample has its own file. The file contains the full electropherogram trace information along with other information about the testing conditions (e.g., date, time, injection time, voltage, temperature, current, the RFU threshold used by the analyst). If you have the electronic data, you can use the DNA analysis software (GeneScan & Genotyper or GeneMapper ID) to independently analyze the electronic data. That allows you to examine the results as closely as possible (zoom in on the electropherogram to evaluate low-level results) and establish the RFU threshold of your choosing.” (emphasis added)
The knowledgable source I quoted above is Jason Gilder, and he and Dan Krane are cosigners of the open letter from a total of nine forensics scientists that is critical of the evidence in this case. I would like to reexamine this issue with respect to how these files are useful. I will have more to say about circumstances of their being withheld from the defense in the future.
Contents of fsa files
The fsa files are created by the DNA analysis instruments of Applied Biosystems, and the program GeneScan can read them. These files contain the times of and dates on which samples were (runhttp://www.nfstc.org/pdi/Subject06/pdi_s06_m01_02.htm). They also contain the peak detection threshold in relative fluorescence units. Perhaps most importantly, they contain the electronic information needed to recreate a DNA electropherogram with the parameters chosen by the analyst.
Electronic data files and the Leskie case
I would like to examine this case more extensively, both for what it tells us about contamination and what it tells us about electronic data files. Jaidyn Leskie was a young boy in Australia who was murdered n 1997. DNA from an alleged rape victim, Ms. P, was found on two items of his clothing, a bib and track pants. There is general agreement that this was the result of contamination (http://viewfromwilmington.blogspot.com/2010/01/forensic-dna-contamination.html), despite the fact that contamination did not show up in the negative control (reagent blank or no-template) samples. It is helpful to know that Jaidyn’s body was submerged in water for several months before its discover, and these conditions are not at all conducive to the stability of DNA. None of Jaidyn’s own DNA was found, only Ms. P’s.
Professor Thompson provided a report for the Leskie case (quoted above). Professor Thompson wrote (http://www.bioforensics.com/articles/index.html), “When I review the casework of forensic DNA laboratories in the United States, I typically ask for and receive copies of the electronic data collected by laboratory instruments during DNA testing. These data show the actual results of the DNA tests. By examining these data, an independent expert can check whether the forensic laboratory interpreted its results correctly and can detect a host of potential problems that would not be apparent from examining the laboratory notes. Electronic data would be particularly helpful in evaluating the present cases. Beyond allowing a cross check of the analysts’ interpretations, it would allow a detailed independent assessment of whether there is evidence of low- level contamination in any samples.”
Professor Krane provided two reports; the supplemental report was written after he was given access to the electronic data files. With respect to the negative controls not showing contamination his first report state, “there is no good reason to expect that contamination would uniformly affect all samples if and when it does occur. In much the same way, Salmonella-tainted meat placed on one part of a countertop at the beginning of food preparation does not mean that all food subsequently prepared for the same (or even a later) meal will be similarly tainted – just those items that also come in contact with the same portion of the countertop can be reasonably expected to have a chance of being tainted.” In previous posts, I have noted that the amount of DNA after it has been amplified by the polymerase chanin reaction (PCR) makes it a serious potential contaminant. However, professor Krane explained why the PCR process itself was not likely to be the source of the contamination in this instance. Professors Thompson and Krane both indicate that substrate controls would have been appropriate in this case.
It is Dr. Krane’s second report that is especially pertinent to the utility of access to the electronic data. He wrote, “My subsequent review of the underlying electronic data associated with the testing performed by the VFSC during their investigation of the death of Jaidyn Leskie in particular leaves me even more convinced that the STR-DNA profile match observed between the condom of the rape investigation and the bib in the Jaidyn Leskie abduction investigation is the result of contamination.” He went on to say, “Now that I have had an opportunity to review the electronic data from the Leskie investigation I, like Professor Thompson, do indeed find low levels of signal that are consistent with Ms. P’s DNA profile and lend substantially more credence to the already compelling proposition that she is the source of the DNA associated with the Leskie bib and track pants.” Professor Krane subsequently wrote in response to one of my inquiries that the observation of these peaks “helped strengthen the case that contamination had occurred by several orders of magnitude.” (emphasis added)
Professor Krane noted that there was a systematic difference in the peak heights depending on the software one used and the analysis options one chose: “However, I thought it might also be helpful to consider the output as it was seen by the testing laboratory primarily for two reasons: 1) no-smoothing with the Macintosh versions of the software systematically makes peak heights larger; and 2) the peak heights generated in this way should be more directly comparable with the threshold established by the testing laboratory in the course of their validation studies. As Professor Thompson points out, “Most laboratories establish a peak height threshold for reporting alleles and make it a practice to ignore peaks falling below that threshold.” I, like him, feel that this practice is appropriate but that low-level signals may also contain useful information in investigations such as this one.” It is possible that peaks could fall above the threshold in the hands of one analyst and below it in the hands of another. The sizes of the peaks in the two figures in this report vary from less than one hundred RFUs to many hundreds of RFUs, documenting the fact that profiles arising from contamination can easily be mistaken for samples arising from genuine contact.
Justification for the release of electronic files in another case
An anonymous DNA forensic expert unaffiliated with the present case had this to say in a case from several years ago:
“The laboratory has provided hard copy printouts of the data that do not allow the possibility of reanalysis by an independent expert. Certain parameters have irrevocably been applied to the data; as such it represents an interpretation by the laboratory rather than the original data. Of additional concern is the fact that the documents provided by the laboratory are represented as fully complying with the discovery request.” The expert gave several areas where independent review requires the electronic data files, including.
1. Determination of the threshold. “Not all qualified experts would necessarily apply the same threshold given identical data…The possibility of false inclusions as well as false exclusions exists if real data that happen to reside below an artificial threshold are ignored.”
2. Scale of viewing. “This ability is an important element in determining whether a particular peak represents and authentic DNA fragment.”
3. Proprietary concerns. “The data itself, as the work product of a government laboratory in a criminal matter, is clearly in the public purview.”
“Honest differences of opinion by qualified experts should be welcomed by the Court. This can only be accomplished if the independent expert is provided full and complete discovery by the government.”
Electronic data files and the Knox/Sollecito case
In response to a question, Dan Krane wrote me to say, “I would like to see that data primarily for two reasons: 1) to determine the actual heights and data collection points of all the peaks (for purposes of mixture resolution and the possibility that some are associated with pull up, respectively), and 2) to calculate a limit of detection from the data in the controls so as to determine if the lab was reliably distinguishing between signal and noise in the evidence samples.”
Professor William Thompson wrote (Tarnish on the 'gold standard:' Understanding recent problems in forensic DNA testing. The Champion. 30(1):10-16, January/February 2006), “A key aspect of discovery in DNA cases is the electronic data produced by the computer-controlled genetic analyzers that are currently used to “type” DNA samples. Analysis of the computer files can not only reveal undisclosed problems and support alternative interpretations of the findings, but also, as discussed above, these files can be crucial for detecting instances of scientific fraud, such as that committed by Jacqueline Blake and Sarah Blair.” Jacqueline Blake was an employee of the FBI whose two-year record of contamination-free work was the result of dumping a portion of the negative control down the sink. Sarah Blair repeatedly substituted a file of a contamination-free blank for the actual blank.
I can think of several things I would look for using the electronic data files. The first is what peak threshold was used for the 400+ runs and whether or not it was the same threshold as the knife blade profile. The second is to zoom in on the small peaks in the bra clasp, as Jason Gilder implied. It is conceivable that the identities of the three additional people who contributed DNA to the clasp could be ascertained. The third is to examine the negative control runs for evidence of fraud, as Professor Thompson noted could be done. The negative controls are the most common place for fraud to be detected.
State of Michigan
One exception to the general rule of complete disclosure of the electronic data files was the state of Michigan (http://www.bioforensics.com/articles/Thompson_Champion_Tarnish.pdf). In 2005 the Michigan State police Issued a statement saying that, “it is the position of the Michigan State Police Forensic Science Division that any release of this (sic) data for processing with non-validated parameters is tantamount to evidence tampering.” Thompson refutes this position: “By analogy, if the police disclosed digital photos of the crime scene, it would hardly be ‘data tampering’ for a defense expert to manipulate the digital images in an effort to enhance them or bring specific details into focus…The use of proper analysis parameters might well become an issue if and when the defense decided to offer into evidence the results of its analysis of the electronic data. But to deny access to digital data on grounds that the defense might analyze it improperly eviscerates the right to discovery.” (emphasis added) I will update this post if I am able to learn whether or not the State of Michigan has changed its policy.
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