View-from-Wilmington

Hank Skinner, the death penalty, and investigative tunnel vision

2011-11-04T11:00:00.006-04:00

Update I, 5 November 2011

The Skeptical Juror wrote, "The hairs found clasped in Twila’s hand, the hairs pronounced by the DA to belong to the killer, turned out to come from a male, maternal relative of Twila. They did not come from Hank Skinner. According to the standard set by the DA before the testing, those hairs exonerated Hank Skinner." Twila's uncle had stalked her the night of her murder. The DNA testing described appears to be mitochondrial DNA forensics (one inherits mitochondrial DNA from one's mother). My tentative interpretation of the mitochondrial DNA is that the data tend toward innocence but are not yet conclusive. As others have said, I am not certain Mr. Skinner is innocent, but I cannot see a persuasive reason not to test the items in question.

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The state of Texas is trying to put Hank Skinner to death for the murder of a family of three people. DNA testing showed that blood smears on his shirt matched two of the victims. Mr. Skinner was undoubtedly at the scene of the crime, but his mental and physical state at the time open the question of whether or not he would have been capable of committing murder. A recent Texas law was designed to apply to this case, to allow further DNA testing.

Radley Balko has been following the case of Hank Skinner for some time. Writing for Reason Balko noted, “In 2000 DNA tests were conducted on blood taken from a roll of gauze and a cassette tape found in the house; that blood didn't match Skinner, his girlfriend, or her sons.” At Huffington Post he wrote, “There is DNA from the crime scene that could exonerate Skinner -- or could affirm his guilt -- that has never been tested. That includes blood from the murder weapon, blood from a jacket left in Busby's home, a rape kit taken from Busby, scrapings from under Busby's fingernails and hairs she was clutching at the time of her death -- hairs that likely came from her killer.”

The State of Texas has argued that since Skinner’s attorney at the time did not press for testing these items. Radley Balko continued, "’They only tested the material they thought would implicate Skinner,’ [Professor David] Protess told me in an interview last year. ‘They fixated on their suspect, and once they thought they had enough for a conviction, they stopped.’” Private investigation several years after the crime turned up a second plausible suspect.

Students of the Knox/Sollecito case should be especially troubled by investigatorial tunnel vision. In the first place, there are good reasons to question the competency of Skinner’s first attorney, apart from his decision not to seek testing. Second, his attorney’s decision was contrary to the wishes of Mr. Skinner, as he expressed in a letter in 1994. Third, the whole issue of whether or not the attorney should have sought testing is misdirection: the investigators should have tested these items as a matter of good forensic science. Here is a link to a petition for full DNA testing.

Some helpful commentary on the acquittal

2011-10-20T21:47:00.007-04:00

Part 33 in the Knox/Sollecito case

On 3 October 2011 a court acquitted Amanda Knox and Raffaele Sollecito of the murder of Meredith Kercher. A few articles stood out. Christiana Patterson’s title, “We prefer a crazy story to the truth,” as good a one-sentence summation of the case as any I have seen. She also indicated one of the main problems with the one of the most significant pieces of evidence against Knox and Sollecito: “One piece of ‘evidence’ wasn't ‘found’ for 47 days. It was found, in fact, the day after a TV programme highlighting flaws in the case.” She also empathized with the Kercher family’s dilemma of whether to continue believing that Knox and Sollecito are somehow culpable or to reconsider their understanding of the case.

Of the prosecution’s version of the murder as a sex game gone wrong Deborah Orr said, “An astonishing number of people around the world were keen to believe this scenario, although there is no evidence to support it. Some still are.” Of the Kercher family she concluded, “A lot of people share blame for the mental torture this family have been through. Amanda Knox is not one of them.” Indeed. Nor is Raffaele Sollecito.

Ms. Knox’s seemingly odd behavior led some to suspect her; A friend of mine recalled a video of Ms. Knox as wildly kissing her boyfriend Mr. Sollecito outside of the apartment shared by Ms. Knox, Ms. Kercher, and two other women. Yet Ian Lesie noted, “In fact, the video is anything but sexy. Knox, looking wan and dazed, exchanges chaste kisses with Sollecito, who rubs her arm consolingly.” He saw this case as “a particularly pungent manifestation of a universal trait, one that frequently leads criminal investigators and juries astray: overconfidence in our ability to read someone else's state of mind simply by looking at them.”

With considerable justification Carole Cadwalladr observed, “The whole case, the prosecution's version of events, the media coverage, and the court of public opinion, has been viewed almost solely through the prism of Knox's looks and sexuality.” Was Meredith Kercher shoved aside? To some degree, but so was Ms. Knox’s then boyfriend, Raffaele Sollecito. Most remarkably, Rudy Guede, the sole person whom the evidence indicates sexually assaulted and killed Ms. Kercher has also been largely ignored. In an alternate universe he would have been the person most vilified, and with complete justification.

Update 1 (11 PM)

Dylan Evans saw "confirmation bias" and "imagination inflation" in the investigation: "Unfortunately, law enforcement officials are as ignorant of this phenomenon [imagination inflation] as they are of confirmation bias. When they ask suspects to imagine their possible role in a murder they do not at first remember, therefore, this very exercise may unknowingly lead the suspect to believe that he or she was really involved."

Amanda Knox and Raffaele Sollecito: There is no mixed blood

2011-09-22T21:16:00.012-04:00

Part 32 in the Knox/Sollecito case

Introduction
The Conti-Vecchiotti report casts further doubt upon the reliability of the bra clasp and the kitchen knife, two of the strongest, yet seriously flawed, pieces of evidence against Ms. Knox and Mr. Sollecito in this case. With the appeals trial expect to wrap up shortly, it is time to reexamine the strength of the other biological evidence against them, especially the mixed DNA traces. An anonymous pro-guilt blogger did so several months ago. The related question of whether or not the luminol-positive areas (some of which had DNA profiles) were truly blood was the subject of a previous entry here and a discussion at Let’s Talk about True Crime.

Which samples contained mixed DNA?
There are two amorphous, luminol-positive spots in Filomena’s room (Reps. 176 and 177), although the alleles which may be Amanda’s are quite weak. There is a shoe print in the hallway (Rep. 183). In the shared bathroom there is a sample from the bidet drain, the cotton flock container on the floor, and from the inside of the washbasin (Rep. 137). There is no DNA from Amanda in the murder room, either by itself or mixed with Meredith’s DNA.

Did the jury in the first trial find the mixed DNA to be significant?
Barbie Nadeau wrote, "The defense's biggest mistake, according to interviews with jurors after the trial, was doing nothing to refute the mixed-blood evidence beyond noting that it is common to find mingled DNA when two people live in the same house. The jurors needed more than that. 'To have mixed blood, you have to both be bleeding,' one of them remarked to me after the verdict. It was obvious that Meredith was bleeding, but why was Amanda bleeding?'" ("Angel Face," pages 152-153)

Does mixed DNA indicate mixed blood?
The passage quoted above implies that at least one juror thought that the two were equivalent, but this is a fallacy. There are three possibilities with respect to mixed DNA and blood: neither source, one source, or both sources of DNA could be blood. A commonly repeated fallacy of this case is to equate a mixture of DNA with a mixture of blood (to assume possibility three). For example in a recent Dateline broadcast Barbie Nadeau said, “I have to say, I live in a house with 3 people, my two sons and my husband, I guarantee you I have no mixed blood with any of them, anywhere in my house. I don't bleed where they bleed, we don't bleed at the same time. There would never be my mixed blood, their blood and my blood anywhere ever.”

The false equivalence between mixed DNA and mixed blood dates back at least to the publication of the book Darkness Descending. In this book Colonel Luciano Garofano, a retired officer of the Carabinieri, said, “However, here is the electropherogram and you can see that the RFU value is very high, so the sample is undoubtedly blood, which is the body fluid that provides the greatest amount of DNA. In some cases you see higher peaks of Amanda's DNA than Meredith's. Amanda has been bleeding. Nor is it old blood, as the defence might say, because blood decays fast. We have the same result on the cotton-bud box. The light switch was over-scrubbed, but from the film the way the cotton-bud was good enough. There too we have mixed blood. So that's pretty significant for Amanda, Unfortunately for her, she bled at the same time Meredith was bleeding. That's a lot to explain." (Darkness Descending, page 371).

There are several reasons why Garofano’s interpretations are wrong. In response to a question of mine, Professor Dan Krane wrote, “Inferring tissue source from peak heights is just plain silly -- to the point of being absolutely outrageous. It hardly bears more comment than that, but if high peaks mean blood then what would you expect from semen which has a ten to one hundred fold higher concentration of DNA?” Professor Greg Hampikian concurred with the view that peak heights were not an indication of whether or not blood was the source of DNA. The peak heights for Raffaele’s profile on the cigarette butt were reported to me as being about the same height as those on the cotton box, and the former are presumably from saliva.

Colonel Garofano’s claim that the DNA from blood decays quickly is difficult to evaluate. A paper (Park et al., “Direct STR Amplification from Whole Blood and Blood- or Saliva-Spotted FTA without DNA Purification,” J. Forensic Sci., March 2008, Vol. 53, No. 2, 335-41) showed that 1-2 year-old blood samples gave strong signals in DNA profiling when stored in the form of FTA cards (which contain stabilizers); therefore, their study does not exactly refute what Colonel Garofano claimed, but it does not support his claim, either. However, this paper also showed that saliva gave tall peaks in DNA profiling, which is one more indication that peak height cannot be used to infer the biological origin of a sample. The rate of decay of a DNA sample depends upon so many factors that dating DNA by its degradation is not practical. Furthermore, even if one were to accept that DNA peaks from blood did degrade very quickly, one might have to conclude that the luminol-positive, mixed-DNA samples were not blood, inasmuch as the luminol was applied on 18 December, more than a month and a half after the crime.

What did Massei conclude with respect to the mixed DNA samples?
In contrast to the juror quoted above, the Massei report did not assume that mixed DNA was equivalent to mixed blood (pp. 278-279, English Translation). “It should then be highlighted that in that same bathroom various [300] trace specimens were found, of a mixed nature and testing positively for blood. It is true that, according to what was asserted and explained, it is not possible with a mixed trace specimen that tested positive for human blood to determine which of the trace’s contributors the blood belongs to. In this case, however, non-mixed traces were also found, which were shown to be of a haematological nature [i.e. blood] and turn out to have the biological profile of the victim.” The report continued (p. 279), “And it is probable - not necessary, but probable - that during the following act of scrubbing the hands to remove the blood, he/she left the mixed trace consisting of Meredith’s blood and of cells which had been removed by rubbing during the act of washing.”

The Massei motivations report acknowledged that Amanda had no wounds and therefore was not bleeding. It also noted that DNA by itself gives no indication of when it was deposited (see below). In summary Massei thought that the mixed DNA did not necessarily indicate mixed blood, but he believed that the traces were deposited simultaneously, at least partially on the basis of Amanda’s declaring that the bathroom was clean on the afternoon of 1 November. Such a position is problematic in that a clean bathroom does not necessarily imply a DNA-free bathroom. Moreover, there is no reason to rule out Amanda’s depositing the DNA on the morning after the crime in addition to the possibility that she deposited it before the crime.

Does mixed DNA have to be deposited at the same time?
In general the presence of DNA almost never gives an indication of how or when it was deposited. The abstract of an article (“DNA profiling of trace DNA recovered from bedding,” Forensic Science International, Volume 159, Issue 1, 25 May 2006, Pages 21-26) on DNA profiling states in part: “The results indicate that the DNA profile of an individual can be obtained from bedding after one night of sleeping in a bed. The DNA profile of the owner of the bed could also be detected in the foreign bed experiments. Since mixed DNA profiles can be obtained from trace DNA on bedding, caution should be exercised when drawing conclusions from DNA profiling results obtained from such samples.” This is a good example of mixed DNA that could not have been deposited simultaneously.

How common is mixed DNA?
Head of the US National Institute of Standards and Technology's genetics group, “[John] Butler has reviewed more than 5000 DNA samples from 14 US labs and found that mixing is a common occurrence: 34 per cent of the samples he studied included DNA from two people, while 11 per cent were three or four-person mixtures.” Although some fraction of the two-person samples are from the victim and the perpretrator, it is not reasonable to suppose that this is the case for all of them, let alone the three or four-person mixtures.

Are there other mixed DNA samples in this case?
In addition to the mixed DNA of Meredith and Amanda at the girls’ flat, there are also three mixed DNA samples containing Amanda’s and Raffaele’s DNA at his flat. One was found in Sollecito’s bathroom, one was found in his bedroom, and one was found on a pair of rubber gloves. The former two are also luminol-positive, but the identity of the luminol-reactive substance is not known. All three mixed samples are likely to be the result of cohabitation. Amanda’s and Raffaele’s DNA was also found on a cigarette butt at the girls’ flat (p. 193, Massei Report, English translation). The cigarette butt is also interesting in that some of the peaks comprising Amanda’s profile are moderate in intensity, despite possibly being the result of secondary DNA transfer (Amanda does not smoke cigarettes).

Do any of the samples contain DNA from a third party?
Sara Gino’s testimony indicated that in sample 177 in Filomena’s room there were alleles besides those of Meredith and Amanda. I have also examined a copy of the electropherogram. In the D19S433 locus, four alleles are marked: 12, 13, 16, and 16.2, but there are unlabeled alleles at 14 and 15 or 15.2. If one acknowledges that it might have been deposited at some other time than the murder, then one must also acknowledge the same possibility for Amanda's DNA.

Could the forensic team have run controls?
Besides the issue of how samples were collected in general, the forensic police could have done substrate controls, where they examined areas for DNA that were a few inches away from putative blood stains, as materials scientist Dr. Mark Waterbury suggested. If they had found Amanda’s DNA in some of those locations, it would have been suggestive of innocent DNA deposition.

They could also have performed or cited studies of DNA deposition in bathrooms, if such studies existed already (I am not aware of any). There are a number of ways that such studies could be performed. For instance, one could take blood from person A and place it in person B’s bathroom, then collect DNA samples. If one found mixed DNA from A and B, it would strengthen the hypothesis that Amanda deposited DNA in the normal course of everyday living.

Is there precedent for mixed DNA arising through contamination?
Many cases of contamination show a mixture of DNA from the analyst and a potential suspect, as discussed in the previous blog entry. One case, the murder of Jane Mixer, showed contamination from two potential suspects, Gary Leiterman and John Ruelas. However, Ruelas was four years old at the time of the murder and lived in a different city. Therefore, this is probably a case in which both profiles arose from contamination.

Could the way the DNA was sampled have resulted in mixed DNA?
The Massei Motivations report (p. 278, English translation) indicates that the defense thought that the mixed traces were meaningless: “All the more so since the samples had been taken using the same blotting paper which had been used for various parts of the bidet and the sink.” Even Colonel Garofano (a strongly pro-prosecution commentator on the case) was dismayed at the way the washbasin trace was collected, noting, “The fact that the sample was collected by wiping both the edge and the plughole is dangerous. You’re likely to find all sorts of stuff in the plughole.” (p. 370, “Darkness Descending”)

Did the police take every precaution to avoid contamination?
No, there are several ways in which the work could have been improved. Ms. Stefanoni’s view was that liquid samples are liable to cross-contamination, but dry traces are not. In the English translation of the Massei report (p. 203) it says that Stefanoni “specified” that gloves were changed “every time an object was touched that was particularly soaked with blood, and when it was obvious that the gloves would be soiled;” On pages 204-205 she indicated that the presence of a liquid is necessary to bring about contamination by touch.

Ms. Stefanoni’s view is out of the mainstream. On page 38 of John Butler's textbook “Forensic DNA Typing,” he wrote, “Use clean latex gloves for collecting each item of evidence. Gloves should be changed between handling of different items of evidence.” At Forensic Magazine in the article “Evidence Handling and Collection” Dick Warrington wrote, “Go about collecting evidence. I can’t say enough about avoiding cross contamination. Put on gloves, use gloves, change gloves. Do that every time you touch a piece of evidence. Likewise, use disposable tweezers, scalpels, etc. Change these each time they are used, as well.” Warrington also wrote an article for Forensic Magazine called “DNA Collection and Packaging,” that discussed the use of gloves and tweezers to avoid contamination. Orchid Cellmark’s guidelines state, “Use clean latex gloves for collecting each item of evidence. It is recommended the gloves be changed between the collection of each item of evidence.” If the police handled an item of evidence with Amanda’s DNA then handled an item with Meredith’s DNA, the glove could carry Amanda’s DNA into the other sample.

Are there innocent explanations for the mixed DNA in Filomena’s room?
The luminol work that first identified some of the areas that later were shown to contain mixed DNA traces was performed on December 18, 2007. By this time many police personnel had been in the girls’ flat, and many of Meredith’s items had been tossed about. This raises the possibility that the forensic police tracked the genetic material of either Knox or Kercher into Filomena’s room from the hall. The forensic police who were recorded on 18 December wore one-piece tyvek garments but did not appear to have any outer shoe covering. Former FBI agent Steve Moore noted that they did not change shoe covers going from one room to another that that this creates the potential for cross-contamination. This is especially worrisome in that several members of the team are quite close to the dried bloodstains in Meredith’s room, as can be seen in parts 10 and 11 of a series of videos taken on 18 December 2007.

In addition the luminol-positive spots are only presumptive blood; these tested negative by tetramethylbenzidine, a second type of presumptive test, and there is no record of confirmatory blood testing. Therefore, it is open to debate whether or not the luminol-positive substance is even blood. One photograph of the luminol-positive footprints in the hallway also show blue specks on the ruler and on the boot of one of the forensic police officers. It is unclear what the luminol-positive substance was in this case, or whether it could have contaminated other items of evidence.

Conclusions
Mixed DNA is commonly observed and is not equivalent to mixed blood. In general DNA samples cannot be dated, and any two profiles within a sample may have been deposited at different times. The mixed DNA in the bathroom may have been created by Meredith's blood falling on Amanda's biological matter that was already there. The chances of this happening might have been lessened if the forensic police had taken a smaller trace with respect to the washbasin, for example. Dirty gloves or dropped swabs (which happened elsewhere) made have mixed DNA during collection. The police or the inhabitants of the flat may have tracked Meredith's blood into Filomena's room. The evidentiary value of these mixed DNA samples is very low.

The likelihood of DNA contamination

2011-09-04T13:07:00.020-04:00

Part 31 in the Knox/Sollecito case

The subject of DNA contamination has been a frequent topic of this blog. DNA contamination is again near the forefront of the Kercher murder and the second trial of Amanda Knox and Sollecito. The court-appointed, independent experts, Drs. Conti and Vecchiotti, have issued a report that raises the strong possibility of contamination. The odds that a forensic DNA sample are contaminated are hard to determine yet very important. Let us first examine a specific statement made with respect to environmental contamination and this case, then look at the question more generally. A subsequent entry will examine the collection practices of the Rome lab and Conti’s and Vecchiotti’s evaluation of their work in this case.

Professor Giuseppe Novelli, a researcher into medical genetics and forensic DNA profiling, said, «Il contaminante va dimostrato, dove nasce e dove è. Il gancetto contaminato dalla polvere? Più probabile che cada un meteorite e butti giù questo tribunale» "The contaminant needs to be demonstrated, where it comes from and where it is. The clasp contaminated by dust? It's more likely that a meteorite comes down and knocks down this courthouse." (translation by komponisto)

Let us assume that Dr. Novelli is specifically referring to household dust. The potential for dust being an issue in forensic DNA testing first came to light with the publication of a paper from Bonnie Brown and coworkers: Toothman et al., “Characterization of human DNA in environmental samples,” Forensic Science International 178 (2008) 7–15. These workers sampled dust from offices, research laboratories, and classrooms.

Figure 3 in this paper is an electropherogram of dust from a classroom, and it shows peaks of 1000 to 3500 RFU corresponding to 3-6 alleles in some loci associated with shorter pieces of DNA. As the length of the DNA fragments increases (moving from left to right on the elecropherogram), the height of the peaks decreased. The authors point out that this is consistent with DNA template that is partially degraded. The combination of a sample’s being a mixture and its yielding only partial profiles makes it very difficult to identify individual profiles.

The authors wrote, “Results of this study have implications regarding the processing of forensic samples. First, the presence of genotypeable human DNA in dust illustrates a significant
potential contamination source in forensic investigations. Twenty-five of 36 samples contained sufficient input human DNA for STR analysis using the AmpFlSTR® Profiler PlusTM assay (~1.0 ng), and 36% (including low-input samples) produced alleles at multiple loci. These results demonstrate that even though anti-contamination measures may be in place at a crime scene and the laboratory, trace DNA derived from dust in the vicinity of other evidence is capable of producing signals higher than background noise in STR analyses.”

Trace DNA and the environment
Secondary transfer is the movement of DNA from a donor to an intermediate object then to another object from which it is collected. Some forensic scientists only classify it as contamination when it occurs subsequently to the object’s being taken into custody; however, other workers prefer to treat innocent secondary transfer as equivalent to contamination on the basis that neither is relevant to the investigation. Both secondary transfer prior to an object’s being collected and contamination need to be understood more thoroughly for trace DNA to be used routinely in DNA forensics. Van Oorshot and colleagues wrote, “Greater effort needs to be made by police/crime investigators to investigate how a DNA sample arrived at the location where it was found, as well as by scientists to better understand the impact of activities on the relative amounts of DNA from particular sources at a crime scene… Some preliminary contributions to our knowledge of transfer in relation to residential burglary and street robbery have recently been made [67].

In their review of trace DNA in forensics Van Oorshot and colleagues suggested six remedies to address the problem of contamination:
“1. perform more studies similar to those of Raymond et al. [67], Cook and Dixon [202], Dowlman et al. [203] and Toothman et al. [201] in order to learn more about the occurrence and persistence of DNA on particular surfaces in different environmental conditions” Understanding how prevalent and persistent background DNA is in the environment is far from being completely understood. Dr. Novelli declined to comment for this report, but his comparison with a meteorite is premature, at best.

The relationship between DNA sample size and the ease of transfer
In their 2010 review article Van Oorshot and colleagues wrote, “Contaminant DNA may appear as either the major or minor sample within a mixture or, alternatively, may overwhelm the target DNA completely.” One explanation for this somewhat counterintuitive statement is that contamination in the laboratory may introduce DNA from previous PCR amplifications by a number of possible routes. However, the two main DNA profiles of interest (Meredith’s on the knife blade and Raffaele’s putative profile on the bra clasp) both involve relatively small amounts of DNA; therefore, we will focus on small samples.

The discussion of low copy number (LCN) testing from the Crown Prosecution Service noted, “This increased sensitivity means ultra-clean laboratories are needed for the testing to minimise contamination of the sample by DNA from any other source.” The New Zealand Institute of Environmental Science and Research has spent $1 million building anticontamination areas for low copy number (LCN) DNA forensics. The New Zealand Herald wrote, “The bogey is contamination. The very sensitivity of the technique which enables it to extract a DNA profile from the tiniest sample also makes it extremely vulnerable to contamination. Stringent measures are needed to minimise that risk… We live in a ‘soup’ of DNA, explains ESR forensic programme manager Keith Bedford. ‘If I were to shed dandruff, massive amounts of dna could fall ... hair could carry DNA. The way I am speaking at the moment, we could probably detect DNA on this pad in front of me.’”

Sara Gino testified for the defense in the trial of the first instance, and some of what she had to say is pertinent to this issue. From the Massei report (p. 258, English translation): “She reaffirmed that [the risk of] contamination exists, and emphasised that in minimal quantities of DNA there is not necessarily a greater risk of contamination but it was easier to notice the effects of the contamination and be misled (‘...It's not that the risk of contamination is greater; but it is easier to see the contamination...’ page 92).” In response to a question on this subject, Professor Dan Krane responded, “There is absolutely no question but that contamination is a much greater problem in LCN cases than conventional DNA testing. The reasons that it is a greater problem are both because it is easier to detect contaminants ([Sara] Gino's point) and because it is easier to transfer (and to transfer without knowing) smaller amounts of DNA than larger amounts of DNA.”

Some examples of DNA contamination
Farah Jama was a young man accused of rape on the basis of his DNA seemingly being found on the alleged victim. Mr. Jama is black and at 21 was too young to have entered the club at which the incident occurred, which catered to people over 28. Moreover, the alleged victim did not recall seeing a black man at the club that night. Yet, as Milanda Rout wrote, “But the judge and the jury did not buy his alibi, despite supporting evidence from his father, brother and friend. Instead, they believed the forensic scientist who testified there was a one in 800 billion chance that the DNA belonged to someone other than the accused man.” After Mr. Jama spent more that eighteen months in prison, he was released because prosecutors said that they could not rule out contamination. The contamination event may have occurred during two forensic medical examinations, one of the victim and the other of Mr. Jama on an unrelated matter that occurred one day earlier.

Perhaps the most thoroughly studied case of contamination is that which occurred in the Jaidyn Leskie case. This blog has covered the Leskie case on two previous occasions. The DNA of a woman who probably never left her village was found on the clothing of the submerged body of a toddler. She was a mentally challenged woman who may have been raped, which is why her DNA was being examined. Because the woman was such an exceedingly unlikely suspect, the only reasonable explanation was contamination. Contamination has been documented on several occasions when evidence items from unrelated cases are examined within a few days in the same lab.

Russell John Gesah was charged with the rape and murder of a mother and child. Kathleen Skeen wrote, “A Victorian Police Forensic Services Centre review found clothing with Mr Gesah's DNA from an unrelated offence had been examined on the same day and same surface as clothing from the Tapp case." The Gesah case, and the murders of Jane Mixer and Jane Durrua (see below) are all examples of DNA cold hits. The Gesah case prompted the State of Victoria to reexamine thousands of cases (see below).

Gregory Turner might have been convicted of murder on the basis of DNA evidence. However, a forensic worker contaminated a key piece of evidence with his and her DNA. She also acknowledged contamination in two other cases on which she had worked. An interesting aspect of the Turner case is that the DNA from the victim came from her fingernails, and Mr. Turner’s DNA came from his wedding ring. These facts suggest that the presence of liquids is not necessary to bring about cross-contamination, in contrast to the implications of Patrizia Stefanoni’s testimony in the present case.

The murder of Jane Mixer was initially attributed to a serial killer. When Gary Leiterman’s DNA was found on the decades-old evidence, he was convicted. However, the presence of the DNA matching then four-year old John Ruelas on the same item of evidence (despite Ruelas’s living in another city) strongly points to this being another example of contamination. This illustrates another important principle. One does not always know the precise moment that contamination occurred, but one can infer contamination when the direct deposit of DNA is shown to be highly unlikely.

A seemingly solved cold case that turned out to be contamination involved the 1968 murder of Jane Durrua. Jerry Lee Bellamy’s DNA was found when the evidence was tested in 1999. Evidence against Mr. Bellamy in an unrelated case was tested on the same day as items from the Durrua case. The actual evidence of contamination was not conclusive, but despite this, charges against Mr. Bellamy were dropped. Alleged serial killer Robert Zarinski was later arrested, but he died before he could be tried.

The difficulties in quantifying the frequency of DNA contamination
Not all labs document contamination events. Some labs argue that contamination that is identified with the use of negative control experiments does not count as contamination. Negative controls will spot wholesale contamination events but will not necessarily catch sporadic contamination. These facts make it difficult to quantify how frequently contamination occurs. However, it does not seem to be an especially rare event. Professor Thompson is a lawyer who specializes in probability theory as it relates to DNA profiling. Maura Dolan reported that he is among the leading authorities on laboratory errors in the United States. In response to a request from the Los Angeles Times to review the records from some California forensics labs, Thompson said, “’on a regular basis, laboratory personnel make mistakes that could lead to false identifications’ of suspects.” He also indicated that what has emerged in recent years is just “the tip of the iceberg.”

In 2008 Professor Thompson wrote an article, “The Potential for Error in Forensic DNA Testing (and How That Complicates the Use of DNA Databases for Criminal Identification"). “Doubt was also cast on a number of convictions in Queensland when a forensic scientist who had previously worked for a state forensic laboratory publicly expressed concerns about the reliability of the lab’s work. He told The Australian newspaper that it was not uncommon for the lab to mix up DNA samples from different cases.[62] For example, he said that analysts’ own DNA, from blood samples used as analytical controls, often was mixed up with (or found its way into) casework samples, creating false matches: “[Q]uite often my (colleague) would walk down the aisle and say, ‘I’ve just committed another rape on the Gold Coast.’”[62] The analyst said that while many such errors were caught, sample limitations made it impossible to resample or retest in some questionable cases.” These remarks underscore the notion that DNA contaminations are not a rare event.
[62. A. McDonald, “DNA evidence claim clouds Australian convictions,” The Australian, July 8, 2006.]

In response to the Russell John Gesah contamination incident (see above), the Victorian police reexamined their cases involving DNA forensics. During the period from 1988 to 2008 the Victorian police service handled 7000 cases involving DNA. According to Peter Gregory and coauthors, “In 2003, Mr Scheffer told an inquest on Moe toddler Jaidyn Leskie that since late 1999, 39 cases had been identified as requiring "diagnostic and corrective action", with most involving contamination.

Finally, testimony reported by Annabelle McDonald (in The Australian) implied that mixing up samples is a not uncommon event. Although mislabeling of samples (if that is what mixing up means) is not itself contamination, it has the potential to lead to the same erroneous judicial result. A mislabeling in Nevada was uncovered during an independent review of the Lazaro Sotolusson case. In addition Dwayne Jackson was also the victim of a similar mistake at the Las Vegas forensics lab.

Conclusions
There is not yet enough information on environmental contamination to make conclusive statements about how common environmental contamination is; however, DNA is deposited routinely in all sorts of ways that are unrelated to criminal activity. The authors of a recent study believe that environmental dust can give rise to extra alleles in evidence samples. The frequency of contamination is difficult to quantify, but it is not an especially rare occurrence. The chances of contamination are greater for DNA in the low template range than they are for larger samples. Historical examples of contamination suggest that it is more likely to occur when items of evidence are processed closely in time. Contrary to the implication of Dr. Novelli's remarks, it is rarely the case that the exact mechanism of contamination is proven.

Forensic tests for the presence of blood

2011-07-07T21:34:00.021-04:00

Part 30 in the Knox/Sollecito case
Updated three times (see below)

Introduction
Blood has a high proportion of red blood cells that are packed with a protein called hemoglobin but are without DNA. Hemoglobin has a helper molecule called heme, which contains iron, and the iron binds and releases oxygen. Roughly 1 in 800 blood cells is a white blood cell that does not have hemoglobin but does have DNA. The detection of blood is an ongoing problem in forensic science, and advances are continually being made. A previous entry in this blog also treated luminol.

Presumptive tests
Two major kinds of presumptive tests are chemiluminescent and chemical. Presumptive tests rely upon the pseudoperoxidase acivity of hemoglobin. Hemoglobin is not an enzyme (catalyst) in its role carrying oxygen, but it can often speed up the reaction of hydrogen peroxide with a reduced molecule. In these tests hemoglobin is mimicking the action of a class of enzymes called peroxidases, thus one refers to the pseudoperoxidase activity of hemoglobin. Peroxidases oxidize organic molecules using peroxides (such as hydrogen peroxide) as the oxidant. Luminol is chemiluminescent, giving off a bluish light in the presence of dilute blood when it is oxidized. Tetramethylbenzidine (TMB) is a chemical test, relying upon a change in color upon oxidation.

The murder of Meredith Kercher may have featured a misuse of the Kastle-Meyer test, a presumptive test for blood. The Kastle-Meyer chemical test relies upon hydrogen peroxide oxidizing phenolphthalin, which is colorless, to phenolphthalein, which is pink.

The police released photos (see above) to the press that some observers, such as Judy Bachrach of Vanity Fair, thought was blood. Based on the discrepancy between Ms. Knox’s description of the bathroom and its seemingly bloody appearance, some observers lost trust in Ms. Knox.***

The actual appearance of the bathroom was unremarkable, except for a small number of droplets of blood and a partial footprint that may have been made in bloody water.

However the pink color may have been from using the Kastle-Meyer reagent over a large surface area and allowing air to oxidize the phenolphthalin. However, the color may have instead been the result of reagents used for latent fingerprint analysis. The pink photo at the top of this page was apparently not entered into evidence at the trial.

Confirmatory tests
Confirmatory tests are typically run after presumptive tests have given a positive result. Their purpose is to distinguish blood from substances that can give false positives for blood. Forensic scientists Dr. Kelly Virkler and Dr. Igor Lednev identify five classes of confirmatory tests: microscope tests, crystal tests, spectroscopic methods, immunological tests, and chromatographic methods. Crystal tests are based on the formation of crystals of heme (or a pyridine-based derivative of heme), and they are not performed as much as in previous years. Immunological tests that are based upon antibodies (immunoglobulins) that bind to hemoglobin, lactate dehydrogenase (more specifically, the distribution of the isozymes of lactate dehydrogenase), glycophorin A, or other biomolecules are more recent innovations. There are many methods which employ antibodies, such as the early double diffusion (Ouchterlony) experiments and more recent immunochemical techniques, such as enzyme-linked immunosorbent assays (ELISAs).

False Positives and the language of forensic reports
Presumptive tests will often give false positives in presence of metal ions or plant material containing peroxidases. Drano and bleach are two of several household products that can yield a false positive with luminol, as noted by Lt. Robin Bratton. Some of the putative bloodstains in the Lindy Chamberlain case (in which she was wrongfully convicted of murdering her infant) may have been the result of copper dust from the atmosphere, discussed by Dr. R. V. Winchester. The Chamberlains lived in Mt Isa, which is home to copper mines.

The case of Greg Taylor in North Carolina illustrates how one’s fate can turn on the choice of which information is revealed and the choice of words the forensic scientists use to convey the results. Joseph Neff and Mandy Locke wrote, “In Taylor's case, an alleged blood stain was the only physical evidence tying him to the murder. The presumptive test was positive; the confirmatory test was negative. The lab report made no mention of the negative confirmatory test…The FBI's written policy directed the analyst first to report the positive presumptive test results. If the confirmatory test is negative, the analyst would write, ‘Further testing could not confirm the presence of human blood.’” Some problems that can arise when a confirmatory test is negative are discussed in Appendix A.

The luminol-positive areas in the murder of Meredith Kercher
There were two luminol-positive areas in Filomena’s room, and both contained mixtures of DNA (the DNA mixtures will be treated in a separate blog article). There were three footprints in the hallway, and all tested negative for DNA. There was also a shoe print that contained both Meredith’s and Amanda’s DNA.

It emerged during the trial that the luminol-positive areas that contained DNA were subjected to a second presumptive blood test, tetramethylbenzidine (TMB). Dr. Sarah Gino noted in her testimony that TMB is negative about 50% of the time when luminol-positive areas are tested (Massei Motivations Report, p. 258, English Translation). Although luminol is more sensitive than TMB, TMB can detect blood that has been diluted up to 10,000-fold.

It is sometimes argued that negative TMB results in the Kercher case can be ascribed to this difference in sensitivity. There are several reasons to reject this explanation. First, if it were the only explanation for TMB giving a negative result, no forensic personnel would ever use TMB after using luminol: A negative result would not rule out the presence of blood, yet a positive result would still require a confirmatory test afterwards. Second, the window of dilution factors for which one would expect a positive luminol reaction but a negative TMB reaction is relatively small. Third, if one did have a sample which fell into this range, the luminol response would be weak, whereas Colonel Garofano remarked upon the sheer luminosity* of the footprints in the book Darkness Descending. A study by Bilous and coworkers showed that the maximum intensity of light emitted fell with decreasing concentration of blood (see Table 1).

With respect to the luminol-positive/TMB-negative/DNA-negative areas, I asked the authors of a recent study on the forensics of body fluid identification for their interpretation. Drs. Virkler and Lednev wrote, “So, there was either no blood and the luminol was wrong, or there was blood and the TMB had interference and the luminol damaged the DNA. We think it is more likely that there was no blood, and that the luminol was reacting with something else, possibly plant matter from the bottom of the shoes causing the footprints (the intensity of the luminol reaction might give some more insight). The prosecution should have used much more convincing evidence to prove the presence of blood.”

Were the luminol-positive areas related to the crime?
The footprints in the hallway are all right feet images** and do not form a trail. No reference footprints were taken from anyone except Amanda, Raffaele, and Rudi, nor can the prints be dated. Yet Judge Massei regards the prints as being made in blood. He said (p. 284 in the English translation of the Massei Motivations Report), “In this regard, one cannot simply disregard the fact that the bloodstains were undeniably abundant in Meredith’s room, from which easily, or indeed inevitably, they must have been exported to other parts of the house by anyone who, coming out of Meredith’s room, went into these other parts.” In some respects this line of reasoning is similar to Dr. Stefanoni’s argument in front of Judge Micheli during the pretrial, as reported in Candace Dempsey’s blog, Let's Talk About True Crime. This argument is extremely poor. It suggests that the footprints should form a continuous trail of right and left footprints away from Meredith’s room, contrary to fact. It treats luminol as if it were a confirmatory test for blood, and it ignores the negative TMB testing that was done on at least some of the luminol-positive areas.

Finally, two other facts lead one to question whether the luminol-positive spots are related to the crime. One is that the luminol data were collected on December 18, not in early November right after the crime but rather after the police had tossed the crime scene. This means that law enforcement personnel may have tracked luminol-positive material into Filomena’s room, for example. Two is that the police found many luminol-positive areas in Sollecito’s flat. There is no reason to associate any of these regions with the murder, and Sarah Gino’s testimony suggests that luminol-positive areas are not uncommon in forensic investigations.

The relationship between DNA testing and confirmatory blood testing
Although DNA typing is a powerful tool in forensics, it is not a test for blood. The National Forensic Science Technology Center said, “For example, while examining the clothing of a suspect, a forensic biologist might visually locate a brown stain that presumptively tested positive for blood and was then DNA typed. The DNA type is found to match the victim. Knowing that the loci tested are higher primate specific, what conclusions can be drawn? The only unqualified conclusion that can be offered is that the stain contains DNA that matches the victim. It has not been proven to be blood.” In response to a question of mine, Dr. Virkler and Dr. Lednev concurred: “It is correct to assume that DNA profiling is not a confirmatory test for blood because it can be found in so many other things. Just confirming the presence of the victim or suspect's DNA has absolutely no bearing on what type of tissue or fluid it is. There could have been skin cells scattered in a pile of ketchup that would match a person's DNA, but that doesn't make it blood.”

In "An Independent of the SBI forensic laboratory" in North Carolina, Chris Swecker and Michael Wolf stated, “It should be noted that the confirmatory ‘Takayama’ blood test that was at issue in the Taylor Innocence Commission proceedings was discontinued in 2003 and replaced with DNA and rapid Stain identification tests.” The Rapid Stain kit manufactured by Independent Forensics of Hillside, IL “uses two mouse monoclonal antibodies specific for human glycophorin A.” Glycophorin A is a protein found on the membranes of red blood cells.

The lack of DNA in a sample suggests that a substance is not blood, but that relationship is not absolute. The sample might contain an inhibitor of the polymerase chain reaction needed to amplify DNA in present-day DNA forensics or the presumptive test itself may have an effect on the DNA profiling. The exact formulation of luminol affects how much DNA is recovered.

Update 2, 6 PM 7/8/11
Conclusions
The luminol-positive areas can be subdivided into those that did and those that did not have DNA. The amorphous regions in Filomena’s room fall into the former category, and the footprints in the hallway fall into the latter category. However, none was subjected to a confirmatory test for blood, and none should be concluded to be blood. The presence of DNA in some of the areas does not constitute a confirmatory test; additionally, the areas with DNA were negative in the TMB tests. The other luminol-positive areas were not confirmed to be blood. Ms. Comodi asked for the jury to decide whether or not the areas were blood. The jury should not have concluded that any luminol-positive area was blood, and that is one reason that the notion that these areas were mixed blood is a fallacy. We will explore this erroneous notion in a subsequent entry.

***A previous version of this sentence was incomplete. It read, "Based on the discrepancy between Ms. Knox’s description of the bathroom and its seemingly bloody appearance." I completed the sentence and added a link to a discussion board.

Update 1 7/7/11, 2 PM EDT
*On page 377 in the book Darkness Descending, Colonel Garofano discussed the luminol-positive prints in Amanda's room and the prints attributed to her in the hallway: "FIrst of all, from their sheer luminosity they are blood. The DNA test showed Meredith's blood in all cases except for two places in which we have a mixed Amanda and Meredith sample." Colonel Garofano's statement implies that the luminol-positive areas all had Meredith's DNA, which is false. They also seem to equate a hypothetically presence of DNA as meaning that blood is also present, and this is also false, as discussed above. Thanks to Rose Montague for asking for the exact quote.
**A reader suggested a different wording, such as "each footprint in the hallway is a right-foot image," would be clearer. I am grateful for this suggestion.

Update 3 6 PM 7/12/11
I added two links on Drs. Virkler and Lednev.

Appendix A, Forensic bias and confirmatory blood tests
The Raleigh News and Observer reported, “Jed Taub, a 30-year veteran of the SBI, said, ’We didn't report the negative result of a confirmatory test because, really, it's misleading,’ said Taub, who now works as a forensic investigator for the Pitt County Sheriff's Office. ‘We couldn't be sure it wasn't blood, so those tests really didn't matter.’’ Reporters Mandy Locke and Joseph Neff continued, “Taub said that the only times he reported the absence of blood was when he got a negative result on that first, presumptive test. Any negative results after that were irrelevant, he said.”

In another article in the series on North Carolina’s SBI forensic laboratory Neff and Locke reported, “Perhaps the biggest challenge facing new SBI Director Greg McLeod is changing the culture of the SBI and the laboratory. Analysts have worked to support the theories of prosecutors, instead of rendering detached scientific analysis. Training manuals, some which have been withdrawn, have coached analysts to support prosecutors and distrust defense attorneys. This bias extended down to the very way analysts reported test results. ‘They were writing reports to law enforcement,’ said Chris Swecker, the former FBI supervisor who audited the blood cases. ‘They were trying not to write any negative test results.’”

These stories suggest that some aspects of forensic bias can be traced to the close relationship between law enforcement and forensic science laboratories. With respect to the forensics there is nothing that happened in Perugia that could not happen in the United States.

Appendix B, Some other presumptive and confirmatory tests

Leucomalachite green: Hemoglobin catalyzes the oxidation of the reduced form of leucomalachite green to the oxidized form, much as in the Kastle-Meyer test.

Leucocrystal violet: This test is very similar to the leucomalachite green test.

Takayama crystal tests: The sensitivity is about 0.001 mL of blood or 0.1 mg of haemoglobin. The crystals are pink in color.

The Independent DNA Experts Weigh In

2011-06-29T17:17:00.007-04:00

Part 29 in the Knox/Sollecito case

Judge Hellmann, who is presiding over the appeal, appointed Conti and Carla Vecchiotti as independent experts to review the bra clasp and knife DNA evidence. The translation of their conclusions was provided by komponisto, who also authored “The Amanda Knox Test.” Their report will be discussed in court next month. The formatting (bold or italics) is in the original.

CONCLUSIONS

Based on the considerations explained above, we are able to respond as follows to the inquiries posed at the assignment hearing:

"Having examined the record and conducted such technical investigations as shall be necessary, the Expert Panel shall ascertain:

1. whether it is possible, by means of a new technical analysis, to identify the DNA present on items 165b (bra clasp) and 36 (knife), and to determine the reliability of any such identification"

- The tests that we conducted to determine the presence of blood on item 36 (knife) and item 165B (bra clasps) yielded a negative result.

- The cytomorphological tests on the items did not reveal the presence of cellular material. Some samples of item 36 (knife), in particular sample "H", present granules with a circular/hexagonal characteristic morphology with a cental radial structure. A more detailed microscopic study, together with the consultation of data in the literature, allowed us to ascertain that the structures in question are attributable to granules of starch, thus matter of a vegetable nature.

- The quantification of the extracts obtained from the samples obtained from item 36 (knife) and item 165B (bra clasps), conducted via Real Time PCR, did not reveal the presence of DNA.

- In view of the absence of DNA in the extracts that we obtained, with the agreement of the consultants for the parties, we did not proceed to the subsequent amplification step.

2. "if it is not possible to carry out a new technical analysis, shall evaluate, on the basis of the record, the degree of reliability of the genetic analysis performed by the Scientific Police on the aforementioned items, including with respect to possible contamination."

Having examined the record and the relevant documents, we are able to report the following conclusions regarding the laboratory analyses performed on Item 36 (knife) and Item 165B (bra clasps):

ITEM 36 (KNIFE)

Relative to the genetic analysis performed on trace A (handle of the knife), we agree with the conclusion reached by the Technical Consultant regarding the attribution of the genetic profile obtained from these samples to Amanda Marie Knox.

Relative to trace B (blade of the knife) we find that the technical analyses performed are not reliable for the following reasons:

1. There does not exist evidence which scientifically confirms that trace B (blade of knife) is the product of blood.

2. The electrophoretic profiles exhibited reveal that the sample indicated by the letter B (blade of knife) was a Low Copy Number (LCN) sample, and, as such, all of the precautions indicated by the international scientific community should have been applied.

3. Taking into account that none of the recommendations of the international scientific community relative to the treatment of Low Copy Number (LCN) samples were followed, we do not accept the conclusions regarding the certain attribution of the profile found on trace B (blade of knife) to the victim Meredith Susanna Cara Kercher, since the genetic profile, as obtained, appears unreliable insofar as it is not supported by scientifically validated analysis;

4. International protocols of inspection, collection, and sampling were not followed;

5. It cannot be ruled out that the result obtained from sample B (blade of knife) derives from contamination in some phase of the collection and/or handling and/or analyses performed.

ITEM 165B (BRA CLASPS)

Relative to Item 165B (bra clasps), we find that the technical analysis is not reliable for the following reasons:

1. There does not exist evidence which scientifically confirms the presence of supposed flaking cells on the item;

2. There was an erroneous interpretation of the electrophoretic profile of the autosomic STRs;

3. There was an erroneous interpretation of the electrophoretic profile relative to the Y chromosome;

4. The international protocols for inspection, collection, and sampling of the item were not followed;

5. It cannot be ruled out that the results obtained derive from environmental contamination and/or contamination in some phase of the collection and/or handling of the item.

THE EXPERTS

Prof. Carla Vecchiotti

Prof. Stefano Conti

The Independent DNA Experts and the Electronic Data Files

2011-05-16T21:37:00.006-04:00

Part 28 in the Knox/Sollecito case

Update, 13 June 2011

In the story “Knox appeal: DNA experts to request more time” from the AFP on 20 May 2011, Knox lawyer Carlo Dalla Vedova said “The experts asked the forensic police to hand over information essential to their report on the DNA. They still haven't received it and will therefore request a 40 days extension.” He added, “It's not the first time we've asked for the police to hand over this information,” He also said, “But they need the raw data they have asked for from the police to do so. We first asked for it in 2009 and it's still not been handed over.” This ends the debate about whether or not the forensic files were ever released to the defense during the trial of the first instance.
____________________

Judge Hellmann appointed two independent experts to review the DNA forensic evidence in Amanda Knox’s and Raffaele Sollecito’s appeal. Recently, the experts asked for more time, and reports suggested that they did not yet have access to documents the felt were necessary to carry out this task.

According to Candace Dempsey, forensic scientist under whose supervision the tests were carried out, Dr. Patrizia Stefanoni, turned aside this request. She wrote to Judge Hellman, “In reference to the request of acquisition of CD RAW DATA, one is obligated to explain that the information in the form of this file in the sequencer is never an integral part of the technical report, as far as the object being tested by the forensic geneticist, namely the DNA profile, and that it is already reported in the electropherogram printout, connected to the technical report on which all of the useful date and an evaluation of the genetic profile are reported… Finally, the request asked for by the expert consultants relative to the acquisition of the CD RAW DATA appears incomplete in so much as the name of the ‘sample file’ requested was not specified…”

To help me consider Dr. Stefanoni's refusal refusal, I have consulted with DNA forensics professionals Dan Krane and Jason Gilder of Forensic Bioinformatics, and I gratefully acknowledge their help. The continued lack of file release with respect to the DNA profiling of this case has been a recurring theme of this blog.

Her arguments against releasing further information are essentially:
(1) All of the necessary data are already in the paper printouts of the electropherograms.
(2) The request for data files is insufficiently specific.

Let us examine point (1) first. Dr. Stefanoni’s position appears to be the same as it was when Dr. Pascali was refused data, as noted in Raffaele’s appeal. Yet some of the electropherograms only provide the number of repeats, not the peak height for each peak. Peak heights are essential to evaluate peak height imbalance within a locus, which bears on the question of whether or not a sample is in the low-template range, and whether two peaks within a locus belong to the same or to two different individuals. Peak heights can also be used to quantify the severity of degradation when one compares DNA fragments of different lengths. Peak height ratios also help one to decide whether or not a small peak is a type of artifact known as a stutter. A careful examination of these small peaks is especially important in helping to judge what other DNA is present on the bra clasp besides Meredith’s and presumably Raffaele’s.

In addition, having the electronic data files allows one to calculate a run-specific limit of detection (Gilder et al., J. Forensic Science, January 2007, 52 (1), 97). This process sets a lower limit on the size of which peaks to accept, based on the amount of noise.

It can also be helpful in detecting a type of artifact known as a pull-up. There are four types of dyes used in DNA profiling, each with a different wavelength (color) of detection. Each dye is ordinarily detected in its own channel. Sometimes a large peak gives a small spurious signal because of bleeding from one channel into another (Butler, Forensic DNA Typing (2005), pp. 336-337; 384). According to Christine Funk and Dr. Simon Ford, “Pull-up can usually be identified through careful analysis of the position of peaks across the color spectrum, but there is a danger that pull-up will go unrecognized, particularly when the result it produces is consistent with what the analyst expected or wanted to find.”

Dan Krane was asked to give his opinion about the release of such files in a separate legal matter. He wrote, “I believe that a defense expert cannot competently evaluate the results of an STR DNA test without having access to the test’s underlying electronic data. In my experience, review of electronic data has often led directly to the discovery of important problems or limitations in the STR testing, or to alternative theories of the evidence, that would not have been apparent based on a review of laboratory reports or other laboratory records… In my opinion, review of the electronic data is as important as review of the laboratory’s written notes…There is no legitimate reason for a laboratory to refuse a defendant’s request to examine the electronic data.” (bolding mine) Finally, this blog has previously noted that the ABA standards explicitly call for release of the electronic data files.

Point (2) is equally difficult to comprehend. Clearly Dr. Stefanoni understands that the electronic data files are being requested, yet apparently wants specific file names. It is difficult to see how the independent scientists would know the file naming convention used in Dr. Stefanoni’s lab. Who does Dr. Stefanoni think can provide the specific file names?

Forensic Bioinformatics has a 10-point standard discovery motion, and point 6 covers files. The material should include:
(6.1) All collection files (such as injection lists and log files for an ABI 310 analysis).
(6.2) All GeneScan® files, including sample files and project files.
(6.3) All Genotyper® files, including templates/macros (see Request 5).
(6.4) All GeneMapper® files, including sample files (.fsa files) and project files (.ser files).
(6.5) If the data you are providing includes files from another case that are not pertinent to the instant case (e.g., sample files from another case included in the same run folder), then please identify those non-pertinent samples by name and laboratory code.

Clearly it is the job of the laboratory that performed the test to provide the file names.

Concluding remarks
The failure of Dr. Stefanoni’s laboratory to provide the data to the independent forensic scientists is a continuation of her refusal to provide them to the defense. There is absolutely no legitimate reason for her to do so. As Dan Krane noted, “It is a fundamental tenet of science that two reasonable experts should be able to independently arrive at the same conclusions after reviewing the same experimental data.”

An analysis of the bra clasp DNA

2011-03-17T21:29:00.010-04:00

Part 27 in the Knox/Sollecito case

Introduction
A previous post has examined the DNA on the bra clasp, which has a strong profile from the victim, Meredith Kercher. In this post we will examine the bra clasp DNA on the basis of the available information with respect to whether or not Raffaele’s DNA is present. We will also look into the uncertainties surrounding whether or not the DNA of a third party’s DNA is present. However, a complete analysis would require electronic data files, not electropherogram images, and the defense never received these or other files. All references to the Massei Motivations report are given with respect to the English translation available at perugiamurderfile.org. Dr. Adriano Tagliabracci was an expert witness for Raffaele Sollecito’s defense, and his interpretation of the bra clasp DNA profile clashed with Dr. Patrizia Stefanoni’s, the chief prosecution witness with respect to DNA forensics. The bra clasp also figured prominently in an open letter coauthored by two DNA forensic experts and cosigned by seven others.

Executive Summary
Y-chromosomal DNA corresponding to Raffaele’s haplotype was found on the clasp as well as many alleles corresponding to his autosomal DNA. Dr. Tagliabracci’s critique of Dr. Stefanoni’s analysis, that it was suspect-centered, is probably valid but is tangential to the more important questions surrounding the collection of the clasp. The reanalysis of the clasp in the appeal will likely conclude that a partial profile corresponding to Raffaele’s autosomal DNA (but possibly not a full profile) is present. However, there are one or more other contributors as well, apart from Meredith, and the more salient question is how this DNA was deposited on the clasp. There is no reason to suppose that the third person’s DNA necessarily arrived via a different mechanism from Raffaele’s: Secondary transfer, contamination at the crime scene, and evidence-tampering are all more likely than Raffaele’s depositing DNA on this dubious piece of evidence during the murder, but not depositing DNA on the bra itself or leaving any other trace in Meredith’s bedroom.

Analyzing Mixtures of DNA
It is worth reiterating that analyses of DNA mixtures are somewhat subjective. With respect to the John Puckett case, Chris Smith reported: “Mixed samples are another flashpoint in the DNA wars. It can be exceedingly difficult to separate one person’s DNA from another’s, especially in a degraded sample like this, and there is no universally accepted way to interpret the resulting profile. As the eminent British researcher Peter Gill told a conference of his fellow forensic scientists in 2005, ‘If you show 10 colleagues a mixture, you will probably end up with 10 different answers.’ Even Cheng’s supervisor, a combative man named Matt Gabriel, reluctantly admits on the stand that there is no agreed-on protocol for handling mixed samples.” With respect to the Puckett case Michael Bobelaian quoted Professor Dan Krane: “’There is a public perception that DNA profiles are black and white,’ he told me. ‘The reality is that easily in half of all cases—namely, those where the samples are mixed or degraded—there is the potential for subjectivity.’”

An article in the Journal of Forensic Sciences provides good discussion of how to minimize observer effects in DNA forensics. Among the authors are co-signers of the Johnson-Hampikian open letter and one person who has written extensively on the problem of investigator bias. Note that the proposal indicates that the investigator should not have access to the reference samples until quite late into the analysis process. In other words, one wrong way to analyze an evidence sample would be to lay reference sample electropherograms on top of it and look for matches. Overlaying the reference sample onto the evidence electropherogram after the analysis is complete simply to present the data is fine.

Stutter peaks
Individuals vary in the number of short terminal repeats of DNA at various locations in their chromosomes, and this is the basis of DNA profiling. Larger fragments of DNA emerge later from the capillary tube and give rise to peaks in an electropherogram. Each peak corresponds with one allele. Stutter peaks are a type of artifact in the electropherogram, and they most often show up at a position on the time-axis (which is proportional to the size of the DNA fragment) that is one repeat unit shorter than the true allele. They are usually in the vicinity of 5% of the height of the true peak with which they are related. For the purposes of this analysis, we will assume that any peak that is one repeat unit shorter than an allele in Meredith’s profile is likely to be a stutter peak.

From the Massei Report, about page 243: "Regarding locus D7S820, he [Dr. Tagliabracci] revealed that Forensics had interpreted it, recognizing the presence of two alleles, 8 and 11; they had not taken into consideration a peak, low, but still higher than 50 RFU, corresponding to allele 10." To whom does it belong? In locus D16S539, Dr. Tagliabracci believes that there is a peak at the 13 locus. This allele is also not part of Meredith’s or Raffaele’s profile, but it is quite possible that both are stutter peaks.

Other DNA on the clasp
However, there are other small peaks besides the one at 10 in the D7S820 locus, and because of their positions along the time-axis, it is difficult to believe that they are stutters. In locus D19S433 there are alleles at 10 and 14 repeats that are not part of Meredith’s or Raffaele’s profile. In locus vWA there appear to be peaks at 9, 11, and 18, that are not part of these individual’s DNA profiles. In other words, there is probably DNA on the clasp that belongs to someone other than Meredith Kercher or Raffaele Sollecito. Although it is difficult to say how many individuals contributed, there would seem to be at least two. The critical question is how it came to be there, taken up below. Some have tried to claim that Amanda was a third contributor to the bra clasp DNA. However, there can be no doubt that Amanda's complete profile is not on the bra clasp.

The presence of these small peaks raises another question. Many of these small peaks were not marked on the electropherogram of the clasp, suggesting the possibility that Dr. Stefanoni’s lab did not consider them to be real peaks. Some of them appear to be in the range of 100 RFUs. Although they are small relative to typical peaks, they are as large or larger than all of the peaks in Meredith’s profile from the kitchen knife. This forces one to ask whether a consistent peak threshold were used for all samples, and if not, one has to question whether peak thresholds were changed ex post facto, something that seems contrary to basic principles.

Raffaele’s putative DNA on the bra clasp
Raffaele and Meredith shared eleven alleles out of about thirty. Because Meredith’s profile is roughly eightfold more intense than Raffaele’s putative profile, it is very challenging at the very least to know whether Meredith’s DNA alone or Meredith’s plus Raffaele’s DNA contributed to the strong (>1000 RFU) peaks in the profile. For one thing, peaks heights can decrease from left to right across an elecropherogram due to degradation, which attenuates peak heights corresponding to large DNA fragments more than smaller loci. For another, small peaks vary in intensity more than large ones due to noise and stochastic effects. An additional complication is that Raffaele’s profile has a few peaks that would show up at the same position as stutter peaks from Meredith’s profile would.

Let us now turn to the alleles in which Raffaele’s reference profile is distinct from Meredith’s profile. “Professor Tagliabracci then maintained that this suspect-centric method was detectible in Dr. Stefanoni’s report and presentation because, he affirmed, it was a case of forcing the profile obtained … eliminating or leaving out alleles [257] solely for the purpose of making that profile compatible with Raffaele Sollecito’s profile.” (Massei Report translation, p. 241)

The presence of Raffaele’s DNA in YSTR testing strengthens the case that Raffaele’s autosomal DNA is present on the clasp, though in low quantity. One way to take some of Dr. Tagliabracci’s objections into account is to acknowledge that Raffaele’s DNA is present in the low template number range, as discussed in the appendix below.

Some problems in the collection techniques
As noted above the key question is how did Raffaele’s DNA and the DNA of one or more other individuals become deposited onto the clasp. Contamination can happen when an item of evidence is collected at the scene of a crime, as well as when it is tested in the laboratory. In this series of photographs the same crease in a glove of a forensics worker is seen, indicating that this glove was not changed. On page 13 of the book “Angel Face” Barbie Nadeau reported on Dr. Stefanoni’s cross-examination by Raffaele’s lawyer Giulia Bongiorno. Ms. Bongiorno noted that Dr. Stefanoni’s bracelet was seen in the same position above her glove, again pointing to gloves not being changed.

Dr. Stefanoni’s view was that contamination was much less likely with dry traces than with liquids (Massei Report translation, pp. 201-202; 204-205). “Regarding the possibility of transferring exfoliated cells that may be found on a hand or a glove, Dr Stefanoni explained that in the abstract, anything could be transferred, but it remained to be seen in practice. So, with specific reference to exfoliated cells, she stressed that it would be necessary to press down with force or scratch over a surface where these would have to be present (for example, the back of a person)… With reference to the single-use gloves, Dr. Stefanoni specified that they were changed, in the course of the search, every time an object was touched that was particularly soaked with blood, and when it was obvious that the gloves would be soiled; ‘otherwise, if it is just an ordinary object…I can move it, but this does not lead to my DNA remaining, let’s say, attached. It depends on the object.’” (Massei Report translation, pp. 202-203). One infers from her comments that in the absence of blood or obvious dirt or grime, gloves were not changed. Dr. Stefanoni’s views on how frequently gloves should be changed are not shared by any forensic scientists that I can identify. On page 38 of “Forensic DNA Typing,” the most authoritative textbook on the subject of DNA profiling, John Butler wrote, “Use clean latex gloves for collecting each item of evidence. Gloves should be changed between handling of different items of evidence.” Other guidelines make the same or similar recommendations.

“She [Dr. Stefanoni] confirmed, therefore, that before having touched the clasp with those gloves, the gloves had not touched any other objects, since they had just been put on.” Yet some of the gloves were dirty, including one used to handle the bra clasp. The clasp was handled by at least two people wearing gloves when it should have been handled by one person using a disposable pair of tweezers. The bra clasp was also recovered more than a meter from where it was originally observed and noticeably dusty. In summary the late-collection and subsequent handling of the clasp substantially weaken its evidentiary value, as noted in the Johnson-Hampikian open letter of 19 November 2009.

Dr. Stefanoni’s view that dehydrated traces are very hard to contaminate is also open to question. In the case of Gregory Turner previously discussed on this blog, a forensic worker contaminated fingernail clippings with both her DNA and Mr. Turner’s DNA from a ring, and there is no reason to believe that liquids were involved. Overall, the techniques in Dr. Stefanoni’s laboratory were not as stringent as they might have been, and this raises the chances of contamination, all other things being equal.

The presence of DNA from one or more persons who are not suspects on the clasp is one of the most serious black marks against the bra clasp as evidence of Mr. Sollecito’s involvement in this crime. It is difficult to see how one or more unknown individuals deposited DNA by primary transfer; therefore, secondary transfer and contamination need to be considered carefully as mechanisms by which both Raffaele’s DNA and the DNA of one or more unknown individuals arrived on the clasp.

Appendix
One way to interpret Dr. Tagliabracci’s remarks is that he criticized Dr. Stefanoni for focusing on peaks in the clasp profile that happened to be in Raffaele's reference profile and ignoring peaks that did not. If Dr. Stefanoni did so because she had prior knowledge of Raffaele’s profile, then such analysis is open to question, as indicated above. Dr. Tagliabracci implied that this was a problem. “He pointed out that that there is a significant subjective element in reading the electropherograms. He focused in particular on locus D5S818, in which two principal alleles are present; together with a third peak with a height of 108 RFU; as this is higher than 50 RFU, it should have been considered an allele. Forensics [la Polizia Scientifica] did not, however, consider this to be the case; instead, they considered the 65 RFU peak to be an allele and observed that, in this way, a compatibility with Raffaele Sollecito’s profile resulted, which otherwise would not have been the case (page 59). With reference to this, Professor Tagliabracci repeated that there was a forced interpretation, which was typical of a suspect-centric attitude (page 60).” (Massei Report translation, p. 242) The quotation above only provides the peak height in RFU, not the number of repeats, which sets the location along the horizontal (time) axis. I do not know which peaks are meant.

Dr. Tagliabracci’s approach seems to be more in line with the spirit of recommendations in the 2008 Journal of Forensic Sciences article cited above, although Dr. Stefanoni denied that she used a suspect-centered approach. The Massei report gives at least five instances where Dr. Tagliabracci differed with Dr. Stefanoni with respect to the interpretation of certain loci. Specifically with respect to D5S818, he challenged her interpretation when she took a smaller peak (65 RFU) in preference to a larger one (108 RFU) to be part of a profile. Because other peaks attributed to Raffaele are generally larger, in the range of 200 RFU, this objection needs to be answered.

The Y-STR testing strengthens the case that Raffaele is indeed a contributor to the bra clasp DNA. Yet how can one explain the inequalities in peak heights in the peaks that correspond with his profile? It is possible for DNA belonging to Raffaele to have highly unequal peak heights for several reasons. One possibility is that this would happen when the non-Meredith DNA is in the low template number range. This could lead to large disparities in peak heights in the two alleles within any single locus because of stochastic effects. Dr. Tagliabracci was aware of this issue, as noted in the Massei Report translation, p. 240. Raffaele's putative DNA on the clasp is very weak, less than 200 pg according to his appeal. The exact amount of DNA depends on the details of the calculation. If the low-template number explanation is invoked to explain differences in peak heights, then the standard protocol for dealing with low template DNA is to run the sample at least twice. A retest has yet to be done but may become part of the appeals process.

Comments on the accuracy of the Lifetime movie about Amanda Knox and Raffaele Sollecito

2011-02-23T10:48:00.005-05:00

Part 26 in the Knox/Sollecito case

Lifetime premiered a movie on the murder of Meredith Kercher this week, called "Murder on Trial in Italy." I would like to hear everyone’s thoughts and possibly collect them into a summary. ABC and Candace Dempsey have reported on this movie.

February Updates

2011-02-19T15:30:00.006-05:00

Eric Volz’s blog has added an interview with Professor Greg Hampikian, one of the two coauthors of the open letter covering the bra clasp and knife. Dr. Hampikian, of Boise State University, is the director of the Idaho Innocence Project. Lifetime is premiering a movie this Monday, “Amanda Knox: Murder on Trial in Italy.” Edda Mellas and Curt Knox, Amanda’s parents, have been indicted for libel. Professor Alan Dershowitz mentioned their indictment in an interview in La Stampa. A translation of what he said is “I love Italy, but in recent times you have made the freedom of expression very weak: the Italian government heavily influences the media and they charged the parents of Amanda Knox, guilty only of having made a public expressing opinions on the process of Perugia, however, tainted by legitimate concerns. On the ground of protection of freedom of the press is not giving Italy a great example.” Update: Another tranlsation can be found here.

Why I believe that Amanda Knox and Raffaele Sollecito are innocent

2011-01-19T22:58:00.002-05:00

Part 25 in the Knox/Sollecito case

The molehill of evidence
It is the evidence that is not there that is the prosecution’s weakest point, as former FBI agent Steve Moore pointed out. Consider blood spatter, for instance: “t is inconceivable that the person stabbing Meredith was not contaminated by blood spatter. Guede was. Anybody holding Meredith (such as was alleged by the prosecution) would be within the spatter zone. Again; blood on clothes and skin.”

There is no evidence that Amanda or Raffaele had any contact with Rudi Guede on the night of the murder. There is no evidence that they took any drugs other than cannabis. There is no DNA of Amanda’s in the murder room, and the only evidence of Raffaele’s is the highly contested bra clasp. Forensic Engineer Ron Hendry refuted the arguments of the prosecution that the break-in was staged. The difference in the amount of evidence against Guede versus Knox and Sollecito can be likened to a strong versus a weak signal, and only by pretending that the strong evidence is no better than the weak evidence can one come to the conclusion that all three are culpable.

The interrogation on the night of the 5th of November
The police seemed to have prior knowledge of Amanda’s text message to Patrick on the night of the murder, and the police may have known that the two of them met on the afternoon of the 5th. We also know from both Amanda’s contemporaneous statements and those of others that she was tired and scared in the days leading up to this interrogation (Candace Dempsey, Murder in Italy, Chapters 5-8).

There are many instances of people making a combined false accusation and confession, and this is one of them. The interrogation started around 11 PM and produced two statements, one around 1:45 AM and the other around 5:45 AM. She asked whether she needed a lawyer and was told that would only make things worse. Her statement the next morning shows considerable confusion. Also, if she had been completely rational during the interrogation, she would never have accused Patrick, whether she were innocent or guilty. She believed that he was at the bar that night, which should give him a rock-solid alibi. Again, Steve Moore’s comments are extremely useful and thought-provoking: “Why would detectives schedule an interrogation overnight? ...the reason they interrogated Amanda all night was to break her. Not get the truth, not get answers, not make Perugia safer; but to break her so that she would say what they wanted her to say.”

An ordinary kitchen knife, not the murder weapon
The large knife from Raffaele's flat did not match at least one and probably not two of the three major wounds. It did not match the bloody outline of a knife in Meredith’s bedroom. The DNA on the handle from Amanda was probably deposited when she used it for cooking at Raffaele’s flat. Although the arguments are sometimes detailed, Meredith’s DNA on the knife is probably due to contamination in the laboratory itself, but it may have been contaminated during its transport.

Shoeprint and footprint evidence
The police tried to insinuate some of the luminol-positive footprints were due to Knox and Sollecito and that all were set in blood. This attempt was intellectually dishonest. All of the shoeprints matched Guede’s sneakers. The luminol-positive footprints in the hall do not appear to be Meredith’s blood, inasmuch as they did not have Meredith’s DNA. The one bloody footprint in the bathroom looks a little bit more like Guede’s foot than Sollecito’s foot, but attributing it to either person unequivocally is questionable at best.

Cognitive bias and tunnel vision
If they are innocent, then how did they get convicted? Amanda and Raffaele were detained and held without charge before the forensic evidence came back implicating Rudy Guede. The day of their arrest the police paraded them through the old town with lights on and horns blaring. This had only happened one time previously in Perugia, according to the memory of one citizen, when a mafia figure was arrested. By the time Guede was becoming a suspect, a major figure in the Rome police department had put Ms. Knox’s picture in the hallway, right next to the arrest of Bernardo Provenzano.

This was not a conspiracy in the sense of a bunch of people sitting around a big table. I think it is a case where the police and public minister (PM) Mignini had made a bold claim about Knox and Sollecito’s involvement and could not back down. It may have been a situation where the forensic police (especially) felt, “To get along, go along.” In addition, the forensic scientists might have really believed that Knox and Sollecito were guilty and subconsciously tilted their results in that direction. Koppl and Balko wrote, “To the extent that it's possible, evidence should be stripped of all context before being sent to the lab.” Given that Knox and Sollecito were already in custody in a high-profile case before some of the evidence was even collected, it is difficult to see how all cognitive bias could have been avoided.

Poor forensics and lack of discovery
The prosecution’s misrepresenting which tests were or were not done and their withholding of electronic data files underlying the DNA forensics suggests that they know how weak their case really is. But it is remarkable how much they did wrong or did not do at all, for no reason that I can understand. There is a possible semen stain on Meredith’s bed that was never followed up with a confirmatory test. There were three computer hard drives that the police so badly mishandled that recovery of the data has been difficult or not even attempted. The collection of the DNA evidence with dirty gloves that were seldom changed is just plain sloppy. There is evidence of Meredith’s blood mixed with Amanda’s DNA in certain places in the flat, but the prosecution misleadingly implied that the samples were from Knox’s blood. Since Amanda lived at the flat, finding her DNA there is not inculpatory at all.

Exculpatory evidence
Meredith is known to have returned home around 9 PM. Many small pieces of evidence point to an earlier time of death, before 10 PM, than the prosecution indicated, about 11:40 PM. Meredith had left a load of laundry in the washing machine, presumably when she left to visit her friends for dinner. Yet the laundry had not been removed. Meredith was probably still wearing her zippered sweatshirt when she was attacked, the garment she wore when she was walking home on a brisk evening. Meredith unsuccessfully tried to call her ailing mother around 8:56 PM but did not attempt to reach her again. Atypically, Meredith did not send any text messages that evening. There were two calls around 10 PM that the Massei motivation report ascribes dubiously to Meredith playing with her cell phone. These activities may be evidence of her attacker trying to turn the phones off. A different cell tower sent a MMS to her phone at 10:13 PM; this falls short of proof that the cell phone had left her flat by this time, but it is consistent with the phone’s being transported at this time.

Meredith’s stomach content and the lack of any material in the duodenum are difficult to reconcile with the time of her last meal (of pizza, then apple crumble), which started around 6:30 PM or earlier. Her friends watched a movie after eating pizza, and they stopped to eat apple crumble. Raffaele’s appeal argues that Meredith’s stomach contents indicate a much earlier time of death, by roughly two hours, to about 9:30 or so. Some argue that TOD cannot be accurately determined by stomach contents alone, but that argument can be taken too far: it is known that Meredith was alive until at least 9 PM. In lieu of a lengthy discussion of physiology, let us take a simple path. Patients are advised not to eat for six to eight hours prior to surgery involving intravenous anesthesia. This avoids the possibility that the patient will vomit and aspirate stomach contents into the lungs. Why would anesthesiology guidelines suggest six hours for a small meal if the stomach remained full after 5 to 5.5 hours?

If her death occurred before 10 PM, then it is somewhere between unlikely and impossible that Amanda and Raffaele are guilty. They were known to be acting normally as of about 8:45 PM, when Ms. Popovic came over. Raffaele’s appeal argues that there was some computer activity long after this time, and the police who examined his computer may have not been experienced with MacIntosh products enough to know where to look. Even if the undisputed computer activity ended around 9:10 PM, it is extremely difficult to see how the two of them had time to get so messed up that they lost control enough to murder someone before 10 PM.

Final thoughts
The appeals process has begun with an examination of the DNA forensics of the kitchen knife and the bra clasp. If the computer evidence is reexamined and the stomach contents are reevaluated, Amanda Knox and Raffaele Sollecito have a reasonable chance of exoneration as a result of their appeal.

The American Bar Association and DNA electronic data files

2010-10-22T18:30:00.004-04:00

Part 24 in the Knox/Sollecito case

It is sometimes claimed that the defense teams of Ms. Knox and Mr. Sollecito failed to show up for the DNA forensic testing in this case. Therefore, they do not know what went on and do not have cause to complain about the testing methods or lack of disclosure. This argument is false on a number of fronts. Ms. Knox’s stepfather Chris Mellas said that the defense was given only a few hours of notification, yet Rome is a considerable drive from Perugia (in addition to the defense having other responsibilities). This argument also ignores the fact that several of the experts from the defense only came aboard long after the testing was over. It is absurd to contend that they should be denied free access to the data. However, another problem with this argument is that it assumes that observing the testing is really that critical in the first place.

I posed the question of whether it would be more useful to observe the testing or to have the electronic data files to Professor Dan Krane, one of the cosigners of the open letter on the DNA forensics of this case. He responded:

“Having the electronic data for review is enormously important. Having the opportunity to witness the testing of samples is of marginal utility at best. Reviews of the underlying data for DNA tests often reveals alternative interpretations of the evidence samples, especially in circumstances were small amounts of DNA are involved and it is difficult to distinguish between signal, noise, and technical artifacts. Observing testing rarely provides any more insights than what should be possible from a review of contemporaneous notes that should be part of a lab's case file. Witnessing testing is far from a cure-all. Problems such as contamination of samples can easily arise before a sample arrives in a laboratory yet could not be detected by an expert observing the testing process itself.”

The subject of the electronic data files has been a major theme of this blog’s coverage of the Knox/Sollecito case. Every expert whom I have contacted has spoken in support of full release, and some private DNA forensic companies even have a standard form for the defense to fill out to obtain them. Another benefit of full release of all case files is that serious clerical errors are occasionally found and corrected.

In addition to forensic experts, legal experts within the United States support complete disclosure of all pertinent information, including but not limited to the electronic data files. Nothing close to full disclosure happened in this case. 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.” He reported on the prosecution’s response: “Deputy prosecutor Manuela Comodi brushed off the request for all forensic documentation and added: ‘They have everything they need. That is enough.’”

The American Bar Association’s Criminal Justice Section Standards on DNA evidence discusses disclosure in section 4.1:
(a) The prosecutor should be required, within a specified and reasonable time prior to trial, to make available to the defense the following information and material relating to DNA evidence:
(iii) the laboratory case file and case notes;
(iv) a curriculum vitae for each testifying expert and for each person involved in the testing;
(viii) all raw electronic data produced during testing;
(ix) reports of laboratory contamination and other laboratory problems affecting testing procedures or results relevant to the evaluation of the procedures and test results obtained in the case and corrective actions taken in response; and

Obviously the Italian courts are not bound by the ABA’s guidelines. However, the ABA guidelines are additional documentation, as if any were required, that release of the electronic data files is a near-universal norm in most nations. Ms. Comodi indicating that she has the right to decide what documentation is enough is remarkable given the unanimity of opinion on the usefulness of full disclosure among DNA forensic experts.

An overview of some DNA evidence in the murder of Meredith Kercher

2010-09-27T21:13:00.010-04:00

Part 23 in the Knox/Sollecito case

Executive summary
The most severe problems with the bra clasp are that three other partial profiles are present, that it was moved by unknown means before it was collected, that it was handled way too much during its collection, and that it might be within LCN range. Massei’s reasoning with respect to the disputed loci is fundamentally flawed. The most severe problems with Meredith’s profile on the knife are lack of blood, the low peak heights, the alleles that dropped in and dropped out, and the fact that an inferior version of low copy number (LCN) DNA analysis was used. Amanda’s DNA found with Meredith’s blood is not inculpatory, because DNA in one’s home is rarely out of the ordinary, and there are collection problems with these samples. Finally, the electronic data files were not released, and this has hampered the ability of the defense to challenge the evidence properly.

General defense arguments
Besides the argument that a profile is insufficient to identify a person (see below), an argument that the defense can use is that the DNA is present due to innocent activity. For example, Amanda’s DNA on the handle of the knife may be due to her using it to cook. In addition, the defense can argue three things with respect to how a defendant’s DNA came to be on an item of evidence: secondary/tertiary transfer, contamination, and evidence tampering.

The legal standard for a DNA profile and low copy number DNA
One argument that the defense can use is to say that a given DNA profile fails to clear the legal bar for identifying someone. One might use the analogy to a partial fingerprint. An example here is the necessity of testing low copy number (LCN) DNA twice, whereas the knife was only tested once. The bra clasp falls into a gray area in terms the amount of Raffaele’s DNA present; the defense is arguing that it, too, falls into the LCN range. Meredith’s profile on the knife also shows other evidence of being in the LCN range, such as peak height imbalance. Moreover, the majority of the peaks are below 50 RFU in peak height, most labs have set a threshold of at least 50 RFU as the minimum height for a peak to be counted. Meredith’s DNA profile should not have been accepted by the court as evidence, and Raffaele’s lawyers may have success with their argument.

Contamination
If we only allowed the contamination argument in cases where the defense could demonstrate the exact mechanism of when and how it happened, we would exclude known cases where it did happen. The prosecution must perform negative controls under the same conditions as the evidence and disclose the results of these control experiments to the defense. If DNA shows up in the negative controls, my understanding is that all evidentiary samples processed at the same time must be performed over. When no rational explanation for the presence of DNA on an item can be offered, one is forced to assume that the DNA arrived via contamination. Some cases of DNA contamination are the Jaidyn Leskie murder, the Jane Mixer murder, the Farah Jama rape case, the Gregory Turner case, and the profile N case in New Zealand.

The lack of frequent glove changes and the handling of the clasp by many forensic technicians are problematic for the prosecution. Moreover, Dr. Stefanoni’s testimony as presented in the Massei report (pp. 202-203 in the English translation at Perugia Murder FIle) on this subject is open to serious challenge. Her argument is that they did not change gloves with respect to a certain item of evidence and this piece of evidence did not show contamination. Therefore, contamination is difficult, requiring either liquids or vigorous rubbing. This view seems to be at odds with the consensus of the field, as well as the facts of the Gregory Turner case, which involved transfer of DNA from fingernails to a wedding ring.

Confirmation bias
Not doing what amounts to substrate controls on the mixed Knox/Kercher DNA samples might have been due to confirmation bias. Not obtaining DNA reference samples from Laura and Filomena are behaviors consistent with confirmation bias. Using a lower peak height threshold for the knife than any other piece of evidence contradicts the words of an introductory textbook on DNA forensics as well as general scientific principles. However, there is an additional reason to suspect that some form of investigator bias was at work with respect to the knife profile. Sample 164 was blood from the wall of a bedroom, but it was not tested because of a “negative preliminary (quantification) result.” One surmises that there was not enough DNA to continue the forensic analysis. Why should testing have been stopped for item 164, which had blood, when it was continued for the knife, which had no blood?

Expert testimony
The prosecution’s witnesses and the defense’s witnesses do not have equal scientific standing. Dr. Stefanoni has not published any articles on DNA forensics of which I am aware. On the other hand the nine signers of the open letter (Dr. Johnson, Dr. Hampikian, and the seven co-signers) publish regularly. That is not to say that publication record or academic prestige is everything; there is also variation in the abilities of expert witnesses to convince a jury that they are correct. In this matter the defense may have not fared as well.

The bra clasp
The following discussion assumes that a full DNA profile corresponding to Raffaele Sollecito’s is present, but that does not answer the question of how or when it got there. One problem with the bra clasp as evidence against Raffaele is that his DNA is not found on the bra itself, a point that his lawyers raised in the Micheli preliminary hearing. A more serious problem is that partial profiles of three other people have also been reported.

An answer to the question of how Raffaele’s DNA was deposited on the clasp is that it might have been deposited the same way as three DNA profiles from unknown individuals. To put it another way, if we acknowledge that DNA from three unknown individuals came to be on the clasp innocently, then what makes Raffaele’s DNA different? It is very unlikely that four people handed the bra clasp as part of a sexual assault and murder. Primary transfer before the assault seems equally unlikely; most people fold their own laundry, and someone else folding it would only account for one profile. So the unknown DNA had to arrive either from secondary transfer or from contamination.

One possibility involving secondary transfer involves the towels. The towels that Rudy probably took from the bathroom might have had DNA from anyone who washed his or her hands in the bathroom and used the towels to dry off, including Raffaele, who had cooked there. If the towel were placed over the clasp and stepped on, it could transfer DNA to the clasp. This might also explain the deformation of the clasp. Another possible route of secondary transfer is that whoever moved the clasp before it was collected deposited Raffaele’s DNA (possibly originating from the door).

There is a good deal of misunderstanding involving DNA contamination and the clasp. It is often said that the only item that tested positive for Raffaele’s DNA was a cigarette butt, and so how could contamination occur? There are several problems with this argument. First, one should not equate the DNA that the investigators found with the total amount of DNA Raffaele left at the cottage. The investigators seemed to be focused on blood, as well as Meredith’s body. They were not taking a random sampling of the cottage. Second, there is no reason to exclude contamination from the cigarette butt in the lab, although if they were tested far apart in time, contamination is less likely. Third, Raffaele’s reference sample is a potentially serious source of contamination. In PCR-based DNA forensics, the DNA is amplified very roughly a millionfold in amount. That is why good labs separate the pre-PCR from the post PCR-samples.

The amount of Raffaele’s DNA on the clasp is borderline LCN. If it is judged to be below the LCN cutoff, it would ordinarily have to be tested twice and only those alleles that showed up in both runs should be counted. It is sometimes said that the amount of Raffaele’s DNA was so large as to mean that it could only arise from vigorous rubbing (primary transfer). The fact that the amount of DNA is actually low would seem contradict such an argument. However, it is the premise that is wrong; the DNA profile itself can rarely give an indication of when and how it was deposited. One cannot rule out primary transfer when the amount of DNA is low any more than one can rule out secondary transfer when the amount of DNA.

Raffaele’s appeal with respect to the bra clasp
The discussion above presumes that a good, complete profile was found. However, Dr. Tagliabracci disputed that the profile matched Raffaele’s for at least six of the loci. If Sollecito’s profile were strong and if the bra clasp DNA were not a mixture, there might be fewer opportunities for disagreement between Dr. Tagliabracci and Dr. Stefanoni. Of the six disputed loci from the bra clasp DNA profile, Massei wrote (pp. 296-297 of the Perugia Murder File English translation):

“Consequently, there are apparently a considerable number of loci that are not the subject of dispute, a number which seems to be greater than the number of disputed loci and greater than the number of six loci with reference to which Professor Tagliabracci had previously declared, before the current systems were available‚ it was enough ... we made hypotheses even with six loci‛ (page [319] 103). The circumstance now exposed allows, it was held, the following consideration: if, despite the subjective contribution of the geneticist, the interpretative disagreement regarding the non-compatibility of Raffaele Sollecito’s profile with the loci that had contributed to forming trace 165B involved those loci indicated by Professor Tagliabracci during the course of the hearing and at pages 20 and 21 of the previously mentioned memorandum conclusions, it must be held that, for the greatest number of loci at least, the peaks were so clear and the interpretation so sound that they could not be contested. Consequently, the overall result should be considered fully reliable, even disregarding the repetition of the analysis. It should however be noted that Dr. Stefanoni, during the hearing at which she testified, had offered suitable explanations and answers which this Court considers acceptable.”

Raffaele’s appeal document correctly notes that Massei’s argument about the numbers of disputed and undisputed loci is contrary to the principles of forensic genetics. Let us assume that the data are clear enough to avoid ambiguity and consider the following analogy. Suppose that a winning lottery number is 12497635834, and I have a lottery ticket that is 12497235834. And suppose I claim that since my ticket has 10 out of the 11 numbers identical, I am a winner. That argument makes as much sense as Massei’s does.

But what of Dr. Tagliabracci’s statement that six loci used to be enough to form hypotheses? Suppose that initially a complete profile consisted of six loci. If a person matched all six loci, he or she would not be excluded as the DNA donor to that sample. However, if that person matched at only 5 loci and failed to match at the sixth locus, then he or she would be excluded. Now suppose an improved test with 10 loci became available. Then a person who matched all ten loci would not be excluded, and the number of other people who could also match would be much smaller than in the case with 6 loci. However, a person who matched at 9 loci but failed to match the tenth locus would still be excluded, even though 9 is greater than 6.

Massei must believe that at all six disputed loci, the DNA is Raffaele’s, or at the very least that the results in all six loci are indeterminate (if the latter were true, it would indicate that Raffaele’s DNA constituted a partial profile, not a complete one). Massei does not provide a clear reason for rejecting Dr. Tagliabracci’s assessment in favor of Dr. Stefanoni’s. It is difficult to see why a sentencing report the fails to provide reasons is any better than no sentencing report at all.

The knife profile
The peak heights on the DNA profile culled from the kitchen knife are all below 100 relative fluorescence units (RFU), and most are below 40 RFU. This is below any threshold of which I am aware. What was the harm in using a lower peak threshold? One can argue that it obliges the forensic scientist to use the same threshold for all the samples on the basis of consistency. It is a dollars-to-donuts bet that some evidence of contamination could be found at this atypically low peak threshold among the hundreds of samples run.

There is no detectable blood on the knife. The open letter asserts that if a bloody knife were cleaned, one would remove detectable traces of DNA before detectable traces of blood. If one claims that the DNA arose from other tissue, then I would ask how it is possible to remove blood cells and not other cells. The cleaning problem only grows more severe if one claims that the knife were cleaned with bleach and that traces of bleach were found. Even trace amounts of bleach are known to destroy DNA for forensic profiling.

The profile shows evidence of alleles dropping in and dropping out. In other words there is one allele where Meredith’s profile is weak or absent, and there is one locus with two peaks that are not part of Meredith’s profile. The peaks within each locus are often very uneven (as much as roughly threefold) in peak height, yet they should be approximately the same height in a good profile. These problems are to be expected when DNA is in the low copy number (LCN) range. When DNA falls into such a low range of amounts, forensic scientists generally test it at least twice and accept only those peaks that appear in both runs.

One can argue that LCN profiling should ordinarily be accepted by a court. However, Dr. Stefanoni used an inferior version of LCN DNA profiling, one that has never appeared in the scientific literature. LCN profiling is typically done in specialized buildings, away from the laboratory doing regular profiling. These precautions are necessary because LCN profiling is more prone to contamination than ordinary PCR-based profiling. These precautions were not followed with respect to the knife, and it was only tested once.

Another problem with the knife is that the second officer to have possession of the knife was at Meredith’s cottage just before receiving it. This raises the odds of contamination outside of the lab. Meredith’s profile probably arose through contamination in the laboratory, but contamination during the time it was taken into custody is also a possibility.

The mixed DNA samples
A number of samples that appeared to be blood had both Meredith’s and Amanda’s DNA. Three of the mixed DNA samples were probably blood and three may or may not have been blood. This would be very weak evidence under most conditions. Amanda’s DNA is expected to be in many locations in her own home. The fact that samples were not taken close to the blood (essentially substrate controls) means that one cannot rule out an innocent explanation for their existence. To argue that these samples are inculpatory, one is almost forced to assume that Amanda’s DNA is from her blood. White blood cells contain DNA; therefore, Amanda’s DNA might have arisen from her blood. Yet without characterizing or quantifying the amount of biological material that gave rise to her DNA, there is no reason to believe that the samples must be from blood. No such tests were done.

However, the prosecution has two additional problems with its case. First, Dr. Stefanoni did not change gloves when collecting multiple samples (see above). Therefore, she might have mixed samples herself. Second, at least one of these samples had a third profile in it, from an unknown individual. If this person’s DNA arose from innocent means, there is no reason to exclude the possibility that Amanda’s did also.

The lack of DNA
The lack of Raffaele’s DNA or Amanda’s DNA on Meredith’s body, when Raffaele is thought to have restrained her and Amanda to have throttled her calls into question this part of the prosecution’s narrative. The number of actual instances where DNA was used in strangulation cases where the DNA originated from the victim’s neck, as opposed to the victim’s fingernails, is small. However, some instances of alleged domestic violence cases have used swabbing of bruised or reddened areas on the alleged victim as evidence.

Conclusions
The way that the bra clasp was handled and the lack of a clear chain of custody cast doubt on this piece of evidence. The lack of blood on the knife calls into grave question whether the DNA got there before or after the police took it into evidence, as argued in the Johnson/Hampikian open letter. Secondary transfer is a likely means for Raffaele’s DNA being in the bra clasp, and contamination, either in the lab or during collection, is a likely means for Meredith’s DNA being found on the knife. The mixed DNA samples are virtually meaningless. The single most troubling aspect of the DNA evidence is the lack of full disclosure of the electronic data files and other documentation relating to the DNA forensics. The prosecution is acting as if it had something to hide.

Eighteen false or misleading claims about Edda Mellas

2010-08-22T15:46:00.005-04:00

Part 22 in the Knox/Sollecito case

In the previous entry I invited my readers to examine the claims that Edda Mellas made eighteen false claims, a view that was advanced at the site True Justice for Meredith by an anonymous individual calling herself “The Machine.” The following condensation is my synthesis of many of those comments. Thanks to Bob, Bruce Fisher, Kate, Mary H, Rose Montague, and all of the other contributors.

False claim 1: “The prosecution had changed the motive four times during the trial. and at the end they finally had to say we don’t have a motive but it doesn’t matter.” (minute 4.22 above)
Barbie Nadeau pointed out that the prosecutors had changed their theory, but only rather slightly:
“The prosecution lawyers began their case in January 2009 by arguing that Kercher was killed during a sex game gone awry. When it came time for closing arguments, they had changed the theory slightly, trying to make the case that Knox resented her prissy British roommate and killed her in hatred” A sex attack was still involved.
Prosecutor Mignini also suggested that a hards (sic) drug like cocaine might have been involved, and certainly never said that they didn’t have a motive. Co-Prosecutor Manuela Comodi said that she didn’t know precisely what the motive was, but certainly never claimed that there was none.

Response
It is misleading to begin the clock at January 2009. The motive progression was: **Beginning motive (Nov. 2007) – Conspired satanic group sex activity.
**Beginning of trial – Conspired group sex activity.
**End of trial per Mignini– Knox’s resentment of her prissy British roommate--i.e., Knox’s hatred of Meredith.
**End of trial per Comodi – No motive but it doesn’t matter.
**Motivation report – Lust and marijuana induced aggression.

Finally, Ms. Nadeau herself reported (Angel Face, p. 158) that Mignini wanted to reintroduce the Satanic ritual, but Comodi blocked this.

False claim 2: “He (Rudy Guede) all of a sudden had money that he didn’t have earlier in the day” (minute 3.22 above)
Edda Mellas is plucking “facts” out thin air with this claim. No evidence was presented at any court hearing that showed that Rudy Guede suddenly had money that he didn’t have earlier in the day on 1 November 2007.

Response
No one knows for sure whether Rudy Guede was able to buy a train ticket to Germany or simply avoided paying. However, he had not worked in two months. The facts that Meredith’s rent money was missing, his DNA was found on the zip of her purse point toward him as the thief. By contrast, neither Amanda nor Raffaele had money problems, despite the latter having a low bank account.

False claim 3: “There is no murder weapon.” (minute 4.32 above)
Judge Massei indicates in the sentencing report that Amanda Knox’s judges concluded that the double DNA knife, the larger of the two indicated by Meredith’s autopsy, is indeed the murder weapon.
It is totally compatible with the deep puncture wound in Meredith’s neck, and according to a number of independent forensic experts, it contained Meredith’s DNA on the blade..

Response
Besides the problems with the DNA on the knife (see Response 13), it neither matched two of the three major wounds nor the bloody outline of a knife on the bed. If this were the murder weapon, it would have had blood on the handle, which would need to be cleaned off. This would remove the putative murderer’s fingerprints at the same time. The forensic police did not disassemble the knife to look for blood, as General Garofano pointed out in the book Darkness Descending. Why not? Perhaps even they doubt that Raffaele’s ordinary kitchen knife is a credible murder weapon.

False claim 4: “The Italian Supreme Court found the interrogation illegal” (minute 7.54 above)
Though this claim has been repeated in different ways, the Italian Supreme Court has NEVER ruled that Amanda Knox’s interrogation either as a witness or a suspect was illegal. In the suspect interview, she had both a lawyer and interpreter present.

Response
The Machine is being cagey with respect to what constituted the suspect interview. The Supreme Court ruled that any information resulting from the interrogation was inadmissible in the Knox/Sollecito trial, but, in a mockery of justice and a violation of basic human rights, interrogation information was entered into the trial due to the Lumumba defamation/slander case.

False claim 5: “They admit to the fact they really have no physical evidence” (minute 7.54 above)
As it took the prosecutors four or five months to present it, they have never admitted that they have no physical evidence. The stop-start-stop nature of the defense phase of the trial showed how very telling the evidence was.

Response
If the prosecution had solid physical evidence they would not be trampling all over Amanda’s rights by withholding evidence and lying as per the following:  
*The prosecution withheld crucial testing information from the defense for the first 6 months of the trial of first instance.
*The prosecution lied for the first 6 months of the trial when they continually repeated that the footprints revealed by luminol were not tested for blood—documents released to the defense by the judge’s order show that the footprints were tested and that the results were negative, i.e., no blood.
*The prosecution is still withholding crucial testing information--the electronic data files (.fsa files), the instrument log files, and (if they exist) the contamination log files.

A succinct description of the lack of evidence for the prosecutor’s case is found here.

False claim 6: “They believe Meredith was killed at about 9.30pm” on Larry King Live (minute 0.54 here)
The prosecutors didn’t claim this at the trial. According to Mignini’s timeline, which he used when presenting his scenario for what happened to the judges and jury at trial, Meredith was killed at about 11.50pm.

Response
The Machine ignores the fact that Public Minister Mignini moved the time of death back an hour during his closing statement. There are several reasons for rejecting Mignini’s revised time of death, not the least of which are the contents of Meredith’s stomach.

However, the cell phone evidence is perhaps the most exculpatory. The cell phone evidence is very clear and Raffaele’s appeal makes a very good argument that it is a good indication of a time of death between  9 and 10 pm. At 8:56 pm there is an attempt to call Meredith’s parents that does not go through. There is no further attempt despite the fact that her normal habits as shown by her phone records has her calling them before she went to bed on a regular basis.  Just a few minutes before 10 pm there is an attempt to call voicemail that is ended before the message was heard and at 10 pm there is an attempt made to call her bank that does not use the international code prefix and does not go through. At 10:13 the cell phone shows there is a GRPS (mms) reception to the cell phone from a tower that does cover Meredith’s place but not as strongly as the tower that normally covers her flat. This is the first time she has gotten a call covered by this particular mast. The next incoming call at 10 past midnight shows the location of the phones in the garden where they were found based on the mast that covers that area.  The Massei report speculates that Meredith was just playing around with her phone at the times all these earlier calls. The defense had the idea of testing an area between Meredith’s apartment and the garden where they were found and discovered that this particular mast (the one showing the 10:13 call) covers an area between Meredith’s flat and the garden where they were found, meaning that at 10:13 the phone was in route to the garden and Meredith was already dead.

False claim 7: Amanda Knox didn’t know Rudy Guede (minute 1.02 here)
Unbelievably, Edda Mellas claimed that Amanda Knox didn’t know Rudy Guede despite the fact that Amanda Knox testified IN COURT that she had met Rudy Guede on several occasions.
Here’s the actual court transcript:
Carlo Pacelli (CP), Patrick Lumumba’s lawyer: In what circumstances did you meet him (Rudy)?
Amanda Knox (AK): I was in the center, near the church. It was during an evening when I met the guys that lived underneath in the apartment underneath us, and while I was mingling with them, they introduced me to Rudy.
CP: So it was on the occasion of a party at the house of the neighbors downstairs?
AK: Yes. What we did is, they introduced me to him downtown just to say “This is Rudy, this is Amanda”, and then I spent most of my time with Meredith, but we all went back to the house together.
CP: Did you also know him, or at least see him, in the pub “Le Chic”, Rudy?
AK: I think I saw him there once.
CP: Listen, this party at the neighbors, it took place in the second half of October? What period, end of October? 2007?
AK: I think it was more in the middle of October.

Response
“To meet” is to be introduced or come together at a particular time and place.  “To know” in this case would be “to be acquainted or familiar with.” in other words she didn’t know Guede personally. She knew who he was but didn’t know him.  Apparently The Machine must havea hard time understanding American English. Amanda met the guy 1 time and might have saw him at a club 1 time. That does not mean she knows him. The Machine is pretending that the there is no difference between the two.

False claim 8: Rudy Guede’s DNA was in Meredith’s purse (minute 3.16 here
Edda Mellas’s claim that Rudy Guede’s DNA was in Meredith’s purse is completely untrue. According to the Micheli report, which was made available to the public in January 2008, Guede’s DNA was found on the zip of Meredith’s purse and not inside it.

Response
The Machine is making a distinction without a difference. Rudy Guede’s DNA was found on her purse, on the sleeve of her sweatshirt and in her body. The lack of Amanda’s or Raffaele’s DNA on Meredith’s body is a problem for the prosecution’s case.

False claim 9: “Even the Italian Supreme Court ruled that her rights were repeatedly violated.” (minute 5:32 here)
The Italian Supreme Court has NEVER ruled that Amanda Knox’s rights were repeatedly violated. Not even her own lawyers claimed that, and no complaint was ever lodged.
The first of Knox’s two written statements couldn’t be used against her simply because she wasn’t represented by a lawyer when she made it – and she volunteered that statement, in a seeming state of panic, when she was told Sollecito was no longer supporting her alibi..
We continue next with Edda Mellas making claims in an interview for the CBS Early Show.
Whilen Edda Mellas was in Perugia, she was interviewed by CBS’s Chris Wragge. (Embedding of this CBS video YouTube on sites like TJMK is disabled, which suggests that CBS might be worried that the claims made were wrong and they should have been challenged on-air.)

Response
An even higher court is beginning to realize that Amanda’s rights were repeatedly violated—society, which demands fundamental justice and the rule of law:  
*Denial of legal representation
*Interrogation statements ruled to be inadmissible by the Supreme Court were thrust into the trial due to the Lumumba defamation/slander case.
*The prosecution withheld crucial testing information from the defense for the first 6 months of the trial of first instance.
*The prosecution lied for the first 6 months of the trial when they continually repeated that the footprints revealed by luminol were not tested for blood—documents released to the defense by a judge’s order revealed that the footprints were tested and that the results were negative, i.e., no blood.
*The prosecution is still withholding crucial testing information--the electronic data files (.fsa files), the instrument log files, and (if they exist) the contamination log files.
*Amanda Knox has been charged with slander for defending herself in court.

False claim 10: The double DNA knife is incompatible with the wounds on Meredith’s body. (minute 0.16 above)
In the interview Edda Mellas made the following claim: “The knife they think is the murder weapon is way too big and demonstrated how it had to have been a much smaller knife that caused all the wounds.”
Edda Mellas’s claim above is simply not true.
Barbie Nadeau reported directly from the courtroom in Perugia that multiple witnesses for the defence, including Dr. Carlo Torre, conceded that the double DNA knife was compatible with the deep puncture wound in Meredith’s neck.
“According to multiple witnesses for the defense, the knife is compatible with at least one of the three wounds on Kercher’s neck, but it was likely too large for the other two.” (Barbie Nadeau, Newsweek).
“He (Dr. Carlo Torre) conceded that a third larger wound could have been made with the knife, but said it was more likely it was made by twisting a smaller knife.” (Barbie Nadeau, The Daily Beast).
Judge Massei categorically states in the judges’ sentencing report that the double DNA knife was compatible with the large wound on Meredith’s neck.

Response
The problems with the knife as evidence are discussed in Responses 3 and 13, however it is worth repeating that any knife could have made the larger wound, including the one that made the other two wounds on Meredith’s neck. What makes no sense is why Amanda and Raffaele would take a knife from his apartment even if their intent were to scare Meredith that night. There were knives at the girls’ flat. The notion that Amanda carried the large kitchen knife for protection (in a cloth bag, no less) is absurd.

False claim 11: Meredith’s room was so tiny, there wasn’t enough room for four people in some kind of tussle. (minute 0.27 above)
In the same interview with Chris Wragge, Edda Mellas asserts that there couldn’t have been an attack on Meredith involving three assailants.
“The space available this crime happened is so tiny you can’t have had four people in that room in some kind of tussle.”
The Violent Crimes Unit itself used detailed images at the trial (this is one below) to show that there was more than enough room for an attack involving three attackers.

Response
Edda may have been questioning whether a struggle involving four people would create more damage in the room than was observed. If three people attacked Meredith, where are Knox’s or Sollecito’s shoeprints or fingerprints? If they restrained her and throttled her, why is there no DNA evidence of this contact?

Update 15 September 2010
It was originally Raffaele Sollecito’s expert witness, Francesco Introna, who argued that the room was too small for three people to assault Meredith Kercher.

False claim 12: There is no evidence of Amanda Knox at the actual crime scene. (minute 2.06 above)
“I fact at the actual crime scene there is no physical evidence of Amanda; not a hair, not a fingerprint, not a nothing.”
The crime scene involves the whole cottage and it isn’t limited to Meredith’s room. Knox and Sollecito were both CONVICTED of staging the break-in and tampering with the crime scene.
Furthermore, there is plenty of evidence actually placing Amanda Knox in Meredith’s room on the night of the murder: the double DNA knife, and the blood she tracked into the bathroom, the hallway, Filomena’s room, and her own room.
According to two imprint experts, there was a woman’s bloody shoeprint on the pillow under Meredith’s body which matched Knox’s foot size.
Even Sollecito’s forensic consultant, Professor Vinci, claimed that he had found Amanda Knox’s DNA on Meredith’s bra.

Response
Because the date at which DNA arrived on an object cannot be known and because Amanda used the knife when she cooked at Raffaele’s flat, the presence of Amanda Knox’s DNA on the handle is strictly meaningless.

Every single shoe print found in the murder room belongs to Rudy Guede. The two imprint experts that The Machine is referring to were proven wrong. The Machine and everyone else at TJMK and PMF are well aware that this information has been refuted but they continue to spread this lie. Raffaele Sollecito’s forensics expert Francesco Vinci showed in great detail, in court, that all of the prints found in the murder room belonged to Rudy Guede.   The prosecution had originally stated that there was one shoe print matching Raffaele Sollecito’s shoes found on the tile floor. They also stated that one shoe print of a woman’s size 37 shoe was found on a pillow case. The shoe print said to be a woman’s shoe was attributed to Amanda.  The truth is, all of the shoe prints match Rudy’s Nike Outbreak 2 shoes.

The Machine’s reasoning with respect to staging the break-in and tampering with the crime scene assumes Knox’s and Sollecito’s guilt, which are the very questions under dispute. In addition, luminol is a presumptive test for blood, no more. The luminol-positive footprints were negative by the TMB test and did not have Meredith’s DNA; therefore, there is no reason to believe that they originated from blood.

If one claimed that the DNA on the bra clasp is conclusive evidence of guilt, one would have to begin searching for the three unidentified individuals also deposited DNA on the clasp. One thing that the bra clasp implies is that contamination might be alive and well in the Rome testing laboratory. Either that or secondary transfer could explain all of the DNA on the clasp.

False claim 13: “The DNA is so insignificant. It’s this tiny spot. It’s not blood.” (minute 2.16 above)
Three independent DNA experts - Dr. Patrizia Stefanoni, Dr. Renato Biondo, and Professor Francesca Torricelli – confirmed that Meredith’s DNA was definitely on the blade of the double DNA.
The DNA charts themselves show a clear and unmistakable match. Edda Mellas doesn’t seem to understand that DNA evidence almost always involves only microscopic traces of DNA.
Dr. Stefanoni testified at the trial that the DNA on the blade could indeed have come from Meredith’s blood.
We continue next with Edda Mellas in an Interview with Linda Byron on Seattle TV station King 5.

Response
The Machine ignores that Meredith’s DNA was in the low copy number (LCN) range, demonstrating that she understands less about DNA profiling than Edda Mellas does. First, LCN samples should be tested at least twice, and only those alleles that show up in both runs are should be counted. Second, Stefanoni did not use standard LCN conditions in other ways, such as the number of cycles of the amplification step and working under lighting and air-handling conditions that minimize the possibility of DNA contamination. New methods are typically vetted in peer-reviewed journals before they are accepted. Third, the Machine also ignores the well known possibility of contamination, as well as the fact that contamination is a greater risk for samples in the LCN range.

There are some problems with The Machine’s assertion that there is a “clear and unmistakable match.” First, in locus D3S1358 there are two peaks, each with peak height of about 20 RFU, which are not seen in Meredith’s reference profile. They have 15 and 16 repeats, respectively, but Meredith’s profile has peaks at 14 and 18 repeats. Second, in the D21S11 locus, the knife profile has a peak at 30 repeats, but Meredith’s profile has peaks at 30 and 33.2 repeats. It is possible to explain the two extra and one missing peak as a consequence of the amount of DNA being in the LCN range. Yet, this explanation only underscores the fact that Stefanoni should have used the services of a lab that has proper facilities and experience, instead of making up her own inferior method.

It is now well known that Stefanoni went ahead with the analysis, despite the fact that her instrument read “too low,” meaning that there was not enough DNA to continue. What is less well appreciated is the fact that Stefanoni treated this sample differently from other samples, where she discontinued the analysis under similar circumstances. The Machine ignores Stefanoni’s apparent inconsistency.

Dr. Stefanoni’s assertion that the DNA could have come from Meredith’s blood is extremely dubious. The knife tested negative for blood with tetramethylbenzidine (TMB), and Dr. Elizabeth Johnson and Professor Gregory Hampikian indicated that the test for blood is more sensitive than the test for DNA. In other words, if a bloody knife were cleaned of all traces of blood, all traces of DNA would also be removed. They and the cosigners of an open letter on the DNA evidence in this case publish regularly in the field of DNA forensics. The same cannot be said of Dr. Stefanoni.

Furthermore, The Machine ignores the fact that Stefanoni did not turn over the electronic data files or the machine logs. This failure to abide by the international standards of discovery of DNA evidence means that any claim about the quality of the results is suspect. The defense expert witnesses did not have all of the information that they would need to evaluate Stefanoni’s dubious results.

False claim 14: Amanda Knox and Raffaele Sollecito maintained the same story (minute 3.17)
Edda Mellas claimed in this interview with Linda Byron that Amanda Knox had maintained the same story for over a year when she was asked whether her daughter had lied. In another interview with Linda Byron in November 2009, Edda Mellas bizarrely claimed that Amanda Knox hadn’t changed her story. KING 5 Investigator Linda Byron asked her: “Did she change her story?”
Edda Mellas responded: “No, no. For this whole year they have maintained the story – what they did that night. They stayed at Raffaele’s, they made dinner, they watched a movie. That’s it, that’s the story.”
Edda Mellas’s statement that Amanda Knox didn’t change her story and that she and Sollecito maintained the same story is yet another incorrect and misleading claim. Knox and Sollecito both gave three different alibis. The posts on their alibis are linked-to up at the top here. Knox gave at least three different times for when she and Sollecito had dinner on the night of the murder.
Knox gave different reasons for writing her handwritten confession, and she gave different accounts of seeing the blood in the bathroom which contradict each other.
And most devastating of all, Sollecito stopped providing Knox with an alibi on 5 November 2007. Sollecito is STILL nearly three years later refusing to corroborate her alibi. He clearly hasn’t maintained that Knox was with him at his apartment – actually he claimed that she went out for four hours.

Response
Amanda has had two basic accounts; before and after the night of 5-6 November, she said that she was with Raffaele. Only on the night of the interrogation did she say anything different, and she almost immediately backed away from what she said that night. Amanda’s own words and actions and the observations of others all indicate that Amanda was physically and emotionally worn out by the time of her interrogation. We will never know how her interrogation progressed, because the police either lost it or never made a recording of it.

The claim that Raffaele stopped providing an alibi for Amanda after 1 November 2007 is among The Machine’s most serious misstatements. The accounts in Murder in Italy and Darkness Descending both indicate that Raffaele backed Amanda up, although Ms. Dempsey indicates that Raffaele got some of the times wrong. Raffaele has always stated that to the best of his knowledge Amanda spent the entire night with him on 1 November 2007. He does add that it would have been possible for Amanda to have sneaked out for maybe an hour without his knowledge.

Raffaele’s lawyers appeared before the Supreme Court in the spring of 2008 to argue for his release, inasmuch as he had not even been formally charged at this point. Their words are sometimes taken as evidence that he was claiming he was not with her on the night of 5 November. His lawyers used words that were translated as “erroneous assumption” at Perugia-Shock that they were together, but a better translation is undeserved or unwarranted assumption. The key to understanding his lawyers’ argument is that they did not call it an erroneous belief, which would be a denial that they were together. The lawyers are saying that any evidence that would place Amanda outside Raffaele’s flat ought not be counted as evidence that Raffaele were outside his flat. As Kate wrote, “She’s not saying they were together or that they weren’t together; she’s challenging the Court to provide the evidence it NEEDS to provide if it’s going to transfer evidence to Sollecito on the basis of an unsupported assumption.”

False claim 15: Amanda Knox wasn’t provided with an interpreter (minute 2.37)
Edda Mellas made this false claim, which has been widely propagated by Knox groupies, in an interview with Linda Byron on King5. It’s not difficult to prove that this claim is completely false. Knox’s interpreter on 5 November 2007, Anna Donninio, even testified at the trial. And Amanda Knox herself spoke about her interpreter when she gave testimony at the trial.
We continue next with the claims of Edda Mellas on ABC TV.

Response
The interpreter in this case was a participant in the interrogation process. According to Andrea Vogt, “But Knox said her interpreter's ‘traumatization’ was actually used to pressure her. ‘Ms. Donnino then later suggested that ... perhaps I didn't remember well because I had been traumatized, and so I should try to remember something else.’”

John Hooper reported on Ms. Donnio’s testimony: “Under cross-examination she described her role as that of a ‘mediator’ rather than a mere translator of words.”  Knox Clashes With Interpreter."   That seems to be an unusual role for an interpreter. One wonders whether there is a defined role that an interpreter can play and if there are limits to what role they can take, as proscribed in Italian law.

False claim 16: “Amanda Knox is incredibly honest” (minute 11.25)
In an interview with ABC’s Elizabeth Vargas (ABC have rendered this video not embeddable) Edda Mellas claimed that her daughter is “incredibly honest”. And Edda Mellas told The Guardian’s Simon Hattenstone that “Amanda doesn’t know how to lie.”
In fact, Amanda Knox’s mobile phone records, data recovered from Sollecito’s computer, and corroborative testimony of numerous witnesses, provide irrefutable proof that Amanda Knox has lied – again and again. For example, her lies about him directly led to Diya Lumumba, an innocent man, spending two weeks in prison – even though as recorded in prison she told her mother Edda Mellas that her claims were not true.

Response
The Machine provides no specifics for her claims. Blaming Ms. Knox for what she said during an interrogation without knowing what went on between 11 PM and 5:45 AM the next morning is jumping to conclusions without facts. The authorities knew that Ms. Knox had already backed away from her statements about Lumumba long before she spoke to her mother. And the fact that this interview was recorded means that ILE knew exactly how Ms. Knox perceived her false statement. If they had decided her statement were false on the basis of what she said to her mother, they could have released Mr. Lumumba. Moreover, the authorities were not proactive with respect to an exculpatory witness for Mr. Lumumba; he came to Perugia on his own initiative.

Amanda’s family and all of her friends have always said that Amanda is ‘honest to a fault’. Why would anyone wish to accuse Amanda’s family and all of her friends of being liars?

False claim 17: Amanda Knox could have left Italy, but she chose to stay and help the police.
In an earlier interview with Larry King in October 2009, Edda Mellas told him that Amanda Knox could have left Italy, but she chose to stay and help the police: “After the murder, Mellas said, friends and family told Knox to leave Italy—to either come home or stay with relatives in Germany—but Knox refused because she wanted to help find the killer and prove that she had nothing to do with it.”
“Many people asked her to leave, but she said no. ‘I’m going to stay. I’m going to try and help. I’m going to try and finish school,’ ” Mellas said.” Edda Mellas’s claim is flatly contradicted by Amanda Knox herself, in the e-mail she wrote to her friends in Seattle on 4 November 2007: “I then bought some underwear because as it turns out I wont be able to leave italy for a while as well as enter my house”
And along with one of Meredith’s friends who walked home with Meredith on the night, the police told Amanda Knox pretty promptly that as her status was (then) a primary witness, she was not to go anywhere. The fact that Knox did stay was of little help to the investigation – in fact, she seemed to work hard to derail it – and one of her main concerns at the time, a pretty callous one, was whether she would be staying or moving out of the house and getting a rent refund.

Response
The following statement from Judge Matteini indicates that Amanda was free to leave Italy and didn’t:  "Your family lives in the United States, so it would be extremely easy for you to leave the country," Matteini wrote. "The fact that you did not do so before you were arrested is totally irrelevant. We must remind you that your arrest was made very early, and was affected purposely before the arrival of your mother in order to avoid just such a possibility."

False claim 18: Amanda Knox and Raffaele Sollecito were not under the influence of drugs on the night of the murder (BBC Radio)
In an interview with BBC Radio after the verdict, Edda Mellas apparently stated that Amanda Knox and Raffaele Sollecito were not under the influence of drugs on the night of the murder.
This is despite the fact that both Knox and Sollecito had both themselves actually claimed they had smoked cannabis. The prosecution believed they might have been on a hard drug like cocaine, which also seems the general belief around Perugia.

Response
The Machine is engaging in rumor-mongering. There was no evidence presented at the trial about cocaine or any other drug. Amanda never used cocaine in her life. Knox and Sollecito have stated that they had smoked cannabis. One suspects that Amanda’s parents were implying that they (Amanda and Raffaele) were not under the influence of ‘hard’ drugs as opposed to mildly euphoriant-like cannabis which does not induce aggressive behavior.

Part 3. And Some Conclusions
The fact that Edda Mellas has been able to propagate so many wrong claims in the media for so long without being challenged seems to speaks volumes about the naivety and unprofessionalism of her interviewers, and of the media organisations they work for. As they usually do, ABC News, CBS News, CNN, King 5, and other media outlets should have interviewed objective crime-case professionals, who don’t have a vested interest in the case.
Instead they have relied again and again on Amanda Knox’s mother and other family members as primary sources.
Amanda Knox is not an innocent political prisoner who was railroaded in some Third World country for some very murky reason. She was unanimously convicted after a lengthy trial at which the evidence was absolutely overwhelming.
As the Christian Longo and Scott Peterson cases that we posted on below go to prove, seemingly quite normal people commit horrific murders. Probably the vast majority of murders are committed by people who to many seemed normal.
It seems downright perverse that some of the journalists who have interviewed Edda Mellas treat Amanda Knox as a victim, and with cloying sympathy ask “How is Amanda doing?” They wouldn’t dream of asking Charles Manson’s mum how the Manson girls are doing.
It is time for the sake of the truth, the legitimacy of the verdict, the relations between the US and Italy, and the peace of mind of Meredith’s family and friends, that from now on they hold Edda Mellas’s feet to the fire..

Response
The premise of The Machine’s article is flawed. The Machine presented no evidence that the press has ever relied heavily on Edda Mellas as a primary source of information. Have they actually relied on family members as “primary sources?” Or are the interviews with Amanda’s parents intended to focus on the subjective, human-interest aspects of the story? The comparison to Charles Manson and the references to cocaine use (again without providing any evidence to support this claim) make it clear that The Machine has no business complaining about another person's lack of impartiality. Moreover, Ms. Knox’s lawyers made many of the same arguments as Edda Mellas; therefore, there is no reason to single her out. The Machine has chosen to personalize the debate for no good reason.

Many of the Non-errors that The Machine cites are repeated in the defense appeals and should not be taken as errors simply because it doesn't fit with the prosecution’s case or the Massei report. Many of these issues are disputed for good reason. The Machine’s credibility for posting accurate and objective information has to be evaluated in light of her many errors in this article and others. Moreover, since the posting of the previous entry, The Machine has neither explained why the arguments are incorrect, nor made any alterations in or retractions to her essay, further damaging her credibility.

Eighteen claims about Edda Mellas’s interviews

2010-08-03T13:21:00.015-04:00

Part 21 in the Knox/Sollecito case

At True Justice for Meredith, The Machine has posted eighteen supposed errors (“Why The Media Are Wrong To Rely On Amanda Knox’s Family For Impartial and Accurate Information”) made by Edda Mellas, Amanda Knox’s mother, in an interview on Larry King Live and in other interviews. I invite readers to examine The Machine’s assertions and evaluate their accuracy. Please add citations where appropriate. I’ll get the ball rolling with my replies to numbers 2, 3, and 8, which are given below the three claims made at TJfM.

False claim 2. “He (Rudy Guede) all of a sudden had money that he didn’t have earlier in the day” Edda Mellas is plucking “facts” out thin air with this claim. No evidence was presented at any court hearing that showed that Rudy Guede suddenly had money that he didn’t have earlier in the day on 1 November 2007.

False claim 3. “There is no murder weapon.”
Judge Massei indicates in the sentencing report that Amanda Knox’s judges concluded that the double DNA knife, the larger of the two indicated by Meredith’s autopsy, is indeed the murder weapon. It is totally compatible with the deep puncture wound in Meredith’s neck, and according to a number of independent forensic experts, it contained Meredith’s DNA on the blade.
False claim 8. Rudy Guede’s DNA was in Meredith’s purse.
Edda Mellas’s claim that Rudy Guede’s DNA was in Meredith’s purse is completely untrue. According to the Micheli report, which was made available to the public in January 2008, Guede’s DNA was found on the zip of Meredith’s purse and not inside.

Responses
2. The Machine’s claims about court hearings may be true, but he or she needs to explain where Rudy Guede, who was jobless, obtained the money for a train ticket to Germany. Because the murder occurred at the end of the day on 1 November, Guede’s actions on 2 November and later are equally relevant to a discussion of whether or not he had more money.

3. The Machine does not list these other supposed experts here but does in claim 13. Dr. Stafanoni’s boss, Dr. Renato Biondo, cannot reasonably be called independent. Amanda’s DNA on the handle is strictly meaningless, since we cannot know when it was deposited. The hypothesis that her DNA was deposited when she cooked with the knife is perfectly reasonable. Meredith’s DNA is highly contested. This banal kitchen knife is not compatible with two of the three wounds, and the third one could have been made with any sharp knife, including the one that made the first two.

8. The Machine makes a distinction without a difference. The fact that Rudy Guede’s DNA was found on the zip of Meredith’s purse makes it parsimonious to assume he took Meredith’s money (see claim 2).

Update 1, 4 August 2010

False claim 13: “The DNA is so insignificant. It’s this tiny spot. It’s not blood.” (minute 2.16 above)
Three independent DNA experts - Dr. Patrizia Stefanoni, Dr. Renato Biondo, and Professor Francesca Torricelli - confirmed that Meredith’s DNA was definitely on the blade of the double DNA. The DNA charts themselves show a clear and unmistakable match. Edda Mellas doesn’t seem to understand that DNA evidence almost always involves only microscopic traces of DNA. Dr. Stefanoni testified at the trial that the DNA on the blade could indeed have come from Meredith’s blood.

Response
The Machine ignores that Meredith’s DNA was in the low copy number (LCN) range, demonstrating that he or she understands less about DNA profiling than Edda Mellas does. First, LCN samples should be tested at least twice, and only those alleles that show up in both runs are should be counted. Second, Stefanoni did not use standard LCN conditions in other ways, such as the number of cycles of the amplification step and working under lighting and air-handling conditions that minimize the possibility of DNA contamination. New methods are typically vetted in peer-reviewed journals before they are accepted. Third, the Machine also ignores the well known possibility of contamination, as well as the fact that contamination is a greater risk for samples in the LCN range.

There are some problems with The Machine’s assertion that there is a “clear and unmistakable match.” First, in locus D3S1358 there are two peaks, each with peak height of about 20 RFU, which are not seen in Meredith’s reference profile. They have 15 and 16 repeats, respectively, but Meredith’s profile has peaks at 14 and 18 repeats. Second, in the D21S11 locus, the knife profile has a peak at 30 repeats, but Meredith’s profile has peaks at 30 and 33.2 repeats. It is possible to explain the two extra and one missing peak as a consequence of the DNA being in the LCN range. Yet, this explanation only underscores the fact that Stefanoni should have used the services of a lab that has proper facilities and experience, instead of making up her own inferior method.

It is now well known that Stefanoni went ahead with the analysis, despite the fact that her instrument read “too low,” meaning that there was not enough DNA to continue. What is less well appreciated is the fact that Stefanoni treated this sample differently from other samples, where she discontinued the analysis under similar circumstances. The Machine ignores Stefanoni’s apparent inconsistency.

Dr. Stefanoni’s assertion that the DNA could have come from Meredith’s blood is extremely dubious. The knife tested negative for blood with tetramethylbenzidine (TMB), and Dr. Elizabeth Johnson and Professor Gregory Hampikian indicated that the test for blood is more sensitive than the test for DNA. In other words, if a bloody knife were cleaned of all traces of blood, all traces of DNA would also be removed. They and the cosigners of an open letter on the DNA evidence in this case publish regularly in the field of DNA forensics. The same cannot be said of Dr. Stefanoni.

Furthermore, The Machine ignores the fact that Stefanoni did not turn over the electronic data files or the machine logs. This failure to abide by the international standards of discovery of DNA evidence means that any claim about the quality of the results is suspect. The defense expert witnesses did not have all of the information that they would need to challenge Stefanoni’s dubious results.

Update 2, 4 August 2010, approximately 10:15 PM

“False claim 14: Amanda Knox and Raffaele Sollecito maintained the same story…And most devastating of all, Sollecito stopped providing Knox with an alibi on 5 November 2007.
Sollecito is STILL nearly three years later refusing to corroborate her alibi.”

The Machine’s claim about Raffaele is exactly false. Raffaele backed up Amanda at their hearing in front of Judge Matteini on 8 November 2007, discussed in Darkness Descending on p. 208.
“Judge Matteini said, ‘There are several points, Mr. Sollecito, that differ between your version of today and your version of events as related on the evening of 5 November just three days ago. Can you explain whether you were with Amanda Knox that evening or not?’
Now it was make-or-break time. Matteini had posed the million-dollar question. The one Mignini had been waiting for.
His pay-off was unexpected, effectively an explosive retraction of his initial confession.
Raffaele said, ‘I’m sorry I told you that crap about not being with Amanda. We were together that evening.’
…But now on the key point of the night in question, he was sticking to her like glue again. Backing her up… ‘I can confirm that I spent the night with Amanda Knox.’”

Murder in Italy, p. 198, summarized his appearance before Judge Matteini by noting that Raffaele got the times wrong, but the events right. “Then the judge asked the Italian student what he did remember, prompting a long, dull discussion about the broken pipe under the sink, which he had showed Amanda, discussing with her the probable cause of the leak, a perennial problem in that flat. He also remembered eating dinner with her, watching a movie, working on his computer, getting tired, and going to sleep. Yes of course they slept together. He just couldn’t remember what time they did each action, because he’d been stoned, in a holiday mood, and not punching a time clock.” Finally in his diary Raffaele recalls Amanda saying to him that if she had not been with him that night, she would also be dead.

It is often said that Raffaele did not support Amanda’s alibi of being with him the night of the murder in his appearance before the Supreme Court in the spring of 2008. It was actually Raffaele’s lawyers who appeared, and one of their jobs was to end Raffaele’s detention without charge by any reasonable legal argument. According to Perugia-Shock (25 April 2008) Raffaele’s lawyers invoked the concept of “erroneous assumption,” rather than “erroneous belief.” If they had said “erroneous belief”, it would mean that Amanda was not with him. But the “erroneous assumption” has to do with making an assumption, not so much with the thing being assumed, and then transferring evidence onto him as a result. His lawyers were saying that evidence that might place Amanda at the scene of the crime should not be used to justify holding Raffaele in custody. Raffaele’s lawyers might have meant that Raffaele obviously could not account for Amanda’s whereabouts after he fell asleep. Thus there is no justification for using his lawyers’ appearance before the Supreme Court as evidence that Raffaele claimed that Amanda was elsewhere.

To those who believe that Amanda Knox and Raffaele Sollecito are guilty, I issue a challenge.

2010-07-20T21:16:00.005-04:00

Part 20 in the Knox/Sollecito case

Francesco Maresco, lawyer for the Kercher family, said after the verdict last December, “We are teaching the whole world and the United States how to collect, analyse and evaluate scientific technical aspects of the case.”

I have previously discussed how the electronic data files are used by independent experts in criminal cases. Those arguments are especially compelling in the murder of Meredith Kercher, in which the amount of DNA in two of the most important pieces of DNA evidence fall near or into the low copy number (LCN) range. The profile from the bra clasp is also a mixture, and it is well known that the analysis of mixtures introduces subjectivity into the analysis. I have also previously given my reasons for believing that these critical files were never released to the defense teams. Since that time some additional information has become available that puts this question to rest.

Raffaele Sollecito’s appeal documents indicate that his defense expert Dr. Pascali requested the raw data in 2008 (presumably the electronic data files). This request was prior to the preliminary hearing, and the lawyers supported their request with a reference to article 415. They also requested the log files. The judge granted the defense teams the right to forensic information in the summer of 2009 that they had been denied until that time. However, the prosecutions did not fully comply with this order, according to a source close to the defense, and this was one of the things that precipitated the defense teams’ asking for a mistrial in September of 2009.

An open letter coauthored by Dr. Elizabeth Johnson and Professor Gregory Hampikian noted that the prosecution failed to release the electronic data files (.fsa files) to the defense. Since the time of the letter’s release on 11/19/09, some have assumed that these two DNA forensic scientists were unrelated to the case and therefore had no standing to ask for these files. This argument is false. An article written by Fiona Ness on 25 April 2010 indicates that Professor Hampikian is a consultant for Amanda Knox’s defense team. As such, he has every reason to request the operating procedures of the lab, as well as the electronic data files that produce the electropherograms.

“The importance of DNA evidence in a conviction is highlighted in one of Hampikian’s cases - that of US student Amanda Knox. Knox was convicted of the murder of British student Meredith Kercher after a high-profile trial in Italy in 2009. Knox’s conviction was partly based on a sample of her DNA discovered on a knife found in the house. However, Hampikian says he is appalled by the standard of DNA evidence used by the Italian courts to convict Knox in the case. ‘The amount of DNA present is far below the normal cut-off for many labs that I know of. A one off spurious piece of DNA evidence shouldn’t be treated as a gold standard profile from a high-profile source. The issue of this low-template DNA sample is really troubling me.’ Trying to obtain the evidence to have it retested, however, is proving difficult. ‘The discovery rules in Italy are different to what I’m used to. It’s fairly routine in the US that I send a request and get what I want. But in the Knox case I haven’t been able to get a copy of the standard operating procedures of the lab and without that, it’s hard to see if they even followed their own guidelines.’ Evidence, Hampikian says, is a matter of science, to be reviewed, not protected.” (emphasis added) An article in the Irish Times confirms that a professional relationship exists between Professor Hampikian and the Knox family.

The words of an anonymous forensic DNA expert unconnected with the murder of Meredith Kercher are apropos here. This individual said with reference to a different case, “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.” Keith Inman and Norah Rudin gave ten ways to improve forensic science. Number five was “Provide transparency. Secrecy and gamesmanship are inappropriate to the work of the forensic scientist. All laboratory notes, data, results, procedures, logs, and records should be open to controlled
and appropriate scrutiny.”

To those who believe Ms. Knox and Mr. Sollecito are guilty, I respectfully issue a challenge: Join me in calling for the release of all of the forensic information that the defense has been denied until now. Some among you have argued that the Italian authorities should not release any more information than that demanded by Italian law. However, it is conceivable that Italian law is not yet settled on the question of whether or not to release the electronic data files. If it is not, why should the precedent be against full disclosure rather than in support of full disclosure? If the case against the defendants is as strong as you say it is, you have nothing to fear. On the contrary, your certainty would be stronger if the release and examination of these files produced nothing.

To the Italian authorities I respectfully issue a related challenge: Make good on Mr. Maresca’s claim. Show the world that forensic evidence is to be shared with the defense. At that point the analysis will be complete. Provide the electronic data files (.fsa files), and the instrument log files, and include the contamination log files if they exist. Then and only then will you indeed be showing the world the right way to treat forensic evidence.

DNA transfer in Strangulation

2010-07-13T22:03:00.008-04:00

Part XIX in the Knox/Sollecito case

Update 1, 22 August 2010

I communicated with an anonymous forensic nurse about their domestic violence program. If an alleged victim complained of an attempted strangulation, complained of a partner’s grabbing their arm, or showed bruising or redness, they have been swabbing that area for DNA, for two years. Positive results in at least one case helped to convict someone. This information confirms the reasonableness of swabbing Meredith’s body in appropriate places, although the bruise on the nape of Meredith’s neck may have been the result of her being thrown against the wall (as some have theorized). We do not know whether swabbing the bruised areas was done or not.
____________________________

PM Guiliano Mignini’s reconstruction of the murder of Meredith Kercher was shown to the jury in the form of an animated video. In his speculation Amanda Knox grabbed Meredith Kercher by the throat and slammed her against a wall. The video superimposed actual shots of Meredith’s bruises with Amanda’s animated hand to imply that Amanda’s action produced the bruises. Later, Rudy Guede and Raffaele Sollecito held Meredith’s arms back, and Amanda stabs her (Barbie Nadeau, Angel Face, p. 160). In forensics professor Carlo Torre’s reconstruction of the crime, the single assailant grabbed Meredith by the throat and stabbed her. The area under Meredith’s chin and her nape were bruised; the former bruising was the result of the knife and the latter when the assailant put Meredith down.

Although Mignini’s theory of the crime suggests a much longer amount of contact between the assailants and victim than does Torre’s, both imply contact. None of Amanda Knox’s DNA was found in Meredith’s bedroom or on her body. Raffaele Sollecito’s DNA was found on a bra clasp (although the defense contests this piece of evidence) but not the bra itself. Rudy Guede’s DNA was found in several places, including on the sleeve of Meredith’s sweatshirt. Let us examine some forensic DNA studies to see if they shed any light on this tragedy.

The study by Wiegand and Kleiber gives a case study in which DNA evidence was collected 48 hours after a strangulation. They wrote, “Strangulation marks were clearly visible on the neck of the victim. Epithelial cells could be removed from the neck of the victim using separate cotton swabs for the left and the right side of the neck. Only the swab from the right side could be typed and included the pattern of the suspect (Fig. 3), a result which corresponded to the autopsy findings (the right neck side showed a higher intensity of bleeding in the muscles than the left side indicating a more intensive pressure against the right side). Altogether clear results could be obtained using four STRs (TH01, VWA, FGA, CD4) demonstrating the high utility and sensitivity of the method described.” These authors also conducted simulated strangulations, and they reported a success rate of better than 70%.

The simulated strangulation study in 2002 by Rutty used both SGMplus and LCN amplification. The simulated strangulation experiment was done with periods between the force and the sampling were 1, 5, 10, 15, 30, and 60 min, 2, 3, 4, 5, 6, 7, 8, 24, and 48 h and 3, 4, 5 and 10 days. When the author used SGMplus, he observed a full profile of the offender 7 out of 29 times, and always in the presence of the victim’s profile. When the author used LCN all 17 experiments yielded offender profiles, with the majority being partial profiles. Dr. Rutty wrote, “Of the test neck swabs, 19 yielded positive amplification results using SGMplus, 12 showed a victim-only profile and 7 a victim and offender profile with a full offender profile detectable up to 6 h after contact. When LCN was used (17 tests) all showed the offender to be present for all time periods i.e. up to 10 days. In the majority of cases it was a partial offender profile with the majority of the amplification result being a full victim profile.”

Dr. Rutty stated that “When considering the apparent time periods of DNA survival, passive transfer of the offender’s DNA onto the victim’s neck could also explain the presence of offender DNA several days after contact.” This study did not break down the results by time periods between simulated strangulation and DNA collection; therefore, it is difficult to draw firm conclusions based solely on the data presented.

A 2008 study by Graham and Rutty reexamined the question of DNA transfer to and from strangulation victims with an emphasis on innocent DNA transfers that might deposit DNA on the neck of a victim. In 24% of samples collected showed nonself DNA on the simulated victim from third party sources. The authors believe that such DNA transfers might confuse an investigation.

Finally, it might be helpful to return to the subject of primary and secondary DNA deposition. The study by Lowe and coworkers in 2002 looked at DNA transfer from a good DNA shedder to a poor DNA shedder to an object. By definition transfer was secondary from the good shedder, and transfer was primary from the poor shedder. When mixtures were observed, secondary transfer from the good shedder provided the major component, not primary transfer from the poor shedder. This study illustrates the dictum that one generally cannot infer the mechanism of how the DNA was deposited from the DNA itself. Along with the study by Graham and Rutty, this work suggests caution in the interpretation of nonself DNA on the body of the victim of strangulation. A similar caution should also be applied in the interpretation of DNA on the bra clasp.

In addition to the case study discussed by Wiegand and Kleiber, there are a small number of news reports of strangulations that mention DNA. One is from greater Detroit, and another is from Chicago. However, these articles do not specify the place on the body that was tested for DNA. In addition to the possibility that DNA was collected from the neck, it is possible that the victim’s fingernails contained the perpetrator’s skin cells or vice versa.

There are no reports that ILE found anyone’s DNA on Meredith’s bare wrists or her neck, and it is unclear whether or not the forensic police swabbed for DNA in these areas. It is also unclear whether some areas on the neck would have been free enough of Meredith’s blood to allow swabbing for the assailant’s DNA. Nevertheless it is difficult to see why the forensic police should not have swabbed the nape of Meredith’s neck or her wrists. If they did and found nothing, it would be strongly exculpatory, although it might fall short of proof of innocence due to uncertainties over collecting enough DNA or collecting it quickly enough after the murder. If the forensic police failed to swab these areas, it would suggest that they did not do as thorough a job as one would wish.

Bibliography
P. Wiegand and M. Kleiber, “DNA typing of epithelial cells after strangulation,” International Journal of Legal Medicine (1997) 110 :181–183. abstract

G. N. Rutty, “An investigation into the transference and survivability
of human DNA following simulated manual strangulation
with consideration of the problem of third party contamination,” International Journal of Legal Medicine (2002) 116 :170–173.
abstract

A. Lowe, C. Murray, J. Whitaker, G. Tully, P. Gill, “The propensity of individuals to deposit DNA and secondary transfer of low level DNA from individuals to inert surfaces.” Forensic Science International (2002) 129(1):25-34. abstract

E. A. M. Graham and G.N. Rutty, “Investigation into ‘normal’ background DNA on adult necks: implications for DNA profiling of manual strangulation victims.” Journal of Forensic Science, (2008) 53(5):1074-82. abstract

Raffaele Sollecito's Appeal

2010-06-21T19:35:00.009-04:00

Part XVIII in the Knox/Sollecito case

Update, 7/12/10

Here is a better translation of a portion of Sollecito’s appeal dealing with the bra clasp, provided by an anonymous translator:

“But there is more. The lack of full discovery was also found during the course of the trial:
- on July 18 2009, during cross-examination of the technical consultant of Raffaele Sollecito’s defence, Prof. Adriano Tagliabracci, there was an astonishing coup de theatre, in which the prosecution formulated a question which generated the suspicion that the Public Minister was in possession of further laboratory data never made available to the defence. In particular, the data relative to the quantity of the extract used for genetic analysis of the biological material found on the bra clasp of the victim;
- confronted with the reaction of the defence, the office of the Public Minister had to admit that there existed documents compiled by the scientific police never deposited at the conclusion of the investigations (contravening in this way the provision of Article 415 bis c.p.p.), nor sent to the Gup with the request for trial (in violation of Article 416, paragraph 2, c.p.p.).
In other words, the office of the PM denied a complete discovery of the documents of the investigation, extending this breach in the rights of the defence into the trial!”

This passage indicates that the prosecution failed to provide the defense with information relating to the single most important piece of evidence against Raffaele Sollecito all through the pre-trial and well into the trial phase. What is unclear from the appeal document alone is whether or not all information was ultimately released. However, other documents indicate that the prosecution never released all of the information that the defense teams sought.
___________________________________________________

The following is Google-translated from Raffaele's appeal document (pp. 51-57) with some minor edits. Although it is hard to decipher the meaning in places, it gives a picture of the defense continually asking for information on the DNA testing all throughout the preliminary hearing and trial, and the prosecution continually refusing. I have previously written about the importance of the electronic data files to a proper defense and about the near universality of this disclosure. I am eager to hear the prosecution’s explanation of how their refusal to hand over log files and electronic data files can be anything other than a trampling upon the right of discovery:

“And there is no doubt that, in terms of 'prosecution, failure to discovery on one of the main aspects of the process has been a considerable advantage over the defense, since the case involved Raffaele Sollecito is building right on genetic testing. In fact, it is useful to make a historical reconstruction of the case at hand:
- Following the conclusion of preliminary investigations, the defense could review the technical report of forensic genetic investigations in the signature of Dr. Patrizia Stefanoni, to which were attached tables who reported only the number of alleles, without which they would specify any other information or scientific data (for clarity, we define each variant allele of a gene, the genotype of an individual gene has a relatively Kit alleles he is in possession);
- Given the extreme importance of this for proof on indication of Prof. Pascali expert defense Raffaele Reminder, on June 24, 2008 - pending the period of 20 days under Article. 415 bis -, was made an initial request to Prosecutor acquisition diagrams in electropherograms whereby the forensic results came in content Technical report on forensic genetics. In particular, this request is have specified the absolute necessity (in order of presentation defensive pleadings and petitions under Article. 415 bis cpp) to have the aforementioned documents available to the consultant of the could examine it in detail;
- However, against all evidence, the prosecutor dismissed the request was deemed inadmissible 'because the option in all.art.415 cpp a cover secured and only those acts ';
- To deal with a similar unjust refusal, the defense made on July 3, 2008, a further instance in which it sought to 'acquire forensic laboratories of the numerical values and RFU peaks on all findings, or alternatively to obtain police Scientific CDROM containing the raw data and peak RFU. It was asked, Moreover, in case it was not possible to obtain copies of these data, that the Prof. Pascali was allowed to go to the police service science for a spot inspection of the data and make it directly computerized copy;
- Even that request, however, was inexplicably rejected on 11 July 2008 with the anodyne statement that 'on the charts of Forensic there are already bars with generic value on fluorescence peaks.
The defense then returned to a preliminary hearing with a serious cognitive gap, due to lack of awareness of scientific data used by the police in their scientific investigations. As we shall see, this story had a further follow:
- Preliminary hearing of 16 September 2008, the defense reiterated request to acquire numerical values RFU and peaks at all findings or, alternatively, to acquire the CD-ROM containing the raw data RFU and peaks. The request filed at that meeting was based upon both the incompleteness detected in the diagrams attached to the report, and by the repeated requests made to the office of the C>P> to obtain the missing data;
- After this request, the Gup could not help but detect need 'for purposes of deciding' to understand 'fully (...) as procedure has been adopted for the analysis in question, and whether there further elaborations that constitute the necessary support conclusions reached. 'Consequently, the Gup has ordered the hearing in heard of Dr. Stefanoni calling 'to accompany their testimony with computer media containing data requested by the defense. "The same judge in that case was aware the extreme importance of data capture whereas the investigations living would receive 'the most important elements all.impianto accusatory;
- On September 25, 2008 in observance of the provision of Gup is was deposited by association. Zugarini on behalf of Dr. Stefanoni, the CD-Rom containing the requested data. In this regard like to highlight as the immediate acceptance of the instance in question proves unequivocally from the outset the importance of having the data available full scientific;
- Hearing on September 27, 2008, was then represented to the Gup need to obtain additional documentation because incomplete data, therefore, was asked to Court to acquire the service files (log files);
- However, the Judge, after seeking an opinion to Dr. Stefanoni has also rejected the application based on an uncritical adherence to its comments, coming to claim that "not be needed information contained in the logs (data nell.esperienza forensic are never identified, resulting standards approved by the parameters internationally and which appear to be in use in all Laboratories engaged in Forensic Genetics).
Such an established procedure is not, of course, acceptable under no point of view, since the unconditional adherence to observations of Dr. Stefanoni, has led to support the contention accusatory, without the technical-scientific comparison of an expert third and impartial.
And indeed, if it had consulted a person not bound by any constraint on the charge (ie a neutral), the parties would certainly have benefitted. And 'quite clear that to ask to review its person (Dr Stefanoni) which produced that result is, in fact, nonsense: can not say, claim of self-discipline science by the same technician who testified that result. Any specialist will of course be pushed, albeit inadvertently, to defend the validity of their work, even in front of a simple request for clarification, and justify - after all, understandably, by his point of view - that all data provided are sufficient.

Was evidence showed the need to provide all documentation scientific defense.
It 'important to note that log files are much scientific data relevant, if not indispensable, especially in situations (such as the case in point) where the peak height must be assessed together with other parameters (such as area) is also higher to determine the plausibility or, conversely, the unlikelihood attribution to a person's DNA. So it is true that during the preliminary hearing in court, the Dr. Stefanoni - at the request of the consultant that the Prosecution asked if it was important given the "peak area" – said "Normally not. "However, what is more surprising is that the very Dr. Stefanoni candidly admitted that it had no other experiences on (p. 68 transcription.'s preliminary hearing Oct. 4, 2009). The opinion of Dr. Stefanoni, in fact, emerged in all its fragility when the consultant has made the defense Reminder noted a recommendation of the International Society of Genetic Lawyers, which states that the method used to interpret traces of mixed DNA and consider l.area l.altezza of peaks "(p. 99 of those transcripts.)
The GUP at this point, he invited Dr. Stefanoni to be received by October 8, 'the data relating to the calculation of peak areas related to the finding 165 / B indicated by prof. Pascali in the third column, in his name, all.allegato referred to the report filed, and diagram on the second run on the sample elettroferografica 36B.
The epilogue of this long run-up occurred on October 8, 2008 with the filing by Dr. Stefanoni the CD-ROM containing the data dell.amplificato electrophoresis sample DNA called 165 / B (finding piece of cloth with hooks), and the CD-Rom containing: Sample data info for the two races dell.amplificato electrophoretic sample of DNA known as 36 / B (Finding knife) electropherograms of the second electrophoresis.
As can be seen from the picture just outlined, the defense did not have provision, at the conclusion of preliminary investigations, all acts of investigation as required by law, so much so that this uncertainty lasted at least for the preliminary hearing stage (and beyond, as you say).
For example, consider the simple analysis of the peak - technical data that was provided to the defense until after the hearing at the hearing Preliminary Dr. Stefanoni, damaging irreparably the rights of defense -revealed that the amount of DNA used for analysis was quite modest, which led the consultant to the defense clarified, that the interpretation given to the forensic graphics has minimally complied with the guidelines laid down by the International Society of Forensic Genetics.
But there is more. The lack of full discovery was also found in during the process:
- On July 18, 2009, during cross-examination technical consultant Defense Raffaele Sollecito, Professor Adriano Tagliabracci, there was an astonishing coup de théâtre, as the accusation made questions that have created the suspicion that the prosecutor had hold additional laboratory data ever made available to parties. It was, in particular, data on the amount of extract used for genetic analysis of biological material found on the hook of the bra of the victim;
- In front of the defense reaction, the Office of Public Prosecutor had to admit that there are acts performed by forensic ever deposited at the conclusion of the investigation (in contravention Thus the provision of art. 415 bis cpp) or sent to Gup with the request of trial (in violation of Article. 416, paragraph 2, cpp).
In other words, the Office of the PM or denied full discovery of documents investigation, pushing this lesion of the right of defense to the debate! We will now give an account of evaluations of the Court of Assizes of Perugia. The sentence I can refer about the motivations of the order of rejection "of All.audience 14/09/2009 defenses of the defendants objected l.avv n the interference with the right defense, arguing in this regard, which were verified the void. After hearing the other party seeking to disregard l.exception, this Court issued l.decree, which read out with which l.exception of nullity was rejected and was available to proceed further "(p.7. above).
Passing the order of 14 September 2009, the Assize Court noted as follows: 'respect of invalidity l.exception advanced and illustrated memory today filed for violation of the right of defense question exception is not admissible, l.activity sampling and comparison of traces biological object activity.exception the nature of prior technical investigation covered with the possibility dall.article 360 for parties to participate in and comment in this context is not apparent that there has been no lesion of the right of defense, for the nullity that would assessed in a case of a 415 dell.article knows nzione not provided by any specific provision or by a 415 Criminal Procedure Code that principle of mandatory nature of the void during preliminary dell.audience compare 1/10/2008 GUP measure included in documents filed today in support the plea of nullity that aspect has been addressed and its exception has not been repeated in terms of which all.article Code 491 Nell.audience of Criminal Procedure also before this Court on 18.7.2009 issue was not raised in terms of the void under the compare the transcripts of the hearing on 18.7.2009, with particular Refer to pages 102 et seq and 114 et seq therefore logical to conclude that l.aspect in all.exception now advances to integrate a nullity ta question But to sanction by the Supreme Court ruled on the matter for example compare Cassation Judgement second section 29573 of 2006 and Section Supreme number 21593 2009 its fifth exception was belatedly raised. As for the broken and also being the subject of advanced today than that penalty is justified in the presence of a omitted on filing all.entire investigations in this case l.omission h a covered part of the supporting documentation'”

DNA contamination and DNA cold hits

2010-06-16T22:01:00.008-04:00

Part XVII in the Knox/Sollecito case

This post returns to the problem of forensic DNA contamination. It also addresses the problem of partial profiles and adventitious matches, especially with respect to cold cases. North Carolinians might want to take special note of the John Puckett and Raymond Easton cases, inasmuch as North Carolina may join other states in demanding DNA samples upon arrest. My prediction is that as the size of a DNA database grows, we will see a greater number of cold case convictions that turn out to be erroneous.

Murder of Jane Mixer
We have previously encountered the conviction of Gary Leiterman of the murder of Jane Mixer. The presence of both Mr. Leiterman’s DNA and that of John Ruelas. The prosecution was unable to come up with a reasonable explanation for Mr. Ruelas’ DNA; he was four years old at the time and lived in another city.

Dr. Theodore Kessis reexamined the DNA forensics of this case:
“Review of the electropherograms associated with this negative control sample (NEG 041902) reveals that it was contaminated, a fact that cannot be disputed since Dr. Milligan himself labeled it with a note indicating as much (Appendix 8 - Electropherogram sample NEG 041902).
Remarkably, Dr. Milligan stated in his 7/15/02 testimony that no contamination events had occurred during the course of his testing and that if any had, he would have documented them in his reports (pg. 141-21 and 142-4). Equally difficult to rectify here is the fact that when asked if he had ever committed an error, Dr. Milligan's replied he could never recall making one. (pg. 162, lines 1-5)”

While agreeing with others that most contamination events happen when two samples are handled closely in space and time, Dr. Kessis also offered a caution, “It must be noted however that contamination errors have been documented where no direct processing link between sample and contaminant have been established, raising the specter that a source of contamination can linger in a laboratory for some time.”

Dr. Kessis found another deficiency: “As previously mentioned, Corrective Action files and Error logs form an important part of a laboratory's quality control and assurance programs by centralizing the documentation of errors within the laboratory. Mandated by the DAB Standards (Appendix 2, section 14.1.1), such data allows laboratory management to quickly and efficiently identify and address systematic problems that affect the reliability of testing results.”

“Given the thousands of samples, hundreds of cases, and number of people handling casework within this laboratory, the lack of a centralize system to track errors and discrepancy indicates that the lab had no mechanism in place to identify and deal with systematic problems such as contamination events.”

There are several take-home messages for students of the Knox/Sollecito case here. Contamination by more than one individual’s DNA is possible. The laboratories in question will sometimes claim to be error-free, as did the Rome lab. In such an instance it would be helpful to check the laboratory’s corrective action files, which are more likely to be accurate than someone’s memory. Whether the Rome lab has such files is unclear. Finally, when DNA results force one to an absurd conclusion (as with the kitchen knife), contamination or misinterpretation should be suspected.

The case of Gregory Turner
Gregory Turner was indicted and jailed for a murder when the DNA from a murdered woman in Newfoundland was found on his wedding ring. The ring also contained DNA from one other contributor, thought to be his accomplice. However, the lawyer sought out the names of the technicians from the lab and determined that the technician working on his ring also worked on the victim’s fingernails. Moreover, the DNA from the second contributor to the ring turned out to be the profile of the technician herself. After many months, Mr. Turner was released from jail. This particular case of DNA contamination is an example of where both primary and secondary transfer of DNA occurred. As did the Mixer case, it shows that contamination can transfer the DNA from more than one person onto an item of evidence. This is worth bearing in mind given the multiple DNA contributors to the bra clasp in the Knox/Sollecito case.

Profile N
As was true in the Jaidyn Leskie case, the victim of one crime can become a suspect in other crimes on the basis of contaminated DNA evidence. Sometimes it takes a major foul-up to prod a laboratory into corrective action. In New Zealand, the Wellington police were investigating two murders, dubbed Rex and Pad, as well as N, the victim of an assault.

Michael Strutt reported, “One caught up in the testing was a mild mannered Christchurch man who had been assaulted outside his local, the Hagley Arms Hotel, on 23 April 1998. Police had taken blood in order to eliminate his DNA from samples taken from the scene of the assault and sent it to ESR for testing. The result of this test came to be dubbed 'Profile N' by the inquiries which were to follow… The Christchurch assault victim was subjected to 'extensive police inquiries' for more than three months and his financial records were seized. This established what he had claimed all along, that he had not left Christchurch around the time of the murders. In fact he hardly left Christchurch at all… Although they never discovered exactly how the mistakes had happened they did determine that the 'Rex' and 'Pad' samples had been accidentally contaminated with DNA from Profile N at an early stage of processing at ESR's Mt Albert laboratories. Extracts from them sent to other laboratories for testing also returned Profile N. Numerous recommendations for improving oversight, record keeping and even laboratory ventilation were made.”

“During the inquiry ESR [Environmental Science & Research Ltd] was asked to check the results of all testing done in July 1998 for any further instances of Profile N. Although they initially reported that none were found, later retests showed a partial profile consistent with N in another sample from 'Pad'. They also revealed 25 other 'unexplained' profiles in 14 of the 36 samples tested that month.”

A group investigating these cases asked a manager of the forensic unit of the ESR lab to comment, “The Wellington murders you refer to were not DNA failures. The problem was picked up and investigated. Five separate investigations failed to find scientific proof for the cause of the anomalies. No direct evidence of either accidental or deliberate contamination has come to light. Existing facilities and protocols were shown to meet independent quality audit requirements. The Ministerial Inquiry recognising the points above concluded that on the balance of probabilities the apparently anomalous results could be ascribed to accidental contamination of DNA extracts within the ESR laboratory. They made a number of recommendations which ESR has either implemented or is planning to implement. This sits comfortably with our continuous improvement management focus.”

The fact that the lab in question met the audit requirements is evidence that simply following accepted protocols does not guarantee that contamination will never happen. The lack of the determination of an exact mechanism of contamination is consistent with Dr. Kessis’s caution in the Mixer case above. People who argue that Amanda Knox and Raffaele Sollecito are guilty sometimes demand a mechanism of contamination; unfortunately, this cannot always be determined.

The first false cold hit case in the UK
Michael Strutt wrote, “A man [Raymond Easton] with advanced Parkinsons disease who could not drive an automobile or dress himself unaided was linked to a burglary which had occurred 200 miles from his home. In spite of protestations of innocence and alibi evidence police arrested him because the DNA profiles matched and 'so it had to be him'. It was several months before10-point DNA tests were done on samples from the suspect and the crime scene. The results exonerated him.

He gained his freedom and a brief note from the prosecutor saying that charges were being dropped because ‘there was not enough evidence to provide a realistic chance of conviction’. He still awaits an official apology. Or even an admission of error.”

The reason why Mr. Easton was initially suspected was an adventitious match, as opposed to contamination. This case shows that adventitious matches can happen especially for partial profiles. The first profile had only six loci, but the second profile had 10 loci. As with DNA contamination, when a cold hit match leads to an absurd result, the DNA evidence needs to be reconsidered.

The Sylvester murder, a cold hit combined with a partial profile
According to Dr. Donald Riley, “A partial profile is one in which not all of the loci targeted show up in the sample. For example, if 13 loci were targeted, and only 9 could be reported, that would be termed, a partial profile…Over-interpretation of partial profiles can probably lead to serious mistakes. Such mistakes could include false inclusions and false exclusions, alike.” Let us examine the rape and murder of a young nurse which ultimately yielded a partial profile of the assailant many years later.

Diana Sylvester was raped and murdered in San Francisco in 1972. After evidence in this case was subjected to forensic DNA analysis, a trawl through California’s DNA database identified a suspect over thirty years later, a cold hit. Of the investigations treated here, the Sylvester murder is the one in which the particulars of the investigation (a cold hit) and the differences in expert opinion on the correct statistical calculation have the least relevance to the Knox/Sollecito case. However, several more subtle points in common can be found.

In this case the suspect was identified on the basis of his DNA matching a partial profile from evidence taken from the victim. This suspect, John Puckett was in the DNA database because of his convictions for rape about five years after Ms. Sylvester was raped and murdered. However, the MO of the crime was consistent with another rapist, Robert Baker, who matched the physical description of the assailant better than Mr. Puckett and who was deceased by the time the case was reopened. The defense was barred from introducing information about Mr. Baker, the original suspect. Over the objections of the defense, the prosecution was allowed to bring in Mr. Puckett’s past convictions. How strong was the DNA evidence against Mr. Puckett?

The main issue in this case is a disagreement among experts over the correct statistical calculation to use in cold hit cases. Another key element in this case is that it made use of a partial, not full, DNA profile. In the United States a full DNA profile has thirteen separate markers (loci). A profile must have seven markers for it to be searched in California’s database. However, only 5 and a half markers were clearly found in the Sylvester murder. The jury was told that the chances of a random person’s matching the DNA found at the crime scene were 1.1 million to one. Yet when the odds were calculated with a different set of statistical assumptions the odds were only one in three, a statistic that the jury was barred from hearing. This is why the odds were only 1.1 million to one, and not substantially higher. However, when one uses a model that takes into account that there were 338,000 profiles in the database, one arrives at the 1-in-3 odds. The question of which model is better is a difficult one, yet it is odd that California courts have taken it upon themselves to decide which model is more appropriate. And the difference between one in 1.1 million and 1 in 3 is huge. It would have probably been enough to move at least one juror from guilty to not guilty beyond a reasonable doubt.

A second issue concerns the number of loci in profile itself. The peaks that were needed to flesh out the profile from 5.5 loci to 8 loci fell below the laboratory’s intensity threshold, but forensic technician Bonnie Cheng wished to interpret them anyway. DNA profiles contain artifact peaks, some of which are known as blobs and others as stutters. Deciding which peaks are true and which are artifacts may contain an element of subjectivity. The prosecution’s outside DNA witness, Dr. Chakraborty used Mr. Puckett’s full profile to interpret the partial profile, a practice that is open to serious question.

A third issue is that the sample was mixed, containing DNA markers from both the victim and assailant. The question of which markers belong to which profiles naturally arises. DNA forensic expert Peter Gill said, “If you show 10 colleagues a mixture, you will probably end up with 10 different answers.” With reference to this case Dan Krane made an important point, “There is a public perception that DNA profiles are black and white. The reality is that easily in half of all cases—namely, those where the samples are mixed or degraded—there is the potential for subjectivity.”

A fourth issue is that the lab used up so much of the sample that the defense could not do its own testing. This is a debatable practice in a DNA case; some guidelines indicate that this should not be done unless the defense agrees in advance.

One lesson for students of the Knox/Sollecito case is that the judge’s decisions might control the outcome of a case. The judge’s decision to exclude one statistical model in the Puckett case can be compared with Judge Massei’s decision not to order an independent review of the forensics of the Knox/Sollecito case. A second message is that DNA profiling is not immune to cognitive bias. In both the Puckett case and the Knox/Sollecito case, the forensic technicians lowered the bar with respect to the intensity threshold. A third fact to bear in mind is that Meredith’s DNA profile from the kitchen knife was a partial profile. However, how many loci should be counted for this piece of evidence depends entirely upon one’s choice of intensity threshold. Fourth, the bra clasp is a mixed sample, and interpreting mixtures contains an element of subjectivity.

Some possible reforms
Australian criminal defense barrister Peter Faris wrote in response to the Benjamin Forbes case, “Faced with a figure of 10 billion, a jury will always convict. The only way that it can be defended is for the defence to demonstrate a doubt arising from contamination, forensic or statistical procedures. In the real world, defence lawyers and legal aid bodies are just not equipped to investigate these matters. Many cases rely (to a greater or lesser extent) on DNA evidence. In some of them, such as Forbes, there is simply no other evidence. Consequently, if there is contamination at the scene, in police or laboratory storage or in the laboratory itself, the defence can never prove it.

Mr. Faris proposed some reforms:
“DNA should never be admitted unless there is corroboration: that is, there must be some other evidence of the identity of the offender. As for the rest of DNA cases, the solution is to put the burden on the prosecution. This can be done by amending the various Evidence Acts around the country to make DNA evidence inadmissible unless the trial judge is first satisfied, by the prosecution, that it should be admitted. The prosecution should apply to the trial judge, in a preliminary hearing, to admit DNA evidence. They must satisfy the judge, on the balance of probabilities, of various matters. The important matters are that the burden of admissibility is upon the crown. No DNA evidence could be led unless this procedure has been completed.
Conditions could be imposed in the legislation to protect the accused. For example, the prosecution would be required to produce evidence to disprove contamination, whether at the scene or in the laboratory. Strict proof of continuity of exhibits would be required. The prosecution would have to call evidence of the current international statistical procedures. Proof by the defence of international articles and learned writings could be relaxed.”

Final Thoughts
We have examined the problems with clerical errors, contamination, statistical manipulation, and outright fraud in this and preceding posts. It must also be borne in mind that the presence of DNA on an object rarely provides information on the time or means (primary, secondary, etc.) of its deposition. Paradoxically, DNA profiling is the branch of forensics with the firmest grounding in science. Much evidence exists to the effect that it is held in particularly high esteem by juries (a possible subject for a future post).

Taking all of these issues into account, I would not convict someone in a case where the sole piece of evidence comes from DNA forensics, but I would give it considerable weight, provided that the data were obtained legitimately and presented to the court in a transparent manner that respected the discovery rights of the defense. The worthy question of whether or not states should demand DNA samples upon felony arrest is outside the scope of this post.

How does the Patricia Stallings case shed light on the murder of Meredith Kercher?

2010-06-02T22:53:00.009-04:00

Part XVI in the Knox/Sollecito case

Patricia Stallings was convicted, then exonerated of poisoning her infant son Ryan with ethylene glycol, the major component of antifreeze. When Ryan was unable to keep food down, Mrs. Stallings took Ryan to Cardinal Glennon Children’s hospital accidentally, which happened to be associated with a toxicology unit. Ryan had metabolic acidosis (the pH of his blood was too low) and the laboratory associated with St. Louis University reported 180 milligrams per liter of ethylene glycol.

Ryan was put into foster care, but Mr. and Mrs. Stallings were allowed weekly visits. Four days after one such unsupervised visit, during which Mrs. Stallings gave Ryan a bottle, Ryan became ill again, having metabolic acidosis and died three days later. The same lab reported finding 911 milligrams per liter of ethylene glycol in Ryan’s serum and also in his baby bottle, which had been put into a dishwashing machine.

What are the odds of the tests being wrong?
There were three separate determinations of ethylene glycol, the original serum, the serum after the second feeding, and the bottle itself. In addition, one or both of the serum samples was also retested by a commercial lab. How could this be just chance? The prosecutor told the jury not to worry about motive, but just to concentrate on the fact that there was no rational explanation for these results except deliberate poisoning. He implied in so many words how unlikely it was for the labs to be wrong.

An alternative explanation begins to emerge
Patricia Stallings was arrested after a half-empty bottle of antifreeze was found in the couple’s basement. Mrs. Stallings was pregnant with her second son at the time of her arrest; her son David was immediately placed in foster care. David began to exhibit the same symptoms as Ryan, but he was taken to a children’s hospital. The hospital diagnosed David with a genetic disease known as methylmalonic acidemia (MMA)*. In this disease, one enzyme in a particular biological pathway is defective, causing a metabolic traffic jam, in which other compounds build up in the bloodstream. Although the odds of any one infant having this disease are about 1 in 48,000, David’s diagnosis meant that there was a one in four chance that Ryan had the disease as well. This fact was not allowed to be presented at her trial however, possibly because the judge and the defense attorney misunderstood each other with respect to what the defense attorney needed to do in order to bring the issue up.

Professor of biochemistry William Sly was one of the citizen-scientists who became involved in the case. Molecular geneticist Piero Rinaldo also reexamined the evidence, with some surprising results. James Shoemaker was involved in gathering evidence prior to the trial and subsequently. Both William Sly and Robert Ritter, Mrs. Stallings’ second attorney, learned of the case from the television show "Unsolved Mysteries.”

How could the analyses of ethylene glycol have been done better?
The gas chromatography (GC) technique measures how much time it takes for substances to pass through a column of stationary liquid (a waxlike substance) over which inert gas flows. This period is the retention time of a substance, and this length of time depends on its chemical properties. Two compounds may have the same retention time but usually do not.

The first analysis of ethylene glycol showed that the unknown compound in Ryan’s serum had a retention time within 30 seconds of a standard of ethylene glycol. A difference of 30 seconds is larger than is typically seen for an identical compound run twice, but let us assume generously that 30 seconds is within experimental error between one GC run and the next. The investigators should not have concluded that they had identified ethylene glycol even under this assumption, rather they should have performed additional tests.

One way to distinguish between two compounds that have identical or almost identical retention times is to run each compound through a mass spectrometer as it emerges from the end of the column. The mass spectrometer measures how heavy a compound is and in some cases how heavy the fragments of the compound are when the compound disintegrates. The combined technique gas chromatography-mass spectrometry (GC/MS) is usually very discriminating between one compound and the next, but it was just coming into widespread use about the time of the Stallings case in 1989.

A second way to distinguish two compounds is to run the gas chromatography experiment three times with three chemically distinct stationary phases. If the retention times of the two compounds, the unknown and the standard, are the same in all three trials, then the two compounds are probably identical. A third way is to spike a portion of the sample with the unknown compound with the reference. This eliminates the factors that cause run-to-run variation in retention times. The labs in question apparently did not do any of these three additional tests.

Shoemaker, Sly, and their coworkers examined a stored sample of Ryan’s blood using gas chromatography/mass spectrometry and showed that the substance believed to be ethylene glycol was actually propionic acid, one of the substances that would be expected to be elevated if Ryan had the same genetic disorder as his brother David. They also spiked a sample of Ryan’s blood with ethylene glycol and showed that it did not have the same retention time as the unknown compound, now identified as propionic acid.

The analysis of Ryan’s blood after the unsupervised visit suggested a very high concentration of ethylene glycol. Yet ethylene glycol is highly water-soluble and clears the body with a half-life of 3.0 hours. The half-life is the time it takes for the concentration of a substance to go from some value x to x/2. Therefore, Ryan would have had to consume 300 liters of ethylene glycol during his unsupervised visit to account for his blood plasma concentration four days later, an absurd volume.

Dr. Rinaldo found evidence of methylmalonic acid in Ryan’s serum. Along with propionic acid, methylmalonic acid would be expected to be in elevated concentrations in a person suffering from MMA. He also reexamined the GC data from the two labs. He found that the commercial lab saw an unknown compound in Ryan’s serum and merely assumed it was ethylene glycol without even running a standard.

He was unable to find evidence of ethylene glycol in the tests that were run on the bottle, but the bottle itself had gone missing. The positive result for ethylene glycol on the baby bottle should have raised a red flag on its own. Ethylene glycol in the bottle would have been washed and rinsed away in the dishwasher. Drs. Shoemaker and Sly believed that the small amounts of ethylene glycol found in some of the samples were due to contamination.

Cognitive bias
Once some of these facts emerged, D.A. McElroy joined with Mrs. Stallings’ new lawyer in a motion of ineffective counsel. First Mrs. Stallings was granted a new trial, and later the charges were dropped.

The first analysis to show ethylene glycol was done in a toxicology laboratory, and they might have been trained to focus on poisonings, not inherited metabolic disorders. Dr. Bob Smith called this an “expectation effect,” and he later referred to the general forensic phenomenon as “investigator bias.” The commercial lab that retested on of the serum samples may have been guilty of confirmation bias. It seems likely but not a certainty that the second lab knew that ethylene glycol poisoning was suspected. In this context it is interesting that Dr. Shoemaker later sent normal plasma spiked with propionic acid to three laboratories and two of the three reported finding ethylene glycol.

The lab that first identified the unknown compound might or might not have been following the standard protocols of the day, but the protocol was insufficiently rigorous in the sense that the identification was only one piece of information, the retention time, as discussed above. However, the commercial lab was deficient by any measure. Clearly, neither lab did a thorough job of examining all information pertaining to Ryan’s serum.

Roger Koppl discussed many of the problems that beset forensic science in the United States. Some of the problems he illuminates, such as dependency bias, were not factors in the Stallings case but may have been at work in the Knox/Sollecito case. He wrote, “the typical forensic worker has psychological incentives to reach findings based on his
close psychological ties with the law enforcement community he serves.” He also treated confirmation and other cognitive biases (p. 13).

“Larry S. Miller demonstrates an excellent example of cognitive bias at play. He asked a group of 14 students trained in hair analysis, all of whom met the basic requirements for expert testimony on human hair identification in courts of law, to examine four cases each. For each student, two cases were presented the usual way: They were given two samples and told that one was from the crime scene and the other from the suspect. The other two cases were presented through a forensic lineup. The known sample from the imaginary crime scene was compared to five suspect-known hair samples. In all 56 cases, there were in reality no true matches. The first group of cases yielded an error rate of 30.8 percent; the second group an error rate of only 3.8 percent.12

Miller’s study illustrates how evidence is often presented to the forensic scientist in a bias-inducing manner. The samples are labeled as coming from the defendant or from the victim and are frequently accompanied by a synopsis of the investigation indicating the reasons that the investigators believe the suspect is guilty. This protocol cues the forensic worker to the expected or correct result.”

The Stallings case in the context of the Knox/Sollecito case
The Johnson/Hampikian open letter criticized both the DNA evidence surrounding the knife and the bra clasp. Some observers of the Knox/Sollecito case have asked what are the odds that both of the DNA results could be the result of contamination or secondary transfer. One might ask what are the odds of at least four identifications of ethylene glycol being wrong, and yet they were in Stallings case. It may be that assigning a probability to the chances of both the bra clasp and the knife being the result of contamination or secondary transfer by standard rules is misleading. When two events are independent, the probability of both occurring are the product of the probabilities of each. So if event A has a 10% probability, and event B has a 10% probability, then the probability of both is 1%. However, when some form of cognitive bias is in play, then this calculation does not apply; in other words, the two events are no longer independent.

Some other parallels can be found. In both cases the investigators seemed oblivious to the contradictory nature of their findings. The second determination of ethylene glycol in Ryan’s serum was so high as to rule out ethylene glycol poisoning four days earlier. The lack of blood on the kitchen knife should have told the forensic DNA analysts that Meredith’s DNA profile was the result of contamination. In both cases the motive for the crime was dubious. Patricia Stallings was thought to be guilty of Munchausen’s by proxy syndrome on the basis of scant evidence. Amanda Knox was accused of trying to get back at Meredith Kercher, because of tensions from rooming together.

References
Michelle Hoffman, “Scientific Sleuths Solve a Murder Mystery,” (1991) Science 253, 931.

Roger Koppl, “CSI for Real: How to Improve Forensics Science”

Dr. Bob Mead, “Accused and Convicted—a case study”

Journal of Pediatrics, The. 1992 Mar;120(3):417-21. Misidentification of propionic acid as ethylene glycol in a patient with methylmalonic acidemia. Shoemaker JD, Lynch RE, Hoffmann JW, Sly WS.

Bill Smith, “Not Guity! How the system failed Patricia Stallings”

Appendix: Methylmalonic acidemia* (MMA)
A metabolic pathway is a series of chemical conversions, in which an enzyme catalyzes each reaction. Enzymes are the products of genes, and an alteration of a gene from its normal form may produce an enzyme that does not function properly. The compound propionyl coenzyme A is the thioester of propionic acid conjugated with coenzyme A (CoA), a thiol. When propionyl coenzyme A is produced in the body, it is converted into succinyl coenzyme A in a pathway that is three steps long: Propionyl CoA carboxylase is the enzyme that changes propionyl CoA into D-methylmalonyl CoA, and this compound is converted into L-methylmalonyl CoA by methylmalonyl CoA epimerase. Finally, this compound is converted into succinyl CoA by the vitamin B12-dependent enzyme methylmalonyl CoA mutase. The gene for this last enzyme is defective in methylmalonic academia, and the inheritance pattern is autosomal recessive. When this happens, the previous compounds build up in concentration. At some point the bond linking propionic acid or methylmalonic acid and coenzyme A is hydrolyed, and the free acids are found in the bloodstream. Among the symptoms of this disease are lethargy, seizures, and vomiting. Metabolic acidosis and ketosis are also observed. Some forms respond to supplementation with vitamin B12.

References to Appendix
Healthline
Nelson, DL and Cox, MM, "Lehninger Principles of Biochemistry," 5th edition.

*update 6/3/10, 4:30 PM. Corrected several spelling errors/typos.

Secondary transfer of DNA and DNA contamination

2010-05-09T13:12:00.014-04:00

Part XV in the Knox/Sollecito case

Introduction
This post returns to the subject of forensic DNA contamination. It will define primary and secondary transfer of DNA and explain how they are related to contamination. It also treats clerical errors and the need for independent review of the forensic DNA data. It reconsiders the lessons of the Leskie case. These concepts will be applied to some of the DNA forensics in the murder of Meredith Kercher, especially as it relates to the evidence against Amanda Knox and Raffaele Sollecito.

DNA contamination
People sometimes confuse DNA contamination with secondary transfer of DNA. Let us define these terms and give a few examples. In Forensic DNA Typing, p. 152, John Butler wrote, “Contamination implies the accidental transfer of DNA.” Implicit in his definition is that the transfer happened after the evidence was collected. In An Introduction to Forensic DNA Analysis, p. 14, Norah Rudin and Keith Inman “define contamination as the inadvertent addition of an individual’s physiological material or DNA during or after collection of the sample as evidence…A contaminated sample is one in which the material was deposited during collection, preservation, handling, or analysis.”

Primary transfer of DNA
According to forensic scientist Suzanna Ryan, “Primary transfer is described as the transfer of DNA from an individual to an item.” Ryan summarized some of the factors that contribute to how much DNA is transferred: “Through studies by Ladd, et al and others, many in the forensic community believe that some individuals just naturally shed more cells when handling an item (‘good’ shedders) than others (‘poor’ shedders). Other factors including the substrate being handled (rougher items collect more DNA), the time since the individual last washed their hands, how nervous the person is (nervousness can lead to increased sweating), and how often they touch their mouth, eyes, hair, face or other body parts (thus gathering DNA on their hands) play a heavy role in whether a DNA profile will be obtained through simply touching an item.” One presumes that rougher items cause more cells to transfer than smoother items, but Ms. Ryan did not give specific examples.

Secondary transfer of DNA
Suzanna Ryan wrote, “In secondary transfer, there is no direct contact between a person and an object. It is instead transferred through an intermediary. This could be another person or another object. An example—expanding upon the same knife example as above—is as follows: Person A shakes Person B's hand. Person B touches the handle of a knife. Secondary transfer theory would allow that Person A's DNA could be transferred first to Person B's hand and second to the knife handle. This would mean that even though Person A never actually touched the knife handle, his DNA could be present on it.”

Secondary transfer at the scene and the lab
Suzanna Ryan continued, “At the laboratory, the analysts are careful to wear gloves when handling evidence items. Great care is generally taken to clean scissors, tweezers, and other utensils between testing items. But what about items that are not cleaned as regularly? For example, is it possible to transfer DNA from an item of evidence to a ruler, and then when the next item of evidence is examined and photographed, could the DNA transfer again from the ruler to this item? A 2006 study by Poy and van Oorschot showed an example of secondary transfer when a mixed DNA profile was found on a swab taken from an examination magnifying lamp. This profile was searched in the lab's database and a match was found with a case that had been worked on the bench-top with the magnifying lamp. It was determined that DNA was transferred from the item being examined to the analyst's gloves and then onto the top of the magnifying lamp.”

This incident should be considered both secondary transfer of DNA (the item transferred DNA to the glove, which transferred it to the lamp) and DNA contamination because it happened in the analysis lab. This incident also illustrates how easy accidental DNA transfer can be in a lab. DNA contamination occurs when an analyst transferred his or her own DNA onto an object, but this would be classed as primary transfer.

Sometimes DNA contamination occurs in ways that do not involve the item of evidence. DNA profiles have been observed because an item of labware (plastic tubes, cotton buds, etc.) was contaminated with DNA from a person who helped to manufacture the item. The chemical reagents and equipment needed to perform the polymerase chain reaction, the DNA amplification step, are occasionally contaminated. These are examples of contamination that are due neither to primary nor to secondary transfer.

Primary and secondary transfer when several people handle an object
In the journal Nature, 387, p. 767 (1997), R. van Oorschot and M. Jones wrote, "Objects handled by many individuals all produced profiles with multiple alleles of varying intensity. To determine the effect of multiple handlers, we exchanged polypropylene tubes between individuals (2 or 3, 10 min each) with different genotypes. Although the material left by the last holder was usually present on the tube, that of previous holders was also retrieved to varying extents. The strongest profile obtained was not always that of the person who last held the object, but was dependent on the individual. We regularly observed profiles of previous holders of a tube from swabs of hands involved in these exchanges, showing that in some cases material from which DNA can be retrieved is transferred from object to hand (secondary transfer).” This article was the first one of which I am aware to document that DNA profiles could be recovered from fingerprints. This may also be the first one to use the term “secondary transfer.”

Primary and secondary transfer of DNA to the bra clasp
Some have argued that the amount of Raffaele Sollecito’s DNA on the clasp can only have been deposited through primary (direct transfer), not contamination or secondary transfer. This argument is false on several grounds. It ignores that that the amount of DNA in primary transfer depends upon several factors (see above). It ignores that contamination can produce strong profiles that analysts have mistaken for genuine ones (see below). It ignores the fact that Mr. Sollecito’s DNA profile on the clasp was relatively weak in intensity, roughly 200 RFUs. Perhaps most fundamentally, this argument runs counter to a principle of DNA forensics. As part of his analysis of the Leskie case (see below), forensic scientist Dan Krane wrote, “In fact, it is quite uncommon for DNA tests themselves to say anything about the circumstances (or even the time frame) associated with the transfer.” Jason Gilder wrote in an email to me, “One of the standard axioms of DNA typing is, the presence of a DNA profile says nothing about the time frame or the circumstances under which DNA was transferred to that item. Contamination falls into is one such instance of an issue that cannot be identified by the electropherogram alone (unless you are dealing with a control sample or other known profile).”

On the other hand, an anonymous commenter on a discussion board offered this hypothetical scenario for secondary transfer of Mr. Sollecito’s DNA: “For example, let's say that DNA from Meredith, Amanda and Raffaele was on the hand towels Rudy took from the bathroom (highly probable, since they'd all used the bathroom in the days before the murder). Drying your hands on a hand towel is exactly the kind of rubbing action that would shed DNA. If Rudy had trodden on one of the towels, then trodden on the bra clasp (one of the hooks was deformed, of course) that could have transferred DNA from the towels to the hook, with no direct contact from Raffaele necessary. In turn, Raffaele's DNA was more easily identified because they could use the more sensitive tests for the Y chromosome, whereas the other DNA would have been mixed female and thus tricky to correctly identify.” This is a speculative scenario, but it is not the only kind of secondary transfer that one could imagine. Sollecito’s DNA was likely on the door to Meredith’s bedroom, for example, because he tried to break the door down.

Clerical errors in DNA forensics
Previously we have explored why the electronic files are important. However, simply having an independent expert review the case file can catch some types of errors even without the electronic files. DNA forensic consultant Norah Rudin encountered a case where two reference samples were switched, due to a clerical error. Lazaro Sotolusson was held for a year and would have been tried for rape involving juveniles, facing multiple life sentences. In a preliminary hearing, one of the female victims identified Sotolusson as her attacker, possibly a case of a mistaken eyewitness. Dr. Rudin examined handwritten notes and computer files (not the sort of files one uses to create a DNA electropherogram, such as a .fsa file) and concluded that the lab had switched the two samples. The lab retested samples from Mr. Sotolusson and Joseph Coppola and confirmed the error. Rudin stated to a reporter, “If I hadn't looked at the original data, I likely wouldn't have found the mistake. That's one of the reasons that I always look at the original data… I believe every case needs to be reviewed by an independent analyst.” (emphasis added)

Errors of a similar kind have occurred elsewhere. Professor William Thompson wrote, “I recently reviewed the corrective action file for an accredited California laboratory operated by the District Attorney’s Office of Kern County (Bakersfield). Although this is a relatively small laboratory that processes a low volume of samples (probably fewer than 1,000 per year), during an 18-month period, it documented multiple instances in which (blank) control samples were positive for DNA, an instance in which a mother’s reference sample was contaminated with DNA from her child, several instances in which samples were accidentally switched or mislabeled, an instance in which an analyst’s DNA contaminated samples, an instance in which DNA extracted from two different samples was accidentally combined into the same tube, falsely creating a mixed sample, and an instance in which a suspect tested twice did not match himself (probably due to another sample-labeling error).” (emphasis added)

Whether or not an independent analysis would have caught possible clerical errors here is an open question. The Knox defense team asked for an independent analysis of all of the forensic data, but the judge denied the request. As long as human beings are part of the testing process, clerical errors are likely to happen at some frequency. This factor and the possibility of contamination ought to be considered when one ponders the astronomical odds that are sometimes used when describing a particular DNA result.

The Leskie case and its relationship to the knife and bra clasp as evidence
Jaidyn Leskie was a toddler who was murdered in Australia over a decade ago. A DNA profile belonging to a Ms. P. was found on two pieces of Jaidyn’s clothing, a bib and some track pants. Ms. P’s profile had varying intensities at different loci, suggesting sample degradation. However, her profile was quite strong in some loci, having peak intensities of over 1000 RFUs. Another example of contamination occurred in State of Illinois v. Sean Evans (2003). In this example a positive control was contaminated with a sample containing a DNA ladder, a series of DNA fragments of increasing length that might be used as a calibration standard. Note that the intensity of the fragments making up the ladder is 500-1500 RFU, similar to a typical evidence sample. The unusual nature of the ladder DNA helps to show that contamination occurred, but this is seldom true for other kinds of contamination.

Ms P’s DNA profile was ultimately attributed to contamination partially on the basis that Ms. P lived hundreds of miles away from the crime and never left her village. Yet she could have lived next door to the Leskie family, and contamination would still be a likely explanation for finding her DNA on the toddler’s clothing. Jaidyn’s body was found submerged in water for months. These conditions are antithetical for the preservation of DNA evidence. Significantly, none of Jaidyn’s DNA was recovered from his clothing. This should have been a reason to suspect contamination on its own.

The bloodless kitchen knife in the Knox/Sollecito case is similar to Jaidyn’s clothing in that no human DNA was likely to have been on the blade at the time of collection at any section that tested negative for blood; therefore, the DNA was most likely deposited in the lab. The Leskie case was one in which the electronic data files were particularly helpful. The Knox/Sollecito case would also benefit by independent examination of these files. For example, one could use the .fsa files to examine other samples along the knife blade and handle using the same threshold value for all samples. One might find profiles belonging to other individuals, and this would strengthen the argument that DNA on the knife arose from contamination or secondary transfer.

Could contamination have occurred in the Leskie case? The evidence with Ms P’s DNA was examined within a few days the evidence from the Leskie case, and Dr. Krane noted “even if evidence samples from the two cases did not come into direct physical contact, secondary transfer (by way of common contact with a surface or implement) of biological material from the condom or articles of Ms. P’s clothing in the rape investigation to the bib and track pants could have occurred.” The lab in question had argued that contamination was unlikely on at least two grounds, one of which was the lack of DNA from Ms P showing up in other profiles. Dr. Krane agreed that “no other samples including negative controls associated with both investigations display indications of Ms. P’s allele’s being present.” However, he rebutted the lab’s point by stating, “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.” Although the amplification of DNA through use of the polymerase chain reaction (PCR) creates the possibility of contamination via the amplified DNA, Dr. Krane did not think it is as likely in this case as secondary transfer.

There is one more point with respect to the bra clasp that needs to be addressed. It is sometimes argued that Mr. Sollecito’s DNA could not have arrived on the clasp by contamination because his DNA was found on no other items except for a cigarette butt. This is essentially the reasoning of Judge Micheli, who oversaw Rudy Guede’s trial. From the Wikipedia article on the murder of Meredith Kercher, “The judge at the trial of Guede acknowledged that the DNA sample was considered small, but described the claim of contamination at the laboratory as making ‘no sense’, since there was no material from which such contamination could have come, and so ‘the risk would have been the loss of traces found there, not the risk of somehow discovering new traces.’” This argument is false for at least two reasons. It ignores the possibility of contamination from Mr. Sollecito’s DNA in the lab, and it ignores the empirical facts of the Leskie case, where Ms. P’s DNA did not show up in other items or controls.

Summary
One way to distinguish between secondary transfer and contamination is to say that the difference between primary and secondary transfer depends upon how the DNA was deposited on the evidence item, but contamination depends upon when the DNA was deposited: if the DNA were deposited before the item was collected as evidence, it would not be contamination. We have also seen that contaminating DNA does not evince a difference in intensity that would allow it to be distinguished from DNA arising from primary or secondary transfer before the item was collected as evidence. Clerical mix-ups are another source of error in DNA forensics, and catching them is one of many reasons to welcome independent reviews of the results. Raffaele Sollecito’s DNA could have arisen on the bra clasp from contamination or secondary transfer, as well as primary transfer. Meredith Kercher’s weak, dubious DNA profile on the knife is almost certain to have arisen from contamination.

Updates 1/13/2012 and 1/19/02

I corrected Suzanna Ryan's name from Suzanne, and I fixed a link to one of her articles. I added a quotation mark and fixed a link to William C. Thompson's article.

The prosecution's failure to release the electronic data files to the defense

2010-04-26T19:23:00.016-04:00

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.

Things said and left unsaid: Barbie Nadeau’s coverage of the Knox/Sollecito case (Part XIII)

2010-04-18T21:54:00.012-04:00

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.

The utility of electronic data files in DNA forensics cases

2010-04-05T23:06:00.003-04:00

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.

Viewpoints on the Italian Justice System

2010-03-21T22:42:00.002-04:00

Part XI in a series on the Knox/Sollecito case

The murder of Meredith Kercher has caused the Italian justice system to come under scrutiny. The first is a letter Count Neri Capponi wrote about the Monster of Florence case, and the second are his comments on the Knox/Sollecito case to Judy Bachrach of Vanity Fair. Count Neri Capponi is a judge and a lawyer, and his son Niccolo is an acquaintance of Douglas Preston and Mario Spezi, authors of The Atlantic article and the book The Monster of Florence.

The travesty of justice undergone by Douglas Preston and Mario Spezi (http://www.theatlantic.com/magazine/archive/2006/07/the-monster-of-florence/4981/) is the tip of the iceberg. The Italian judiciary (which includes the public prosecutors) is a branch of the civil service. This particular branch chooses its members, is self-ruling, and is accountable to no one: a state within the state! This body of bureaucrats can be roughly divided into three sections: a large minority, corrupt and affiliated to the former Communist Party; a large section of honest people who are too frightened to stand up to the political minority (which controls the offices of the judiciary); and a minority of brave and honest men with little influence. Political and dishonest judges have an infallible method of silencing or discrediting opponents, political or otherwise. A bogus indictment, the tapping of telephones, the conversations (often doctored) fed to the press to start a smear campaign, a spectacular arrest, prolonged preventive detention under the worst possible conditions, third-degree interrogations, and finally a trial that lasts many years and ends in the acquittal of a ruined man. Spezi was lucky, because the powerful Florentine public prosecutor is no friend of the Perugia prosecutor’s and, I am told, “suggested” that Spezi be freed; the Perugia court, I am told, accepted the “suggestion.”
Count Neri Capponi
Florence, Italy
http://www.theatlantic.com/magazine/archive/2006/10/letters-to-the-editor/5197/

The Italian legal system, ecclesiastical judge Count Neri Capponi informs me, will not work in Amanda’s favor. “Our system stems from the Inquisition and also from medieval law,” he explains. What this means, in effect, he says, is that justice in Italy “is based on the supremacy of the prosecution. This nullifies the fact—written in our constitution by the way—that you’re innocent until proven guilty.
http://www.vanityfair.com/culture/features/2008/06/perugia200806?currentPage=6

Amanda Knox was accused of slander for her allegation of police abuse (http://perugia-shock.blogspot.com/2010/01/new-proceedings-against-amanda-knox.html). Based on Frank Sfarzo’s report, one is skeptical about how objectively her allegations were investigated. From a report prepared by the human rights group EveryOne on police violence in Italy, “When human rights activists report episodes of violence or abuse of power being perpetrated by rogue officers to local or national institutions, a worrying phenomenon nearly always takes place. Instead of collecting precise reports of the episodes in order to investigate and identify those responsible for the abuse, the superiors shut up like a clam, denying without question that such disgraceful acts could have taken place. They assume a threatening tone with the associations and threaten to report them for slander, libel and defamation etc. This attitude, which the leaders of EveryOne themselves have witnessed on several occasions, prevents the rogue officers being isolated and their behaviour discouraged. On the contrary, it makes them feel part of an agency in which they are allowed to act above the law using violence, threats and acts of gratuitous coercion. According to the activists, after reporting misconduct by uniformed police officers towards racial minorities, it is not rare for the activists themselves to be followed by plain clothes policemen or summoned to police stations or headquarters and “advised” not to take any further action.” (thanks to Observer for pointing out this report*)

Commentator Peter Popham has written a couple of articles on the Italian system. Comparing the British and Italian systems Popham wrote (http://www.independent.co.uk/opinion/commentators/peter-popham-will-knox-find-justice-in-perugia-1826533.html), “One of the great virtues of the British judicial system is that, whatever ideas a detective or prosecutor may have about a case, he is not allowed to voice them until the case comes to court. And a very good thing too.

They manage these things differently in Italy, where prosecutors regularly leak their theories to the newspapers, often in extraordinary detail. Reporters compete for the juiciest tit-bits. As a result, by the time the trial comes around, the public already know what they think about a case, and why. This makes miscarriages of justice horribly likely. Take the Perugia murder: Mr Mignini made up his mind about it, and got his theories splashed across the media, in early November 2007. But weeks later forensic evidence led the police to another suspect who had little or no connection to Knox, Sollecito and their African friend. Rudy Guede, unlike the original three, was tied to the crime scene by fingerprints, hand prints and DNA evidence. In a separate trial he has already been convicted of the murder.

When Guede exploded on the scene, the investigators should have torn up their work and started again. But by this time the "guilt" of Knox and Sollecito was so well established in the media and in the public's mind that there was no going back. The jury sitting on the case absorbed all those early reports. As a result, justice may be done in Perugia next week, but I wouldn't bank on it.”

Popham also brought up (http://www.independent.co.uk/news/world/europe/the-big-question-should-italian-justice-be-in-the-dock-over-the-conviction-of-amanda-knox-1836076.html) an aspect of the Italian system that might work in Knox and Sollecito’s favor, “The good news for them is that the appeal is essentially a re-trial: every aspect of the case will be examined afresh. It is very common for convictions at the first trial to be overturned on appeal. A conviction is not considered "definitive" until it is confirmed by the Court of Cassation.” Another commentator has indicated that Knox’s incriminating statement was thrown out before her trial in a way that might not have happened until after her trial in another country.

With respect to the broad latitude given to the prosecutor for his summation, Scott H. Greenfield (http://blog.simplejustice.us/2009/12/05/a-trial-without-evidence.aspx) lamented, “During the summation, the prosecutor told the jury about the things Amanda Knox might have said to Meredith Kercher before the alleged drug-induced orgy that ended with her throat being slashed.

‘You are always behaving like a little saint. Now we will show you. Now we will make you have sex.’

This would be a horrible thing to say, except that it never happened. No one says that such a statement was ever made. But summations in Perugia aren't limited to evidence, as they are here. Rather, this is a permissible indulgence into fantasy, a made up dramatization of what the prosecutors contend might have happened. It's used to inflame the jury. It's what prosecutors try to do everywhere, except that there are no restrictions on such fabrications in Italy. Still, arousing passion gets a far better visceral response that appealing to reason.”

I have a relatively limited number of facts on which to base an evaluation of the Italian justice system. Broadly speaking, it has things to admire and areas for improvements. My comments here should not be construed as a blanket indictment of the Italian justice system.

*update 3/22/10
www.statewatch.org/.../EveryOne%20-%20Report%20Police%20Violence%20in%20Italy_ENG.pdf

Luminol and some of the footprint evidence

2010-03-16T23:56:00.005-04:00

Part X in a series on the Knox/Sollecito case

The story surrounding the footprints in the murder of Meredith Kercher is complex, and it may take more than one post to cover it. However, the recent jury’s statement included a reference to the footprint evidence as one indicator of guilt. In this post we will summarize the analyses of both pro-prosecution and pro-defense points of view with respect to a bloody footprint found on a bathmat and the three luminol-positive footprints in the hallway.

Chemistry and forensics of luminol
Luminol was used to visualize some of the footprints. Luminol is typically used as a mixture that includes sodium carbonate and sodium perborate. Luminol reacts with the iron atom in hemoglobin, and also reacts with other substances, such as bleach and fruit juice, or with substances that contain a metal ion that can catalyze the light-producing chemistry. Fruit pulp is rich in certain peroxidase enzymes that have an iron ion that has much in common with the iron in hemoglobin. In hemoglobin and in the peroxidase family of enzymes the iron ion is bound to four nitrogen atoms of an organic molecule called protoporphyrin IX. The combination of iron and protoporphyrin IX is called heme, which is tightly bound to the protein portions of hemoglobin or catalase, respectively. A fifth nitrogen atom from a histidine residue within the protein also coordinates the iron ion (Frey and Hegedus, Enzymatic Reaction Mechanisms, pp. 203-209). Heme is called a prosthetic group, a nonprotein molecule that helps a protein to do its job.

Both hemoglobin and peroxidases are proteins, but only peroxidases are enzymes (biological catalysts). In the luminol reaction however, both hemoglobin and peroxidases are acting catalytically. A paper by Barni et al., “Forensic application of the luminol reaction as a presumptive test for latent blood detection,” Talanta 72 (2007) 896–913, is a review of luminol chemistry and forensics. Hydrogen peroxide oxidizes luminol with the production of light. The iron ion within hemoglobin or other substances is a catalyst; in other words, one molecule of hemoglobin converts many molecules of luminol and hydrogen peroxide to produce 3-aminophthalate. Thus the catalytic behavior of metal ions partially explains the sensitivity of this test. Since photons of light are emitted in this reaction, the process is classified as a chemiluminescent reaction.

This paper discusses whether one can tell whether or not the substance reacting with luminol is really blood:

“Due to the possible presence of these substances at the crime scene, the luminol test must not be considered sufficiently specific to permit an unequivocal identification of blood [15,18,51,88,89]….

Generally visual examination is used when the luminol test is employed in a forensic situation, rather than instrumental detection of the luminescence. An experienced practitioner may distinguish the true blood-catalyzed chemiluminescence from that produced by other substances by the evaluation of parameters observable to the naked eye such as emission intensity, duration and spatial distribution. However this approach may also lead to misinterpretation, due to a subjective, informal and non-quantitative evaluation, for example, because its intensity is qualitatively much weaker than that expected for blood. In other circumstances an emission of similar intensity may be thought to derive from diluted bloodstains and is accepted. Therefore, caution should be exercised when using the test.”

Thus the Luminol test is a presumptive test and should be confirmed by one that is more specific for blood. However (http://www.friendsofamanda.org/luminol.html), “The prosecution's key forensic witness told the court she can tell by looking at a luminol reaction whether it involves blood or something else, but she did not perform any scientific tests to validate this claim.”

Perugia-Shock
The prosecution attributed one hallway footprint to Raffaele Sollecito. Francesco Vinci testified that the luminol footprint in the hallway is a human footprint but one that cannot be attributed to anyone in particular (http://perugia-shock.blogspot.com/2009/09/sollecitos-expert-questions-all.html). The shape of the big toe and the print of the putative second toe were key elements to his conclusions. Frank Sfarzo wrote, “With such limited elements Vinci is only able to rule out Raffaele (or the girls) and to say that the print is compatible with Rudi. And we can only admire his honesty and consistency.”

Additional posts on the footprints by Frank Sfarzo
http://perugia-shock.blogspot.com/2009/05/footprint-is-mr-sollecitos.html
http://perugia-shock.blogspot.com/2008/06/footprints-are-amandas.html
http://perugia-shock.blogspot.com/2009/07/coroner-sarah-gino-accuses.html

Darkness Descending
Now let us turn to the analysis of the footprints that Colonel Luciano Garofano gave to the author of the book Darkness Descending, by Paul Russell and Graham Johnson (Pocket Books, 2009). Colonel Garofano is a well-known forensic scientist who recently retired from the Carabinieri. He was much friendlier to the prosecution’s case than to the defense’s case, and I do not agree with everything that he said in this book, particularly with respect to the footprint on the blue bathmat discussed below.

“The other problem I have is the way the Luminol was applied. The size of the blobs shows that it was not carefully vaporized but squirted. That creates two problems. It dilutes the sample and it dilates the print. We have a print attributed to Sollecito, which matches his foot in the size of the big toe, the width of the metatarsus and the width of the heel, but does not present the characteristic details each of our feet present. The print can be said to be compatible, but not 100 per cent.”

“Now let’s have a look at the prints attributed to Amanda Knox. There’s one in her bedroom facing the exit to the room, and there are two right feet in the corridor walking in the direction of the victim’s room. The same goes here. The method of application of the Luminol is insufficiently subtle to positively identify a foot, but the result can be said to be generally compatible with Amanda Knox’s.

“But I didn’t see who else they compared the prints with. Just Rudy, Amanda, and Raffaele? So we only have a choice between those? We don’t have the footprint of other women or men, as a comparison? Pity.”

Colonel Garofano believed that it is likely that Raffale’s foot made the print on the blue bathmat, but he did not sound certain. However, he did not discuss the fatal criticism that the prosecution’s expert witness made a serious error in the measurement of this print, discussed below. Colonel Garofano did not address the fact that Rudy’s big toe looks nothing like Raffaele’s, and the bathmat print. Nor did he seriously entertain the possibility that the prints are not even blood. He also did not explain why the print attributed to Ms. Knox points toward Meredith’s room and why there is not a full set of prints. These are serious omissions in that it is difficult to picture how the prints could have been made during the commission of the murder.

Science Spheres
Mark Waterbury discussed some of the problems in the footprint evidence in the hallway and elsewhere (http://www.sciencespheres.com/2009/10/methods-of-polizia-pseudoscientificaa.html):
“Luminol glowing footprints were found in a hallway, and some may have been Amanda's, it is hard to know for sure because they were only compared with her feet, and found to be ‘compatible.’ Again, no controls. Meredith, Laura, Filomena, none of the other resident's feet were compared to these footprints. The footprints were tested for blood, and it came out negative. No blood. So, why are they important? Amanda lived there, after all.”

“Amanda's DNA was said to be found in one of these footprints. Did they also test a meter away from the footprints, to see if her DNA was all over the apartment where she lived? No. That would have been another control experiment. Was the DNA actually associated with the footprint, or did it just happen to be there, because the resident's DNA was all over their apartment, as people's DNA usually is? We will never know. They skipped the control experiments, and presented results without any reference.”

With respect to Meredith’s DNA and the luminol-enhanced footprints, I would argue that not finding her DNA is evidence against the proposition that the substance is her blood. However, finding her DNA would be not conclusive evidence that the substance is her blood. That is because there could be non-blood derived biological material from Meredith mixed into the footprint. In other words finding her DNA would have been consistent with blood being responsible for the luminol reaction but would not demand that conclusion.

Perugia Murder File
A powerpoint, Dear-Mr-Marriott-I-Shrunk-the-Black-Kid.pps, authored by Kermit (http://www.perugiamurderfile.org/viewtopic.php?f=5&t=36) attempted to rebut arguments presented at the Friends of Amanda website. The first of these is that the prosecution’s expert witness Mr. Rinaldi, made a serious error in his size measurements. Kermit’s presentation also addresses two of the problems in ascribing the bloody footprint to Mr. Sollecito, the narrowness of the big toe (http://www.friendsofamanda.org/footprint.html) and the appearance of a mark near the big toe. Mr. Guede’s big toe is shorter than his second toe, but Mr. Sollecito’s second toe does not even show up in his footprint. Mr. Guede’s big toe is narrower than Mr. Sollecito’s. According to Kermit, the reason that the bloody imprint of the big toe seems narrower than Mr. Sollecito’s is that the raised tufts of the blue bathmat have picked up more blood than the unraised portions. Likewise, the mark Sollecito’s expert witness Francesco Vinci would ascribe to a second toe (http://perugia-shock.blogspot.com/2009/09/sollecitos-expert-questions-all.html), Kermit claims is Mr. Sollecito’s big toe. Kermit said elsewhere that his reason for writing his powerpoint presentations were to refute the lone wolf theory of the crime, because the prints were of varying sizes.

I do not find Kermit’s arguments about the raised tufts to be convincing. There is a raised tuft of lighter color in between the big toe and the second mark, possibly from Guede’s second toe. If Kermit were correct, that portion of the bathmat should be as dark as the rest. The validity of Kermit’s measurements has also been questioned by two commenters at a forum at James Randi Educational Foundation (http://forums.randi.org/showthread.php?t=161229&page=126).

Defense-friendly blogs
Charlie Wilkes of the website Friends of Amanda presented the argument that the bathmat footprint measurements made by the prosecution’s witness, Lorenzo Rinaldi, contained a critical error. (http://www.friendsofamanda.org/footprint_measurements.html). Mr. Wilkes also discussed the footprints elsewhere (http://knoxarchive.wordpress.com/2009/11/27/manuela-comodi-asks-for-common-sense/). The site Injustice in Perugia gives a detailed account with images of the footprints (http://www.injusticeinperugia.org/footprints.html). These two sites make several telling points, especially with respect to the luminol-positive footprints in the hallway. The footprint L9 (in the knoxarchive numbering scheme) is attributed to Amanda by Rinaldi. Yet is alone, and it points toward, not away from Meredith’s room. L6 and L7 are two right feet, one of which is attributed to Raffaele. The footprint in the hallway attributed to Raffaele look quite indistinct to me. The other one is attributed to no one at all, and one wonders to whom it belongs. None of the footprints tested positive for blood and none were positive for Meredith’s DNA.

None of the three footprints were part of a trail. It is difficult to see how Amanda Knox and Raffaele Sollecito could have removed other footprints (as part of an alleged cleanup) without also cleaning up Rudy Guede’s nearby bloody shoeprints.

Prosecutorial tunnel vision
The failure to obtain reference footprints is disturbingly reminiscent of the lack of reference DNA from Laura or Filomena, the other two flatmates. It suggests that once the investigators locked onto Amanda and Raffaele, they did not reopen their field of vision. Crime journalist Mario Spezi said about the word “compatible,” in Douglas Preston’s book, The Monster of Florence, which covers a serial murderer in that city.

“Compatible, not compatible, and incompatible are the baroque inventions of Italian experts who don't want to take responsibility. Using 'compatible' is a way to avoid admitting they haven't understood anything. Was the bullet in Pacciani's garden inserted into the monster's pistol? 'It is compatible.' Was that laryngeal break inflicted by someone who intended to kill? 'It is compatible.' Was that painting done by a monstrous psychopath? 'It is compatible.'”

“Perhaps yes, perhaps no--in short, we don't know! If the experts are chosen by the investigators, they say their results are 'compatible' with the theories of the prosecution; if they are chosen by the defendants they say that their results are 'compatible' with the theories of the defense. That adjective should be outlawed!”

Conclusions
Luminol was overapplied to the footprints in the hallway, and a full set of reference footprints was not taken. These two points alone make the prosecution’s attribution of two the footprints to Ms. Knox and Mr. Sollecito, respectively, impossible to accept as solid conclusions. The unattributed footprint forces one to ask who else was in the hallway and when. Moreover, the luminol-visualized footprints did not contain Meredith’s DNA and cannot be said to be blood. The failure to obtain a positive test for blood is possibly the most serious problem for the prosecution’s case. Although I do not claim to be an expert in the analysis of footprints, the bathmat footprint looks like a better match to Rudy Guede than to Raffaele Sollecito. The footprints in the hallway may date from a time prior to the murder, or on the following morning. The lack of reference footprints is one more indication that the forensics in this case was not pursued in an entirely objective manner.

An interim evaluation of the evidence against Knox and Sollecito

2010-03-01T09:36:00.002-05:00

Part IX in a series on the Knox/Sollecito case

Here is an interim overview of some of the evidence in the murder of Meredith Kercher; individual issues may be covered in greater depth once the reasons for the verdict have been announced. We have already examined some of the problems with the DNA of the knife and bra clasp. Problematic as the LCN DNA of the knife and the weak, mixed DNA of the clasp are, they are the only things that tie Mr. Sollecito to the room and Ms. Knox to a supposed murder weapon. Without them the whole case looks insubstantial.

Forensic evidence
The investigators failed to perform and especially to report the DNA forensics to the usual degree of completeness, and this leaves many questions unanswered. The investigators did not take Filomena’s or Laura’s reference DNA samples, even though they were Meredith’s roommates. Chris Mellas, Amanda’s stepfather, said that despite a court order in the summer of 2009, the investigators failed to disclose the electronic data files of the DNA evidence (called .fsa files) and logs to the defense. The lack of disclosure of evidence concerning the DNA forensics was one of the reasons that the defense essentially moved for a mistrial in the fall, a motion which was denied. According to Barbie Nadeau (http://www.thedailybeast.com/blogs-and-stories/2009-09-14/no-mistrial-for-knox/), “Just as court adjourned in July, it was revealed that the prosecution had held back key evidence from the defense and civil attorneys. On Monday, clutching the Italian constitution, Sollecito’s lead defense attorney, Giulia Bongiorno, told the judge: ‘My client has been denied his right to adequate representation.’”

Although Ms. Nadeau does not indicate the nature of the evidence withheld, the subsequent Johnson/Hampikian open letter of 19 November 2009 noted specifically lack of disclosure of the .fsa files. Because it is difficult to see why the defense would not share such files with Dr. Johnson and Professor Hampikian (or at least make them aware that the files had been finally disclosed), the open letter tends to corroborate Mr. Mellas’ account. In addition, Bob Graham wrote (http://www.dailymail.co.uk/news/article-1233539/Amanda-Knox-victim-anti-American-trial-campaigners-urge-Hillary-Clinton-launch-investigation.html), “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.”

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.”

One leaves DNA by many mechanisms including shedding hair and skin. Finding Ms. Knox’s DNA in her own flat is a very unsurprising result, whether or not it happened to be mixed with Meredith’s blood. Her DNA was found in Mr. Sollecito’s flat as well. The lack of their DNA in Meredith’s room on all but the bra clasp is a silence that shouts. In a pretrial hearing, Mr. Sollecito’s lawyers argued that it would have been very unlikely for him to be able to leave DNA on the bra clasp without also leaving it on the bra as well, yet none was found there (http://www.telegraph.co.uk/news/3255101/DNA-on-Meredith-Kerchers-bloodied-bra-was-due-to-lab-contamination-claims-Sollecito.html).

The other biological forensics was also problematic. Luminol was overapplied to one of the footprints, according to Colonel Garofano in the book Darkness Descending, leading to a loss of detail in the image. Moreover, luminol is a presumptive test for blood, one that should be confirmed by further testing. Although some claim to have the ability to tell blood from other substances via luminol alone, this claim is controversial in the forensic literature. Moreover, defense expert witness Sara Gino stated "We were not told that, first of all, the prints were treated with a substance which should have indicated whether they were blood, and the result was very uncertain." In addition, the investigators did not obtain reference footprints from all of the roommates. The temperature of Meredith’s body was taken about two days after death had occurred, making it harder to estimate the time of death.

The investigators could have performed the electronic forensics much more professionally. For example, the investigators damaged three hard drives, Meredith’s, Amanda’s, and one of Raffale’s, (http://www.dailymail.co.uk/news/article-1234298/Amanda-Knox-The-troubling-doubts-Foxy-Knoxys-role-Meredith-Kerchers-murder.html). Amanda’s hard drive is said to have pictures of her and Meredith, evidence that would belie the impression that the two roommates did not get along, but her drive has not yet been salvaged. Her defense team has offered to pay for a different group of experts to attempt to retrieve the information, but this offer was rebuffed. The investigators also inadvertently erased a piece of potential alibi information (http://www.lastampa.it/redazione/cmsSezioni/cronache/200909articoli/47691girata.asp), the time that the file Stardust was accessed (http://perugia-shock.blogspot.com/2009/09/computer-places-knox-and-sollecito-at.html).

Non-forensic evidence
The prosecution would have us believe that a gang rape occurred, despite the fact that this is an unusual occurrence. Ms. Knox and Mr. Guede had met only twice, the two men had never met, and neither Ms. Knox nor Mr. Sollecito communicated with Mr. Guede in any documented way. It strikes me as extraordinarily risky to commit a crime with someone one does not know. Then Ms. Knox and Mr. Sollecito are imagined to have removed evidence linking them to the crime but not evidence linking Mr. Guede to the crime. In addition, the prosecution changed the motive during the trial but did not have evidence to support either motive.

Raffaele’s kitchen knife is too large to have made the bloody outline of the knife on the sheet. It is too large to make two of the three wounds, and any knife could have made the third. There is no reason for Raffaele and Amanda to have transported the knife in the first place. On top of that we are asked to believe that Raffaele and Amanda would not dispose of this knife, even though Rudy would have seen them use it and could rat them out, and even though the other knife was disposed of. We are also asked to believe that they would clean the blade of the knife but not the handle. This whole scenario would be risible if it were in a third-rate mystery novel.

Raffaele and Amanda are said to have faked evidence of the flat’s being burglarized. I do not find the argument that the break-in was staged to be convincing. There is little evidence pointing that way. Filomena’s room was tidy when she left it, but she recalled that when she returned, there was glass on her clothes. This suggests that someone put the clothes on the floor to simulate a break-in, then broke the window in her room. However, the photographic evidence is not definitive, and it is possible to imagine a number of explanations. Suppose the window were broken, and glass ended up on the laptop. Then suppose that the laptop were moved from the desk to the floor, where some of the glass slid off to some clothing and some remained on the computer. Also, Filomena was allowed back into her room to retrieve some items, and it is possible that she inadvertently did something to put glass on the strewn clothes and remembers the room as though she found it that way.

It has been argued that Raffaele called the Carabinieri after the unexpected arrival of the Postal Police, in an attempt to portray himself as a concerned but innocent citizen, then lied and said that his call to the Carabinieri preceded the appearance of the Postal Police (who were returning missing cell phones). The prosecution wants us to believe that Mr. Sollecito lied to the police about when he placed the call, before he was a suspect. The explanation for what probably did happen is complex, but unless one believes that Mr. Sollecito is very stupid, the prosecution’s theory does not make much sense. Attempting to lie about when the call to the Carabinieri would have little upside (he could have said to the postal police that he was just about to call them or the Carabinieri), and has a huge downside. One would generally believe that the police would be meticulous record keepers about the times of calls and other matters. If Mr. Sollecito were tempted to concoct this story, a moment’s thought should have been enough to convince him of the likelihood of being found out. The two defendants did do some dumb things, but I do not believe that they are that stupid.

Ms. Knox’s incriminating statements were thrown out as evidence for the murder trial; therefore, they cannot be used to assess her legal guilt or innocence. However, suppose we consider her incriminating statements against Lumumba in assessing factual innocence and ask why she made them. Her subsequent comments about the interrogation are similar to those made by people who have been pressured into making false confessions. Francesca Bene’s interrogation provides a modest amount of support for what Ms. Knox said, as discussed in a previous post. In addition, we have Douglas Preston’s account of his being interrogated in a foreign language, and his evaluation that his halting answers made him sound like a liar. It is quite possible that Ms. Knox’s interrogators misperceived similar behaviors of hers as evidence that she had something to hide and therefore pressed harder. Moreover, her later statement, “But I've said this many times so as to make myself clear: these things seem unreal to me, like a dream,” implicitly disavows Lumumba’s involvement.

The investigators claim that no undue coercion was used, but Dr. Giobbi said that he heard Amanda screaming. The investigators claim that they did not record the key interrogations with Amanda that night, despite having previously recorded her interviews and phone calls. Furthermore, they lied when they said that Amanda came in to the police headquarters of her own volition (http://perugia-shock.blogspot.com/2009/05/giobbi-i-gave-order.html). Therefore, Ms. Knox’s account of her interrogation is more credible than theirs is.

Ms. Knox’s allegedly performing a cartwheel at the police station was the fodder for a great deal of negative publicity. Her own explanation of that episode, as relayed through Chris Mellas to Frank Sfarzo of Perugia-Shock, is that she was stretching to relieve stress when a policeman commented on her flexibility. They fell into a conversation, and he asked her what other gymnastics or exercises she knew. Ms. Knox’s testimony at her trial mentioned meeting the policeman but did not say whether or not he asked her to demonstrate other gymnastic moves. Elsewhere, she implied that she did at least some exercises or stretches of her own accord. Therefore, her testimony neither contradicts nor confirms the version Mr. Sfarzo reported. In any case, her yoga or gymnastics have little or no bearing on her guilt or innocence.

What about Raffaele’s probable lie about his cooking with Meredith and his pricking her finger? Does this not generate suspicion? His statement was made only after he had heard that her DNA was found on the knife blade, not before, and it was made without knowledge of the quality of the data. His statement was stupid, but understandable. Therefore, I would say that there is reason to be suspicious of Amanda and Raffaele, probably not enough to indict, and certainly not enough to convict.

The defense have argued that this tragic crime was the work of a lone assailant, Rudy Guede. The evidence linking Mr. Guede to the crime is much stronger; there is a bloody handprint, the bowel movement in the toilet, and there are several pieces of DNA evidence. I am puzzled by the sexual aspect of the crime, but despite this reservation, Mr. Guede acting alone in the rape and murder is the most logical explanation to me. If information about Rudy’s involvement had come back earlier, I doubt that the investigators would have ever moved for an indictment against Raffaele or Amanda. In other words, this is an instance of garden-variety tunnel-vision on the part of the investigators.

Farah Jama and forensic DNA contamination

2010-02-21T21:33:00.001-05:00

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 (http://www.heraldsun.com.au/news/man-jailed-for-rape-has-conviction-overtuned-after-revelation-that-dna-evidence-may-have-been-contaminated/story-e6frf7jo-1225807656413).

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 (http://www.theaustralian.com.au/news/features/dna-in-the-dock/story-e6frg6z6-1225809214024).

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 (http://www.news.com.au/couriermail/story/0,,26542662-27197,00.html).

The Monster of Florence and the Tragedy in Perugia

2010-02-14T17:30:00.002-05:00

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).

http://www.theatlantic.com/doc/200607/florence-murder/6.

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.”

http://cpj.org/2006/04/crime-journalists-imprisonment-raises-alarm.php

“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.”

http://www.cpj.org/2006/05/italian-court-frees-journalist-held-after-writing.php

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.”

http://blog.seattlepi.com/dempsey/archives/131443.asp

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.

http://blog.seattlepi.com/dempsey/archives/140460.asp

An ordinary kitchen knife or a murder weapon?

2010-02-05T17:12:00.007-05:00

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 (http://www.istitutoaffarisociali.it/flex/AppData/Redational/Ejournal/Articoli/Files/D.7e1010a4daa67d625c63/indagini_genetico_forensi.pdf). 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 (http://www.friendsofamanda.org/articles.html).

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 (http://perugia-shock.blogspot.com/2009/09/psychiatrist-and-coroner-for-amanda.html), and changing the limit after the experiment was done opens the door to bias, as discussed in the previous post on the knife (http://viewfromwilmington.blogspot.com/2010/01/amanda-knox-and-raffaele-sollecito-and.html).

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, 2^nd 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 http://abcnews.go.com/GMA/AmandaKnox...cutorswitched-motives/story?id=9215634. 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 (http://www.scientific.org/tutorials/articles/riley/riley.html):

(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 (http://perugia-shock.blogspot.com/2009/09/neutral-expert-dismisses-murder-weapon.html). 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.

Meredith Kercher’s Bra Clasp

2010-01-30T11:21:00.001-05:00

Part V in a series on the Knox/Sollecito case

Meredith Kercher’s bra clasp was separated from her bra, presumably by the murderer. The first problem with the bra clasp in this case is the fact that it was not collected as evidence until about 47 days after the crime, on 18 December 2007. This might not matter if the crime scene had been secure. However, someone had moved the clasp had from its original location (by a meter in some estimates). Someone had broken into the house on two separate occasions in early 2008, after the clasp was in police custody. The lack of control over the bra clasp alone might be enough to disqualify it as evidence.

A second problem is that the clasp became dusty because it was found in a pile of clutter. Human epithelial cells are a major component of dust; indeed, dust itself has recently become of forensic interest (http://www.newscientist.com/article/mg19826584.200-telltale-dna-sucked-out-of-household-dust.htm). A third problem with the clasp is that it was handled with dirty gloves. Here is a video that documents this fact, as well as the dust on the clasp itself:

http://www.youtube.com/watch?v=gLE4s3jXTVU&feature=related

The glove might have touched the same door or door handle that Raffaele Sollecito used when he attempted to break the door down after Meredith’s murder. This is one possible route of secondary DNA transfer. In addition, note how it was treated in a second video:

http://www.youtube.com/watch?v=UMaTI0SiuLw

The clasp should have been handled with disposable tools. Moreover, the clasp is being passed to and fro unnecessarily, and even put on the ground, both of which increase the likelihood of contamination. One wonders why the clasp is being put on such an elaborate display.

The mixture of DNA

The clasp had Meredith’s profile as the strongest component. A relatively weak component (200 relative fluorescence units) appears to be Raffaele’s DNA. There are reports of DNA from at least three other people (http://www.dailymail.co.uk/news/article-1234298/Amanda-Knox-The-troubling-doubts-Foxy-Knoxys-role-Meredith-Kerchers-murder.html

The 19 November 2009 letter coauthored by Drs. Hampikian and Johnson said, “Transfer of Raffaele’s DNA to the clasp could have occurred through several innocent means as a result of his DNA being in the apartment or via Amanda’s clothing or belongings. DNA testing cannot determine how biological material was deposited onto an item of evidence: whether by direct deposit, or by secondary transfer through an intermediary. DNA testing cannot determine how long biological material may have been on an item, or whether contamination occurred during collection.”

http://www.friendsofamanda.org/files/KnoxSollecitoDNAPetitionSubmitted11.19.09b.pdf

The presence of a mixture leads to several questions. First because I cannot envision how so many people could have handled the bra clasp directly, I think that indirect transfer of DNA is the more likely explanation. Second, it is difficult to see why the three individuals who deposited DNA on the clasp should not be considered potential suspects. Third, suppose that the police had taken other dusty items into evidence at the same time as the bra clasp. If these had been utterly clean of DNA, the results on the clasp would carry more weight. From what I can gather, no such items were taken into custody on the same day.

The lack of other DNA

At a pretrial hearing Mr. Sollecito’s defense team argued that the lack of his DNA on the bra itself is significant (http://www.telegraph.co.uk/news/3255101/DNA-on-Meredith-Kerchers-bloodied-bra-was-due-to-lab-contamination-claims-Sollecito.htmlhttp://www.telegraph.co.uk/news/3255101/DNA-on-Meredith-Kerchers-bloodied-bra-was-due-to-lab-contamination-claims-Sollecito.html), “But defence lawyers used a mannequin's bust and a white bra to argue that it would be impossible for Mr Sollecito's DNA only to have ended up on the tiny clasp and not the rest of the bra if he had touched it or handled it.”

The Hampikian/Johnson open letter said, “Neither Raffaele Sollecito’s nor Amanda Knox’s DNA was found on: the remainder of the bra that was found with the victim, other items of victim’s clothing, objects collected from the room where the victim was found, or in samples from the victim’s body. These evidentiary samples were all collected the day the body was discovered.”

The lack of Sollecito’s or Knox’s DNA on anything in Meredith’s room except the bra clasp is hard to square with an attack that the prosecution claims to have lasted at least 20 minutes.

Conclusions

The main issues I have with the clasp are that it must have been handled by at least one unknown person, that it picked up dust during the 47 days, and that there are deposits of DNA from other individuals on it.

The Johnson/Hampikian letter deserves the last word: “Handling and movement of this sample has compromised its probative value. The laboratory results for this sample cannot reliably be interpreted to show that the DNA of Raffaele Sollecito was actually on the bra clasp at the time of Meredith Kercher’s murder, and it does not establish how or when this DNA was deposited or transferred.”

Forensic DNA contamination

2010-01-24T18:00:00.002-05:00

Part IV in a series on the Knox/Sollecito case

Before we examine the bra clasp in the murder of Meredith Kercher, we need to explore the problems of forensic DNA contamination. This background may also help to explain the problems relating to the DNA sample culled from a kitchen knife discussed in part I of this series.

Definition

In An Introduction to Forensic DNA Analysis, p. 14, Norah Rudin and Keith Inman “define contamination as the inadvertent addition of an individual’s physiological material or DNA during or after collection of the sample as evidence…A contaminated sample is one in which the material was deposited during collection, preservation, handling, or analysis.” When this is done deliberately, this constitutes evidence-tampering, although there is no bright line between tampering and contamination.

Proper collection of evidence

Dick Warrington has written two useful articles on contamination for Forensics magazine. He stresses the importance of changing gloves frequently and using disposable tools. If disposable tools are not available, one must clean them between handling different pieces of evidence. In the 2009 article he cautions, “If you pick up one piece of evidence and then pick up another piece of evidence you can transfer evidence from the first item to the second item. You can avoid this kind of cross-contamination if you remember to change your gloves before handling each piece of evidence.”

Sources of contamination

The polymerase chain reaction (PCR) technique is used to increase the amount of (amplify) DNA by a maximum of 2ⁿ times, where n is the number of cycles of PCR. Because n is typically greater than twenty, this process amplifies the amount of DNA in every sample by over one-millionfold.

In Forensic DNA Typing, p. 152, John M. Butler notes “Contamination implies the accidental transfer of DNA. There are three potential sources of contamination when performing PCR: sample contamination with genomic DNA from the environment, contamination from samples during preparation, and contamination of a sample with amplified DNA from a previous PCR reaction (Lygo et al. 1994). The first source of contamination is largely dependent on sample collection at the crime scene and the care taken there by the evidence collection team (see Chapter 3). Environment contamination can be monitored only in a limited sense by ‘substrate controls’ (Gill 1997). The latter two sources of contamination can be controlled and even eliminated by using appropriate laboratory procedures and designated work areas (see Chapter 4).”

Footnotes for Butler

Gill, P. (1997) Forensic Science International, 85, 105-111.

Gill, P. and Kirkham, A. (2004) Journal of Forensic Sciences, 49(3), 485-491.

Lygo, J.E. et al., (1994) International Journal of Legal Medicine, 107, 77-89.

Dr. Donald Riley writes, “It is often said that the most critical source of PCR contamination is DNA from previous PCRs. Again, a PCR produces many DNA copies of the target DNA sequences. Due to shear number, these copies (called amplicons) are a hazard for future PCRs… However, a more dangerous source of contamination is what is called genomic DNA. This is DNA that hasn't yet been amplified. Genomic DNA doesn't have the high concentration of the target DNA copies but is a hazard because genomic DNA could produce an entirely false DNA profile. Full profile contaminants have been documented on multiple occasions and in multiple laboratories. Partial profile contaminants are more common and sometimes constitute a poorly recognized risk in using partial profiles in evidentiary samples as evidence. When contamination occurs there is rarely any way to confirm how it happened.” (emphasis added) The wonder of the PCR technique, its ability to make almost unlimited quantities of DNA, is also its danger.

Preventing and detecting contamination in the lab: the limits of negative controls

Donald Riley delineates some parallels between sterile technique and the techniques used in DNA forensics lab to minimize contamination. However, he also notes that clinically sterile equipment or reagents might still harbor DNA and that DNA samples lack an immune system to ward off contaminants. Moreover, good technique does not ensure a zero probability of contamination. Hence, there is a need for negative control experiments.

Terri Sundquist and Joseph Bessetti of Promega Corporation write:

“A ‘reagent blank’ control consists of all reagents used during sample processing but contains no sample. This control is used to detect DNA contamination of the analytical reagents used to prepare the sample for analysis. In a separate negative control reaction, water is used instead of extracted sample or reagent blank. This negative control reaction is often referred to as the ‘no-template’ control and allows identification of contamination in the amplification reagents themselves.”

However, Donald Riley noted some deficiencies in negative controls, “Alternatively, the blank may show no profile, consistent with, but not proving that contamination didn't occur. Unfortunately, a few forensic DNA laboratories omit their controls…Good PCR technique is no guarantee that contamination didn't influence the results. Steps must be taken to try and detect contamination. Negative controls are blank PCRs that have all the components of the evidentiary PCRs but have no other DNA added intentionally. Fortunately, there are often two negative controls used, one when the DNA is extracted, and another when the PCR is set up. Any PCR signal in the negative control would warn that contamination has occurred. Unfortunately, the negative controls are virtually the only warning of PCR contamination. Negative controls may alert the analyst to general contamination occurring within the lab or the lab reagents. These controls don't offer protection against contamination occurring before the samples arrived at the PCR lab. Negative controls also can't rule out contamination of individual samples. The individual samples lack individual signs of contamination if it occurs. Unlike a human patient, a PCR is incapable of showing signs of infection (contamination) such as fever or undue pain. PCRs also have no immune system to ward off contaminants.”

Butler, pp. 152-154, implicitly recognizes the problems associated with the PCR amplification process:

“The possibility of laboratory contamination is assessed with ‘negative controls’ that test for contamination of PCR reagents and tubes. Basically, a negative control involves running a blank sample through the entire process in parallel with the forensic case evidence. The same volume of purified water as DNA template in the other samples is added to a negative control PCR reaction. If any detectable PCR products are observed in the negative control, then sources of contamination should be sought out and eliminated before proceeding further…To reduce contamination problems during the laboratory examination of DNA samples, all pre-PCR and post-PCR amplication reactions should be kept physically separate. Laboratory contamination is probably impossible to avoid completely, but can be proactively assessed with negative controls and staff elimination databases (Gill and Kirkham, 2004).”

Norah Rudin and Keith Inman (p. 15) state: “Once the sample is in the laboratory where it can be dried and chilled, the potential for contamination is mostly from other samples undergoing processing at the same time…Precautions include processing evidence and reference samples separately in space and time, restricting PCR product to an isolated room, and using controls to detect contamination in any batch of samples.” (emphasis added)

But William C. Thompson is clear about the limitations of negative controls,

“A false incrimination can also occur through cross-contamination among evidentiary samples. Even labs that are careful to test reference samples separately from evidentiary samples often process all of the evidentiary samples from a case together, creating the potential for false matches. I recently reviewed a case processed by the Los Angeles Police Department DNA laboratory in which samples from a bloody murder scene were being processed in the same batch as samples from items collected in a suspect’s house. Due to an analyst’s error in the case, DNA from the murder victim accidentally ended up in a control sample. This error was detected because the control sample was a “blank” which was supposed to contain no DNA. However, it was merely happenstance that the accidental transfer of DNA ended up in a blank control rather than another sample in the same batch. If the victim’s DNA had instead ended up in one of the samples from the suspect’s house, I believe that the error would not have been detected and would have led to a false laboratory report saying that the murder victim DNA had been found on an item collected in the suspect’s house. Defense lawyers need to think carefully about the potential for such errors because experience shows that they can and do occur.” (emphasis added)

Riley concurs, writing, “These controls don't offer protection against contamination occurring before the samples arrived at the PCR lab. Negative controls also can't rule out contamination of individual samples. The individual samples lack individual signs of contamination if it occurs.” The bottom line is that some instances of contamination probably go undetected.

Dishonesty involving controls

William C. Thompson delineates another problem:

“While most of the problems are due to inadvertent mistakes, a number of cases involving dishonesty have also come to light. DNA analysts have recently been fired for scientific misconduct, and specifically for falsification of test results, by a number of forensic laboratories, including labs operated by the FBI,¹⁴ Orchid-Cellmark (another large private DNA laboratory),¹⁵ the Office of the Chief Medical Examiner in New York City,¹⁶ and the United States Army.¹⁷ In all of these cases, the analysts were caught faking the results of control samples designed to detect instances in which cross-contamination of DNA samples has occurred.”

Footnotes for Thompson

14. See, U.S. Department of Justice, Office of the Inspector General, The FBI DNA Laboratory: A Review of Protocol and Practice Vulnerabilities, May 2004. Available online at: http://www.usdoj.gov/oig/special/0405/index.htm

15. Laura Cadiz, Md.-based DNA lab fires analyst over falsified tests, Baltimore Sun, Nov. 18, 2004.

16. Author’s interview with Robert Shaler, former Director of the OCME DNA Laboratory.

17. Associated Press, Worker in Army lab may have falsified DNA test result. Aug. 27, 2005; Memorandum For All Staff Judge Advocates Re: Brady Notice by Lisa Kreeger, Staff Attorney, Department of the Army, October 17, 2005 (on file with the author).

When the investigators and the DNA laboratory are in communication, the investigators sometimes make it clear that a certain result is desired. Thompson and colleagues (2003) write:

“Part of the problem is that forensic scientists refuse to take appropriate steps to ‘blind’ themselves to the government’s expected (or desired) outcome when interpreting test results. We often see indications, in the laboratory notes themselves, that the analysts are familiar with facts of their cases, including information that has nothing to do with genetic testing, and that they are acutely aware of which results will help or hurt the prosecution team. A DNA analyst in one case wrote:

‘Suspect-known crip gang member — keeps ‘skating’ on charges-never serves time. This robbery he gets hit in head with bar stool — left blood trail. [Detective] Miller wants to connect this guy to scene w/DNA …’

In another case, where the defense lawyer had suggested that another individual besides the defendant had been involved in the crime, and might have left DNA, the DNA laboratory notes include the notation: ‘Death penalty case. Need to eliminate [other individual] as a possible suspect.’”

The problem of having the laboratory be independent from the prosecution is a well-known one (http://learn.genetics.utah.edu/content/labs/gel/forensics/): “The [National Research Council] recommends that forensic DNA analysis be conducted by an unbiased outside laboratory that maintains a high level of quality control and a low error rate.”

Case Studies of Contamination from Co-Processing of Samples

Thompson gives two examples of suspect identification on the basis of dubious cold hits:

“In one particularly interesting Australian case, DNA on the clothing of a murdered toddler named Jaidyn Leskie was linked, via a ‘cold hit,’ to a young ‘mentally challenged’ woman who lived hundreds of miles away and who, by all accounts, had never left her own village. Police could find no way to link the young woman to the Leskie murder and at first dismissed the ‘cold hit’ as an ‘adventitious’ (coincidental) match. However, a coroner’s investigation established that DNA from the young woman had been processed through the same laboratory at about the same time as the toddler’s clothing. The young woman had allegedly been the victim of a sexual assault involving a condom. Although laboratory personnel maintain that accidental transfer of samples between cases is impossible, it now appears almost certain that the young woman’s DNA from the outside of the condom accidentally contaminated samples from the toddler’s clothing.

“The facts of some recent cases in the United States have also raised suspicions about false cold hits due to contamination across cases. For example, in 2002, while investigating the 1969 murder of University of Michigan law student Jane Mixer, the Michigan State Police Crime Laboratory in Lansing found DNA of two men on her clothing. The profiles were searched through a database and matched two Michigan men, Gary Leiterman and John Ruelas. Police immediately suspected that Leiterman and Ruelas had been involved in the murder, but there was a problem — Ruelas was only four years old when Mixer was killed and had been living with his parents in another city. According to news accounts, police could find no link between young Ruelas and Mixer.²⁹ That did not deter Washtenaw County Assistant Prosecutor Steven Hiller who charged Leiterman with the murder. Hiller ‘created a scenario placing a young Ruelas at the [murder] scene as a chronic nose-bleeder whose blood dropped on Mixer.’³⁰ There is, however, another possible explanation for this ‘cold hit.’ Examination of laboratory records revealed that known samples of DNA from both Leiterman and Ruelas were being processed in the Michigan State lab on the same day as the old samples from the Mixer murder.³¹ Both men were being tested in connection with other cases unrelated to the Mixer murder. Although the Michigan State laboratory maintains that cross-contamination of samples across cases was impossible, it seems a very strange and unlikely coincidence that two men who, according to the prosecutor, were present when Mixer was murdered in 1969 just happened to have their DNA tested (for other cases) on the very same day as samples from the Mixer case were tested. Leiterman was nevertheless convicted of Mixer’s murder in 2005.” (emphasis added)

Footnotes for Thompson

29. Maryanne George, Murder case mystery deepens. Detroit Free Press, Jan 15, 2005.

30. According to news accounts, Hiller offered no evidence to support this theory. Liz Cobbs, Judge raises possibility evidence may have been contaminated at State Police lab, Ann Arbor News, May 11, 2005.

31. Author’s interview with Professor Dan Krane (a defense expert in the case). Also, Thersa Mask, Mixer’s dad is clear on one thing, Detroit Free Press, July 13, 2005.

Contamination is surely an unlikely event, at least in that it happens less frequently than it does not happen. Yet, which is less likely in these two cases, contamination or the involvement of the suspect identified by these cold hits? And even if improbable, how does this speak to a reasonable doubt?

Borderline situations

Suppose that a technician runs evidentiary samples and reference samples in the same batch out of laziness or ignorance. Suppose a different technician runs these samples together knowing that there is a greater chance of contamination. These two cases are distinguishable only if one knows the intent of the technicians. The second case is close to outright evidence tampering, but the similarity of the two situations implies that there is no bright line between sloppiness and outright fraud.

Frequency of Contamination

This is difficult to estimate for a variety of reasons. Donald Riley reports that some laboratories omit controls or perform them in such a way as to lessen the chances of detection. Thompson reports that many laboratories fail to record instances of contamination in a log book, despite the advice of the FBI. Some labs take the overly sanguine approach that if they detect contamination, it is not really an error. Thompson writes, “The surprise for defense lawyers who have managed to gain access to these files is how voluminous they are. Errors occur regularly.”

Summary

Forensic DNA contamination is a well-known phenomenon that good labs attempt to minimize, and to document when it does happen.
PCR-amplified DNA is one of the most serious contamination threats in a DNA forensics lab.
Keeping a clean DNA lab is a little like maintaining a sterile environment, only more difficult.
It is difficult to estimate the frequency of contamination for a variety of reasons. However, many instances have been documented.
Negative controls can be used to identify contamination, but they only detect contamination in blanks, not evidentiary samples.
Fradulent DNA forensics often takes the form of falsifying negative controls.

Bibliography

John M. Butler, Forensic DNA Typing (2005), 2^nd ed., Elsevier.

Terri Sundquist and Joseph Bissetti

http://www.promega.com/profiles/802/ProfilesinDNA_802_11.pdf

Donald Riley

http://www.scientific.org/tutorials/articles/riley/riley.html

Nora Rudin and Keith Inman, An Introduction to Forensic DNA Analysis, 2^nd ed. (2002).

William C. Thompson 2006

http://www.nacdl.org/public.nsf/0/6285f6867724e1e685257124006f9177

William C. Thompson; Simon Ford; Travis Doom; Michael Raymer; Dan E. Krane (2003)

http://www.nacdl.org/public.nsf/698c98dd101a846085256eb400500c01/c1d63d2bd1a582cf85256e540074c146?OpenDocument&Highlight=0,rape

Dick Warrington Forensics April/May 2005

http://www.forensicmag.com/articles.asp?pid=41

Dick Warrington Forensics April/May 2009

http://www.forensicmag.com/articles.asp?pid=275

Occam's razor versus Knox's behavior

2010-01-19T17:59:00.006-05:00

First, kudos to Observer for some fine links. I especially liked http://lesswrong.com/lw/1j7/the_amanda_knox_test_how_an_hour_on_the_internet/ and I hope that everyone takes the time to read the postscript. Second, the comments thread for the previous post on Dr. Kekule has drifted into a discussion of Knox’s behavior. That’s OK; I was considering hosting an open thread on her behavior/credibility anyway. So, let’s keep using the Kekule thread for questions of behavior and try to stay more on topic in future forensics threads. Comments are disabled for this very brief post.

Update (22 January 2010)
I will consider submissions on the subject of the Knox/Sollecito case. Here is your chance to be a guest blogger.

Commentary on the Knox and Sollecito case from Dr. Alexander Kekule

2010-01-16T18:59:00.003-05:00

Professor Alexander S. Kekule wrote following commentary for the German newspaper Der Tagesspiegel on 9 December 2009 (http://www.tagesspiegel.de/meinung/kommentare/Amanda-Knox-DNA-Spur;art141,2970520). Professor Kekule holds both M.D. and Ph. D. degree and is a virologist. I am very grateful to two anonymous friends, who did most of this translation.

Amanda Knox - on ice angel’s trail
The verdict against the “icy-eyed angel” has met with criticism, especially in the US. Actually, the evidential value of DNA tests is over estimated.

Last Friday one of the most controversial murder trials of recent years ended. A jury in Perugia, Italy sentenced 22-year-old Amanda Knox, and 25-year-old Raffaele Sollecito to 25 years imprisonment. The Court regarded it as proven that the American student and her boyfriend in the town of Puglia, Italy in November 2007 brutally abused and murdered a fellow student. Another accomplice, 23-year-old Rudy Guede, in a separate case, was already sentenced to 30 years. The conviction of the "icy-eyed angel" met with criticism, especially in the U.S., because the evidence was allegedly insufficient.

Under Italian law, the judge must justify the verdict within three months following the trial. However, if the reports of the process observers are correct, already the prosecution relied mainly on forensic evidence. The version presented by the prosecutor, who in the court appears to have followed essentially something that sounds bizarre, but not impossible: during the night of the crime, Knox was to have pushed her British flatmate Meredith Kercher to organize a sort of belated Halloween orgy with the two men. When she refused, Sollecito held her tightly, Guede raped her, and Knox cut her throat.

The evidence against the Ivorian Guede, who has a criminal record, appears overwhelming. Traces of his sperm were found on the dead woman, his finger and footprints in her blood. Afterwards he fled to Germany. However, he denies the murder and accuses Knox. The evidence is more scant against the American woman and her boyfriend. Knox herself came under suspicion because she claimed to have first seen a Congolese bar owner at the scene. Meanwhile, she claims not to having been at home at all that night, and to have found the corpse only the next morning. Evidence of her and her boyfriend’s finger- and footprints in the shared home are no proof since both were frequently in the apartment. Also, the smashing of the window from the inside, presumably executed by the perpetrator to fake a forced entry, could have been the doing of Guede, whom Knox and Sollecito accuse of the crime.

All this would hardly suffice for a conviction - if there were not three tiny DNA traces. Sollecito's genetic material was found on a bra closure of the victim, which had apparently come loose during a violent opening. And in Sollecito's apartment, investigators found a kitchen knife with a traces of the victim's DNA on the blade and Knox’s DNA on the handle.

Indeed, confusion of individuals through "genetic fingerprinting" is almost impossible. It examines not the actual genes in the DNA (they are quite similar in all humans), but the useless segments between them (satellite DNA). Because it carries no genetic information, satellite DNA is copied sloppily and often repeatedly during the formation of egg and sperm. This results in regions of repetitive DNA, the repeat pattern of which is unique for each person. The likelihood of confusion is smaller than for fingerprinting.

But the forensic DNA analysis has its pitfalls. While a real fingerprint shows that the person has actually touched an object, DNA evidence may arise in many different ways. In the Italian murder case, the DNA on the bra clasp could also have originated from a skin scale, lost by Sollecito days earlier in the apartment. The DNA traces on the knife blade could have been transmitted through the hands of Amanda Knox, who lived together with the victim and used her boyfriend’s knife for cooking. The evidence would have more weight if in addition blood stains were found.

All three convicted have appealed the convictions. In that case, the DNA traces have to be re-evaluated, because the presumption of innocence also applies to ice angels. As the mother of the victim has rightly said: "At the end of the day only evidence counts, nothing else."

The author is Professor of Medical Microbiology and Virology at Halle, Germany, and Director of the Institute for Medical Microbiology. Photo: J. Peyer

Ominous Parallels: Comparing the Duke lacrosse case to the Knox/Sollecito case

2010-01-10T21:19:00.003-05:00

Amanda Knox and Raffaele Sollecito were convicted of murdering Meredith Kercher, Amanda’s flatmate in Perugia, Italy, in 2009. Both Ms. Kercher and Ms. Knox were studying abroad. Ms. Kercher was from Great Britain, Ms. Knox is from Seattle, Washington; Mr. Sollecito is an Italian student. A third suspect, Rudy Guede, was convicted in 2008. To some students of the Duke lacrosse (DL) case, the Amanda Knox/Raffaelo Sollecito (KS) case is playing like a sequel they did not wish to see.

DNA evidence

In the Duke lacrosse case the only DNA that even might have been from one of the three indicted players was on a fake fingernail found in a trashcan in one of the bathrooms. The DNA was a weak match to David Evans; however, the most likely explanation was that it arose from transfer from items of his in the trashcan, such as dental floss or facial tissue. In the Perugia murder case there are two pieces of evidence, the kitchen knife discussed in part I of this series, and the bra clasp, which will be treated in a future post. The kitchen knife is alleged to have DNA from Ms. Knox on the handle and a trace of DNA from Ms. Kercher on the blade (http://viewfromwilmington.blogspot.com/2010/01/amanda-knox-and-raffaele-sollecito-and.html). The bra clasp is said to have DNA from Ms. Kercher, Mr. Sollecito and possibly three other individuals. Its value as evidence is disputed.

The Prosecutor

DA Michael Nifong not only withheld exculpatory DNA information, but also made inflammatory statements to the press. His conduct was so egregious that a new verb, to Nifong, has entered the English language. Giuliano Mignini has the distinction of having had a book written about his conduct during a murder investigation, The Monster of Florence, by Douglas Preston and Mario Spezi (http://opinionator.blogs.nytimes.com/2009/06/10/an-innocent-abroad/?ref=opinion). Mr. Mignini was indicted in 2006 based upon his actions in the Monster of Florence murder case (http://www.cbsnews.com/blogs/2009/12/07/crimesider/entry5928444.shtml). Mr. Mignini denied any wrongdoing (http://news.bbc.co.uk/2/hi/europe/7883286.stm).

Changing Storyline

After Reade Seligmann’s attorneys released evidence of the younger Mr. Seligmann’s whereabouts at the time of the alleged rape, Mr. Nifong implied that he had a different timeline, a transparent attempt to get around an unimpeachable alibi. In December of 2006, the alleged victim said that she was no longer sure that she had been penetrated by a penis. Many students of the DL case saw this as an attempt to explain away the lack of players’ DNA even in the presence of DNA from other individuals in the AV’s body.

The RS case has been through more changes in storyline than a movie script handled by a dozen writers. Pulitzer Prize winning reporter Timothy Egan wrote in the summer of 2009, “‘Case closed,’ the Italian authorities said in those first days of November, 2007, even though they had yet to arrest the only man [Rudy Guede] who has ever been found guilty of the murder.” At one point the possibility that the murder was related to a Halloween ritual was floated; at the close of the trial this was not mentioned. In both the DL and RS cases the only constant was that the defendants must be guilty.

Presumption of Innocence

A prominent southern writer, Alan Gurganous, wrote an article for the New York Times titled, “Blue Devils Made Them Do It.” Mr. Gurganous said (http://www.nytimes.com/2006/04/09/opinion/09gurganus.html?ex=1302235200&en=97bf0167bd611343&ei=5088&partner=rssnyt&emc=rss), “From north of here, this story must seem like yet another involving Southern frat boys run wild.” Mr. Gurganous does no more than to pay lip service to the principle that a defendant is innocent unless proven guilty. If anyone doubts that many leading figures in Durham and elsewhere trod the presumption of innocence into the ground in this case (in other words, if one doubts that Mr. Gurganous’ view was representative), Taylor and Johnson’s book Until Proven Innocent will disabuse him or her of this notion.

With respect to the KS case “Judge Paolo Michelli, during the pretrial, took the conspiracy for granted. He boasted that he began his reasoning with all three suspects in the murder room. So much for innocent until proven guilty (http://blog.seattlepi.com/dempsey/archives/179047.asp).”

Character assault

Nifong gave about seventy interviews in the first weeks of the DL case. Among his many false assertions was that the players were stonewalling the investigation. The Durham police aided and abetted him.

One of the criticisms leveled against Ms. Knox is that she failed to act appropriately after the murder. Attorney Scott Greenfield posted an essay on the judicial weakness of such an argument (http://blog.simplejustice.us/2009/06/11/how-is-she-supposed-to-act.aspx). Greenfield also wrote (http://blog.simplejustice.us/2009/12/05/a-trial-without-evidence.aspx), “During the summation, the prosecutor told the jury about the things Amanda Knox might have said to Meredith Kercher before the alleged drug-induced orgy that ended with her throat being slashed. ‘You are always behaving like a little saint. Now we will show you. Now we will make you have sex.’ This would be a horrible thing to say, except that it never happened. No one says that such a statement was ever made. But summations in Perugia aren't limited to evidence, as they are here. Rather, this is a permissible indulgence into fantasy, a made up dramatization of what the prosecutors contend might have happened.” Indeed, many of the incidents that have been used to paint Ms. Knox in an unfavorable light are either untrue or misleadingly portrayed, and may be the subject of separate posts.

Irrelevant or false leaked information

Unindicted sophomore Ryan McFayden made an ill-judged allusion to the book and movie “American Psycho” in a private email. Virtually everything written about the hard-to-stomach contents of this email had to do with the character and mental health of its author (I have firsthand knowledge, however, that Ryan McFayden is a polite, thoughtful, and intelligent young man). Too few people have pointed out that the email had nothing to do with the case and that the authorities were wrong to release it.

Amanda Knox’s journal, which was written during her pretrial incarceration, was leaked to the press. Apparently, it had been translated into Italian then back-translated into English. Along the way the meaning changed in ways that were unfavorable to her (http://www.sciencespheres.com/2009/11/crucible-of-perugia.html). Moreover, upon being informed that she was HIV-positive (which was not true), she wrote about her sexual partners in her journal. This information has contributed to her public image as a person of low sexual morals. However, the ethics of leaking her journal have received scant attention. Some of the leaks in the K/S case, such as the claim of receipts for bleach (http://www.timesonline.co.uk/tol/news/world/europe/article2894139.ece), were not presented at the trial and are probably false (http://www.friendsofamanda.org/cleanup.html).

Wendy Murphy

Among the pundits who got the Duke lacrosse case wrong, Wendy Murphy ranks close to the top (http://durhamwonderland.blogspot.com/2006/12/wendy-murphy-file.html). She made numerous factual errors, and speculated wildly and with an unchecked anti-player bias. Her defense of DA Michael Nifong was bizarre (http://liestoppers.blogspot.com/2006/12/wendy-murphy-strikes-again.html).

Students of the DL case might expect similar behaviors with respect to the Knox/Sollecito (KS), and Ms. Murphy does not disappoint (http://www.patriotledger.com/opinions/x1682953943/WENDY-J-MURPHY-Is-Foxy-Knoxy-an-innocent-coed-or-manipulative-murderer). She wrote,” DNA on the handle of the knife that killed the victim matched Knox - and blood on blade matched the victim…Pro-Amanda forces also forget to note that the knife was found hidden in a shoebox, far back inside a closet at Sollecito's apartment - and that the knife had been scrubbed clean with bleach and an abrasive substance - like a Brillo Pad. The defense claimed the sample of Knox's DNA was too small to matter, but ANY DNA is damning evidence - especially on a knife that's been intentionally cleaned and hidden away deceptively in a shoe box, tucked deep inside the closet of a suspect's home.”

Let us focus only on her factual errors about the knife, the subject of Part I of this series (http://viewfromwilmington.blogspot.com/2010/01/amanda-knox-and-raffaele-sollecito-and.html). There was no blood on the blade, and this is one of the main reasons to doubt that DNA signals arising from when the knife was swabbed did not really originate with the blade at all (http://www.sciencespheres.com/2009/10/lcn-dna-profiling-part-ii-watch-where.html). The knife was found in a kitchen drawer with other knives. The police stored it in a shoebox. Ms. Murphy does not explain how she divined that Ms. Knox and Mr. Sollecito used bleach to clean the knife, nor does she bother to tell us that bleach is so effective at destroying DNA that it is routinely used in DNA labs for that very reason. If bleach and a brillo pad were used to clean the knife, it is very difficult to see how any DNA could remain. Finally, the amount of DNA observed was so small that to say it matched Ms. Kercher’s profile is a stretch; calling it a partial match is a better description, and it is quite possible that it originated from Ms. Kercher’s DNA in the laboratory itself.

Courtroom Demeanor

In Until Proven Innocent Taylor and Johnson wrote (p. 180) about Collin Finnerty facing a wall of photographers while awaiting his first appearance before a judge: “He tried to remain expressionless. In that atmosphere, if he had smiled the media would have called it a smirk; if he had frowned they would have called it an angry glare.” Nevertheless one sportswriter wasn’t sure if the younger Mr. Finnerty’s expression was one of shock and fear or or smugness (http://www.usatoday.com/sports/columnist/saraceno/2006-04-18-duke_x.htm).

Frank Sfarzo wrote (http://perugia-shock.blogspot.com/2009/11/migninis-rage-against-knox-and.html) wrote of Amanda Knox, “If she smiles it's wrong, if she cries it's wrong, if she moves it's wrong, if she's still it's wrong, if she watches it's wrong, if she doesn't watch it's wrong."

The role of the blogosphere

In the Duke lacrosse case the blogosphere was able to go into issues in greater depth than the mainstream media and correct a number of important errors. Here is a partial honor roll: Bill Anderson, CrystalMess, Durham in Wonderland, John In Carolina, LaShawn Barber, Liestoppers, and TalkLeft. In the Amanda Knox case, Dr. Mark Waterbury (http://www.sciencespheres.com/2009/10/seven-deadly-sins-of-knoxsollecito.html) and Candace Dempsey (http://blog.seattlepi.com/dempsey/archives/129925.asp) have been covering forensics and general aspects of the case, respectively. Ms. Dempsey may have been the first to point out the similarities between the DL and RS cases.

Final Thoughts

This post is intended as an overview of some of the problems in the Knox/Sollecito case. Any one of these points could easily be expanded into its own post. We will try to explore some of them in the coming months, especially those involving forensics.

Part II in a series.

Update (22 January 2010)

Seattle, WA (USA), near where Amanda Knox's family lives, and Perugia, Italy are sister cities. Maybe Durham, NC should be Perugia's sister city, instead.