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.
Tuesday, January 19, 2010
Saturday, January 16, 2010
Commentary on the Knox and Sollecito case from Dr. Alexander Kekule
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
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
Sunday, January 10, 2010
Ominous Parallels: Comparing the Duke lacrosse case to the Knox/Sollecito case
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 KS 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.
Sunday, January 3, 2010
Amanda Knox and Raffaele Sollecito and the murder of Meredith Kercher, Part I
Introduction to the case
This post will be the first in a series of articles on the Amanda Knox/Raffaele Sollecito case. Amanda Knox is an American student, and Italian Raffaele Sollecito is her former boyfriend. Both of these two individuals were convicted of the murder of British student Meredith Kercher in late 2009. Rudy Guede was previously convicted of her murder in a separate, fast-track trial in 2008. Many in the United States have criticized the prosecutor’s summation (http://blog.simplejustice.us/2009/12/05/a-trial-without-evidence.aspx) and the forensics (http://www.sciencespheres.com/2009/10/methods-of-polizia-pseudoscientificaa.html).
The DNA forensics in this case centers around two items, Meredith Kercher’s bra clasp and Raffale Sollecito’s kitchen knife. This article will focus on some of the issues surrounding the knife. The kitchen knife had Amanda’s DNA on the handle, which is not surprising given that Amanda cooked at Raffaele’s house. But the prosecution claims that their forensics investigators found a small amount of Meredith’s DNA on the blade. This claim is dubious at best, but even if it were true, the knife cannot be the sole murder weapon. Let’s take up the second question first.
Problems with the knife
First, Mr. Sollecito’s kitchen knife was too large to have made two of the three wounds on Ms. Kercher’s body. The smaller knife, the one that made the first two wounds, may have also made the third wound. Second, the kitchen knife does not match the bloody outline of a knife at the crime scene (http://www.newsweek.com/id/216903/page/2). Third, Newsweek reported that, “an officer testifying at the trial said he used ‘police intuition’ when choosing that knife from Sollecito's cutlery.” If there were multiple knives in the drawer, why choose one that had a different outline from the one whose outline was on Ms. Kercher’s sheets? The claim of police intuition does not make any sense.
But possibly the most serious reason for doubting that DNA was really on the knife is that it tested negative for blood (http://www.sciencespheres.com/2009/12/why-knife-was-not-knife.html. Dr. Stefanoni opined that the knife had been cleaned with bleach. This is a puzzling claim even at the outset, because bleach does not leave a corrosive mark on stainless steel; however, the prosecution’s argument becomes even more questionable upon further inspection. Drs. Elizabeth A. Johnson and Greg Hampikian, both experts in DNA forensics, coauthored an open letter about some of the evidence in this case (http://www.friendsofamanda.org/articles.html). About the cleaning of the knife, they said:
This DNA does not originate from blood. A highly sensitive chemical test for blood was negative, and it is unlikely that all chemically detectable traces of blood could be removed while retaining sufficient cells to produce a DNA profile consistent with the victim.
Indeed, bleach is so effective at destroying DNA that it is used in research laboratories for that very purpose (A. M. Prince, L. Andrus PCR: How to kill unwanted DNA, Biotechniques, Vol. 12, No. 3, 358-360). It far more effective than acid! Bleach is also used in some anthropological work to destroy unwanted DNA on the surface of an object that would contaminate valuable DNA inside. The very fact that there was no blood on the knife suggests that there was also no DNA on the knife; therefore, contaminating DNA is the most likely source for the signals that were observed. These three reasons call into question whether the kitchen knife had anything to do with the murder.
What the laboratory of Dr. Patrizia Stefanoni should have done is to save some of the material for a retest. As mentioned previously, this lab should have tested other knives, and perhaps other, random implements, in Raffele Sollecito’s drawer in the same way. Would DNA have also shown up on a different knife? These control experiments would have clarified whether Meredith Kercher’s DNA was really on the knife or not. However, we can at least examine the data that were produced from the knife.
Introduction to DNA forensics
Modern DNA forensic analysis (birg.cs.wright.edu/talks/Human Identification 2008.ppt) produces fluorescent signals that must be observed and interpreted properly to exclude or not exclude a person as a DNA contributor. The fluorescent signals arise from a collection of DNA molecules of various lengths (sizes) that are produced by chopping the DNA strands at a set of specific locations, and then separated using capillary electrophoresis. The pattern of signals from the DNA form what is called an electropherogram. The electropherogram from a piece of evidence is compared against reference samples from various individuals.
Fluorescence Spectroscopy
Spectroscopy is the study of how light interacts with matter. All spectroscopic experiments involve the observation of photons of light above a background of random noise. All forms of spectroscopy must contend with the fact that signal-to-noise (S/N) ratios are not infinite. The S/N ratio is a measure of the strength of the signal and is often related to the concentration of the chemical species that produces it. DNA forensics makes use of chemical labels that produce fluorescence. In a DNA electropherogram the S/N ratio is measured in relative fluorescence units (RFUs). Why are S/N ratios so important in regards to the DNA sample on the knife blade in the Amanda Knox/Raffaele Sollicito case?
The open letter coauthored by Dr. Elizabeth and Professor Gregory Hampikian and cosigned by several others had this to say about the knife DNA:
An extremely low level, partial DNA profile was developed for the blade swabbing using the Identifiler kit. The alleles detected were consistent with the DNA of the victim. The highest peak in the electropherogram was approximately 100 relative fluorescence units (rfu), while 21 of the 29 peaks that were detected and labeled as alleles fell between 20 and 50 rfu….No credible scientific evidence has been presented to associate this kitchen knife with the murder of Meredith Kercher. (emphasis added)
Signal-to-Noise Ratios
To understand their conclusion we need to know more about signals and noise. Suppose you are driving your car away from your home town and you have tuned in your favorite FM radio station. As you travel farther away, the music gets fainter (the signal is now weaker), so you turn up the gain (amplification). Now the music is more audible, but you start to hear crackles (the noise). Amplification affects both signal and noise. Eventually, you will travel so far away that the noise becomes more unpleasant and you switch to a different station (the S/N ratio has become unacceptably low).
Now let us ask what would happen if you were 200 miles away and you tuned to the frequency of your favorite FM station in your home city. You would hear nothing but noise, sometimes called static. Based only on your observation, you could not say that the station was even broadcasting. It is not that you would deny that the station was broadcasting, it is just that you cannot affirm it on the basis of your observation; your observation is indeterminate.
Each DNA forensic laboratory establishes a threshold value for the size of acceptable peaks, but the threshold values are not identical from lab-to-lab. Setting a minimum threshold does not automatically favor the defense or the prosecution. The lowest such value of which I am aware is 40 (http://www.bioforensics.com/articles/champion1/champion1.html). At first this seems large, since peaks smaller than this are still greater than noise, but these peaks are small relative to those typically encountered in DNA electropherograms.
Instead of examining the specific choice of a threshold value, let us discuss why setting them in advance of the experiment is so important. Scientists set up their experiments to test (falsify) their hypotheses. If the signal-to-noise level in any spectroscopic experiment falls below the threshold, any hypothesis requiring that the signal be above the threshold must be rejected. The reason one sets the threshold first is to avoid bias. The textbook An Introduction to Forensic DNA analysis, 2nd ed. (Rudin, N. and Inman, K., CRC Press 2002, p. 121) states (emphasis added), “It is important to have some predetermined limit to distinguish what is signal and what is noise.” If one treats the threshold as flexible, the very purpose for setting it prior to running the experiment is defeated.
How does this relate to the DNA electropherogram of the knife sample (http://www.friendsofamanda.org/articles.html, Figure 1)? 16 out of 29 peaks are lower than 40 in S/N, and 22 are lower than 50 RFU. Dr. Stefanoni herself wrote (http://www.thedailybeast.com/blogs-and-stories/2009-09-14/no-mistrial-for-knox/) the words “too low” with respect to the knife. In other words these peaks are too small to count as music in the car radio analogy above.
It would be helpful to know the threshold value regularly employed in Dr. Stefanoni’s lab, but it could have been as high as 150 RFU and is very unlikely to be below 40 RFU. The signals above the threshold might constitute a partial profile of Ms. Kercher’s DNA. However, such a partial match is very problematic (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.
Conclusions
The kitchen knife cannot be the sole murder weapon, and it most likely had nothing to do with the crime whatsoever. The only evidence that it might have played any role is the finding of DNA that is at best a partial match to Ms. Kercher’s DNA on the blade, and that almost certainly came from contamination during the test. Given the weakness of the fluorescence signals and especially the lack of blood on the knife, the signals observed do not tie the knife to the crime. No wonder that the open letter quoted above ends its section on the kitchen knife by concluding that there is no forensic evidence to link it to the crime. But an equally troubling problem with the prosecution’s theory is that Ms. Knox and Mr. Sollecito would bother to take this knife from his flat to the dwelling occupied by Ms. Knox, Ms. Kercher, and their two roommates in preference to using knives found in the kitchen of these four roommates. What sense does that make? It is typical of this case that Occam’s razor is so often ignored.
Update, 01/18/2010
The prosecuation's theory would also have us believe that Knox would not dispose of the supposed murder weapon, and despite cleaning the blade extensively, would not clean her fingerprints from the handle. This strikes me as unlikely.
This post will be the first in a series of articles on the Amanda Knox/Raffaele Sollecito case. Amanda Knox is an American student, and Italian Raffaele Sollecito is her former boyfriend. Both of these two individuals were convicted of the murder of British student Meredith Kercher in late 2009. Rudy Guede was previously convicted of her murder in a separate, fast-track trial in 2008. Many in the United States have criticized the prosecutor’s summation (http://blog.simplejustice.us/2009/12/05/a-trial-without-evidence.aspx) and the forensics (http://www.sciencespheres.com/2009/10/methods-of-polizia-pseudoscientificaa.html).
The DNA forensics in this case centers around two items, Meredith Kercher’s bra clasp and Raffale Sollecito’s kitchen knife. This article will focus on some of the issues surrounding the knife. The kitchen knife had Amanda’s DNA on the handle, which is not surprising given that Amanda cooked at Raffaele’s house. But the prosecution claims that their forensics investigators found a small amount of Meredith’s DNA on the blade. This claim is dubious at best, but even if it were true, the knife cannot be the sole murder weapon. Let’s take up the second question first.
Problems with the knife
First, Mr. Sollecito’s kitchen knife was too large to have made two of the three wounds on Ms. Kercher’s body. The smaller knife, the one that made the first two wounds, may have also made the third wound. Second, the kitchen knife does not match the bloody outline of a knife at the crime scene (http://www.newsweek.com/id/216903/page/2). Third, Newsweek reported that, “an officer testifying at the trial said he used ‘police intuition’ when choosing that knife from Sollecito's cutlery.” If there were multiple knives in the drawer, why choose one that had a different outline from the one whose outline was on Ms. Kercher’s sheets? The claim of police intuition does not make any sense.
But possibly the most serious reason for doubting that DNA was really on the knife is that it tested negative for blood (http://www.sciencespheres.com/2009/12/why-knife-was-not-knife.html. Dr. Stefanoni opined that the knife had been cleaned with bleach. This is a puzzling claim even at the outset, because bleach does not leave a corrosive mark on stainless steel; however, the prosecution’s argument becomes even more questionable upon further inspection. Drs. Elizabeth A. Johnson and Greg Hampikian, both experts in DNA forensics, coauthored an open letter about some of the evidence in this case (http://www.friendsofamanda.org/articles.html). About the cleaning of the knife, they said:
This DNA does not originate from blood. A highly sensitive chemical test for blood was negative, and it is unlikely that all chemically detectable traces of blood could be removed while retaining sufficient cells to produce a DNA profile consistent with the victim.
Indeed, bleach is so effective at destroying DNA that it is used in research laboratories for that very purpose (A. M. Prince, L. Andrus PCR: How to kill unwanted DNA, Biotechniques, Vol. 12, No. 3, 358-360). It far more effective than acid! Bleach is also used in some anthropological work to destroy unwanted DNA on the surface of an object that would contaminate valuable DNA inside. The very fact that there was no blood on the knife suggests that there was also no DNA on the knife; therefore, contaminating DNA is the most likely source for the signals that were observed. These three reasons call into question whether the kitchen knife had anything to do with the murder.
What the laboratory of Dr. Patrizia Stefanoni should have done is to save some of the material for a retest. As mentioned previously, this lab should have tested other knives, and perhaps other, random implements, in Raffele Sollecito’s drawer in the same way. Would DNA have also shown up on a different knife? These control experiments would have clarified whether Meredith Kercher’s DNA was really on the knife or not. However, we can at least examine the data that were produced from the knife.
Introduction to DNA forensics
Modern DNA forensic analysis (birg.cs.wright.edu/talks/Human Identification 2008.ppt) produces fluorescent signals that must be observed and interpreted properly to exclude or not exclude a person as a DNA contributor. The fluorescent signals arise from a collection of DNA molecules of various lengths (sizes) that are produced by chopping the DNA strands at a set of specific locations, and then separated using capillary electrophoresis. The pattern of signals from the DNA form what is called an electropherogram. The electropherogram from a piece of evidence is compared against reference samples from various individuals.
Fluorescence Spectroscopy
Spectroscopy is the study of how light interacts with matter. All spectroscopic experiments involve the observation of photons of light above a background of random noise. All forms of spectroscopy must contend with the fact that signal-to-noise (S/N) ratios are not infinite. The S/N ratio is a measure of the strength of the signal and is often related to the concentration of the chemical species that produces it. DNA forensics makes use of chemical labels that produce fluorescence. In a DNA electropherogram the S/N ratio is measured in relative fluorescence units (RFUs). Why are S/N ratios so important in regards to the DNA sample on the knife blade in the Amanda Knox/Raffaele Sollicito case?
The open letter coauthored by Dr. Elizabeth and Professor Gregory Hampikian and cosigned by several others had this to say about the knife DNA:
An extremely low level, partial DNA profile was developed for the blade swabbing using the Identifiler kit. The alleles detected were consistent with the DNA of the victim. The highest peak in the electropherogram was approximately 100 relative fluorescence units (rfu), while 21 of the 29 peaks that were detected and labeled as alleles fell between 20 and 50 rfu….No credible scientific evidence has been presented to associate this kitchen knife with the murder of Meredith Kercher. (emphasis added)
Signal-to-Noise Ratios
To understand their conclusion we need to know more about signals and noise. Suppose you are driving your car away from your home town and you have tuned in your favorite FM radio station. As you travel farther away, the music gets fainter (the signal is now weaker), so you turn up the gain (amplification). Now the music is more audible, but you start to hear crackles (the noise). Amplification affects both signal and noise. Eventually, you will travel so far away that the noise becomes more unpleasant and you switch to a different station (the S/N ratio has become unacceptably low).
Now let us ask what would happen if you were 200 miles away and you tuned to the frequency of your favorite FM station in your home city. You would hear nothing but noise, sometimes called static. Based only on your observation, you could not say that the station was even broadcasting. It is not that you would deny that the station was broadcasting, it is just that you cannot affirm it on the basis of your observation; your observation is indeterminate.
Each DNA forensic laboratory establishes a threshold value for the size of acceptable peaks, but the threshold values are not identical from lab-to-lab. Setting a minimum threshold does not automatically favor the defense or the prosecution. The lowest such value of which I am aware is 40 (http://www.bioforensics.com/articles/champion1/champion1.html). At first this seems large, since peaks smaller than this are still greater than noise, but these peaks are small relative to those typically encountered in DNA electropherograms.
Instead of examining the specific choice of a threshold value, let us discuss why setting them in advance of the experiment is so important. Scientists set up their experiments to test (falsify) their hypotheses. If the signal-to-noise level in any spectroscopic experiment falls below the threshold, any hypothesis requiring that the signal be above the threshold must be rejected. The reason one sets the threshold first is to avoid bias. The textbook An Introduction to Forensic DNA analysis, 2nd ed. (Rudin, N. and Inman, K., CRC Press 2002, p. 121) states (emphasis added), “It is important to have some predetermined limit to distinguish what is signal and what is noise.” If one treats the threshold as flexible, the very purpose for setting it prior to running the experiment is defeated.
How does this relate to the DNA electropherogram of the knife sample (http://www.friendsofamanda.org/articles.html, Figure 1)? 16 out of 29 peaks are lower than 40 in S/N, and 22 are lower than 50 RFU. Dr. Stefanoni herself wrote (http://www.thedailybeast.com/blogs-and-stories/2009-09-14/no-mistrial-for-knox/) the words “too low” with respect to the knife. In other words these peaks are too small to count as music in the car radio analogy above.
It would be helpful to know the threshold value regularly employed in Dr. Stefanoni’s lab, but it could have been as high as 150 RFU and is very unlikely to be below 40 RFU. The signals above the threshold might constitute a partial profile of Ms. Kercher’s DNA. However, such a partial match is very problematic (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.
Conclusions
The kitchen knife cannot be the sole murder weapon, and it most likely had nothing to do with the crime whatsoever. The only evidence that it might have played any role is the finding of DNA that is at best a partial match to Ms. Kercher’s DNA on the blade, and that almost certainly came from contamination during the test. Given the weakness of the fluorescence signals and especially the lack of blood on the knife, the signals observed do not tie the knife to the crime. No wonder that the open letter quoted above ends its section on the kitchen knife by concluding that there is no forensic evidence to link it to the crime. But an equally troubling problem with the prosecution’s theory is that Ms. Knox and Mr. Sollecito would bother to take this knife from his flat to the dwelling occupied by Ms. Knox, Ms. Kercher, and their two roommates in preference to using knives found in the kitchen of these four roommates. What sense does that make? It is typical of this case that Occam’s razor is so often ignored.
Update, 01/18/2010
The prosecuation's theory would also have us believe that Knox would not dispose of the supposed murder weapon, and despite cleaning the blade extensively, would not clean her fingerprints from the handle. This strikes me as unlikely.
New Comments Policy
We will try a new comments policy and see how it goes. I will not moderate comments; you will be entirely responsible for what you say. However, my strongest possible recommendation is that all commenters adopt the following philosophy: If you would not say it in front of your mother, don’t say it here. I reserve the right to ban any commenter for any reason without prior warning.
Wednesday, September 9, 2009
More on the Willingham case
Janet Jacobs of the Corsicana Daily Sun interviewed a number of people who took part in the trial of Cameron Todd Willingham (http://www.corsicanadailysun.com/thewillinghamfiles/local_story_250180658.html). Her article fails to mention the phenomenon of crazed glass, which was mistakenly used as evidence of arson. Indeed, her article fails to grapple with one of the main points of Mr. Grann’s piece, that the forensic science of arson is far more advanced than it was seventeen years ago. Despite twice mentioning Mr. Willingham’s moving his car and suggesting that it was evidence he cared for his car more than his children, Ms. Jacobs neglects to give Mr. Willingham’s own explanation, namely that he did not want the gasoline to exacerbate the fire. Ms. Jacobs does not discuss the role of psychiatrist James Grigson in labeling Mr. Willingham as a sociopath (http://www.corsicanadailysun.com/thewillinghamfiles/local_story_248104331.html). Yet she quotes Sergeant Hensley dismissing an arson expert’s opinion as something to be bought without delving into Mr. Grigson’s unethical behavior, for which he was expelled from the American Psychiatric Association. Indeed, most of the people whom Ms. Jacobs interviewed have an interest in portraying Mr. Willingham in the most unfavorable light possible.
Ms. Jacobs indicates that Mr. Willingham’s attorney, David Martin, only became convinced of Mr. Willingham’s guilt after the trial was over. How is this possible when the evidence (at least that with which I am familiar) produced after the trial was exculpatory? Mr. Martin goes on to call the Innocence Project an “absolute farce,” despite the Innocent Project’s having a role in releasing over one hundred people. A defense attorney who calls the Innocence Project a “bunch of hype” is a little bit like a chemist who asserts that there are four elements (earth, air, water, fire), and that the periodic table is a scam.
But equally problematic for me is the strong likelihood that Mr. Martin defended Mr. Willingham while believing him to be guilty. One might be tempted to say that when a lawyer believes his own client is guilty, it is damning. However, my previous blog entry (http://viewfromwilmington.blogspot.com/2009/08/execution-of-cameron-todd-willingham.html) gives an example of a lawyer who did not believe his client, and was unrepentant when later DNA evidence exonerated him. Did Mr. Willingham or Mr. Lloyd (http://www.scpr.org/news/2009/08/17/not-enough-money-or-time-defend-detroits-poor/) get the effective counsel to which they are entitled? I have to wonder.
Ms. Jacobs indicates that Mr. Willingham’s attorney, David Martin, only became convinced of Mr. Willingham’s guilt after the trial was over. How is this possible when the evidence (at least that with which I am familiar) produced after the trial was exculpatory? Mr. Martin goes on to call the Innocence Project an “absolute farce,” despite the Innocent Project’s having a role in releasing over one hundred people. A defense attorney who calls the Innocence Project a “bunch of hype” is a little bit like a chemist who asserts that there are four elements (earth, air, water, fire), and that the periodic table is a scam.
But equally problematic for me is the strong likelihood that Mr. Martin defended Mr. Willingham while believing him to be guilty. One might be tempted to say that when a lawyer believes his own client is guilty, it is damning. However, my previous blog entry (http://viewfromwilmington.blogspot.com/2009/08/execution-of-cameron-todd-willingham.html) gives an example of a lawyer who did not believe his client, and was unrepentant when later DNA evidence exonerated him. Did Mr. Willingham or Mr. Lloyd (http://www.scpr.org/news/2009/08/17/not-enough-money-or-time-defend-detroits-poor/) get the effective counsel to which they are entitled? I have to wonder.
Monday, August 31, 2009
The execution of Cameron Todd Willingham
The case of Cameron Todd Willingham illustrates several of the themes that have appeared on this blog, as well as in my comments at other blogs. Among them are the unreliability of some kinds of forensic evidence, the problem of inadequate legal representation of indigent defendants, and the malleability of eyewitness accounts to fit post hoc narratives. A recent article in the New Yorker (http://www.newyorker.com/reporting/2009/09/07/090907fa_fact_grann?currentPage=1) casts grave doubt on the quality of initial finding that Mr. Willingham murdered his three children by setting their house on fire. “What’s more, [fire scientist] Beyler determined that the investigation violated, as he put it to me, ‘not only the standards of today but even of the time period.’”
The author, David Grann, notes that indigent defendants on death row must “depend on court-appointed lawyers, many of whom are ‘unqualified, irresponsible, or overburdened,’ as a study by the Texas Defender Service, a nonprofit organization, put it. In 2000, a Dallas Morning News investigation revealed that roughly a quarter of the inmates condemned to death in Texas were represented by court-appointed attorneys who had, at some point in their careers, been ‘reprimanded, placed on probation, suspended or banned from practicing law by the State Bar.’” A recent NPR report implies that Michigan and Florida also have problematic public defender systems (http://www.scpr.org/news/2009/08/17/not-enough-money-or-time-defend-detroits-poor/). “In Miami, they say the only way they can squeeze in jail visits is if they work every weekend. And in Detroit, public defenders haven't seen a raise in more than 30 years.”
“Former Supreme Court Justice Sandra Day O’Connor has said that the ‘execution of a legally and factually innocent person would be a constitutionally intolerable event.’” Mr. Grann concludes, “There is a chance, however, that Texas could become the first state to acknowledge officially that, since the advent of the modern judicial system, it had carried out the ‘execution of a legally and factually innocent person.’”
I approach the criminal justice system as a private citizen, not as one with any special training in the law or politics. I have previously indicated that my suggestions for reforms could benefit from advice from those with greater expertise. Nevertheless, I have seen so much that is troubling that, along with others, I have to ask whether a refusal to look at evidence of innocence is sometimes motivated from cognitive dissonance.
The author, David Grann, notes that indigent defendants on death row must “depend on court-appointed lawyers, many of whom are ‘unqualified, irresponsible, or overburdened,’ as a study by the Texas Defender Service, a nonprofit organization, put it. In 2000, a Dallas Morning News investigation revealed that roughly a quarter of the inmates condemned to death in Texas were represented by court-appointed attorneys who had, at some point in their careers, been ‘reprimanded, placed on probation, suspended or banned from practicing law by the State Bar.’” A recent NPR report implies that Michigan and Florida also have problematic public defender systems (http://www.scpr.org/news/2009/08/17/not-enough-money-or-time-defend-detroits-poor/). “In Miami, they say the only way they can squeeze in jail visits is if they work every weekend. And in Detroit, public defenders haven't seen a raise in more than 30 years.”
“Former Supreme Court Justice Sandra Day O’Connor has said that the ‘execution of a legally and factually innocent person would be a constitutionally intolerable event.’” Mr. Grann concludes, “There is a chance, however, that Texas could become the first state to acknowledge officially that, since the advent of the modern judicial system, it had carried out the ‘execution of a legally and factually innocent person.’”
I approach the criminal justice system as a private citizen, not as one with any special training in the law or politics. I have previously indicated that my suggestions for reforms could benefit from advice from those with greater expertise. Nevertheless, I have seen so much that is troubling that, along with others, I have to ask whether a refusal to look at evidence of innocence is sometimes motivated from cognitive dissonance.
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